commit 895be127
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-29

    Bump version to 2.57

configure.ac

commit ca39bf43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-29

    Add missing file: graph_blockmodel_dynamics_ising_glauber_mcmc_h.cc
    
    This fixes #757

Makefile.am
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc_h.cc

commit e8af661f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-29

    Fix remaining numpy 1.25 incompatibility

src/graph_tool/clustering/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/inference/planted_partition.py

commit 6faec236
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-29

    Fix compatibility issue with numpy 1.25
    
    This fixes #758

src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/ranked.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 7ff21297
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-18

    generate_knn(): add support for hints

src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh

commit 9d748594
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-10

    generate_knn(): reduce memory usage

src/graph/generation/graph_knn.hh

commit c800e949
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-10

    generate_knn(): replace distance cache with visited list

src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph_tool/generation/__init__.py

commit 8fe54544
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-18

    blockmodel: add default values for entropy_args_t

src/graph/inference/blockmodel/graph_blockmodel_entropy.hh

commit 3ce5d419
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-29

    cache.hh: improve multithreaded performance

src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/graph_inference.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/util.hh
src/graph_tool/__init__.py
src/graph_tool/inference/__init__.py

commit c41e2156
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-09

    Bump version to 2.57dev

configure.ac

commit 1170c71a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-09

    Bump version to 2.56

configure.ac

commit dab03a06
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-09

    CI: fix docker copy

.gitlab-ci.yml

commit 4d7a1310
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-09

    CI: increase job number for doctests

.gitlab-ci.yml

commit 9e6dcf9d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-09

    inference.rst: fix table alignment

doc/demos/inference/_background.rst

commit b0c1f598
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Fix string termination

src/graph/numpy_bind.hh

commit dd889b21
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Preserve compatibility with Python < 3.10

src/graph/graph_bind.cc
src/graph/numpy_bind.hh

commit 35addb30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Fix docstring

doc/demos/inference/_reconstruction.rst

commit d4af7eba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    arf_layout(): add OpenMP barrier

src/graph/layout/graph_arf.hh

commit 430888fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    arf_layout(): change initialization

src/graph/layout/graph_arf.hh
src/graph_tool/draw/__init__.py

commit 2a89edee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Fix doctest

src/graph_tool/draw/__init__.py

commit 7a931ec9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Add missing flow-example.xml.gz

doc/flow-example.xml.gz

commit 08f17c43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    CI: fix test pipeline

.gitlab-ci.yml

commit afa823a5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Fix docstrings

doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
src/graph_tool/draw/__init__.py
src/graph_tool/topology/__init__.py

commit 803fc78c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    CI: copy build directory via docker cp

.gitlab-ci.yml

commit fef6b91b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    CI: use GNU parallel for doctests

.gitlab-ci.yml

commit 8e0e837e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Fix docstring tests after prng update

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_sampling.rst
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/clique_decomposition.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 00ade327
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Fix vector-valued property map assignment

src/graph/graph_bind.cc

commit f2ea2dbe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    uncertain_blockmodel: rename max_w to max_m

src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 5759284b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    graph_state.hh: add std::forward() calls

src/graph/inference/support/graph_state.hh

commit 58ee1c51
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Implement dispatch for map(), rmap(), and contiguous_map()

src/graph/inference/graph_inference.cc
src/graph_tool/inference/util.py

commit 114b746a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    Add openmp.hh convenience header

Makefile.am
src/graph/graph_python_interface.hh
src/graph/openmp.hh
src/graph/parallel_rng.hh

commit cd52cc01
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-08

    graph_blockmodel.hh: fix modify_edge_dS()

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 95532db5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-04

    generate_knn(): fix nearest implementation and improve knn

src/graph/generation/graph_knn.hh

commit 8303f7c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-06-03

    numpy_bind.hh: check for array object

src/graph/graph_bind.cc
src/graph/numpy_bind.hh

commit 230057e5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-30

    fibonacci_search.hh: fix includes and namespace

src/graph/inference/support/fibonacci_search.hh

commit f7ea5eac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-30

    Update uncertain_marginal.cc

src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc

commit 0d77c3a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-29

    Refactor PRNG state handling
    
    This ensures that multiple threads always point to different streams of
    the same global PRNG state. In particular, this works when both pthreads
    and OpenMP threads are spawned simultaneously.

src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.hh
src/graph/generation/graph_knn.hh
src/graph/graph_bind.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc
src/graph/parallel_rng.hh
src/graph/random.cc
src/graph/random.hh
src/graph_tool/__init__.py

commit 85a5eb8c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-29

    parallel_rng.hh: fix race condition when using Python threads

src/graph/parallel_rng.hh

commit 587637f9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-27

    Preserve compatibility with numpy < 1.17

src/graph_tool/__init__.py

commit 64eef106
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-26

    Implement multithreaded RNGs

src/graph_tool/__init__.py

commit ec21483e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-26

    dynamics: release GIL during iteration

src/graph/dynamics/graph_discrete.cc

commit 0e8bceb6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-25

    generate_knn(): implement 'local' and 'max_rk' parameters

src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph_tool/generation/__init__.py

commit 6336e079
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-25

    graph_util.hh: move parallel loops threshold to regular parameter

src/graph/graph_util.hh

commit 0273139f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-25

    Fix compilation error with clang

src/graph/inference/support/fibonacci_search.hh

commit 43157d5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-15

    generate_knn(): introduce max_cache_size parameter

src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph_tool/generation/__init__.py

commit 6a8c93eb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-20

    cache.hh: solve race condition via local thread storage
    
    This also enables size doubling for amortized constant growth.

src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh

commit a2f534c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-25

    pmap(): handle empty array

src/graph_tool/inference/util.py

commit 9f01a22c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-25

    Externalized Fibonacci search from multilevel.hh

Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/loops/multilevel.hh
src/graph/inference/support/fibonacci_search.hh

commit bd9d227a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-07

    CI: add latest tag to docker images

.gitlab-ci.yml

commit 4581ead9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-07

    CI: fix docker tag

.gitlab-ci.yml

commit 6c91e007
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-07

    CI: use tags for docker builds

.gitlab-ci.yml

commit ccbf9b01
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-07

    Remove redundant std::move() call

src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc

commit 95bf57ab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-02

    Fix typo in doc

src/graph_tool/topology/__init__.py

commit 7b36c88c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-01

    Small doc improvement

doc/demos/inference/_background.rst

commit 328e1afe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-01

    Bump version to 2.56dev

configure.ac

commit a065b259
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-01

    Bump version to 2.55

configure.ac

commit a622409c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-01

    Graph.edge(): fix docstring

src/graph_tool/__init__.py

commit d6a994f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-05-01

    EdgePropertyMap: Add support for (source, target) indexing

doc/quickstart.rst
src/graph_tool/__init__.py

commit 4587af39
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-30

    LayeredBlockState.get_edges_prob(): fix typo

src/graph_tool/inference/layered_blockmodel.py

commit 9940f08c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-27

    blockmodel: fix directed edge update entropy delta

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit 89218de8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-24

    global_clustering(): implement `sampled` option

src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph_tool/clustering/__init__.py

commit 7e151328
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-24

    idx_map.hh: confine position sizes to multiples of two

src/graph/idx_map.hh

commit eeec5180
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-23

    Cosmetic whitespace

src/graph/centrality/graph_pagerank.cc

commit 574e26b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-23

    Disable size checking for idx_map<> in some places

src/graph/generation/graph_contract_edges.hh
src/graph/generation/graph_price.hh
src/graph/topology/graph_similarity.hh

commit 790a0043
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-23

    idx_map.hh: remove resize bottleneck()
    
    Resizing one item at a time can lead to O(N) insertion. This switches to
    size doubling, which gives us O(1).

src/graph/idx_map.hh

commit 3dac0bfc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-23

    global/local_clustering(): small speedup

src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh

commit 8d2e2030
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-21

    Documentation: remove invalid :no-member:

doc/generation.rst
doc/spectral.rst

commit bf69f1a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-21

    Change spelling: indexes -> indices
    
    Both are correct, but latin version is more pleasing.

doc/gt_format.rst
doc/quickstart.rst
src/graph/graph_adjacency.hh
src/graph/graph_filtering.cc
src/graph/graph_io.cc
src/graph_tool/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/topology/__init__.py

commit 876736ad
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-21

    Small doc improvements

doc/conf.py
doc/demos/animation/animation.rst

commit 31cc1369
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-20

    Fix docstrings and enable opengraph tags

doc/centrality.rst
doc/clustering.rst
doc/collection.rst
doc/conf.py
doc/correlations.rst
doc/draw.rst
doc/dynamics.rst
doc/flow.rst
doc/graph_tool.rst
doc/inference.rst
doc/quickstart.rst
doc/stats.rst
doc/topology.rst
doc/util.rst
src/graph_tool/collection/__init__.py

commit 6672e37a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-20

    Bump version to 2.55dev

configure.ac

commit 2c209160
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-20

    Bump version to 2.54

configure.ac

commit 31b1d5a8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-20

    Fix docstringc

.gitlab-ci.yml
doc/.templates/graph.rst
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/search/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 17316525
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-20

    graph_blockmodel.hh: fix edge entropy delta computation with self-loops

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 20b1e07d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-20

    Revamp documentation

Makefile.am
doc/.templates/class.rst
doc/.templates/graph.rst
doc/.templates/layout.html
doc/centrality.rst
doc/clustering.rst
doc/collection.rst
doc/conf.py
doc/correlations.rst
doc/demos/animation/animation.rst
doc/demos/cppextensions/cppextensions.rst
doc/demos/index.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/matplotlib/matplotlib.rst
doc/draw.rst
doc/dynamics.rst
doc/flow.rst
doc/generation.rst
doc/graph_tool.rst
doc/index.rst
doc/inference.rst
doc/modules.rst
doc/quickstart.rst
doc/search_module.rst
doc/spectral.rst
doc/stats.rst
doc/topology.rst
doc/util.rst
src/graph/generation/graph_parallel.cc
src/graph/generation/graph_parallel.hh
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 8de571ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-16

    idx_map.hh: implement check_size parameter

src/graph/generation/graph_knn.hh
src/graph/idx_map.hh

commit 47abc0f9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-15

    generate_knn(): remove sync mode

src/graph/generation/graph_knn.hh

commit 6f18002b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-13

    generate_knn(): fix bug with clear_vertex()

src/graph/generation/graph_knn.hh
src/graph/shared_heap.hh
src/graph_tool/generation/__init__.py

commit 1f07fd28
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-10

    CI: fix problem with multiple deb files

.gitlab-ci.yml

commit 113f0ef3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-13

    generate_knn(): add 'verbose' option and sync mode

src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph_tool/generation/__init__.py

commit 52407ad1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-11

    blockmodel: optimize edge modification delta computation

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh

commit 06180aab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-10

    CI: fix arm64 builds

.gitlab-ci.yml

commit 27085a6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-06

    similarity(): improve documentation

src/graph_tool/topology/__init__.py

commit 0a7975d1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-03

    similarity(): improve documentation
    
    Include relationship with set operations

src/graph/topology/graph_similarity.hh
src/graph_tool/topology/__init__.py

commit ebc5ecbc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-06

    gererate_knn(): fix distance caching

src/graph/generation/graph_knn.hh

commit e3b4fb58
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-10

    contract_parallel_edges(): fix bug with parallel self-loops

src/graph/generation/graph_contract_edges.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh

commit 446226da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    dynamics: fix doctests

src/graph_tool/dynamics/__init__.py

commit 99f1910f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    Bump version to 2.54dev

configure.ac

commit be7ccc5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    Bump version to 2.53

configure.ac

commit 043cde6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    graph_ranked.hh: remove unused variable

src/graph/inference/ranked/graph_ranked.hh

commit 6232dfd7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    CI: fix debian name collision

.gitlab-ci.yml

commit bed1299e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    CI: safeguard from inocuous aplty errors

.gitlab-ci.yml

commit eb2366c5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-09

    CI: add remaning debian/ubuntu builds

.gitlab-ci.yml

commit a3bfe2db
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: fix aptly publish

.gitlab-ci.yml

commit 37bfeaf2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: Fix debian build

.gitlab-ci.yml

commit d80217c2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: disable '-flto' and enable opnemp in clang build

.gitlab-ci.yml

commit 015ad002
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: add --pull option to docker build

.gitlab-ci.yml

commit fb9c2ac1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: change nice to 19 and enforce `NJOBS`

release/debian/Dockerfile
release/docker/Dockerfile

commit 3e00f30e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: change debian package version from ~dev to ~git

.gitlab-ci.yml
release/debian/Dockerfile

commit f40b950c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: fix version computation in debian Dockerfile

release/debian/Dockerfile

commit 74936369
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: remove '-flto' from docker build

release/docker/Dockerfile

commit 53b85399
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: fix debian Dockerfile

release/debian/Dockerfile

commit cf737981
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: implement continuous debian::sid build

.gitlab-ci.yml
release/debian/Dockerfile

commit 43e71849
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: fix details in docker build

release/docker/Dockerfile
release/docker/PKGBUILD

commit 2dbd2f9f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    CI: add continuous docker build
    
    This adds a continous docker build with linux 4 support for HPC systems.

.gitlab-ci.yml
release/docker/Dockerfile

commit 7b87cd76
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    Fix doctests

doc/demos/inference/_layers.rst
doc/gt_format.rst

commit 641f336d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    Change default colormap heuristic

src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/nested_blockmodel.py

commit 1eaa8537
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    draw_hierarchy(): document 'node_weight' parameter

src/graph_tool/draw/cairo_draw.py

commit be6bfeac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-08

    RankedBlockState: fix issue with NestedBlockState

src/graph/inference/ranked/graph_ranked.hh

commit 75dd86a2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-07

    MeasuredClosureBlockState: fix 'max_w' parameter

src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh

commit 6125e208
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-07

    Update doctests

doc/demos/inference/_ranked.rst
doc/demos/inference/_reconstruction.rst

commit 11df6714
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-07

    Fix compilation warning

src/graph/inference/ranked/graph_ranked.hh

commit 447dd6d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-07

    Bump version to 2.53dev

configure.ac

commit 220c1095
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-07

    Bump version to 2.52

configure.ac

commit bd33452b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-07

    RankedBlockState: fix MCMC updates

src/graph/inference/ranked/graph_ranked.hh
src/graph_tool/inference/ranked.py

commit 44ce1e83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-06

    Bump version to 2.51

configure.ac

commit c765a8c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-05

    Bump version to 2.51

configure.ac

commit 146e4440
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-05

    Re-institute [[gnu::pure]] annotations

src/graph/inference/support/cache.hh

commit ddcfcc52
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-09-14

    uncertain_blockmodel.py: Add `max_w` parameter
    
    This parameter limits the maximum edge multiplicity during inference.

src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 4e802f29
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-05

    Fix GIL release for multithreaded case

src/graph/graph_python_interface.hh

commit 0a2f90de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-04

    Bump version to 2.51dev

configure.ac

commit a357cb52
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-04

    Bump version to 2.50

configure.ac

commit 6e7caab3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-04

    cache.hh: disable [[gnu:pure]] in cached functions
    
    The usage of [[gnu:pure]] should be allowed in these instances, but
    their presence causes segfault (and invalid reads according to valgrind)
    with GCC, including version 12 (the latest at the time of this writing).

src/graph/inference/support/cache.hh

commit 6c4c1184
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-02

    Bump version to 2.50dev

configure.ac

commit c2b30835
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-01

    Bump version to 2.49

configure.ac

commit fd505551
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-01

    inference/uncertain: fix issue with directed graphs and ``deg_corr``

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 2958e123
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-01

    MeasuredBlockState: Implement parameters ``lp`` and ``lq``

src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 463bce42
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-01

    Add missing ``[[gnu::const]]`` attribute to log_sum_exp()

src/graph/inference/support/util.hh

commit f178a172
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-04-01

    graph_blockmodel.hh: fix edge update for ``deg_corr == False``

src/graph/inference/blockmodel/graph_blockmodel.hh

commit c8bb540f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-31

    Improve selection of graph views for specific cases

src/graph/graph_filtering.hh
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/ranked/graph_ranked.cc
src/graph/inference/ranked/graph_ranked_gibbs.cc
src/graph/inference/ranked/graph_ranked_mcmc.cc
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.cc
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.cc

commit eeeb40d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-16

    log_sum_exp(): implement multivariate function

src/graph/inference/support/util.hh

commit e5140348
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-07

    log_sum_exp(): ensure appropriate return value type

src/graph/inference/support/util.hh

commit 3bb8eb30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-07-02

    load_from_csv(): fix hash_type != "string" conversion

src/graph_tool/__init__.py

commit 1e3ed05d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-06-10

    graph_draw(): fix automatic ink setting with mplfig

src/graph_tool/draw/cairo_draw.py

commit 2df9fa2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-31

    RankedBlockState: fix hierarchical drawing

src/graph_tool/inference/ranked.py

commit 19fa9988
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-31

    ranked.rst: use contract_parallel_edges() in example

doc/demos/inference/_ranked.rst

commit 6db4293f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-30

    configure.ac: remove trailing spaces

configure.ac

commit 5e808a16
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-30

    Graph(): add ``fast_edge_removal`` option to constructor
    
    This setting will now also be saved with the graph.

src/graph_tool/__init__.py

commit 162bb479
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-30

    inference: implement cached m_entries optimization

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/loops/merge_split.hh
src/graph/inference/loops/multilevel.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/norm_cut/graph_norm_cut.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/ranked/graph_ranked.hh
src/graph/inference/ranked/graph_ranked_mcmc.hh
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.hh
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.hh

commit 46a04521
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-30

    filt_graph<>: accept boost::keep_all as predicate

src/graph/graph_filtered.hh

commit 385cd0b2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-30

    graph_adjacency.hh: Add optional number of vertices to constructor

src/graph/graph_adjacency.hh

commit 23a17e76
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-30

    Improve generate_knn() and add `pairs` option for nearest pairs

Makefile.am
src/graph/generation/graph_contract_edges.hh
src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph/shared_heap.hh
src/graph/shared_map.hh
src/graph_tool/generation/__init__.py

commit 8669c5ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-21

    Add Graph.__len__() alias to Graph.num_vertices()
    
    This fixes #755.

src/graph_tool/__init__.py

commit fc43b0a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-19

    Bump version to 2.49dev

configure.ac

commit b4993dc1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-19

    Bump version to 2.48

configure.ac

commit 2a23bee8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-19

    CI: add template for debian builds and split platforms

.gitlab-ci.yml

commit 4b6d560f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-19

    Fix log_sum_exp() bind issue with clang

src/graph/inference/graph_inference.cc

commit 80609875
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-19

    dl_import.py: cleanup old dl_flags cruft

src/graph_tool/dl_import.py

commit a723584b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-19

    module_registry.hh: avoid static initialization issue on MacOS
    
    This implements the more elegant 'Construct On First Use Idiom' to
    avoid the static initialization race condition, instead of relying on the
    ``init_priorty`` attribute, which does not seem to work propery in
    MacOS.

src/graph/module_registry.hh

commit 6859f9c5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-17

    Bump version to 2.48dev

configure.ac

commit 9a1db7be
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-17

    Bump version to 2.47

configure.ac

commit 57f0adb8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-16

    Graph.add_edge_list(): fix issue with hashed or `None` descriptors

src/graph_tool/__init__.py

commit 9feb4a94
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-16

    Graph.add_edge_list(): Accept any object which can be converted to vertex indexes
    
    This fixes #754

src/graph_tool/__init__.py

commit 573678d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-16

    module_registry: implement priorities

src/graph/centrality/graph_eigenvector.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/module_registry.hh
src/graph/topology/graph_bipartite.cc

commit ac70179a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-16

    Implement module registry infrastructure

Makefile.am
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_trust_transitivity.cc
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_dynamics.cc
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_contract_edges.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_knn.cc
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_maxent_sbm.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_random_edges.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_triadic_closure.cc
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/cliques/graph_clique_decomposition.cc
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_modularity.cc
src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/modularity/graph_modularity_gibbs.cc
src/graph/inference/modularity/graph_modularity_mcmc.cc
src/graph/inference/modularity/graph_modularity_multiflip_mcmc.cc
src/graph/inference/modularity/graph_modularity_multilevel_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut.cc
src/graph/inference/norm_cut/graph_norm_cut_gibbs.cc
src/graph/inference/norm_cut/graph_norm_cut_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut_multiflip_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multilevel_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multilevel_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multilevel_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition.cc
src/graph/inference/planted_partition/graph_planted_partition_gibbs.cc
src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multilevel_mcmc.cc
src/graph/inference/ranked/graph_ranked.cc
src/graph/inference/ranked/graph_ranked_gibbs.cc
src/graph/inference/ranked/graph_ranked_mcmc.cc
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.cc
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/layout/graph_arf.cc
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/module_registry.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/stats/graph_average.cc
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_stats_bind.cc
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_matching.cc
src/graph/topology/graph_maximal_cliques.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc

commit 8ba65467
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-03-04

    Fix cairo_draw() with matplotlib 3.7+
    
    This fixes #751

src/graph_tool/draw/cairo_draw.py

commit c5e0f38e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-27

    pcg-cpp: sync with upstream

src/pcg-cpp/include/pcg_extras.hpp
src/pcg-cpp/include/pcg_random.hpp
src/pcg-cpp/include/pcg_uint128.hpp

commit 00547f98
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-27

    Doc updates

doc/demos/inference/_reconstruction.rst
doc/demos/inference/inference.rst
src/graph_tool/generation/__init__.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/ranked.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 6473ba87
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-27

    CI: fix docker build

release/docker/Dockerfile

commit 2ebc6823
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-27

    CI: remove outdated ubuntu versions

.gitlab-ci.yml

commit dbffc83b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-27

    Bump version to 2.47dev

configure.ac

commit ab460df4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    Bump version to 2.46

configure.ac

commit bc427809
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    generate_sbm(): add error if non-integer arguments are passed

src/graph_tool/generation/__init__.py

commit 3a26d148
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    Update ubuntu releases

.gitlab-ci.yml

commit bda86df8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    inference.rst: add reference to [peixoto-descriptive-2021]_

doc/demos/inference/inference.rst
doc/faq.rst

commit ea5b4586
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    Small doc fixes

doc/faq.rst
src/graph_tool/inference/modularity.py

commit 0f4557ee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    Implement contract/expand_parallel_edges()
    
    This replaces the implementation of remove_parallel_edges().

Makefile.am
src/graph/generation/graph_contract_edges.cc
src/graph/generation/graph_contract_edges.hh
src/graph/generation/graph_generation.cc
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/stats/__init__.py

commit 213f478c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    Add add/remove_random_edges() to generation module

Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_random_edges.cc
src/graph/generation/graph_random_edges.hh
src/graph_tool/generation/__init__.py

commit 2efb709a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-26

    Add operator() to sampler algorithms

src/graph/generation/dynamic_sampler.hh
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh

commit 36076083
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Add small graph atlas to collection.atlas

Makefile.am
src/graph_tool/collection/__init__.py
src/graph_tool/collection/atlas.dat.gz

commit 8eeb74cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Graph.__init__(): allow for initialization with the number of vertices

src/graph_tool/__init__.py

commit 171d9c3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Doc reference fixes

src/graph_tool/__init__.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/ranked.py

commit b2e9ab35
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Add small graph collection in collection.small

Makefile.am
src/graph_tool/all.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/small.py

commit bf344b3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Graph.__init__() fix unrecognized keyword argument error

src/graph_tool/__init__.py

commit 5254c5e2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Accept tuple as argument for Graph.remove_edge()

src/graph_tool/__init__.py

commit 895f8556
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Add FAQ and admonition about modularity maximization

doc/faq.rst
src/graph_tool/inference/modularity.py

commit 9fd79406
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-25

    Add FAQ about vertex lookup from property map value

doc/faq.rst

commit ae275cf4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-22

    Add support for passing edge properties during graph construction

doc/quickstart.rst
src/graph_tool/__init__.py

commit 676b644e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-22

    Small doc updates

doc/demos/index.rst
doc/quickstart.rst

commit bab39bd6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-22

    Implement Graph() initialization from edge/adjacency lists

doc/quickstart.rst
src/graph/graph_python_interface_imp1.cc
src/graph_tool/__init__.py

commit 50b7ffec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-22

    Fix remaining copyright notices

release/debian/debian/copyright
src/graph_tool/__init__.py

commit d4535936
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-21

    Fix Makefile.am

Makefile.am
doc/.static/graph-tool-logo.svg

commit 18294238
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-21

    Update doc theme to pydata

doc/conf.py
doc/demos/inference/_ranked.rst
doc/faq.rst
doc/gt_theme/static/flasky.css
doc/gt_theme/static/font-awesome-4.2.0/css/font-awesome.css
doc/gt_theme/static/font-awesome-4.2.0/css/font-awesome.min.css
doc/gt_theme/static/font-awesome-4.2.0/fonts/FontAwesome.otf
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.eot
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.svg
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.ttf
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.woff
doc/gt_theme/static/font-awesome-4.2.0/less/bordered-pulled.less
doc/gt_theme/static/font-awesome-4.2.0/less/core.less
doc/gt_theme/static/font-awesome-4.2.0/less/fixed-width.less
doc/gt_theme/static/font-awesome-4.2.0/less/font-awesome.less
doc/gt_theme/static/font-awesome-4.2.0/less/icons.less
doc/gt_theme/static/font-awesome-4.2.0/less/larger.less
doc/gt_theme/static/font-awesome-4.2.0/less/list.less
doc/gt_theme/static/font-awesome-4.2.0/less/mixins.less
doc/gt_theme/static/font-awesome-4.2.0/less/path.less
doc/gt_theme/static/font-awesome-4.2.0/less/rotated-flipped.less
doc/gt_theme/static/font-awesome-4.2.0/less/spinning.less
doc/gt_theme/static/font-awesome-4.2.0/less/stacked.less
doc/gt_theme/static/font-awesome-4.2.0/less/variables.less
doc/gt_theme/static/font-awesome-4.2.0/scss/_bordered-pulled.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_core.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_fixed-width.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_icons.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_larger.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_list.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_mixins.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_path.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_rotated-flipped.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_spinning.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_stacked.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_variables.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/font-awesome.scss
doc/gt_theme/static/gt_style.css
doc/gt_theme/theme.conf
doc/index.rst
doc/modules.rst
doc/quickstart.rst

commit af4f06f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    Update copyright information

configure.ac
doc/conf.py
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/draw/pycairo_aux.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/dynamics/graph_dynamics.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_maxent_sbm.cc
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triadic_closure.cc
src/graph/generation/graph_triadic_closure.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/idx_map.hh
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/cliques/graph_clique_decomposition.cc
src/graph/inference/cliques/graph_clique_decomposition.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram.hh
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/histogram/graph_histogram_mcmc.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_split.hh
src/graph/inference/loops/multilevel.hh
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/modularity/graph_modularity_gibbs.cc
src/graph/inference/modularity/graph_modularity_mcmc.cc
src/graph/inference/modularity/graph_modularity_multiflip_mcmc.cc
src/graph/inference/modularity/graph_modularity_multilevel_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut.cc
src/graph/inference/norm_cut/graph_norm_cut.hh
src/graph/inference/norm_cut/graph_norm_cut_gibbs.cc
src/graph/inference/norm_cut/graph_norm_cut_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut_multiflip_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multilevel_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multilevel_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multilevel_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition.cc
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/planted_partition/graph_planted_partition_gibbs.cc
src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multilevel_mcmc.cc
src/graph/inference/ranked/graph_ranked.cc
src/graph/inference/ranked/graph_ranked.hh
src/graph/inference/ranked/graph_ranked_gibbs.cc
src/graph/inference/ranked/graph_ranked_gibbs.hh
src/graph/inference/ranked/graph_ranked_mcmc.cc
src/graph/inference/ranked/graph_ranked_mcmc.hh
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.cc
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.hh
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.cc
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.hh
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/contingency.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/int_part.hh
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/openmp_lock.hh
src/graph/parallel_rng.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_matching.cc
src/graph/topology/graph_maximal_cliques.cc
src/graph/topology/graph_maximal_cliques.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/netzschleuder.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/clique_decomposition.py
src/graph_tool/inference/histogram.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/norm_cut.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/ranked.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit bdb82fec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    all_shortest_paths(): select correct edge for weighted multigraphs
    
    This fixes #744

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit b109ce58
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    cairo_draw.py: raise ImportError if wrong Gtk version is available
    
    This fixes #743

src/graph_tool/draw/cairo_draw.py

commit 570f8c79
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    graph_blockmodel_partition.hh: fix DL of empty partition
    
    This fixes #747

src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit b0be0c31
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    collection.LazyData: fix __getitem__()

src/graph_tool/collection/__init__.py

commit c046b71c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    collection: implement lazy __contains__()
    
    This fixes #745.

src/graph_tool/collection/__init__.py
src/graph_tool/collection/netzschleuder.py

commit 0faed322
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    NestedBlockState.mcmc_sweep(): do not propagate 'vertices' parameter
    
    This fixes #748.

src/graph_tool/inference/nested_blockmodel.py

commit 8b229be6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-01-05

    multilevel.hh: ensure B_min/B_max constraints are enforced

src/graph/inference/loops/multilevel.hh

commit ff958480
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-19

    Fix lack of numpy.float type in recent numpy versions

src/graph_tool/__init__.py

commit 21947578
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2023-02-18

    Add support for cairomm 1.16

configure.ac
src/graph/draw/graph_cairo_draw.cc

commit 924e40b3
Merge: e3ca8cf6 2359848f
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2023-01-05

    Merge branch 'debian/2.45+ds-10/fix/python311' into 'master'
    
    Use inspect.getfullargspec instead of inspect.getarcspec
    
    See merge request count0/graph-tool!69

commit 2359848f
Author: Jerome Benoit <quartermaster@rezozer.net>
Date:   2023-01-04

    Use inspect.getfullargspec instead of inspect.getarcspec

src/graph_tool/generation/__init__.py

commit e3ca8cf6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-07-30

    dynamics: update Voter model

src/graph/dynamics/graph_discrete.hh

commit 83c69885
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-08-01

    Fix truncated copyright headers

src/graph/inference/support/int_part.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh
src/graph/search/graph_dfs.cc

commit 187b21e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-08-16

    topology: improve docstring consistency

src/graph_tool/topology/__init__.py

commit 7b63b7a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-09-26

    edge_reciprocity(): fix typo

src/graph/topology/graph_reciprocity.cc
src/graph_tool/topology/__init__.py

commit 0303009e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-08-16

    edge_reciprocity(): add support for edge weights

src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 3cb5a970
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-09-14

    cache.hh: limit maximum cache size to 500MB

src/graph/inference/support/cache.hh

commit 7dc13fdd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-09-26

    ModularityState: add support for edge multiplicities

src/graph/inference/modularity/graph_modularity.hh
src/graph_tool/inference/modularity.py

commit 8b6be10e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-10-11

    mutual_information(): Implement adjusted mutual information

src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph_tool/inference/partition_centroid.py

commit fc8202c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-12-11

    price.py: fix errorbar computation

doc/price.py

commit ff5266b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-12-11

    graph_blockmodel_entries.hh: fix possible out-of-bounds read
    
    This fixes a possible out-of-bounds read, which would happen only if
    optimization are not enabled. This can trigger failed assertions if
    _GLIBCXX_ASSERTIONS is defined.

src/graph/inference/blockmodel/graph_blockmodel_entries.hh

commit 8151f1f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-23

    RankedBlockState: Add missing documentation index

src/graph_tool/inference/__init__.py

commit 609992dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-23

    Bump version to 2.46dev

configure.ac

commit cc4b7c3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    Bump version to 2.45

configure.ac

commit ae608508
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    CI: build arm64 packages

.gitlab-ci.yml

commit 1c016bc7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    inference: update expected test results

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst

commit d8007e21
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    uncertain: fix edge sampling and updating

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh

commit 70545896
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    get_hierarchy_tree(): fix empty branches pruning

src/graph_tool/inference/nested_blockmodel.py

commit 9f538563
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    BlockState: improve initialization of array-valued parameter `b`

src/graph_tool/inference/blockmodel.py

commit 1d8167da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-22

    Fix planarity test with noncontiguous edge indexes
    
    This fixes issue #712

src/graph/layout/graph_planar_layout.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_planar.cc
src/graph_tool/draw/__init__.py

commit ee939bb6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-21

    get_hierarchy_control_points(): fix docstring

src/graph_tool/draw/cairo_draw.py

commit 5d851ae0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-21

    distance_histogram(): fix bug with openmp
    
    This fixes issue #721

src/graph/histogram.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh

commit 31050f10
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-21

    get_hierarchy_tree(): fix behavior for filtered graphs
    
    This fixes issue #737

src/graph_tool/inference/nested_blockmodel.py

commit d2493cde
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-21

    Fix B_max/B_min behavior for NestedBlockState.multilevel_mcmc_sweep()

src/graph_tool/inference/nested_blockmodel.py

commit bafec6e5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-21

    Add missing _ranked.rst documentation

doc/demos/inference/_ranked.rst

commit 181d0b15
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-21

    blockmodel: fix degree description length delta computation

src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit f4d03d03
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    blockmodel: copy branch

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph_tool/inference/nested_blockmodel.py

commit eefb2c4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    bfs_search(): honor initialize_vertex() from visitor
    
    This fixes issue #729.

src/graph/search/graph_bfs.cc

commit 1fa4fea4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    shortest_distance(): fix `max_dist` logic
    
    This fixes issue #734

src/graph/topology/graph_distance.cc

commit daae776b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    shortest_distance(): fix 'return_reached' behavior
    
    This fixes #730.

src/graph/topology/graph_distance.cc

commit 4cce0696
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    shortest_distance(): fix docstring
    
    This fixes issue #731.

src/graph_tool/topology/__init__.py

commit 8ebea2ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    Remove whitespace

src/graph_tool/inference/norm_cut.py

commit 68374523
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    Fix bug with all_edge_iterator and reversed graphs
    
    This fixes issue #728

src/graph/graph_adjacency.hh
src/graph/graph_filtered.hh
src/graph/graph_reverse.hh

commit 02e1ca46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    graph_blockmodel.hh: remove check_node_counts()

src/graph/inference/blockmodel/graph_blockmodel.hh

commit f03b9b48
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    merge_split: fix issue with clabel
    
    This fixes issue #736

src/graph/inference/loops/merge_split.hh

commit b947294c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    minimize_blockmodel_dl(): fix documentation
    
    This fixes #735.

src/graph_tool/inference/minimize.py

commit 54370b70
Author: Jerome Benoit <quartermaster@rezozer.net>
Date:   2022-03-27

    enhance doc/Makefile
    
    Slightly enhances doc/Makefile.

doc/Makefile

commit 19cee4ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    ModularityState: minor fixes

src/graph_tool/inference/modularity.py

commit 05eb1d20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    sfdp_layout(): implement preferential ordering along y direction

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 79d8f45b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    Fix docstring typo

src/graph_tool/inference/partition_modes.py

commit 358ba2f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    blockmodel: fix in/out-degree description length for directed graphs

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit 3dbe58ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-10

    NestedBlockState: fix pickling

src/graph_tool/inference/nested_blockmodel.py

commit 6cef5f93
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-10

    graph_inference.cc: expose lbinom()/lbinom_fast()

src/graph/inference/graph_inference.cc

commit 7470ea4f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    nested_blockmodel.py: fix copy with edge covariates

src/graph_tool/inference/nested_blockmodel.py

commit f01f29f5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    blockmodel: fix add/remove edge

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 37e1083e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    Minor fixes to inference tests

doc/test_inference.py
doc/test_inference_mcmc.py

commit 8072a1fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    NestedBlockState: fix initialization

src/graph_tool/inference/nested_blockmodel.py

commit ba388c14
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    NestedBlockState: simplify copying and preserve base state params

src/graph_tool/inference/nested_blockmodel.py

commit dc121f25
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    MultiflipMCMCState: add pmovelabel default variable

src/graph_tool/inference/base_states.py

commit 7816cec9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    blockmodel: simple indentation fix

src/graph/inference/blockmodel/graph_blockmodel_entries.hh

commit 81e7ad4c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-06

    blockmodel: edge count amend

src/graph/inference/blockmodel/graph_blockmodel.hh

commit c46c6ae6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-05

    sfdp_layout(): fix mu and gamma parameters

src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 7907bd2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-05

    pmap(): add support for double

src/graph/inference/graph_inference.cc
src/graph_tool/inference/util.py

commit 47225bdc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-03

    base_states.py: fortify DrawBlockState

src/graph_tool/inference/base_states.py

commit c5ba81b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-03

    NestedBlockModel: query state.get_N() instead of state.g.num_vertices()

src/graph_tool/inference/nested_blockmodel.py

commit eca41895
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-03

    blockmodel: add simple _E counter

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 05027736
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-01

    Implement Ranked SBM

Makefile.am
doc/demos/inference/inference.rst
src/graph/inference/graph_inference.cc
src/graph/inference/loops/merge_split.hh
src/graph/inference/ranked/graph_ranked.cc
src/graph/inference/ranked/graph_ranked.hh
src/graph/inference/ranked/graph_ranked_gibbs.cc
src/graph/inference/ranked/graph_ranked_gibbs.hh
src/graph/inference/ranked/graph_ranked_mcmc.cc
src/graph/inference/ranked/graph_ranked_mcmc.hh
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.cc
src/graph/inference/ranked/graph_ranked_multiflip_mcmc.hh
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.cc
src/graph/inference/ranked/graph_ranked_multilevel_mcmc.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/ranked.py

commit e24b5387
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-05-20

    Documentation: add ns macro for netzschleuder links

doc/conf.py

commit cbf8c367
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-02

    blockmodel: edge list test fix

src/graph/inference/blockmodel/graph_blockmodel_elist.hh

commit e43b957a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-01

    UncertainBaseState.get_edge_prob(): fix error

src/graph_tool/inference/uncertain_blockmodel.py

commit 30342d88
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-02-01

    uncertain_blockmodel: improve addition/removal of multiple edges

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh

commit 8645b67a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-04

    vf2_sub_graph_iso.hpp(): avoid uncessary O(N) in get_num_vertices()

src/boost-workaround/boost/graph/vf2_sub_graph_iso.hpp

commit af64085d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    doctests: fix double execution and references

doc/demos/inference/_assortative.rst
doc/demos/inference/_edge_weights.rst
doc/demos/inference/_layers.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst
doc/inference.rst
src/graph_tool/draw/cairo_draw.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/norm_cut.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 9b01da33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    Fix docstrings

doc/conf.py
doc/inference.rst
src/graph_tool/inference/__init__.py

commit d6f1dcf7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    doc/demos/cppextensions/Makefile: update Python version

doc/demos/cppextensions/Makefile

commit 9f170d6e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    Minor fixup to doc css

doc/gt_theme/static/flasky.css

commit 45d97a29
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    CI: remove Ubuntu groovy

.gitlab-ci.yml

commit 5a12463e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    Bump version to 2.45dev

configure.ac

commit ab3fb7fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    Bump version to 2.44

configure.ac

commit 02d3bee6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    CliqueState(): fix docstring

src/graph_tool/inference/clique_decomposition.py

commit dc26d472
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    subgraph_isomorphism(): fix bug when subgraph is filtered
    
    This fixes issue #715

Makefile.am
src/boost-workaround/boost/graph/vf2_sub_graph_iso.hpp
src/graph/topology/graph_subgraph_isomorphism.cc

commit c80b9af0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    CliqueState: fix log-likelihood computation

src/graph/inference/cliques/graph_clique_decomposition.cc
src/graph/inference/cliques/graph_clique_decomposition.hh
src/graph_tool/inference/clique_decomposition.py

commit 324b5495
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    inference: implement normalized cut

Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/norm_cut/graph_norm_cut.cc
src/graph/inference/norm_cut/graph_norm_cut.hh
src/graph/inference/norm_cut/graph_norm_cut_gibbs.cc
src/graph/inference/norm_cut/graph_norm_cut_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut_multiflip_mcmc.cc
src/graph/inference/norm_cut/graph_norm_cut_multilevel_mcmc.cc
src/graph_tool/inference/__init__.py
src/graph_tool/inference/norm_cut.py

commit 7822a48f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    CI: add Debian bookworm and Ubuntu impish builds

.gitlab-ci.yml

commit 2307f04b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-02

    multilevel.hh: fix B_min/B_max enforcement

src/graph/inference/loops/multilevel.hh

commit 49e099a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    distance_histogram(): fix docstring typo

src/graph_tool/stats/__init__.py

commit 05ac1ef7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    shortest_distance(): check for valid source/target
    
    This fixes issue #722

src/graph_tool/topology/__init__.py

commit b4b05785
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    all_pairs_search(): fix initialization for filtered graphs
    
    This fixes issue #723

src/graph/topology/graph_all_distances.cc

commit 3b8a8c5c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    Update copyright information

configure.ac
doc/conf.py
release/debian/debian/copyright
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/draw/pycairo_aux.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/dynamics/graph_dynamics.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_maxent_sbm.cc
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triadic_closure.cc
src/graph/generation/graph_triadic_closure.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/idx_map.hh
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/cliques/graph_clique_decomposition.cc
src/graph/inference/cliques/graph_clique_decomposition.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram.hh
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/histogram/graph_histogram_mcmc.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_split.hh
src/graph/inference/loops/multilevel.hh
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/modularity/graph_modularity_gibbs.cc
src/graph/inference/modularity/graph_modularity_mcmc.cc
src/graph/inference/modularity/graph_modularity_multiflip_mcmc.cc
src/graph/inference/modularity/graph_modularity_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multilevel_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multilevel_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multilevel_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition.cc
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/planted_partition/graph_planted_partition_gibbs.cc
src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multilevel_mcmc.cc
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/contingency.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/openmp_lock.hh
src/graph/parallel_rng.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_matching.cc
src/graph/topology/graph_maximal_cliques.cc
src/graph/topology/graph_maximal_cliques.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/netzschleuder.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/clique_decomposition.py
src/graph_tool/inference/histogram.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit b56963c2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    multilevel.hh: enforce B_min/B_max bounds
    
    This fixes issue #725

src/graph/inference/loops/multilevel.hh

commit a0399483
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2022-01-01

    Implement DrawBlockState base state

src/graph_tool/draw/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/planted_partition.py

commit 38e6fab9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-20

    base_states.py: docstring fixup

src/graph_tool/inference/base_states.py

commit d92cb1e6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-20

    spectral: add Bethe Hessian implementation

src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph_tool/spectral/__init__.py

commit bca4052a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-14

    Cleanup configure.ac

configure.ac

commit f92c1fbf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-10

    mcmc_loop.hh: support state variable by reference

src/graph/inference/loops/mcmc_loop.hh

commit 4df1d212
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-10

    Move std::array<> hash support out of graph_histogram.hh

src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/inference/histogram/graph_histogram.hh

commit cd14eebf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-08

    partition_overlap(): check input lengths

src/graph_tool/inference/partition_modes.py

commit 1caa3bde
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-10-08

    Add Graph.own_property() to documentation

doc/graph_tool.rst

commit 6202a226
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-18

    spectral: add 'csr' optional parameter

src/graph_tool/spectral/__init__.py

commit a4960e70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-18

    graph_union(): improve docstring

src/graph_tool/generation/__init__.py

commit 13187ce2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-13

    sfdp_layout(): remove power() usage in favor of pow2()

src/graph/layout/graph_sfdp.hh

commit d9dbec01
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-05

    mcmc_loop.hh: take node by reference

src/graph/inference/loops/mcmc_loop.hh

commit 7f8492bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-05

    Detach tuple_apply() to util.hh

src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/support/util.hh

commit 66ac9026
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-04

    Fix doctests

src/graph_tool/__init__.py
src/graph_tool/topology/__init__.py

commit f06e8def
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-03

    SBMEdgeSampler: forbid copying

src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh

commit 55e1e08a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-03

    test_inference.py: cleanup

doc/test_inference.py

commit e7a702bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-09-01

    inference: remove __deepcopy__() from state objects

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 18a1dbf4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-08-15

    graph_draw(): automatically enable edge "sloppy" mode when equivalent

src/graph/draw/graph_cairo_draw.cc

commit 44b33e2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-08-13

    PPBlockState: fix usage with directed graphs

src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph_tool/inference/planted_partition.py

commit f0c33061
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-08-13

    graph_blockmodel_partition: small speedups

src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit dff2f5a3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-08-13

    multilevel_mcmc: remove unused variable

src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh

commit c043734c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-08-13

    Graph.add_edge_list(): remove unnecessary check

src/graph/graph_python_interface_imp1.cc

commit b07d0a91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-30

    copy_state_wrap: make test option explicit

src/graph_tool/inference/base_states.py

commit c3dcaca6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-30

    inference: pass by reference to MCMC loops

src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh

commit 4d8d77f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-30

    idx_map.hh: fixed shared position bug and clearing behavior

src/graph/idx_map.hh

commit 26f90d63
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-27

    ModularityState: fix initialization

src/graph_tool/inference/modularity.py

commit 31ccb470
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-26

    inference: minor test check improvement

src/graph_tool/inference/base_states.py

commit ceccb7a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-26

    graph_adjacency.hh: simplify edge index recycling

src/graph/graph_adjacency.hh

commit 74532ee1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-11

    inference: avoid state copying by keeping a shared_ptr

src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/modularity/graph_modularity_gibbs.cc
src/graph/inference/modularity/graph_modularity_mcmc.cc
src/graph/inference/modularity/graph_modularity_multiflip_mcmc.cc
src/graph/inference/modularity/graph_modularity_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multilevel_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multilevel_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multilevel_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition.cc
src/graph/inference/planted_partition/graph_planted_partition_gibbs.cc
src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multilevel_mcmc.cc
src/graph/inference/support/graph_state.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc

commit 21e34981
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-11

    CI: prevent default CXXFLAGS in debian builds

release/debian/debian/rules

commit db31ab1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-11

    CI: disable cache in container builds

.gitlab-ci.yml

commit 6c542b85
Merge: 424e27bb ea7e1caf
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-07-11

    Merge branch 'fixes' into 'master'
    
    Fixes
    
    See merge request count0/graph-tool!65

commit ea7e1caf
Author: David Seifert <soap@gentoo.org>
Date:   2021-07-11

    configure.ac: modernise

configure.ac

commit 424e27bb
Merge: c3cb31c9 c6de615c
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-07-09

    Merge branch 'non-recursive-Automake' into 'master'
    
    Switch to non-recursive Automake
    
    See merge request count0/graph-tool!64

commit c6de615c
Author: David Seifert <soap@gentoo.org>
Date:   2021-07-09

    Switch to non-recursive Automake

Makefile.am
configure.ac
src/Makefile.am
src/graph/Makefile.am
src/graph/centrality/Makefile.am
src/graph/clustering/Makefile.am
src/graph/correlations/Makefile.am
src/graph/draw/Makefile.am
src/graph/dynamics/Makefile.am
src/graph/flow/Makefile.am
src/graph/generation/Makefile.am
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/layout/Makefile.am
src/graph/search/Makefile.am
src/graph/spectral/Makefile.am
src/graph/stats/Makefile.am
src/graph/topology/Makefile.am
src/graph/util/Makefile.am
src/graph_tool/Makefile.am

commit c3cb31c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-07

    Bump version to 2.44dev

configure.ac

commit 9d41331e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-07

    Bump version to 2.43

configure.ac

commit e5828864
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-06

    Latent layers: fix entropy difference computation

src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh

commit 1f80b1fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-06

    Trivial simplification

src/graph/inference/blockmodel/graph_blockmodel_emat.hh

commit 74ab77ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-06

    Recover missing functions: BlockState.add/remove_vertex()

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py

commit 80878919
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-06

    Bump version to 2.43dev

configure.ac

commit 458bd492
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    Bump version to 2.42

configure.ac

commit 60b36065
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    (Nested)BlockState: fix clabel propagation

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 03a8fa2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    NestedBlockState: remove 'sampling' parameter

src/graph_tool/inference/nested_blockmodel.py

commit a2189994
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    blockmodel: cleanup partition_stats usage

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh

commit 02203e8e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    graph_blockmodel_entries.hh: slight performance improvements

src/graph/inference/blockmodel/graph_blockmodel_entries.hh

commit d90b4d8b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    inference: remove outdated functions and function parameters

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py

commit d514bf27
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-07-02

    graph_blockmodel_partition.hh: fix copy bug

src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit 627f6ea0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    Update docstests

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst

commit 950fca54
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    Bump version to 2.42dev

configure.ac

commit cd6c697e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    Bump version to 2.41

configure.ac

commit ac2e8608
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    CI: disable lto in Debian builds

release/debian/debian/rules

commit 8c93acec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    Update doctests

src/graph_tool/inference/blockmodel.py

commit 97c05ac8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    Add missing MultilevelMCMCState._get_bclabel()

src/graph_tool/inference/base_states.py

commit 75556a9a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    get_hierarchy_tree(): change default to empty_branches=False

src/graph_tool/inference/nested_blockmodel.py

commit 7be93ef4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    inference: fix issue with clabel in multilevel MCMC
    
    This fixes issue #706

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/loops/multilevel.hh
src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 98d213e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    inference: simplify and improve EGroups update performance

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/planted_partition/graph_planted_partition.hh

commit 18caad84
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-28

    Bump version to 2.41dev

configure.ac

commit 3994a2ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-24

    Bump version to 2.40

configure.ac

commit 76769a8a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-24

    CI: re-enable FLTO in Debian/Ubuntu builds

release/debian/debian/rules

commit 894fbe90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-24

    Put operator<< overload implementation in correct namespace
    
    This fixes a segfault in some targets (e.g. conda).

src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/histogram/graph_histogram_mcmc.hh

commit 82190914
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-12

    sfdp_layout(): improve performance and update group behavior

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 7c4379bf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-23

    Bump version to 2.40dev

configure.ac

commit dec169a3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-23

    Bump version to 2.39

configure.ac

commit 78a18de6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-23

    Makefile.am: add missing contingency.hh

src/graph/inference/Makefile.am

commit 2afb7ae7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-22

    Bump version to 2.38

configure.ac

commit b6c929f5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-22

    Fix debian build

release/debian/debian/rules

commit 70c28423
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-22

    Fix docker build

release/docker/Dockerfile

commit ca8ed481
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-22

    Fix compilation with boost versions older than 1.76

src/graph/graph_python_interface.hh

commit 3b1cbac6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-22

    Graph.__setstate__(): call explicit __init__()
    
    This makes it easier to subclass Graph while chaning the __init__()
    signature. This fixes issue #696.

src/graph_tool/__init__.py

commit b601f401
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-22

    Fix docstring tests

doc/conf.py
doc/pyenv.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/minimize.py

commit c9dcca6a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Remove stale reference to old bisection submodule

src/graph_tool/inference/__init__.py

commit 458bf830
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    graph_io_binary.hh: suppress compilation warnings

src/graph/graph_io_binary.hh

commit a851ca15
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    multilevel_mcmc: fix initial bracketing

src/graph/inference/loops/multilevel.hh

commit 14ad85a8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Fix clang compilation errors

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/loops/multilevel.hh

commit 594ed6f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    CI: disable openmp with clang

.gitlab-ci.yml

commit 68ce16ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Fix missing copyright headers

src/graph/inference/loops/merge_split.hh
src/graph/inference/loops/multilevel.hh

commit 24e32369
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Add clique decomposition implementation

doc/inference.rst
src/graph/inference/Makefile.am
src/graph/inference/cliques/graph_clique_decomposition.cc
src/graph/inference/cliques/graph_clique_decomposition.hh
src/graph/inference/graph_inference.cc
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/clique_decomposition.py

commit b95a253f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Avoid multiple declarations of move_t

src/graph/inference/loops/merge_split.hh
src/graph/inference/loops/multilevel.hh

commit 08722cf7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Fix graph_histogram.cc compilation

src/graph/inference/support/graph_state.hh

commit 518182a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    multicanonical_equilibrate(): fix callback function
    
    This fixes issue #700

src/graph_tool/inference/mcmc.py

commit 6a2c8b3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Fix mulicanonical_mcmc_sweep() with NestedBlockState
    
    This fixes issue #699

src/graph_tool/inference/base_states.py
src/graph_tool/inference/nested_blockmodel.py

commit bab2be6b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Fix docstrings

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst
doc/inference.rst
src/graph_tool/draw/cairo_draw.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py

commit fdefb758
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-01

    MCMC test cleanup

doc/test_inference.py
doc/test_inference_mcmc.py

commit ea4ff28f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Implement nested_contiguous_map()

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/util.py

commit ecd607db
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-21

    Remove dead multilevel code

src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py

commit e4cb3500
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-15

    Change continuous_map() to contiguous_map()

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/util.py

commit ee5cd8e8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-15

    Fix compilation errors and warnings with Boost 1.76
    
    This fixes issue #703

configure.ac
src/boost-workaround/boost/graph/adjacency_iterator.hpp
src/graph/Makefile.am
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_trust_transitivity.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_dynamics.cc
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_rewiring.cc
src/graph/graph.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_python_interface.hh
src/graph/graphml.cpp
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/layout/graph_bind_layout.cc
src/graph/read_graphviz_new.cpp
src/graph/search/graph_search_bind.cc
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/stats/graph_stats_bind.cc
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/util/graph_util_bind.cc

commit bda49830
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-15

    inference: cleanup deg_ops

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh

commit 5a3aada4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-15

    Implement Gibbs moves for ModularityState

src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/graph_inference.cc
src/graph/inference/modularity/graph_modularity_gibbs.cc
src/graph_tool/inference/modularity.py

commit 43a0de90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-15

    inference: simplify random neighbor sampling

src/graph/generation/sampler.hh
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/graph_inference.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/loops/multilevel.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph_tool/inference/minimize.py

commit 90041be8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-14

    Improve elist implementation

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py

commit ca8b4bb7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-14

    Remove unneeded OpenMP locks

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/planted_partition/graph_planted_partition.hh

commit 78c7d0c2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-14

    dynamic_sampler.hh: add update() and get_prob()

src/graph/generation/dynamic_sampler.hh

commit f804c544
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-15

    Refactor mutilevel MCMC inference
    
    This moves the entire algorithm into C++, and includes a faster
    initialization heuristic.

doc/demos/inference/_assortative.rst
doc/demos/inference/_edge_weights.rst
doc/demos/inference/_layers.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_sampling.rst
doc/demos/inference/inference.rst
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/graph_inference.cc
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/loops/merge_loop.hh
src/graph/inference/loops/multilevel.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/modularity/graph_modularity_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/planted_partition/graph_planted_partition_multilevel_mcmc.cc
src/graph/inference/support/int_part.cc
src/graph/inference/support/int_part.hh
src/graph_tool/Makefile.am
src/graph_tool/draw/cairo_draw.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/base_states.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/histogram.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 498e63c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-07

    generate_knn(): fix docstring

src/graph_tool/generation/__init__.py

commit 4c9359ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-13

    merge_split: do not restrict single-node moves to current hierarchy

src/graph/inference/loops/merge_split.hh

commit 08c38f3f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-13

    Release the GIL during MCMC sweeps

src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh

commit 6e87fc05
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-13

    Add GILRelease support to release the GIL as appropriate

src/graph/graph_python_interface.hh

commit e6b9d702
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-02

    reduced_mutual_information(): fix docstring w.r.t. normalization

src/graph_tool/inference/partition_centroid.py

commit cd8ea9e3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-02

    Histogram: implement conditional histograms

src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram.hh
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/histogram/graph_histogram_mcmc.hh
src/graph_tool/inference/histogram.py

commit ca5486a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-02

    Implement Bayesian histogram inference

src/graph/inference/Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/histogram/graph_histogram.cc
src/graph/inference/histogram/graph_histogram.hh
src/graph/inference/histogram/graph_histogram_mcmc.cc
src/graph/inference/histogram/graph_histogram_mcmc.hh
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/histogram.py

commit d5450d85
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-01

    planted_partition: fix MCMC detailed balance

src/graph/inference/planted_partition/graph_planted_partition.hh

commit 9a40e524
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-01

    planted_partition: implement Gibbs sampling

src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/graph_inference.cc
src/graph/inference/planted_partition/graph_planted_partition_gibbs.cc
src/graph_tool/inference/planted_partition.py

commit c4ff6d79
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-07

    Refactor multilevel MCMC into pure C++

src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/graph_inference.cc
src/graph/inference/layers/graph_blockmodel_layers_multilevel_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multilevel_mcmc.cc
src/graph/inference/loops/multilevel.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/modularity/graph_modularity_multilevel_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multilevel_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_multilevel_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multilevel_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_multilevel_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multilevel_mcmc.cc
src/graph/inference/support/contingency.hh
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py

commit ed484b0e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-06-07

    idx_set: fix iterator constness

src/graph/idx_map.hh

commit 785e77da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-05-13

    blockmodel: add_empty_block() returns the new group

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 9f75d21d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-26

    dynamic_sampler.hh: decouple index and element sampling

src/graph/generation/dynamic_sampler.hh

commit 6b09274e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-04-26

    PropertyDict: fix missing attribute exception

src/graph_tool/__init__.py

commit fc15128a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-04-15

    PropertyDict: propagate attribute lookup

src/graph_tool/__init__.py

commit 51a48300
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-21

    Refactor empty/candidate groups into using idx_set

src/graph/idx_map.hh
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/support/util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 0532729a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-09

    Refactor multiflip_mcmc() as a stand alone code with specializations

doc/test_inference_mcmc.py
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/loops/merge_split.hh
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/support/util.hh
src/graph_tool/inference/blockmodel.py

commit 5f778bca
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-26

    cairo_draw(): fix position transformation with more than two coordinates

src/graph_tool/draw/cairo_draw.py

commit 754f6100
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-21

    Inference HOWTO: fix edge weigth example

doc/demos/inference/_edge_weights.rst

commit 9dbc0547
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-09

    test_inference_mcmc.py: fix parallel tests

doc/test_inference_mcmc.py

commit 9f620ac1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-06

    log_sum_exp(): handle -inf case

src/graph/inference/support/util.hh

commit b7babcf8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-06

    graph_blockmodel_multiflip_mcmc.hh: revert beta=inf behavior

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 61b956b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-06

    graph_blockmodel_emat.hh: simplify and speedup group edge lookup

src/graph/inference/blockmodel/graph_blockmodel_emat.hh

commit e405a575
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-02

    Fix PPBlockState.get_Be()

src/graph_tool/inference/planted_partition.py

commit 54a4dfb9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-03-02

    graph_latent_multigraph.hh: remove unused include

src/graph/inference/graph_latent_multigraph.hh

commit 5676812b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-28

    Docstring fixup

doc/demos/inference/_model_class_selection.rst
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/search/__init__.py

commit aba9d112
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-28

    blockmodel: multiflip_mcmc_sweep() speedup for beta=inf

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit c5840b5d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-28

    blockmodel: sparse matrix load-factor tune-up

src/graph/inference/blockmodel/graph_blockmodel_emat.hh

commit 55c58156
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-28

    Fix inference test

doc/test_inference.py

commit af79a7f3
Merge: 36c61ec2 2ba32db7
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-03-02

    Merge branch 'prop_to_size' into 'master'
    
    Handle property maps of length 0 in prop_to_size and clarify its documentation
    
    See merge request count0/graph-tool!63

commit 2ba32db7
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-24

    Handle property maps of length 0 in prop_to_size

src/graph_tool/draw/__init__.py

commit 832a9ada
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-24

    Clarify documentation of prop_to_size function

src/graph_tool/draw/__init__.py

commit 36c61ec2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-16

    graphviz_draw(): fix encoding bug
    
    This fixes issue #687

src/graph_tool/draw/graphviz_draw.py

commit 4908e139
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-16

    EHash: remove ineffective index randomization

src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 7b4d03d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-15

    EHash: remove const reference

src/graph/inference/blockmodel/graph_blockmodel_emat.hh

commit 8efe5ded
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-15

    EntrySet: replaced assumed optimization with constexpr

src/graph/inference/blockmodel/graph_blockmodel_entries.hh

commit 7cb3816e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-15

    gt_format.rst: small typo

doc/gt_format.rst

commit 894617b7
Merge: 2d06d47b f930bce1
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-06

    Merge branch 'abc' into 'master'
    
    Use collections.abc.Iterable instead of collections.Iterable
    
    See merge request count0/graph-tool!62

commit f930bce1
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-06

    Use collections.abc.Iterable instead of collections.Iterable

src/graph_tool/dynamics/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/topology/__init__.py

commit 2d06d47b
Merge: 0b49af73 2403c922
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-06

    Merge branch 'dict' into 'master'
    
    Use dict instead of OrderedDict
    
    See merge request count0/graph-tool!61

commit 2403c922
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-05

    Use dict instead of OrderedDict
    
    Since Python 3.6, all dicts are ordered.

doc/test_inference.py
src/graph_tool/inference/blockmodel.py

commit 0b49af73
Merge: b8e8c0f2 bd80203d
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-04

    Merge branch 'unused_functions' into 'master'
    
    Remove more unused functions
    
    See merge request count0/graph-tool!58

commit bd80203d
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-03

    Remove unused file graph_closure.hh

src/graph/generation/graph_closure.hh

commit f8bfde86
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-03

    Remove unused power function from graph_katz.hh

src/graph/centrality/graph_katz.hh

commit 7f9cd1b2
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-03

    Remove unused hash_value function from graph_generation.hh

src/graph/generation/graph_generation.hh

commit 64f5f906
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-03

    Remove unused move_radially function from graph_cairo_draw.cc

src/graph/draw/graph_cairo_draw.cc

commit b8e8c0f2
Merge: fbe5f2d7 5170e126
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-03

    Merge branch 'ubuntu14' into 'master'
    
    Fixes for old versions of Ubuntu
    
    See merge request count0/graph-tool!57

commit 5170e126
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-02

    Increase minimum Boost version from 1.55 to 1.58
    
    boost::container::small_vector is not available before Boost 1.58.

configure.ac

commit e9bfea8f
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-02

    Fix CGAL version checks
    
    Periodic_3_Delaunay_triangulation_traits_3.h is only present in CGAL 4.7
    and later.

src/graph/generation/graph_triangulation.cc

commit aae627ba
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-02

    Add missing insert_range.hpp includes

src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_vavg.cc

commit fbe5f2d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-02

    modularity.py: fix wrong reference to numpy
    
    This fixes issue #692.

src/graph_tool/inference/modularity.py

commit 8639365b
Merge: 8459c610 57a53cec
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-02

    Merge branch 'static' into 'master'
    
    Make more functions static
    
    See merge request count0/graph-tool!56

commit 8459c610
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-02-02

    netzschleuder.py: fix URL encoding of datasets with spaces and other special characters

src/graph_tool/collection/netzschleuder.py

commit 57a53cec
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-02

    Make more functions static

src/graph/draw/graph_tree_cts.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_discrete.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_sfdp.hh
src/graph/read_graphviz_new.cpp
src/graph/search/graph_astar.cc
src/graph/stats/graph_average.hh
src/graph/str_repr.hh

commit 2ac08632
Merge: 1648cb97 cb844a60
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-02

    Merge branch 'dist' into 'master'
    
    Remove unused dist function
    
    See merge request count0/graph-tool!54

commit 1648cb97
Merge: 36605ccd 2d462145
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-02

    Merge branch 'python2' into 'master'
    
    Remove checks for Python 2 from configure.ac
    
    See merge request count0/graph-tool!55

commit 2d462145
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-01

    Remove checks for Python 2 from configure.ac

configure.ac

commit cb844a60
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-01

    Remove unused dist function

src/graph/draw/graph_tree_cts.cc

commit 36605ccd
Merge: 1f141ef9 76b17efb
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-01

    Merge branch 'python2' into 'master'
    
    Remove checks for PY_MAJOR_VERSION >= 3
    
    See merge request count0/graph-tool!53

commit 1f141ef9
Merge: f22e9697 6ae59083
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-01

    Merge branch 'boost' into 'master'
    
    Remove workarounds for Boost < 1.44
    
    See merge request count0/graph-tool!52

commit 76b17efb
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-01

    Remove checks for PY_MAJOR_VERSION >= 3

src/graph/draw/pycairo_aux.cc
src/graph/graph_python_interface.hh

commit 6ae59083
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-02-01

    Remove workarounds for Boost < 1.44

src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_kolmogorov.cc
src/graph/graph_io.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.hh
src/graph/read_graphviz_new.cpp

commit f22e9697
Merge: 95a79575 e95ec9f2
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-02-01

    Merge branch 'lt_operator' into 'master'
    
    Remove unused < operator for vectors
    
    See merge request count0/graph-tool!51

commit 95a79575
Merge: 89114c4a d4584a3e
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-30

    Merge branch 'master' into 'master'
    
    partition_centroid.py: fix normalization in mutual_information
    
    See merge request count0/graph-tool!50

commit e95ec9f2
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-29

    Remove unused < operator for vectors

src/graph/graph_properties_imp2.cc

commit 89114c4a
Merge: c3ac15e5 427128d0
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-30

    Merge branch 'includes' into 'master'
    
    Remove unused includes
    
    See merge request count0/graph-tool!49

commit d4584a3e
Author: Rodrigo L.C <rodrigolealc@ciencias.unam.mx>
Date:   2021-01-29

    partition_centroid.py: fix normalization in mutual_information

src/graph_tool/inference/partition_centroid.py

commit 427128d0
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-28

    Remove unused includes

src/graph/dynamics/graph_continuous.hh
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_price.hh
src/graph/graph.hh
src/graph/graph_properties_copy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/topology/graph_distance.cc

commit c3ac15e5
Merge: a5b6f7b0 1f8c25d1
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-28

    Merge branch 'max' into 'master'
    
    Remove custom definition of std::max<bool>
    
    See merge request count0/graph-tool!48

commit 1f8c25d1
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-27

    Remove custom definition of std::max<bool>

src/graph/graph_util.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_maximal_vertex_set.cc

commit a5b6f7b0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-23

    all_circuits(): accept undirected graphs

src/graph_tool/topology/__init__.py

commit 32a7d340
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-23

    all_circuits(): update docs and small cleanups

src/boost-workaround/boost/graph/hawick_circuits.hpp
src/graph_tool/topology/__init__.py

commit f92781d2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-23

    all_circuits(): change from recursive to stack-based implementation
    
    This removes a stack overflow bug.

src/boost-workaround/boost/graph/hawick_circuits.hpp
src/graph/Makefile.am
src/graph/topology/graph_all_circuits.cc

commit ba70639f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-22

    Unify redundant log_sum_exp() implementations

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh

commit 2ed6703d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-10

    generate_sbm(): fix issue with micro_degs=False

src/graph/generation/graph_sbm.hh
src/graph_tool/inference/blockmodel.py

commit 01475cf9
Merge: 65eb4eb0 9b242ea0
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-22

    Merge branch 'clang' into 'master'
    
    Remove CGAL_CFG_ARRAY_MEMBER_INITIALIZATION_BUG
    
    See merge request count0/graph-tool!47

commit 9b242ea0
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-21

    Remove CGAL_CFG_ARRAY_MEMBER_INITIALIZATION_BUG

src/graph/generation/graph_triangulation.cc

commit 65eb4eb0
Merge: 49d57e39 ddd02a29
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-21

    Merge branch 'logsum' into 'master'
    
    Make logsum function static
    
    See merge request count0/graph-tool!46

commit 49d57e39
Merge: 75fde990 89c217b1
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-21

    Merge branch 'scxx' into 'master'
    
    Remove unused struct scxx_to_python
    
    See merge request count0/graph-tool!45

commit 75fde990
Merge: 2bfbde52 6746d064
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2021-01-21

    Merge branch 'clang' into 'master'
    
    Remove workaround for old versions of Clang
    
    See merge request count0/graph-tool!44

commit ddd02a29
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-20

    Make logsum function static

src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh

commit 89c217b1
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-20

    Remove unused struct scxx_to_python

src/graph/graph_bind.cc

commit 6746d064
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2021-01-20

    Remove workaround for old versions of Clang

src/graph/hash_map_wrap.hh

commit 2bfbde52
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-10

    Bump version to 2.38dev

configure.ac

commit 1d377b3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Bump version to 2.37

configure.ac

commit 6bedc3c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Fix noninteractive Debian build

release/debian/Dockerfile

commit 06bf51be
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Fix missing file in Makefile.am

src/graph/inference/Makefile.am

commit d2d0c547
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Fix docker build with new mirrorlist URL

release/docker/Dockerfile

commit c997235e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Remove ubuntu aeon build after EOL

.gitlab-ci.yml

commit 403561fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Fix noninteractive Debian build

release/debian/Dockerfile

commit c906f124
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Bump version to 2.37

configure.ac

commit 0fe8fed3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Bump version to 2.36

configure.ac

commit 64f6945d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Update copyright information

configure.ac
release/debian/debian/copyright
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/draw/pycairo_aux.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/dynamics/graph_dynamics.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_closure.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_maxent_sbm.cc
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triadic_closure.cc
src/graph/generation/graph_triadic_closure.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/idx_map.hh
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/modularity/graph_modularity_mcmc.cc
src/graph/inference/modularity/graph_modularity_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition.cc
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/openmp_lock.hh
src/graph/parallel_rng.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_matching.cc
src/graph/topology/graph_maximal_cliques.cc
src/graph/topology/graph_maximal_cliques.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/netzschleuder.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 40b80af6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Add ubuntu hirsute build

.gitlab-ci.yml

commit 605424ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    Docstring fix

doc/demos/inference/_reconstruction.rst
src/graph_tool/generation/__init__.py

commit 772e31dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-09

    graph_draw(): fix bug with drawing a single node
    
    This fixes issue #688

src/graph_tool/draw/cairo_draw.py

commit 31fafd57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-08

    Update docstrings

doc/demos/cppextensions/Makefile
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/inference.rst
doc/inference.rst
doc/pyenv.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/uncertain_blockmodel.py

commit f7a38bba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-08

    Implement latent triadic closure

src/graph/generation/Makefile.am
src/graph/generation/graph_closure.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_triadic_closure.cc
src/graph/generation/graph_triadic_closure.hh
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/graph_inference.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.cc
src/graph/inference/uncertain/graph_blockmodel_latent_closure.hh
src/graph/inference/uncertain/graph_blockmodel_latent_closure_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_latent_layers.hh
src/graph/inference/uncertain/graph_blockmodel_latent_layers_mcmc.hh
src/graph_tool/Makefile.am
src/graph_tool/generation/__init__.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/latent_layers.py
src/graph_tool/inference/nested_blockmodel.py

commit 31428695
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-08

    TemperingState: fix verbose output

src/graph_tool/inference/mcmc.py

commit 9a39a155
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-12-16

    PPBlockState: fix entropy computation for multigraphs

src/graph/inference/planted_partition/graph_planted_partition.hh

commit bbe57308
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-12-12

    _background.rst: fix typo

doc/demos/inference/_background.rst

commit f97b2dbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-12-10

    netzschleuder.py: simplify token

src/graph_tool/collection/netzschleuder.py

commit bfd0999e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-12-09

    assortativity(): fix bug for non-integer weighted graphs

src/graph/correlations/graph_assortativity.hh

commit a10237b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-08

    graph_draw(): fix issue with foreign property maps

src/graph_tool/draw/cairo_draw.py

commit 9c1a703e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-08

    graph_blockmodel_dynamics_mcmc.hh: improve multigraph moves

src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh

commit 694f4369
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2021-01-03

    uncertain SBM: fix edge sampling

doc/test_inference_mcmc.py
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh

commit 79dd3b1f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-12

    graph_blockmodel.hh: add constexpr

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 0fe4d18c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-12

    Graph.copy_property(): improved error message

src/graph_tool/__init__.py

commit 15a33b72
Merge: 860e9f86 716172b2
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-11-30

    Merge branch 'patch-3' into 'master'
    
    Small refactoring of graphviz_draw.
    
    See merge request count0/graph-tool!42

commit 860e9f86
Merge: 9cba323a 70f0e42c
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-11-30

    Merge branch 'patch-2' into 'master'
    
    Update docstring of graphviz_draw.
    
    See merge request count0/graph-tool!41

commit 9cba323a
Merge: cce083bc e07f74c6
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-11-30

    Merge branch 'patch-1' into 'master'
    
    Fix GraphWidget.update() crashing when called without vprops or eprops argument.
    
    See merge request count0/graph-tool!40

commit cce083bc
Merge: 4e66070a e351c829
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-11-30

    Merge branch 'includes' into 'master'
    
    Remove unused includes
    
    See merge request count0/graph-tool!43

commit e351c829
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-11-23

    Remove unused includes

src/graph/generation/graph_generation.hh
src/graph/generation/graph_knn.hh
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triangulation.hh
src/graph/gml.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_filtered.hh
src/graph/graph_properties.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graphml.cpp
src/graph/histogram.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/graph_latent_multigraph.hh
src/graph/inference/graph_modularity.hh
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.hh
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/layout/graph_arf.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/random.cc
src/graph/random.hh
src/graph/read_graphviz_new.cpp
src/graph/stats/graph_parallel.cc
src/graph/str_repr.hh
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_matching.cc
src/graph/topology/graph_transitive_closure.cc

commit 716172b2
Author: Malte R <m.renken@tu-berlin.de>
Date:   2020-11-17

    Small refactoring of graphviz_draw.
    
    The only observable effect should be that calling with output=None and (output_format="xlib" or fork=True) no longer causes an AttributeError.

src/graph_tool/draw/graphviz_draw.py

commit 70f0e42c
Author: Malte R <m.renken@tu-berlin.de>
Date:   2020-11-17

    Update docstring of graphviz_draw.
    
    The effect of setting "output" to None should be more clear now.

src/graph_tool/draw/graphviz_draw.py

commit e07f74c6
Author: Malte R <m.renken@tu-berlin.de>
Date:   2020-11-13

    Fix GraphWidget.update() crashing when called without vprops or eprops argument.
    
    This fixes interactive_window() crashing when called with window argument but without vprops or eprops.

src/graph_tool/draw/gtk_draw.py

commit 4e66070a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-08

    Fix docstrings

doc/quickstart.rst
src/graph_tool/__init__.py

commit b395146c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-08

    Fix Graph.iter_out/in/all_neighbors()

src/graph/graph_python_interface.cc

commit 30bafd49
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-05

    CI: fix docker build

release/docker/Dockerfile
release/docker/PKGBUILD

commit a9fbbe1a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-08

    Preserve reference to graph during vertex/edge iteration
    
    This fixes issue #685.
    
    This also exposes the non-descriptor based iteration in the documentation.

doc/graph_tool.rst
doc/quickstart.rst
src/graph_tool/__init__.py

commit 326a176b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-02

    Remove support for defunct konect.cc

src/graph_tool/Makefile.am
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py

commit 5d38ec1d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-11-01

    PropertyDict(): hide attributes via mangling
    
    This removes a problem with properties named 't' or 'properties' being
    accessed via attributes.

src/graph_tool/__init__.py

commit 96fb62d8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-10-31

    graph_draw(): fix bug with pen_width
    
    Fix issue with a global pen_width given for vertices.

src/graph_tool/draw/cairo_draw.py

commit d989f401
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-10-23

    CI: add ubuntu:groovy build

.gitlab-ci.yml

commit d9f9b513
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-10-13

    variation_information(): fix docstring default

src/graph_tool/inference/partition_centroid.py

commit 9798528d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-10-13

    generate_knn(): add to docstring summary

src/graph_tool/generation/__init__.py

commit 3f177dfc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-10-13

    generate_knn(): fix problem with equal distances

src/graph/generation/graph_knn.hh

commit 31038455
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-10-13

    Fix typo in inference HOWTO
    
    This fixes issue #683

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_layers.rst
doc/demos/inference/_reconstruction.rst

commit 6ddf1e63
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-17

    CI: fix job_clang_cxx_amd64

.gitlab-ci.yml

commit e8251e81
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-17

    collection: add example to docstring

src/graph_tool/collection/__init__.py

commit e05e93ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-17

    CI: add test against clang + libc++

.gitlab-ci.yml

commit 37210ba9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-17

    Bump version to 2.36dev

configure.ac

commit a06d49a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    Bump version to 2.35

configure.ac

commit 7455caa4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    Fix compilation error with clang + libc++

src/graph/graph_properties.hh

commit 4dd4f8a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    Makefile.am: remove reference to removed file

Makefile.am

commit a12fbb39
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    CI: fix Dockerfile

release/docker/Dockerfile

commit e3191a70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    demos/inference: fix figure spacing

doc/demos/inference/_sampling.rst

commit 164a0286
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    doc: switch from Mathjax 2 to 3

doc/conf.py
doc/mathjax.py

commit 68e1234a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    Bump version to 2.35dev

configure.ac

commit 96575038
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    Bump version to 2.34

configure.ac

commit 58cc8b08
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-16

    draw_hierarchy(): fix problem with undirected graphs

src/graph_tool/draw/cairo_draw.py

commit a573d13d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    Dockerfile: add missing dependency

release/docker/Dockerfile

commit 73b62d72
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    LayeredBlockState: fix behavior for overlapping states with filtered graphs
    
    This fixes issue #679

src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/util.py

commit 32746cc8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    inference/support/util.hh: use rvalue references

src/graph/inference/support/util.hh

commit dbc8e6f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    Fix initialization of overlapping NestedBlockState
    
    This fixes issue #678

src/graph_tool/inference/nested_blockmodel.py

commit 711f2f3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    Add python-zstandard dependency to docker build

release/docker/PKGBUILD

commit 5549a7d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-15

    Raise exception if zstandard module is not available

src/graph_tool/__init__.py
src/graph_tool/collection/netzschleuder.py

commit a405ceb3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-14

    graph_util.hh: implement random_permutation_range()

src/graph/graph_util.hh

commit 8472a7c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-18

    generation: implement generate_knn()

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_knn.cc
src/graph/generation/graph_knn.hh
src/graph_tool/generation/__init__.py

commit e1f7a120
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    Implement access to netzschleuder via API

src/graph_tool/Makefile.am
src/graph_tool/collection/__init__.py
src/graph_tool/collection/netzschleuder.py

commit 64f62690
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-09-01

    label_parallel_edges(): reduce memory usage for very large graphs

src/graph/stats/graph_parallel.hh

commit b7f0788e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-29

    UrnSampler.sample(): use if constexpr

src/graph/generation/urn_sampler.hh

commit 52a48622
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-28

    graph_adjacency.hh: slightly speedup edge removal

src/graph/graph_adjacency.hh

commit 2de7ad34
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-28

    graph_parallel.hh: cosmetic functor -> function conversion

src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh

commit 2b51e4b5
Merge: 9c3246a4 d1562f86
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-08-29

    Merge branch 'coverity' into 'master'
    
    Simplifications identified with the help of Coverity
    
    See merge request count0/graph-tool!38

commit d1562f86
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-08-28

    Remove unused variable Sampler._size

src/graph/generation/sampler.hh

commit 42a4170e
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-08-28

    Turn UrnSampler._temp into a local variable

src/graph/generation/urn_sampler.hh

commit 9c3246a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-25

    graph_adjacency.hh: improve removal or last vertex

src/graph/graph_adjacency.hh

commit e30fbc4f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-25

    Update __license__ and __URL__

src/graph_tool/__init__.py

commit 23b6457d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-23

    graph_draw(): add option fit_view_ink

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit e3c57b27
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-23

    graph_draw(): fix bounding box calculation when using small line widths

src/graph_tool/draw/cairo_draw.py

commit 70eb73d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-21

    BlockState.sample_graph(): add `sample_params` option

src/graph_tool/inference/blockmodel.py

commit e3ccf063
Merge: 925b7a39 68dccad9
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-08-21

    Merge branch 'expat-pkg-config' into 'master'
    
    Detect expat using pkg-config
    
    See merge request count0/graph-tool!37

commit 68dccad9
Author: David Seifert <soap@gentoo.org>
Date:   2020-08-21

    Detect expat using pkg-config
    
    * `AX_LIB_EXPAT` has a big practical issue: It tries to detect expat
      by injecting various paths, among which is /usr/lib. This is extremely
      problematic, as /usr/lib usually contains 32-bit libraries on 64-bit
      systems and thereby kills linkers such as LLD that reject 32-bit
      binaries when linking 64-bit binaries. `pkg-config` does not inject
      /usr/lib, and can also be overridden at configure time.
    
    Closes: https://bugs.gentoo.org/737974

configure.ac
m4/ax_lib_expat.m4

commit 925b7a39
Merge: ffe0d50a 4cb32514
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-08-19

    Merge branch 'arity' into 'master'
    
    Increase Boost Python function arity only when necessary
    
    See merge request count0/graph-tool!36

commit 4cb32514
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-08-18

    Increase Boost Python function arity only when necessary

src/graph/generation/graph_generation.cc
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc

commit ffe0d50a
Merge: 14995a22 2dd0e5ce
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-08-18

    Merge branch 'bugfix/graphviz-read-graph-properties' into 'master'
    
    Fix dot graph reader
    
    Closes #450
    
    See merge request count0/graph-tool!35

commit 14995a22
Merge: 682b4f46 52fe287a
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-08-18

    Merge branch 'bugfix/graphviz-draw' into 'master'
    
    Adjust use of libgvc to fix two graphviz_draw issues
    
    Closes #597
    
    See merge request count0/graph-tool!34

commit 2dd0e5ce
Author: Jeff Trull <edaskel@att.net>
Date:   2020-08-17

    Fix dot graph reader
    
    The correct type for the dynamic property map key is actually
    graph_property_tag, not multigraph_t*. It looks like graph property maps
    only store a single value...

src/boost-workaround/boost/graph/graphviz.hpp

commit 52fe287a
Author: Jeff Trull <edaskel@att.net>
Date:   2020-08-17

    Adjust use of libgvc to fix two graphviz_draw issues
    
    One issue was reported to the mailing list on 2020-08-17 by Rolf
    Sander; the testcase is:
    
    import graph_tool.all as gt
    g = gt.Graph()
    v0 = g.add_vertex()
    v1 = g.add_vertex()
    e01 = g.add_edge(v0,v1)
    e11 = g.add_edge(v1,v1) # loop
    gt.graphviz_draw(g)
    
    The other is issue #597 "Graphviz_draw core dumping when using HTML labels"
    
    Basically these changes add extra type information for interacting
    with libgvc.

src/graph_tool/draw/graphviz_draw.py

commit 682b4f46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-12

    graph_draw(): handle int16_t types

src/graph_tool/draw/cairo_draw.py

commit 4523e238
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-11

    sfdp_layout(): avoid unnecessary position copying

src/graph/layout/graph_sfdp.hh

commit 015b85b2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-11

    price_network(): make nonlinear preferential attachment consistent with documentation

src/graph/generation/graph_price.hh

commit ce624e5a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-06

    CompactHashimotoOperator: fix case with zero-degree vertices

src/graph/spectral/graph_nonbacktracking.hh

commit e17f7aaa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-06

    spectral: implement more efficient linear operator interface

src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph_tool/spectral/__init__.py

commit fe602358
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-04

    graph_draw(): honor bg_color parameter

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit df4e2faf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-08-02

    Improve speed of GML writing
    
    Remove uncessary exception throwing and property map checking.

src/graph/gml.hh

commit 23228363
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-31

    Add UTF8 support to GML parser
    
    UTF8 is not strictly valid for GML, but it doesn't hurt.

src/graph/gml.hh

commit 5e31e5f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    uncertain_blockmodel.py: simplify super() usage

src/graph_tool/inference/uncertain_blockmodel.py

commit f4b7c076
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    UncertainBaseState: change state_args semantics for nested=True

src/graph_tool/inference/uncertain_blockmodel.py

commit 6781ab3f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    inference.rst: remove old reference

doc/demos/inference/inference.rst

commit cdcadbfb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    Graph: fix vorder parameter when not contiguous

src/graph/graph_copy.cc
src/graph_tool/__init__.py
src/graph_tool/inference/blockmodel.py

commit 66086427
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    Graph.copy_property(): remove 'compatible graphs' semantics for edge properties
    
    With this, edge properties with convertible types are always copied,
    regardless if the edge set is the same between target and source
    graphs. In case the edge set is not the same, the properties are copied
    only for the edges in the intersection.

src/graph/graph_properties_copy.hh
src/graph_tool/__init__.py

commit 24f38401
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-29

    Fix some compilation warnings

src/boost-workaround/boost/graph/graphml.hpp
src/graph/gml.hh
src/graph/graphml.cpp

commit 7067c4fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-23

    global_clustering(): add `ret_counts` parameter

src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph_tool/clustering/__init__.py

commit 65142f35
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-19

    uncertain_blockmodel: remove unneeded dummy parameter

src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh

commit 4082cdb1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-19

    Graph.copy_property(): fix compatible graph semantics for edge properties

src/graph/graph_properties_copy.hh

commit a182344c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-19

    inference.rst: update reference

doc/demos/inference/inference.rst

commit d0646aa4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-13

    graph_io_binary.hh: figure out endianess at compile-time

src/graph/graph_io_binary.hh

commit e81cdd98
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-11

    PPBlockState(): add compatibility functions
    
    This fixes issue #668

src/graph_tool/inference/planted_partition.py

commit d546bb2b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-11

    similarity(): fix issue with asymmetric option

src/graph/topology/graph_similarity.cc

commit cff7450e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-11

    Fix some clang warnings

src/boost-workaround/boost/graph/maximum_weighted_matching.hpp
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/layout/graph_arf.hh
src/graph/topology/graph_subgraph_isomorphism.cc

commit 6891e399
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-11

    run_action(): slight simplifications and code style changes

src/graph/graph_filtering.hh

commit c55a2801
Merge: 66d1db43 e67702c9
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-07-11

    Merge branch 'improved-action-dispatch' into 'master'
    
    Use lambdas and pack expansion to reduce template instantiations in action_dispatch
    
    This change produces significant reductions in compiler memory use (4.15GB to 2.81GB in my `graph_assortativity` testcase) and compiler runtime (180m to 168m overall, 206s to 188s in the testcase) by:
    
    1. Performing type iteration with parameter pack expansion where possible
    2. Testing the stored `boost::any` types sequentially instead of all at once (M+N instead of M*N operations)
    
    I see no significant change in runtime with this approach, though it should in theory be an improvement.
    
    See merge request count0/graph-tool!33

commit e67702c9
Author: Jeff Trull <edaskel@att.net>
Date:   2020-07-10

    Use lambdas and pack expansion to reduce template instantiations in action_dispatch

src/graph/graph_filtering.hh
src/graph/mpl_nested_loop.hh

commit 66d1db43
Merge: bc1ada4b 3438f227
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-07-10

    Merge branch 'header-cleanup' into 'master'
    
    Improve build times through header removal and relocation
    
    See merge request count0/graph-tool!31

commit 3438f227
Author: Jeff Trull <edaskel@att.net>
Date:   2020-07-08

    Improve build times through header removal and relocation
    
    - Eliminate unused headers
    - reduce dependencies among headers (slightly)
    
    The include-what-you-use tool (IWYU) was used to analyze header
    dependencies and recommend fixes; some additional manual work was
    then performed.
    
    Add missing include

src/graph/centrality/graph_closeness.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/dynamics/graph_discrete.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_vprop.cc
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_copy.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_group.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graphml.cpp
src/graph/histogram.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/int_part.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_sfdp.cc
src/graph/numpy_bind.hh
src/graph/read_graphviz_new.cpp
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_distance.cc
src/graph/topology/graph_maximal_cliques.hh
src/graph/util/graph_search.hh

commit bc1ada4b
Merge: eabd9979 0b9ddea9
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-07-10

    Merge branch 'bugfix/planar-layout-pos' into 'master'
    
    Ensure supplied position map for planar_layout is owned by view
    
    See merge request count0/graph-tool!32

commit 0b9ddea9
Author: Jeff Trull <edaskel@att.net>
Date:   2020-07-09

    Ensure supplied position map for planar_layout is owned by view

src/graph_tool/draw/__init__.py

commit eabd9979
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-09

    CI: disable LTO with clang

.gitlab-ci.yml

commit f5902d73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-09

    README.md: fix reference to COPYING and COPYING.LESSER

README.md

commit 1a3b804c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-09

    Refer to numpy instead of ~numpy in docstrings

src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit fe232c9d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-09

    load_graph_from_csv(): Synchronize options with Graph.add_edge_list()

src/graph_tool/__init__.py

commit 3db1d2d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-09

    Graph.add_edge_list(): improve handling of hashed=True for arbitrary types

src/graph/graph_python_interface.cc
src/graph/graph_python_interface_imp1.cc
src/graph_tool/__init__.py

commit 541f949c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-08

    Fix PropertyMap.coerce_type() with python::object

src/graph_tool/__init__.py

commit d2990fbf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-08

    Add missing documentation file

doc/demos/inference/_assortative.rst

commit dfe6ee99
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-08

    graph_clustering.hh: fix jackknife variance

src/graph/clustering/graph_clustering.hh

commit 43853fdb
Merge: 1a4c00b9 4c3b87a8
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-07-08

    Merge branch 'feature/lambda-conversion-WIP' into 'master'
    
    Mass bind -> lambda conversion
    
    See merge request count0/graph-tool!30

commit 1a4c00b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-08

    ModularityState: fix docstring typo

src/graph_tool/inference/modularity.py

commit cd6966c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-08

    Graph.list_properties(): fix spacing

src/graph_tool/__init__.py

commit cfd37051
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-08

    graph_clustering.hh: improve speed of triangle counting

src/graph/clustering/graph_clustering.hh

commit 4c3b87a8
Author: Jeff Trull <edaskel@att.net>
Date:   2020-07-06

    Mass conversion of bind() calls to lambdas
    
    Source file work done with custom-modified versions of clang-format
    and clang-tidy, via the modernize-avoid-bind checker. Headers were
    modified by hand. A script removed uses of <functional> and <boost/bind.hpp>.

src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_trust_transitivity.cc
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/correlations/graph_assortativity.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_dijkstra.cc
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_parallel.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/util/graph_search.cc

commit 1f792136
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-02

    Graph.list_properties(): do not sort properties

src/graph_tool/__init__.py

commit 64520e73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-02

    Fix PropertyDict.clear()

src/graph_tool/__init__.py

commit 867d13c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-07-02

    konect.py: decrease memory usage when loading networks
    
    This implements buffered io, instead of loading the entire edge list to memory.

src/graph_tool/collection/konect.py

commit 399d74aa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-29

    konect.py: fix parsing of node properties

src/graph_tool/collection/konect.py

commit 16af6550
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-29

    Add support for zstandard compression

src/graph/graph_io.cc
src/graph_tool/__init__.py

commit 3ad01bce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-26

    Bump version to 2.34dev

configure.ac

commit 2ee45bd6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-26

    Bump version to 2.33

configure.ac

commit 49caa89d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-26

    Fix debian release build

release/debian/Dockerfile
release/debian/debian/copyright

commit 54bdd816
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-26

    dynamics: fix docstrings

src/graph_tool/dynamics/__init__.py

commit 8e161132
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-26

    Documentation update

doc/demos/inference/_background.rst
doc/gt_theme/static/flasky.css

commit fda2eafd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-26

    planted_partition: update docstrings and add convenience methods

doc/demos/inference/inference.rst
src/graph_tool/inference/planted_partition.py

commit f9684ed2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-25

    Fix problem in (Vertex/Edge)PropertyMap.__eq__() when compared to other types

src/graph_tool/__init__.py

commit 9e70cee8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-25

    modularity(): add ``gamma`` parameter

src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph_tool/inference/modularity.py

commit 4059c511
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-25

    GraphView: slight clarification to docstring

src/graph_tool/__init__.py

commit 4e68901c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-25

    load_graph_from_cvs(): add ``strip_whitespace`` option

src/graph_tool/__init__.py

commit 668f14c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-25

    Implement equality operator for (Vertex/Edge)PropertyMap

src/graph/graph_bind.cc
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph_tool/__init__.py

commit 14011da1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-25

    Implement PropertyMap.coerce_types()

src/graph_tool/__init__.py

commit 836b86fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-16

    Fix entropy_args in PartitionCentroidState and ModeClusterState

src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py

commit 89bcbbf6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-16

    Improve documentation for assortative community inference

doc/demos/inference/inference.rst
doc/inference.rst
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/planted_partition.py

commit ef3b921e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-16

    inference: implement ModularityState

src/graph/inference/Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/modularity/graph_modularity.cc
src/graph/inference/modularity/graph_modularity.hh
src/graph/inference/modularity/graph_modularity_mcmc.cc
src/graph/inference/modularity/graph_modularity_multiflip_mcmc.cc
src/graph_tool/inference/__init__.py
src/graph_tool/inference/modularity.py

commit a5ba1166
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-15

    Graph.copy_property(): default `g` to graph that owns `src`

src/graph_tool/__init__.py

commit 48759a07
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-14

    PropertyMap.get/set_2d_array(): Improve docstring

src/graph_tool/__init__.py

commit 4bcfb3ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-13

    Graph.add_edge_list(): Add docstring example

src/graph_tool/__init__.py

commit c9dd78bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-09

    CI: adjust LTO concurrency for GCC/clang

.gitlab-ci.yml

commit 819ad625
Merge: c40329b2 b129862b
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-06-09

    Merge branch 'gtk' into 'master'
    
    Allow graph_tool.draw.draw_hierarchy to be used without GTK installed
    
    See merge request count0/graph-tool!29

commit b129862b
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-06-08

    Allow graph_tool.draw.draw_hierarchy to be used without GTK installed

src/graph_tool/draw/__init__.py

commit c40329b2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-08

    CI: avoid race condition in parallel sphinx-build

.gitlab-ci.yml

commit 2c87c01d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-07

    Change license from GPL3 to LGPL3

COPYING
COPYING.LESSER
Makefile.am
README.md
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/draw/pycairo_aux.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
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src/graph/fast_vector_property_map.hh
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src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
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src/graph/generation/graph_geometric.cc
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src/graph/generation/graph_lattice.cc
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src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_maxent_sbm.cc
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src/graph/generation/graph_predecessor.cc
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src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
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src/graph/generation/graph_sbm.cc
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src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
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src/graph/generation/sampler.hh
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src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
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src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
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src/graph/inference/graph_latent_multigraph.cc
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src/graph/inference/partition_centroid/graph_partition_centroid.cc
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src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
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src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
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src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
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src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
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src/graph/inference/planted_partition/graph_planted_partition.cc
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src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
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src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
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src/graph/random.cc
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src/graph/shared_map.hh
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src/graph/spectral/graph_incidence.cc
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src/graph/spectral/graph_laplacian.cc
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src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
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src/graph/spectral/graph_transition.cc
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src/graph/stats/graph_average.cc
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src/graph/topology/graph_diameter.cc
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src/graph/topology/graph_dominator_tree.cc
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src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
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src/graph/topology/graph_similarity.hh
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src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/planted_partition.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 97b45f86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-07

    CI: run sphinx tests in parallel

.gitlab-ci.yml

commit 463dfbb4
Merge: 42e857bc 4c8a80b5
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-06-06

    Merge branch 'simplify-shared-any' into 'master'
    
    Remove boost::any wrapper around std::shared_ptr
    
    See merge request count0/graph-tool!28

commit 42e857bc
Merge: 46993132 8ba30ef3
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-06-06

    Merge branch 'UB-constness' into 'master'
    
    Remove const qualifier from object that can be modified
    
    See merge request count0/graph-tool!27

commit 8ba30ef3
Author: Jeff Trull <edaskel@att.net>
Date:   2020-06-06

    Rename newly-private data member appropriately

src/graph/graph_properties.hh

commit 4c8a80b5
Author: Jeff Trull <edaskel@att.net>
Date:   2020-06-06

    Remove boost::any wrapper around std::shared_ptr
    
    std::shared_ptr provides a limited amount of type erasure natively
    based on void* and the fact that it stores the original type in the
    deleter. As a result, if you know the original type, you can call
    std::static_pointer_cast and recover a legitimate shared_ptr of the
    right type, very efficiently.
    
    It looks like the use of boost::any in this code is:
    
    1) to hide the pointed-to type so a uniform container can be used
    2) to represent "no pointer"
    
    both of which can be handled natively by shared_ptr<void> with a small
    performance gain from removing one indirection.

src/graph/graph.hh
src/graph/graph_filtering.hh

commit 46993132
Merge: 6f8ba179 e2827d35
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-06-06

    Merge branch 'pythonedge-final' into 'master'
    
    Mark PythonEdge as "final" per clang-tidy
    
    See merge request count0/graph-tool!26

commit ac746100
Author: Jeff Trull <edaskel@att.net>
Date:   2020-06-05

    Remove const qualifier from object that can be modified
    
    Modifying an object declared const is technically undefined behavior,
    and compilers are entitled to do as they like with such code. The most
    likely result - in the event of some future optimizer - would be
    elimination of the code performing the modification, although it could
    theoretically be anything.
    
    Given that ConstantPropertyMap defines an assignment operator already,
    simply changing the underlying data member to non-const (while making
    it private) seems to achieve the same result as the current code while
    avoiding UB.

src/graph/graph_properties.hh

commit e2827d35
Author: Jeff Trull <edaskel@att.net>
Date:   2020-06-05

    Mark PythonEdge as "final" per clang-tidy
    
    Classes and methods marked final have some optimization possibilities
    for the compiler, as some vtable lookups can be eliminated.

src/graph/graph_python_interface.hh

commit 6f8ba179
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-05

    NestedBlockState: fix bfield influence for higher levels
    
    This fixes issue #662

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 164ac5f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-05

    release: Increase NJOBS in Dockerfile

release/debian/Dockerfile

commit 0ca5f78f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-02

    inference: implement assortative SBMs

src/graph/inference/Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/planted_partition/graph_planted_partition.cc
src/graph/inference/planted_partition/graph_planted_partition.hh
src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc
src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/planted_partition.py

commit 32951567
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-02

    inference: isolate entropy_args

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py

commit 96af75c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-06-02

    sampler.hh: fix uniform_sample()

src/graph/generation/sampler.hh

commit 6bc2aa62
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-30

    CI: remove ubuntu disco

.gitlab-ci.yml

commit 46465e45
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-30

    Bump version to 2.33dev

configure.ac

commit 781cd4e8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-29

    Bump version to 2.32

configure.ac

commit 5b6034b0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-29

    isomorphism(): fix bug with large vertex invariants
    
    This fixes issues #653 and #655

src/graph_tool/topology/__init__.py

commit ac6a7a71
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-29

    graph_draw(): fix issue with property maps being changed
    
    This fixes issue #658

src/graph_tool/draw/cairo_draw.py

commit c0b1794f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-29

    inference: update cookbook and docstrings

doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst
doc/demos/inference/inference.rst
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py

commit 100f01d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-10

    Implement partition modes, centroid and manipulation functions

doc/inference.rst
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/graph_inference.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi.hh
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_rmi_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/uncertain_blockmodel.py

commit d5f2e2c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-28

    Fix compilation warnings with GCC 10

src/graph/graph_adjacency.hh
src/graph/graph_properties.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/layout/graph_arf.hh

commit 068d66d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-28

    graph_draw(): Fix automatic edge gradient for pie vertex shapes

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/__init__.py

commit 0996ea8b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-28

    CI: add ubuntu focal build

.gitlab-ci.yml
release/debian/Dockerfile

commit 25270bf5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-05

    Fix Graph.copy_property() for undirected graphs
    
    This fixes a problem which occurs when copying external property maps
    when using undirected graphs.

src/graph_tool/__init__.py

commit 162b8c06
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-01

    uncertain_blockmodel: fix state copying

src/graph_tool/inference/uncertain_blockmodel.py

commit 7008f4ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-05-01

    blockmodel: fix copying with new graph

src/graph_tool/inference/blockmodel.py

commit 2f049ff6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-27

    Fix computation and sampling from marginal multigraph

src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit f2d4b756
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-26

    uncertain_blockmodel: avoid copying uentropy_args_t

src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh

commit d329acf4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-26

    uncertain_blockmodel: implement set_state()

src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit bf3c8e36
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-26

    uncertail_blockmodel: implement marginal_multigraph_sample and marginal_graph_sample

src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 36917e1f
Merge: d2dc156a 67f7464d
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-05-18

    Merge branch 'imports' into 'master'
    
    Remove unused imports
    
    See merge request count0/graph-tool!25

commit 67f7464d
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-05-17

    Remove unused imports

src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/search/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit d2dc156a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-21

    mpl_nested_loop.hh: minor code-style changes

src/graph/mpl_nested_loop.hh

commit 3a03ce46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-21

    nested_for_each(): fix version without value arguments
    
    The version of nested_for_each() without boost::any arguments must be
    called for every type, not only the first. This means the wrapped action
    must return false, otherwise the compiler will omit the remaining calls.

src/graph/mpl_nested_loop.hh

commit df5da3c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-21

    graph_draw(): fix fit_view=False behavior
    
    This fixes issue #651

src/graph_tool/draw/cairo_draw.py

commit 9f3fc571
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-15

    Maximum-weight bipartite matching: improve performance

src/graph/topology/graph_bipartite_weighted_matching.hh

commit a72dc4ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-15

    dynamics: fix behavior of epidemic models with constant_beta=True

src/graph/dynamics/graph_discrete.hh
src/graph_tool/dynamics/__init__.py

commit 7ddc03f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-10

    use inspect.getfullargspec instead of inspect.getargspec

src/graph_tool/decorators.py

commit 343c7b61
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-10

    Fix docstring typos

doc/demos/matplotlib/matplotlib.rst
src/graph_tool/dynamics/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 6b062a27
Merge: 77c95cc2 bf16ec13
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-04-21

    Merge branch 'speedup/remove-dispatch-exceptions' into 'master'
    
    Remove exception throwing from hot path in dispatch
    
    See merge request count0/graph-tool!24

commit bf16ec13
Author: Jeff Trull <edaskel@att.net>
Date:   2020-04-18

    Remove exception throwing from hot path in dispatch
    
    Eliminate fail_cast and stop_iteration exceptions, replacing their
    use with bool success codes and fold expressions.

src/graph/mpl_nested_loop.hh

commit 77c95cc2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-02

    Remove deprecated Python 2 compatibility

src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit f758e17e
Merge: 12bdfb90 dfa0fa1d
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2020-04-01

    Merge branch 'warnings' into 'master'
    
    Fix deprecation warnings
    
    See merge request count0/graph-tool!23

commit dfa0fa1d
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-04-01

    Use collections.abc.Iterable instead of collections.Iterable

src/graph_tool/__init__.py

commit 3c47097d
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-04-01

    Use inspect.getfullargspec instead of inspect.getarcspec

src/graph_tool/decorators.py

commit 5d5f626d
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2020-04-01

    Turn off escape sequences in docstrings

src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/topology/__init__.py

commit 12bdfb90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-04-01

    dynamics: fix unwanted graph modification in doctests

src/graph_tool/dynamics/__init__.py

commit 03744120
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-31

    central_point_dominance(): fixup docstest

src/graph_tool/centrality/__init__.py

commit 33abde0e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-30

    CI: remove cosmic build

.gitlab-ci.yml

commit 07b32023
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-30

    CI: add cosmic and disco builds

.gitlab-ci.yml

commit de6d1d4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-30

    CI: fix debian build and add debian versioning
    
    This fixes issue #642

release/debian/Dockerfile
release/debian/debian/rules

commit 80d54833
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-30

    CI: enable -flto to speedup compilation

.gitlab-ci.yml

commit 9b9d74ee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-29

    CI: fix repository issue with docker release

.gitlab-ci.yml
release/docker/Dockerfile

commit 2cb4eea4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-29

    CI: prevent tests being run for relase tags

.gitlab-ci.yml

commit 2fa3ce82
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-29

    Bump version to 2.32dev

configure.ac

commit 8561bac9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    Bump version to 2.31

configure.ac

commit bdb172d2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-28

    Fix CI release base

.gitlab-ci.yml

commit 00e73e78
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    all_predecessors(): fix docstring
    
    This fixes issue #619

src/graph_tool/topology/__init__.py

commit 54b7fb85
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    central_point_dominance(): fix doctest

src/graph_tool/centrality/__init__.py

commit 5d433574
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    graph_draw(): fix 'bg_color' when drawing to file
    
    This fixes issue #641

src/graph_tool/draw/cairo_draw.py

commit 5da1cee9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    dynamics: change notation from 'infected' to 'infections'

src/graph_tool/dynamics/__init__.py

commit ef39caab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    dynamics: add vertex-specific parameters for epidemic models

src/graph/dynamics/graph_discrete.hh
src/graph_tool/dynamics/__init__.py

commit a1b97fbe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    dynamics: implement weighted versions of epidemic models
    
    This fixes issue #624

src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph_tool/dynamics/__init__.py

commit 3fb37596
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-27

    betweenness(): fix issue with normalization and central point dominance

src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/graph/centrality/graph_betweenness.cc
src/graph_tool/centrality/__init__.py

commit 50559493
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-26

    Add 'edges' parameter to all_shortest_paths()
    
    This fixes issue #622

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 1f67a67f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-26

    Fix get_edges_prop() for layered NestedBlockState
    
    This fixes issue #544

src/graph_tool/inference/layered_blockmodel.py

commit 5571264d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-26

    Diminish docker cpu-shares in CI

.gitlab-ci.yml

commit 611ff5a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-26

    Change max_clique() doctest

src/graph_tool/topology/__init__.py

commit f98c0604
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-26

    Add small test graph to doc/

doc/g_small.gt

commit 5d34f982
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    Fix tarball CI

.gitlab-ci.yml

commit 215139ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    Reduce CI parellelism

release/debian/Dockerfile
release/debian/debian/rules
release/docker/Dockerfile

commit 046a379e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    Add tarball build to CI

.gitlab-ci.yml

commit eacedf72
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    Remove inferfence.rst from CI tests

.gitlab-ci.yml

commit 092e3058
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    Add docker image build to CI

.gitlab-ci.yml
release/docker/Dockerfile
release/docker/PKGBUILD

commit 90357a3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    Add debian release CI integration

.gitlab-ci.yml
release/debian/Dockerfile
release/debian/debian/compat
release/debian/debian/control
release/debian/debian/rules
release/debian/git2debchangelog.sh

commit 4ddc1459
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-25

    ax_boost_python.m4: do a better job of identifying the correct object file

m4/ax_boost_python.m4

commit 9fbbe293
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-23

    Update documentation

doc/demos/cppextensions/cppextensions.rst
doc/demos/matplotlib/matplotlib.rst
doc/pyenv.py
src/graph_tool/inference/uncertain_blockmodel.py

commit af5c99b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-23

    Bump version to 2.31dev

configure.ac

commit 087aace0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-23

    Bump version to 2.30

configure.ac

commit 3b9299e2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-23

    Fix wrong copyright info

configure.ac
src/graph_tool/decorators.py

commit 26903a78
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-23

    Update documentation

doc/demos/inference/_minimization.rst
doc/demos/inference/_model_selection.rst
doc/demos/matplotlib/matplotlib.rst

commit 83db893e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-23

    Update documentation

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/inference.rst
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 9bbcb771
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Forward boost LD_FLAGS
    
    This fixes #554 and #555

configure.ac
m4/ax_lib_cgal_core.m4

commit 8ffeeb12
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    motifs(): fix bug with 'return_maps=True`
    
    This fixes issue #627

src/graph_tool/clustering/__init__.py

commit 83ef9971
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    sfdp_layoyt(): check type of 'groups' parameter
    
    This fixes issue #632

src/graph_tool/draw/__init__.py

commit d1cdc9da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Update remaining copyright information

src/graph_tool/__init__.py

commit 1408c345
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    graph_draw(): fix fit_to_view()

src/graph_tool/draw/cairo_draw.py

commit 5c75fd6d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Add matplotlib integration cookbook

doc/demos/index.rst
doc/demos/matplotlib/matplotlib.rst

commit 807c64df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Improve animation cookbook documentation

doc/demos/animation/animation.rst
doc/demos/animation/animation_dancing.py
doc/demos/animation/animation_sirs.py
doc/demos/animation/animation_zombies.py

commit 97c70930
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Update copyright information

doc/conf.py
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/draw/pycairo_aux.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/dynamics/graph_dynamics.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
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src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_maxent_sbm.cc
src/graph/generation/graph_maxent_sbm.hh
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
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src/graph/generation/graph_rewiring.cc
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src/graph/generation/graph_sbm.cc
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src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
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src/graph/graph_properties_imp1.cc
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src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/idx_map.hh
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
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src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
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src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
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src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
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src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
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src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
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src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/openmp_lock.hh
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src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
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src/graph/spectral/graph_incidence.cc
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src/graph/spectral/graph_laplacian.cc
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src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
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src/graph/spectral/graph_transition.cc
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src/graph/stats/graph_parallel.cc
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src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_components.cc
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src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
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src/graph/topology/graph_matching.cc
src/graph/topology/graph_maximal_cliques.cc
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src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
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src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 557588b1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Update documentation

.gitlab-ci.yml
doc/demos/cppextensions/Makefile
doc/demos/cppextensions/cppextensions.rst
doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst
doc/demos/inference/inference.rst
doc/gt_theme/static/flasky.css
doc/inference.rst
doc/pyenv.py
doc/quickstart.rst
src/graph_tool/centrality/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/topology/__init__.py

commit c4c7e675
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    graph_draw(): revamp fit_view and matplotlib support
    
    This fixes issues #628, #516, #461, #418, #280.

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit a3f51090
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Improve MCMC testing

doc/test_inference_mcmc.py

commit 75418ae1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    graph_draw(): implement text outline color and width

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 1e3b2e38
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    collection: fix error when parsing Konect metadata

src/graph_tool/collection/konect.py

commit b1f60a24
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Fix conversion error in EdgePropertyMap

src/graph_tool/__init__.py

commit 60ee75ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    LatentMultigraphBlockState: fix self-loop marginal collection

src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh

commit 71357981
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-22

    Makefile.am: add missing file

src/graph/Makefile.am

commit bd167765
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-08

    Improve MCMC tests

doc/test_inference_mcmc.py

commit ac607229
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-08

    multiflip_mcmc(): fix detailed balance

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph_tool/inference/nested_blockmodel.py

commit 2da36167
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-08

    gibbs_sweep(): fix detailed balance

src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph_tool/inference/blockmodel.py

commit 70f6e1bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-01

    blockmodel: change paramter 'max_BE' to a more explicit 'dense_bg'

doc/test_inference.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 5a041681
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-29

    multiflip: remove O(N^2) corner case with coalescence

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph_tool/inference/blockmodel.py

commit 5062d1e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-21

    inference: keep track of entropy range in mcmc_equilibrate() when force_niter is not None

src/graph_tool/inference/mcmc.py

commit 08dfc58c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-20

    inference: implement coealescence split stage in multiflip_mcmc_sweep()

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh

commit 4eee3d0d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-05

    Fix Graph.__repr__ with property maps

src/graph_tool/__init__.py

commit fcd6f2b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-05

    Fix includes in Makefile.am

Makefile.am
src/graph/inference/Makefile.am

commit 49ea6aa0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-28

    Paritition mode: implement nested partitions

src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph_tool/inference/__init__.py
src/graph_tool/inference/partition_modes.py

commit 918ae899
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-23

    Initial implementation of partition modes

src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_inference.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_modes/graph_partition_mode.cc
src/graph/inference/partition_modes/graph_partition_mode.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering.hh
src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc
src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/partition_centroid.py
src/graph_tool/inference/partition_modes.py

commit 2d134e6d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-05

    Implement bipartite maximum weighted matching

src/boost-workaround/boost/graph/maximum_weighted_matching.hpp
src/graph/topology/Makefile.am
src/graph/topology/graph_bipartite_weighted_matching.hh
src/graph/topology/graph_matching.cc
src/graph_tool/topology/__init__.py

commit cc5d0046
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-14

    Add support for maximum weight matching
    
    This also adds more consistency with the heuristic version of the code.

src/boost-workaround/boost/graph/maximum_weighted_matching.hpp
src/graph/flow/Makefile.am
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/topology/Makefile.am
src/graph/topology/graph_matching.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_topology.cc
src/graph_tool/draw/__init__.py
src/graph_tool/topology/__init__.py

commit ad33169d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-23

    Implement UncertainBaseState.collect_marginal_multigraph() and marginal_multigraph_entropy()

src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit ca3ba6bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-23

    Fix bug in LayeredBlockState.get_edges_prob()

src/graph_tool/inference/layered_blockmodel.py

commit abfc17cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-23

    Fix bug in PropertyDict.items()

src/graph_tool/__init__.py

commit ebe35be5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-23

    Improve numpy binding to boost::multi_array

src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/numpy_bind.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh

commit 6a5b5703
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    graph_adjacency.hh: force inlining of edge iterator dereferencing

src/graph/graph_adjacency.hh

commit 2a175140
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    inference: NestedBlockState constructor defaults to sampling=True

src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py

commit 8d546347
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    inference: speedup addition of new groups

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit 85d8c6c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    Improve test_inference_mcmc.py

doc/test_inference_mcmc.py

commit 48b231bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    Implement VICenterState

src/graph/inference/Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/partition_centroid/graph_partition_centroid.cc
src/graph/inference/partition_centroid/graph_partition_centroid.hh
src/graph/inference/partition_centroid/graph_partition_centroid_mcmc.cc
src/graph/inference/partition_centroid/graph_partition_centroid_multiflip_mcmc.cc
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/partition_centroid.py

commit 550ab951
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    inference: optimize multiflip_mcmc() by disabling uncessary edge list updates

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit bf0e2475
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-07

    Switch to C++ syntax for function attributes

src/graph/fast_vector_property_map.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_filtered.hh
src/graph/graph_selectors.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/support/cache.hh
src/graph/inference/support/int_part.hh
src/graph/inference/support/util.hh
src/graph/mpl_nested_loop.hh

commit 161d5214
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-02

    inference: fix split-merge bias in multiflip MCMC

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 1cc4bfb1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-01

    inference: modify LatentMultigraphBlockState.collect_marginal() to gather multiedges

src/graph_tool/inference/uncertain_blockmodel.py

commit daf7502b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-01-01

    inference: Add LatentMultigraphBlockState as a wrapper to UncertainBlockState

src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 4822ba5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-29

    inference: fix clabel enforcement in mcmc/multiflip_mcmc

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 3ca7df5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-27

    inference: fix mergesplit with clabel in multflip_mcmc_sweep()

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit de8556fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-14

    inference: add scatter stage split to multiflip_mcmc

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 8918329f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-14

    inference: preserve pclabel in mcmc

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit 1d780746
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-13

    PropertyMap: fix pickle backwards compatibility

src/graph_tool/__init__.py

commit 91954a2d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-11

    Fix typo in inference HOWTO

doc/demos/inference/_minimization.rst

commit 72cb613d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-11

    inference: prevent clabel invalidation in multiflip_mcmc_sweep()

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 6bffcc02
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-12-10

    inference: add random imbalance to split staging in multiflip_mcmc_sweep()

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 8062aa44
Author: Stuart Berg <bergs@janelia.hhmi.org>
Date:   2020-01-30

    hierarchy_minimize(): Fix NameError when the caller supplies a hierarchy that is missing the top level

src/graph_tool/inference/nested_blockmodel.py

commit 95c0d9f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-02

    Fix autoconf detection of CGAL 5
    
    This fixes issue #625

m4/ax_lib_cgal_core.m4

commit 57793779
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-03-02

    Add missing 'raise' in group_vector_property()
    
    This fixes issue #633

src/graph_tool/__init__.py

commit 9aeba521
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2020-02-17

    configure: workaround for boost 1.72 coroutine bug

m4/ax_boost_coroutine.m4

commit ed3d3c25
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-11-22

    test_inference_mcmc: change figure size

doc/test_inference_mcmc.py

commit b694522e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-11-22

    inference: refactor multiflip MCMC

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph_tool/inference/blockmodel.py

commit 080938d8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-27

    Fix swap counting in TemperingState

src/graph_tool/inference/mcmc.py

commit cdcddcc4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-20

    Add option 'window' and 'return_window' to interactive_window()
    
    This makes it easier to do interactive animations, e.g. when using IPython.

src/graph_tool/draw/gtk_draw.py

commit 6a62cc4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-20

    Add internal property map information to Graph.__repr__()

src/graph_tool/__init__.py

commit 5a5a9a57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-20

    Implement random_shortest_path() and count_shortest_paths()

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 12691b83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-13

    blockmodel: add 'recombine' move to multiflip_mcmc()

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph_tool/inference/blockmodel.py

commit 95dad5c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-21

    blockmodel: add if constexpr

src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit 53fe126e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-21

    blockmodel: Fix issue with OverlapBlockState

src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph_tool/inference/overlap_blockmodel.py

commit a7a220ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-21

    TemperingState: count swap attempts and improve swap performance

src/graph_tool/inference/mcmc.py

commit 775878d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-10-01

    blockmodel: avoid copying of entropy_args_t

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/support/cache.hh
src/graph/inference/support/int_part.hh

commit 2fe5bab4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-27

    blockmodel: change set_blocks() to set_state()

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit c2133547
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-26

    test_inference_mcmc.py: add diverse initializations

doc/test_inference_mcmc.py

commit 3797adfb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-26

    blockmodel: modify verbose information

src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh

commit 822db1f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-22

    blockmodel: simplify random neighbor sampling

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/support/graph_neighbor_sampler.hh

commit 8477c7ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-17

    blockmodel: small tweaks to egroups and forced inlining

src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh

commit a7496657
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-17

    blockmodel: performance improvements to neighbor sampler

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/support/graph_neighbor_sampler.hh

commit be0fc677
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-25

    General improvements to multiflip and gibbs mcmc

doc/test_inference_mcmc.py
src/graph/fast_vector_property_map.hh
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 9b24872c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-20

    inference: fix gibbs_sweep()

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit a6152ebf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-09-05

    vertex_similarity(): fix overflow error
    
    This fixes issue #608

src/graph/topology/graph_vertex_similarity.cc

commit 74eb5b3c
Merge: 878fb5b6 ab795217
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2019-08-22

    Merge branch 'avoid-std-max_element' into 'master'
    
    Replace std::max_element with boost::first_max_element.
    
    See merge request count0/graph-tool!19

commit ab795217
Author: Stuart Berg <bergs@janelia.hhmi.org>
Date:   2019-08-19

    adjacency and blockmodel: On clang, replace std::max_element with boost::first_max_element where necessary to avoid #576

src/graph/graph_adjacency.hh
src/graph/inference/blockmodel/graph_blockmodel.hh

commit 878fb5b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-19

    inference: remove 'allow_empty' option

doc/test_inference.py
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/util.py

commit 67372fc8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-17

    inference: improve multicanonical sampling

src/graph_tool/inference/mcmc.py

commit 3f0baa5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-17

    inference: remove dead code

src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh

commit fa9122a2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-17

    inference: add constexpr

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/int_part.cc

commit 4a8d6f3c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-12

    blockmodel: fix issue with pickling in corner case

src/graph_tool/inference/blockmodel.py

commit 930333bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-08-11

    correlations: fix weighted standard deviation

src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_correlations.hh

commit 69151d75
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-29

    Fix doctring for UncertainBaseState.get_edge[s]_prob()

src/graph_tool/inference/uncertain_blockmodel.py

commit 2ddfaaba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-21

    int_part.cc: add constexpr

src/graph/inference/support/int_part.cc

commit d544fdab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-21

    Remove 'ignore_degrees' remnant

src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit d9a6289b
Merge: b89a4b3e f1d8726b
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2019-07-18

    Merge branch 'konect-cc' into 'master'
    
    Updated the link to KONECT in documentation to the main URL
    
    See merge request count0/graph-tool!18

commit f1d8726b
Author: Mikuláš Poul <mikulaspoul@gmail.com>
Date:   2019-07-18

    Updated the link to KONECT in documentation to the main URL

src/graph_tool/collection/__init__.py

commit b89a4b3e
Merge: de26e3f8 97d964a5
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2019-07-17

    Merge branch 'shortest-distance-docs' into 'master'
    
    Small tweaks to topology.shortest_distance docstrings
    
    See merge request count0/graph-tool!17

commit 97d964a5
Author: Mikuláš Poul <mikulaspoul@gmail.com>
Date:   2019-07-17

    Small tweaks to topology.shortest_distance docstrings

src/graph_tool/topology/__init__.py

commit de26e3f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-15

    pcg-cpp: sync with git head (871d0494ee9c9)

src/pcg-cpp/include/pcg_extras.hpp
src/pcg-cpp/include/pcg_random.hpp
src/pcg-cpp/include/pcg_uint128.hpp

commit b063c337
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-15

    Bump version to 2.30dev

configure.ac

commit 6f58fbed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-12

    Bump version to 2.29

configure.ac

commit 79e2c523
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-13

    graph_draw(): Propagate vertex/edge properties in multilevel interactive layout
    
    This fixes issue #595

src/graph_tool/draw/gtk_draw.py

commit f4520a95
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-13

    boykov_kolmogorov_max_flow(): Fix problem with parallel reciprocal edges
    
    This fixes issue #598

src/graph/flow/graph_augment.hh

commit f3ec0a54
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-13

    Doctest fixes

doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/quickstart.rst
src/graph_tool/centrality/__init__.py
src/graph_tool/topology/__init__.py

commit 2d483063
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-13

    collection: Default to konect.cc with fallback to konect.uni-koblenz.de

src/graph_tool/collection/konect.py

commit 38d70115
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-13

    cppextensions: Fix example code

doc/demos/cppextensions/cppextensions.rst
doc/demos/cppextensions/kcore.py

commit e8be2a92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-13

    generate_maxent_sbm(): Fix problem with directed graphs without self-loops

src/graph/generation/graph_maxent_sbm.hh

commit 25c7ee92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-12

    Fix Graph.get_out_degrees() and Graph.get_out_degrees()
    
    This also adds the missing Graph.get_total_degrees() and missing
    documentation.
    
    This fixes issue #596

doc/graph_tool.rst
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 061dabed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-07-05

    graph_maxent_sbm.hh: Fix sampling with self-loops

src/graph/generation/graph_maxent_sbm.hh

commit 54a93039
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-29

    max_cliques(): Remove 'iterator' parameter

src/graph_tool/topology/__init__.py

commit a7d49aa2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-28

    configure.ac: Change --enable-cgal-valgrind to --enable-valgrind

configure.ac

commit 16cbc3bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-28

    topology: Fix issue with returned iterators leaving dangling references

src/graph/topology/graph_maximal_cliques.cc
src/graph_tool/topology/__init__.py

commit 07196449
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-27

    Implement max_cliques()

src/graph/topology/Makefile.am
src/graph/topology/graph_maximal_cliques.cc
src/graph/topology/graph_maximal_cliques.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 3c84519f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-27

    numpy_bind.hh: Avoid direct memory allocation; delegate to numpy

src/graph/numpy_bind.hh

commit 878fb933
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-26

    load_graph_from_csv(): Fix loading from compressed files with Python 3
    
    This fixes issue #593

src/graph_tool/__init__.py

commit 354c0a1a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-23

    vertex_similarity(): Add salton, hub-promoted, hub-suppressed, resource-allocation and leicht-holme-newman

src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph_tool/topology/__init__.py

commit 9137c542
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-23

    vertex_similarity(): Add support for weighted and multigraphs
    
    This fixes issue #592.

src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph_tool/topology/__init__.py

commit 2c084876
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    solve_sbm_fugacities(): Improve numerical stability with zero degrees

src/graph_tool/generation/__init__.py

commit 6a60a564
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    .gitlab-ci.yml: Disable Python 2 tests

.gitlab-ci.yml

commit e9cc8f1c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    Implement generate_maxent_sbm()

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_maxent_sbm.cc
src/graph/generation/graph_maxent_sbm.hh
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py

commit 0b01305b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    latent_multigraph(): Add `verbose` parameter

src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph_tool/inference/latent_multigraph.py

commit 36d81582
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    label_largest_component(): Remove no-op line

src/graph_tool/topology/__init__.py

commit 4b08c433
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    graph_eingenvector.hh: Fix compilation warning

src/graph/centrality/graph_eigenvector.hh

commit 57716b90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    Implement Vector_cdouble

src/graph/graph_bind.cc
src/graph/graph_util.hh
src/graph_tool/__init__.py

commit c3a5066b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-19

    Fix compilation problem with GCC 9
    
    This fixes issue #580.

src/graph/graph_io.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/layout/graph_sfdp.cc

commit c353b76e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-12

    README.md: Update minimal compiler requirements
    
    This fixes issue #585.

README.md

commit 76a71484
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-10

    Bump version to 2.29dev

configure.ac

commit e5760dfc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-06

    Bump version to 2.28

configure.ac

commit 292a8aaa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-07

    Add missing files to inference/Makefile.am

Makefile.am
src/graph/inference/Makefile.am

commit a2e43308
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-06

    Change doc copyright info

doc/conf.py

commit c86f39ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-06

    Include cppextensions cookbook section

doc/demos/cppextensions/Makefile
doc/demos/cppextensions/cppextensions.rst
doc/demos/cppextensions/kcore.cc
doc/demos/cppextensions/kcore.hh
doc/demos/cppextensions/kcore.py
doc/demos/index.rst
src/graph_tool/topology/__init__.py

commit 084f6cf3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-05

    Update copyright information

configure.ac
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/draw/pycairo_aux.cc
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/dynamics/graph_dynamics.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/idx_map.hh
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/openmp_lock.hh
src/graph/parallel_rng.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit dc8030a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-05

    Deprecate custom _wraps() decorator for Python 3
    
    This fixes issue #547

src/graph_tool/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/inference/layered_blockmodel.py

commit 2cbad3d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-05

    str_repr.hh: Switch to decimal represenation of floating types
    
    Instead of hexadecimal, use (exact) decimal representation of floating
    points to achieve compatibility with other graphml readers.
    
    This fixes issue #570.

src/graph/str_repr.hh

commit 28fee35d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-05

    graph_draw(): Avoid drawing selected vertices, when none exist
    
    This fixes issue #551

src/graph_tool/draw/gtk_draw.py

commit 55355c90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-05

    Small documentation fixes

doc/demos/inference/_minimization.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst

commit de0cf806
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-05

    Fix pickling of OverlapBlockState with edge covariates
    
    This fixes issue #550.

src/graph_tool/inference/overlap_blockmodel.py

commit bfba6608
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-04

    scalar_assortativity(): Raise exception for non-scalar properties

src/graph_tool/correlations/__init__.py

commit b22e65f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-04

    Fix issue with multiflip_mcmc()

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 3dbc7b5a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-06-02

    Fix assortativity() for non-scalar property types
    
    This fixes issue #503.

src/graph/correlations/graph_assortativity.cc

commit c732cbf7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-28

    Fix syntax error with Python 2

src/graph_tool/inference/uncertain_blockmodel.py

commit 7bdf4c13
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-27

    eigenvector(): Remove stopping criterion for non-convergence

src/graph/centrality/graph_eigenvector.hh

commit 546ed663
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-27

    Fix compilation issue with clang

src/graph/dynamics/graph_discrete.hh

commit 81c01e75
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-26

    Rename scoped_lock to openmp_scoped_lock
    
    This avoids a collapse with std::scoped_lock.
    
    This fixes issue #511.

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/openmp_lock.hh

commit 0a497c91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-26

    load_graph_from_csv(): Change default to directed=False

src/graph_tool/__init__.py

commit ebd18179
Merge: 5f1c1364 daa99068
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2019-05-27

    Merge branch 'patch-1' into 'master'
    
    Fix m4 recipe for boost::context to work with boost >=1.68
    
    See merge request count0/graph-tool!15

commit 5f1c1364
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-26

    numpy_bind.hh: Replace new with malloc
    
    Numpy will use free() not delete, so we need to use malloc to avoid a
    mismatch.
    
    This fixes issue #579.

src/graph/numpy_bind.hh

commit 803bf8ba
Merge: 4695c1d0 c2b87007
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2019-05-26

    Merge branch 'master' into 'master'
    
    Call cairo.get_include() to find py3cairo.h
    
    See merge request count0/graph-tool!16

commit 4695c1d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-26

    Fix compilation warning

src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh

commit cedfd97f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-26

    Fix issue with measured reconstruction

src/graph_tool/inference/uncertain_blockmodel.py

commit 265e9635
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-26

    Documentation improvements and fixes

doc/demos/inference/_background.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst
doc/gt_theme/static/gt_style.css
doc/pyenv.py
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/inference/latent_multigraph.py
src/graph_tool/topology/__init__.py

commit be6f450d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-05-09

    collection: Revert KONECT url to http://konect.uni-koblenz.de

src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py

commit 8812863d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-28

    Improve label_parallel_edges() and label_self_loops()

src/graph/stats/graph_parallel.hh

commit f8ffd9c1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-28

    inference: Fix issues with reconstruction from epidemic dynamics

src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph_tool/inference/uncertain_blockmodel.py

commit 3512df30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-27

    Documentation improvements and fixes

doc/conf.py
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_reconstruction_dynamics.rst
doc/demos/inference/_sampling.rst
doc/demos/inference/inference.rst
doc/draw.rst
doc/gt_theme/static/flasky.css
doc/pyenv.py
doc/quickstart.rst
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/dynamics/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 9d71c105
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-27

    inference: Fix multiflip MCMC with NestedBlockState

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit 3d854565
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-15

    Documentation improvements

doc/.templates/layout.html
doc/conf.py
doc/gt_theme/static/flasky.css
doc/pyenv.py
doc/quickstart.rst

commit b7d0ea46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-15

    polblogs.gt.gz: cosmetic change to layout

src/graph_tool/collection/polblogs.gt.gz

commit 0e958d61
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-03-30

    Implement Bfield parameter

src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit aebfabed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-03-30

    Add 'edges_only' options to UncertainBlockModel

src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 1d09752d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-03-30

    Implement latent multigraph inference via EM (WIP)

src/graph/inference/Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/graph_latent_multigraph.cc
src/graph/inference/graph_latent_multigraph.hh
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/latent_multigraph.py

commit a4d7dcf3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-02-25

    Add parameter 'b' to collect_vertex_marginals()
    
    This allows arbitrary partitions to be used in the calculation.

src/graph_tool/inference/blockmodel.py

commit 9045c372
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-02-25

    Implement BlockState.get_Be()
    
    This returns the effective number of groups, taking into consideration
    their sizes.

src/graph_tool/inference/blockmodel.py

commit f7e0ec7b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-01-31

    Implement smarter merge-split MCMC

src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/util.hh
src/graph_tool/inference/blockmodel.py

commit e7446106
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-04-15

    Implement reconstruction from dynamics

src/graph/generation/dynamic_sampler.hh
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_multilevel_mcmc.hh
src/graph/inference/graph_inference.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_cising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_continuous.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_discrete.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_epidemics_mcmc_r.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_ising_glauber_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_cising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.cc
src/graph/inference/uncertain/graph_blockmodel_dynamics_pseudo_ising_mcmc_h.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_util.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit c2b87007
Author: Alex Henrie <alexhenrie24@gmail.com>
Date:   2019-04-23

    Call cairo.get_include() to find py3cairo.h
    
    If pycairo was installed from source, py3cairo.h may not have been
    copied to /usr/include/pycairo. It's better to ask the pycairo module
    itself where py3cairo.h is by calling cairo.get_include().

configure.ac

commit 6ea36ec4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-08-07

    Dynamics submodule implementation
    
    This adds the "dynamics" submodule, with implementation of several
    dynamical processes.

configure.ac
doc/dynamics.rst
doc/graph_tool.rst
src/graph/Makefile.am
src/graph/dynamics/Makefile.am
src/graph/dynamics/graph_continuous.cc
src/graph/dynamics/graph_continuous.hh
src/graph/dynamics/graph_discrete.cc
src/graph/dynamics/graph_discrete.hh
src/graph/dynamics/graph_dynamics.cc
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/dynamics/__init__.py

commit 2b749c41
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-01-23

    Improve copying of edge properties

src/graph/graph_bind.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph_tool/__init__.py

commit 1495bc72
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-03-30

    Implement weighted clustering and assortativity

src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py

commit 81232cbf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-02-26

    TemperingState: Add `beta_dl` option

src/graph_tool/inference/mcmc.py

commit 320ee7b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-12-28

    Fix Graph.get_out_edges()

src/graph_tool/__init__.py

commit f7bfd064
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-12-05

    Split PropertyMap into Vertex/Edge/GraphPropertyMap
    
    This improves performance of the Python API.

doc/graph_tool.rst
doc/quickstart.rst
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph_tool/__init__.py
src/graph_tool/draw/graphviz_draw.py

commit daa99068
Author: Alexey <ostrokach@gmail.com>
Date:   2019-02-23

    Import "context/detail/fcontext.hpp" instead of "context/all.hpp" when testing for the presence of boost::context.
    
    "context/all.hpp" has been removed in recent versions of boost::context.
    
    See:
    
    - https://github.com/boostorg/context/issues/81
    - https://github.com/boostorg/context/commit/2e37599461912cc1679f106a25456a493f7f0b27

m4/ax_boost_context.m4

commit d04f8187
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-01-31

    centrality: Fix simple doc inconsistency

src/graph_tool/centrality/__init__.py

commit ef1ed6c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-01-31

    pagerank(): Fix problem with sink nodes
    
    Nodes with out-degree zero are now assumed to connect to every other
    node.

src/graph/centrality/graph_pagerank.hh
src/graph_tool/centrality/__init__.py

commit 3f7ca407
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-12-22

    Implement extract_largest_component() convenience wrapper

src/graph_tool/topology/__init__.py

commit 012787ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2019-01-27

    Add `dag` parameter to shortest_distance()/shortest_path()/all_shortest_paths()
    
    This enables linear-time computation of shortest distances on DAGs that
    also allows for negative weights.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 7342a3ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-12-08

    Fix compilation error with Python 2
    
    This re-enables the 'register' keyword with C++17, which is still
    required for Python 2.

configure.ac

commit c1a7bdf3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-12-07

    More docstring fixes

doc/demos/inference/_reconstruction.rst

commit ab4b82b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-11-29

    Update docstring tests

doc/demos/inference/_edge_weights.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_sampling.rst
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit e39910a5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-11-29

    Update mathjax sphinx option

doc/conf.py

commit f52e0fa9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-11-29

    Add "compact" optional parameter to hashimoto()

src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph_tool/spectral/__init__.py

commit 1c478957
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-10-24

    graph_blockmodel.hh: Small improvement to sample_block()

src/graph/inference/blockmodel/graph_blockmodel.hh

commit f8af5762
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-10-18

    MixedMeasuredBlockState: Improve numerical stability
    
    Use gammaln() in place of log(gamma()).

src/graph_tool/inference/uncertain_blockmodel.py

commit aa39e4a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-10-03

    Fix compilation with CGAL 4.13
    
    This fixes issue #509

src/graph/generation/graph_triangulation.cc

commit 7ab047ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-27

    Modify Graph.add_edge_list() to ignore extra rows

src/graph/graph_python_interface_imp1.cc
src/graph_tool/__init__.py

commit 8e7b5ca3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-26

    Fix issue with Graph.remove_vertex() when contiguous regions are given

src/graph_tool/__init__.py

commit db474cff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-21

    Fix quoting bug in graphviz.hpp
    
    This fixes issue #507.

src/boost-workaround/boost/graph/graphviz.hpp

commit 5457d04f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-21

    Add 'edges' parameter to all_paths()
    
    This fixes issue #505.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 7b85fa40
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-20

    Fix GraphArtisit.draw()
    
    This fixes issue #504

src/graph_tool/draw/cairo_draw.py

commit b9eac005
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-08-07

    Switch PRNG from std::mt19937 to PCG

configure.ac
src/graph/Makefile.am
src/graph/generation/sampler.hh
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/parallel_rng.hh
src/graph/random.cc
src/graph/random.hh
src/graph_tool/__init__.py
src/pcg-cpp/CONTRIBUTING.md
src/pcg-cpp/LICENSE-APACHE.txt
src/pcg-cpp/LICENSE-MIT.txt
src/pcg-cpp/LICENSE.spdx
src/pcg-cpp/README.md
src/pcg-cpp/include/pcg_extras.hpp
src/pcg-cpp/include/pcg_random.hpp
src/pcg-cpp/include/pcg_uint128.hpp

commit 0d86003c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-08-07

    Fix in_neighbor selector

src/graph/graph_adjacency.hh
src/graph/graph_selectors.hh

commit e0153068
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-08-07

    Implement ProperyMap.swap()

src/graph/fast_vector_property_map.hh
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph_tool/__init__.py

commit dd46ba20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-08-07

    idx_map.hh: Fix random access

src/graph/idx_map.hh

commit 7041c30f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-19

    Inference HOWTO minor text improvements

doc/demos/inference/_background.rst
doc/demos/inference/_edge_weights.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_sampling.rst

commit 7849a23e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-05

    spectral: Change to SVG plots in the docstrings

src/graph_tool/spectral/__init__.py

commit 8deecf0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-05

    spectral: Add hashimoto() implementation

src/graph/spectral/Makefile.am
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_nonbacktracking.cc
src/graph/spectral/graph_nonbacktracking.hh
src/graph_tool/spectral/__init__.py

commit a60bd73c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-09-12

    Use and require C++17

configure.ac
m4/ax_cxx_compile_stdcxx_17.m4

commit 41bae98c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-19

    NestedBlockState: Remove uncessary filter synchronization
    
    This fixes issue #495.

src/graph_tool/inference/nested_blockmodel.py

commit 247ecf5c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-10

    price_network(): Improve performance and clarify documentation

src/graph/generation/graph_price.hh
src/graph_tool/generation/__init__.py

commit 9d1777af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-03

    Remove inference.rst from clang tests

.gitlab-ci.yml

commit 4ce6f522
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-03

    _reconstruction.rst: Limit output precision
    
    This fixes tests with Python 2.7.

doc/demos/inference/_reconstruction.rst

commit 1d7916cd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-03

    interactive_window(): change paramter 'no_main' to 'main'

src/graph_tool/draw/gtk_draw.py

commit 0407f41a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-07-03

    Fix incompatibility with Python 3.7
    
    Changes 'async' to 'sync', as the former is now a keyword.

src/graph_tool/draw/gtk_draw.py

commit d7fce730
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-29

    Bump version to 2.28dev

configure.ac

commit ce258562
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-28

    Bump version to 2.27

configure.ac

commit d2cde4cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-28

    Add network reconstruction to inference HOWTO

doc/conf.py
doc/demos/inference/_background.rst
doc/demos/inference/_edge_weights.rst
doc/demos/inference/_layers.rst
doc/demos/inference/_minimization.rst
doc/demos/inference/_model_class_selection.rst
doc/demos/inference/_model_selection.rst
doc/demos/inference/_prediction.rst
doc/demos/inference/_reconstruction.rst
doc/demos/inference/_sampling.rst
doc/demos/inference/inference.rst
src/graph_tool/inference/uncertain_blockmodel.py

commit 57d7c7ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-26

    Remove C++ and Python signatures from boost::python docstrings

src/graph/centrality/graph_centrality_bind.cc
src/graph/clustering/graph_clustering.cc
src/graph/correlations/graph_correlations_bind.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/flow/graph_flow_bind.cc
src/graph/generation/graph_generation.cc
src/graph/graph_bind.cc
src/graph/inference/graph_inference.cc
src/graph/layout/graph_bind_layout.cc
src/graph/search/graph_search_bind.cc
src/graph/spectral/graph_matrix.cc
src/graph/stats/graph_stats_bind.cc
src/graph/topology/graph_topology.cc
src/graph/util/graph_util_bind.cc

commit d70825df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-26

    Docstring cross-reference cleanup

doc/conf.py
doc/demos/inference/inference.rst
doc/inference.rst
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/search/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit b7f1f2a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-24

    Fix problem with gibbs sampling

src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit 0eb27fe5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-23

    blockmodel: Improve performance by disabling group mapping for non-layered SBMs

src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp3.cc
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py

commit 809432af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-21

    LayeredBlockState: Fix pickling typo bug

src/graph_tool/inference/layered_blockmodel.py

commit 22f37bf1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-21

    LayeredBlockState: Fix copying and pickling with pclabel and bfield

src/graph_tool/inference/layered_blockmodel.py

commit 1cf7ad12
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-21

    BlockState: Fix copy and pickle with bfield

src/graph_tool/inference/blockmodel.py

commit 31421e3c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-17

    Fix problem with Graph.purge_vertices(in_place=True)
    
    This fixes issue #485.

src/graph/graph_filtering.cc

commit 544e3624
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-17

    Properly quote ids in DOT outputs
    
    This fixes issue #466

src/boost-workaround/boost/graph/graphviz.hpp

commit e712876b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-16

    mcmc_multilevel(): Fix verbose reporting of cached entries

src/graph_tool/inference/mcmc.py

commit b96ce829
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-15

    graph_draw(): Fix inline SVG drawing with jupyter notebooks
    
    This fixes issue #469

src/graph_tool/draw/cairo_draw.py

commit 4473f385
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-15

    mcmc_multilevel(): Fix problem with empty groups

src/graph_tool/inference/mcmc.py

commit a60612ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-12

    Fix compilation issue with Python 2

src/graph/draw/pycairo_aux.cc

commit e5ba44c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-12

    uncertain_blockmodel: Update docstrings

src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 8daec366
Merge: 2c8c9899 feaa50f1
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2018-06-12

    Fix compilation without pycairo
    
    See merge request count0/graph-tool!10

commit feaa50f1
Author: Ale Abdo <abdo@member.fsf.org>
Date:   2018-06-12

    Fix compilation without cairo

src/graph/draw/pycairo_aux.cc

commit 2c8c9899
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-06-01

    Fix bug with EMBlockState.learn()
    
    This fixes issue #475.

src/graph_tool/inference/blockmodel_em.py

commit 84e0715c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-05-22

    Fix issue with UncertainBaseState.collect_marginal()

src/graph_tool/inference/uncertain_blockmodel.py

commit d3054de6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-05-15

    Fix issue with UncertainBlockState.__init__()

src/graph_tool/inference/uncertain_blockmodel.py

commit deafb2f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-05-12

    Implement UncertainState.collect_marginal()

src/graph/inference/Makefile.am
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_marginal.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit b7793fcc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-05-08

    Add generalized L^p norm to similarity()

src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph_tool/topology/__init__.py

commit 9bd68ef9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-05-08

    Fix compilation issues with GCC 8

src/graph/clustering/graph_extended_clustering.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/generation/graph_community_network.hh
src/graph/gml.hh
src/graph/graph_io.cc
src/graph/graph_properties_copy.hh
src/graph/graph_reverse.hh
src/graph/inference/support/graph_state.hh
src/graph/topology/graph_all_distances.cc

commit 91b8743c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-05-03

    Fix bug in similarity() when using weighted graphs

src/graph_tool/topology/__init__.py

commit f90b3ae1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-30

    Fix problem with BlockState pickling

src/graph_tool/inference/blockmodel.py

commit d6a7557a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-30

    Fix problem with BlockState.copy()

src/graph_tool/inference/blockmodel.py

commit f5a3e59a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-24

    Fix MixedMeasuredBlockState.mcmc_sweep()

src/graph_tool/inference/uncertain_blockmodel.py

commit d29ea506
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-24

    Change gt_pycairo_aux to libgt_pycairo_aux

src/graph/draw/Makefile.am
src/graph_tool/draw/cairo_draw.py

commit 1570ae2f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-21

    Fix problem with recent pycairo

src/graph/draw/Makefile.am
src/graph/draw/pycairo_aux.cc
src/graph_tool/draw/cairo_draw.py

commit 17802dd9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-17

    uncertain_blockmodel.py: Replace relative parameter 'phi' by absolute 'aE'

src/graph_tool/inference/uncertain_blockmodel.py

commit eb3fe62a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-15

    BlockState.sample_graph(): Fix problem with unweighted graphs

src/graph_tool/inference/blockmodel.py

commit 20244ea5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-15

    Fix bug with Graph.shrink_to_fit()
    
    This fixes issue #457

src/graph/graph_adjacency.hh

commit b6f8c18d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-11

    uncertain_blockmodel: Switch to static move proposals

src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh

commit 3172e99e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-11

    uncertain_blockmodel.py: Fix issue with entropy computation
    
    This also adds the "density" entropy argument.

src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit f1193f1b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-10

    UncertainBaseState: Add support for direct state initialization

src/graph_tool/inference/uncertain_blockmodel.py

commit 139b5859
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-09

    MeasuredBlockState: Improve numerical stability

src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_measured.hh

commit d8e5fdf9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-09

    MeasuredBlockState: Fix problem with fn/fp_params

src/graph_tool/inference/uncertain_blockmodel.py

commit f27799a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-07

    similarity(): Improve speed for bounded integer labels

src/graph/Makefile.am
src/graph/idx_map.hh
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph_tool/topology/__init__.py

commit 4f9e4785
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-07

    similarity(): Implement 'asymmetric' parameter

src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph_tool/topology/__init__.py

commit f466b829
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-07

    uncertain_blockmodel: Implement latent_edges entropy argument

src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py

commit ea5052e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-06

    uncertain_blockmodel: Update edges according to SBM probabilities

src/graph/generation/urn_sampler.hh
src/graph/inference/Makefile.am
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_sample_edge.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh

commit 4186030c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-06

    uncertain_blockmodel: Fix issue with clear_egroups()

src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 78e6d500
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-04

    MeasuredBlockState: Fix get_p/q_posterior()

src/graph_tool/inference/uncertain_blockmodel.py

commit e3d185f9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-03

    uncertain_blockmodel: Fix issue with edge mapping

src/graph/inference/uncertain/graph_blockmodel_measured.hh

commit 29b5caa7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-03

    Simplify BlockState.sample_graph()

src/graph_tool/inference/blockmodel.py

commit 2fb6822f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-03

    similarity(): Return integer when norm=False

src/graph_tool/topology/__init__.py

commit ab9168fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-03

    UncertainBaseState: Implement get_graph() method

src/graph_tool/inference/uncertain_blockmodel.py

commit e089bebb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-04-03

    uncertain_blockmodel: Fix sampling issues

src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh

commit 710f08bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-30

    uncertain_blockmodel.py: Toggle fast edge removal

src/graph_tool/inference/uncertain_blockmodel.py

commit d67c1a12
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-30

    collect_vertex_marginals(): Add parameter 'unlabel'

src/graph_tool/inference/blockmodel.py

commit 75d04ad9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-30

    draw_hierarchy(): Fix interactive re-ordering

src/graph_tool/draw/cairo_draw.py

commit c331840c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-27

    uncertain_blockmodel: Implement 'init_empty' parameter

src/graph_tool/inference/uncertain_blockmodel.py

commit 06e61849
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-22

    Fix docstring for similarity()

src/graph_tool/topology/__init__.py

commit 373af413
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-15

    inference.blockmodel: Fix problem with pickling MixedMeasuredBlockState

src/graph_tool/inference/uncertain_blockmodel.py

commit 5b681832
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-15

    inference.blockmodel: Fix typo in MeasuredBlockState.set_hparams()

src/graph_tool/inference/uncertain_blockmodel.py

commit cd44b291
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-15

    vertex/edge_percolation(): Add support for second-largest component

src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph_tool/topology/__init__.py

commit c08bbf86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-13

    inference.blockmodel: Move UncertainBaseState.get_edge_prob() to C++
    
    This also implements UncertainBaseState.get_edges_prob().

src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 60e235e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.blockmodel: Fix issue with MixedMeasuredBlockState

src/graph_tool/inference/uncertain_blockmodel.py

commit e703c29c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.blockmodel: Implement MixedMeasuredBlockState

src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 5bbbfc4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    collection: Update konect URL

src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py

commit f32baccc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.uncertain_blockmodel: Fix pickling bug

src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 8efb5176
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.blockmodel: Fix pickling problem with BlockState

src/graph_tool/inference/blockmodel.py

commit 7e43294e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.MeasuredBlockState: Reflect missing edge probability

src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 40c76afc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    Fix docstrings

src/graph_tool/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/topology/__init__.py

commit 41dc36a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.mcmc.TemperingState: Keep track of state indices

src/graph_tool/inference/mcmc.py

commit d37c0de0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-12

    inference.uncertain_blockmodel: make edge prior optional

src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph_tool/inference/uncertain_blockmodel.py

commit 332ac74d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-11

    Fix bug in motifs()
    
    This fixes issue #431

src/graph_tool/clustering/__init__.py

commit ed348374
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-11

    Fix doctests

src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 669e3448
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-11

    Fix compilation warning

src/graph/graph_adaptor.hh

commit 5c370c56
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-10

    Fix issue with motif_significance()
    
    This fixes issue #444.

src/graph_tool/clustering/__init__.py

commit 00de67ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-03-08

    Sphinx cleanup and docs update

Makefile.am
doc/conf.py
doc/demos/inference/inference.rst
doc/sphinxext/LICENSE.txt
doc/sphinxext/MANIFEST.in
doc/sphinxext/README.txt
doc/sphinxext/__init__.py
doc/sphinxext/docscrape.py
doc/sphinxext/docscrape_sphinx.py
doc/sphinxext/numpydoc.py
doc/sphinxext/setup.py
doc/sphinxext/tests/test_docscrape.py

commit 4f0c7fe6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-10

    inference.blockmodel: Improve nested SBM equilibration
    
    This modifies the MCMC code to allow simultaneous update of
    all hierarchy levels, improving equilibration speed.

doc/test_inference.py
doc/test_inference_mcmc.py
src/graph/generation/dynamic_sampler.hh
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph_tool/flow/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 749572d8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-14

    Fix docstrings

doc/demos/inference/inference.rst
src/graph_tool/draw/__init__.py
src/graph_tool/search/__init__.py

commit 50b7f803
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-14

    inference: Add parameter r to TemperingState

src/graph_tool/inference/mcmc.py

commit afd7243a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-14

    Fix compilation problem with clang

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph_tool/inference/mcmc.py

commit 35b3bf30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-14

    inference: Fix problem with coupled states

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 8f16e8ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-11

    Update copyright date

configure.ac
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/parallel_rng.hh
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/openmp_lock.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit d25f8d92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-19

    inference: Implement code for uncertain networks

src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/graph_inference.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/support/util.hh
src/graph/inference/uncertain/graph_blockmodel_measured.cc
src/graph/inference/uncertain/graph_blockmodel_measured.hh
src/graph/inference/uncertain/graph_blockmodel_measured_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain.hh
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.cc
src/graph/inference/uncertain/graph_blockmodel_uncertain_mcmc.hh
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/uncertain_blockmodel.py

commit 2d5051a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-11

    inference: Cleanup propagate delta

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit f606acc2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-10

    inference: Slightly improve entry computation performance

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit e7363032
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-25

    inference: Fix issues with overlapping SBM and self-loops

doc/test_inference.py
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py

commit 54fa4532
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-15

    inference: Implement 'bfield' parameter

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit ecb5088e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-20

    inference: Fix issue with overlapping groups and self-loops

src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh

commit 19d1b8d8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-20

    Fix compilation issue with clang

src/graph/inference/support/cache.hh
src/graph/inference/support/util.hh

commit f22bdb74
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-18

    Disambiguate between is_directed_ metafunction and is_directed()
    
    This fixes compilation with older GCC versions (ca. 5.0.0).

src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_motifs.hh
src/graph/generation/graph_generation.hh
src/graph/generation/graph_price.hh
src/graph/graph_copy.cc
src/graph/graph_util.hh
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh

commit d9ddaf60
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-15

    inference: Cosmetic fix to log_q_approx()

src/graph/inference/support/int_part.cc

commit 5bf396b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-13

    inference: Improve block entry delta computation

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh

commit f44e89c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-04

    inference: Implement parallel sweeps for TemperingState with NestedBlockState

src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py

commit 5369eb34
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-04

    inference: Improve caching of lgamma()/log()/xlogx()

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/util.hh

commit a3c332d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-04

    inference: Delete unused block edges

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit fe8b6724
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-04

    inference: Reset m_entries and skip no-op virtual move

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh

commit 536b3c3b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-20

    inference: Add self-loops and parallel edges to test_inference.py

doc/test_inference.py

commit 79190e65
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-04

    graph_blockmodel_elist.hh: Clear empty buckets

src/graph/inference/blockmodel/graph_blockmodel_elist.hh

commit 385e8f86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-04

    dynamic_sampler.hh: Fix rebuild()

src/graph/generation/dynamic_sampler.hh

commit 621322fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-03

    inference: Implement parallel sweeps for TemperingState

src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/overlap_blockmodel.py

commit 69b74660
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-03

    inference: Fix multiflip mcmc probabilities
    
    This also makes niter correspond to number of sweeps

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

commit 68989431
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-03

    Remove superfluous template parameter from parallel loop helpers

src/graph/graph_util.hh

commit 92794ce6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-29

    inference: Restrict temperatures to priors only in TemperingState

src/graph_tool/inference/mcmc.py

commit d226ac61
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-29

    inference: Implement beta_dl parameter
    
    This also re-organizes entropy() w.r.t. entropy_args.

doc/test_inference.py
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 1c48aec8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-26

    inference: Return number of attempted moves for mcmc sweeps

doc/test_inference_mcmc.py
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 1c155fb7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-26

    inference: Improve partition update

src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh

commit 25200e72
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-19

    Force-inline degree selectors

src/graph/graph_selectors.hh

commit 72e74070
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-19

    Cosmetic improvements to Sampler and DynamicSampler

src/graph/generation/dynamic_sampler.hh
src/graph/generation/sampler.hh

commit 7bb82a5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-12-26

    Improve BlockState.multiflip_mcmc() move proposals

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph_tool/inference/blockmodel.py

commit 9138901a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-02-01

    Fix inconsistent degree()/in_degree()/in_neighbours() semantics for undirected graphs

src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/graph_adaptor.hh
src/graph/graph_filtered.hh
src/graph/graph_python_interface.cc
src/graph/graph_selectors.hh
src/graph/spectral/graph_incidence.hh
src/graph/topology/graph_distance.cc

commit 977b4516
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2018-01-27

    Fix degree() for filtered undirected graphs
    
    This fixes issue #435

src/graph/graph_filtered.hh

commit 635b9675
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-22

    urn_sampler.hh: Fix wrong return type for size()

src/graph/generation/urn_sampler.hh

commit 09ce8c24
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-20

    Fix compilation problem with clang
    
    Clang still has buggy issues with constexpr...

src/graph/generation/graph_sbm.hh

commit 3c0bfdb4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-19

    generate_sbm(): Slight performance improvement

src/graph/generation/graph_sbm.hh
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh

commit a9a2ba7f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-19

    Implement graph_tool::is_directed()

src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/correlations/graph_assortativity.hh
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_generation.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_python_interface.cc
src/graph/graph_util.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_distance.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/util/graph_search.hh

commit 314bc212
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-09

    Fix docstring test

doc/demos/inference/inference.rst

commit 20cb270c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-09

    Bump version to 2.27dev

configure.ac

commit b89e6b4e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-09

    Bump version to 2.26

configure.ac

commit 8ea751f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-09

    blockmodel: Fix segfault with edge prediction
    
    This fixes issue #426

src/graph/inference/blockmodel/graph_blockmodel.hh

commit 95c33f1f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-07

    Increase coroutine default stack size to 5 MB

configure.ac

commit f8eb4a2d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-07

    Fix compatibility with coroutine for boost < 1.62

src/graph/coroutine.hh
src/graph/graph_python_interface.hh

commit 69810889
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-02

    Trivial docstring fix

src/graph_tool/centrality/__init__.py

commit 27a1411d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-02

    betweenness(): Ignore self-loops

src/boost-workaround/boost/graph/betweenness_centrality.hpp

commit 2a8034cc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-11-02

    betweenness(): Add `pivots` parameter
    
    This enables the fast computation of unbiased estimators.

src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/graph/centrality/graph_betweenness.cc
src/graph_tool/centrality/__init__.py

commit 2c920ab5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-25

    Fix autoconf check for sparsehash
    
    This fixes issue #423

configure.ac

commit 20eb89e8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-25

    Sync doctests with newer matplotlib

src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/topology/__init__.py

commit 9962dadc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-23

    Improve inline __attribute__ annotation

src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh

commit adc8937c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-15

    Fix compilation problem with OpenMP disabled

src/graph/openmp_lock.hh

commit 8edceb70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-13

    draw_hierarchy(): Allow for explicit non-inline mode

src/graph_tool/draw/cairo_draw.py

commit a8741e0f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-13

    Bump version to 2.26dev

configure.ac

commit 8a3a6b2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    Bump version to 2.25

configure.ac

commit fd099314
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    draw_hierarchy(): Fix warnings for inline drawing

src/graph_tool/draw/cairo_draw.py

commit 2ee3e527
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    graph_union(): Ensure property map ownership
    
    This fixes issue #416

src/graph_tool/generation/__init__.py

commit 405e8c87
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    GraphWidget: Fix problem with multilevel layouts

src/graph_tool/draw/gtk_draw.py

commit 8bf627bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    Increase default boost::coroutine stack size to 1 MB
    
    This fixes a problem with stack corruption in graph_draw().

configure.ac
src/graph/coroutine.hh
src/graph/graph_python_interface.hh

commit 8846ca81
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    cairo_draw.cc: Cosmetic changes

src/graph/draw/graph_cairo_draw.cc

commit 7f45db05
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    Force-link against boost::context
    
    This works around a problem in Debian/Ubuntu.

configure.ac
m4/ax_boost_context.m4

commit 89e805d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-12

    Update m4 macros

m4/ax_boost_base.m4
m4/ax_boost_coroutine.m4
m4/ax_boost_python.m4
m4/ax_boost_regex.m4
m4/ax_create_pkgconfig_info.m4
m4/ax_cxx_compile_stdcxx.m4
m4/ax_cxx_compile_stdcxx_14.m4
m4/ax_lib_expat.m4
m4/ax_openmp.m4
m4/ax_python_devel.m4
m4/ax_python_module.m4

commit e4d243fa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-09

    quickstart.rst: `assert` is not a function call

doc/quickstart.rst

commit cae5227e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-09

    generate_sbm(): Improve docstring

src/graph_tool/generation/__init__.py

commit b0427a6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-08

    Bump version to 2.25dev

configure.ac

commit 9642dd05
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-07

    Bump version to 2.24

configure.ac

commit b4307f43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-07

    Remove unnecessary typename

src/graph/generation/graph_sbm.hh

commit 7581ee16
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-07

    Improve Graph.remove_edge()
    
    It now accepts edge descriptors from all graph views and invalidates
    them after removal.

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh

commit 6323a77d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-07

    Fix bug with Graph.remove_edge() for undirected graphs

src/graph/graph_adjacency.hh
src/graph/graph_python_interface.cc

commit 1c9cd293
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-04

    {scalar_}assortatitivy(): Return NaN if undefined

src/graph/correlations/graph_assortativity.hh

commit d4a8428b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-02

    Fix compilation with clang

src/graph/inference/support/int_part.cc

commit c738d441
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-02

    generation: Remove redundant alias code

src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit 62424bf0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-10-02

    int_part.hh: Improve numerical stability

src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/support/int_part.cc
src/graph/inference/support/int_part.hh
src/graph/inference/support/spence.cc

commit b93fa303
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-30

    Update doctests

src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 581ba9fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-29

    random_rewire(): Add "blockmodel-micro" model and implement maximum entropy sampling

src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit aeaff00d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-29

    Fix problem with removal of self-loops

src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh

commit 8a35de17
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-28

    generate_sbm(): Implement microcanonical model

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/sampler.hh
src/graph/generation/urn_sampler.hh
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py

commit fbb1d5c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-27

    int_part.cc: Avoid unnecessary resize

src/graph/inference/support/int_part.cc

commit 9489f197
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-27

    int_part.cc: Improve numerical stability for very large cache sizes

src/graph/inference/support/int_part.cc

commit bb49bd98
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-27

    Fix docstring of load_graph_from_csv()
    
    This fixes issue #415

src/graph_tool/__init__.py

commit 918ba352
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-26

    Hide aliases Vertex.{out,in,out}_neighbours from documentation

src/graph_tool/__init__.py

commit e9a1b2e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-26

    Enforce consistent American spelling in API and documentation
    
    This essentially replaces "neighbours" by "neighbors" throughout.
    
    Aliases using the British spelling (e.g. Vertex.out_neighbours()) are
    preserved for compatibility.

README.md
doc/demos/animation/animation_dancing.py
doc/demos/animation/animation_sirs.py
doc/demos/animation/animation_zombies.py
doc/graph_tool.rst
doc/gt_format.rst
doc/price.py
doc/quickstart.rst
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_imp1.cc
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_filtered.hh
src/graph/graph_python_interface.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.hh
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/support/graph_neighbor_sampler.hh
src/graph/layout/graph_sfdp.cc
src/graph/topology/graph_kcore.hh
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/topology/__init__.py

commit ae68c0c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-25

    Docstring tweaks

src/graph_tool/generation/__init__.py

commit de9e7adb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-25

    Bump version to 2.24dev

configure.ac

commit b669e1b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-24

    Bump version to 2.23

configure.ac

commit fe5ec4e9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-24

    Fix compilation with Boost < 1.60

src/graph/topology/graph_distance.cc

commit 8180fd35
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-24

    Documentation tweaks

doc/price.py
doc/quickstart.rst
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/minimize.py

commit b42ee3f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-24

    Fix compilation issue with Boost 1.58

src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh

commit 7417054c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-24

    Add tar-pax option to AM_INIT_AUTOMAKE

configure.ac

commit 1fcff03a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-23

    inference.rst: Change rng seed

doc/demos/inference/inference.rst

commit 2483cbb2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-23

    blockmodel_overlap: Avoid repeated dense_hash_map construction

src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh

commit 55bccee5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-22

    inference.rst: Initialize rng before doctest

doc/demos/inference/inference.rst

commit 064a9add
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-22

    blockmodel_overlap: Use boost::container::small_vector for group mixtures

src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh

commit 3ebca6c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-22

    Honor parameter 'bs' in minimize_nested_blockmodel_dl()
    
    This fixes issue #396

src/graph_tool/inference/minimize.py

commit f4a24fcb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-21

    Reorganize graph/inference source tree

configure.ac
src/graph/inference/Makefile.am
src/graph/inference/blockmodel/graph_blockmodel.cc
src/graph/inference/blockmodel/graph_blockmodel.hh
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
src/graph/inference/blockmodel/graph_blockmodel_em.cc
src/graph/inference/blockmodel/graph_blockmodel_em.hh
src/graph/inference/blockmodel/graph_blockmodel_emat.hh
src/graph/inference/blockmodel/graph_blockmodel_entries.hh
src/graph/inference/blockmodel/graph_blockmodel_entropy.hh
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.cc
src/graph/inference/blockmodel/graph_blockmodel_exhaustive.hh
src/graph/inference/blockmodel/graph_blockmodel_gibbs.cc
src/graph/inference/blockmodel/graph_blockmodel_gibbs.hh
src/graph/inference/blockmodel/graph_blockmodel_imp.cc
src/graph/inference/blockmodel/graph_blockmodel_imp2.cc
src/graph/inference/blockmodel/graph_blockmodel_marginals.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_merge.cc
src/graph/inference/blockmodel/graph_blockmodel_merge.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.cc
src/graph/inference/blockmodel/graph_blockmodel_multicanonical.hh
src/graph/inference/blockmodel/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/blockmodel/graph_blockmodel_partition.hh
src/graph/inference/blockmodel/graph_blockmodel_util.hh
src/graph/inference/blockmodel/graph_blockmodel_weights.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/layers/graph_blockmodel_layers.cc
src/graph/inference/layers/graph_blockmodel_layers.hh
src/graph/inference/layers/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_imp.cc
src/graph/inference/layers/graph_blockmodel_layers_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_merge.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/layers/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/layers/graph_blockmodel_layers_util.hh
src/graph/inference/loops/bundled_vacate_loop.hh
src/graph/inference/loops/exhaustive_loop.hh
src/graph/inference/loops/gibbs_loop.hh
src/graph/inference/loops/mcmc_loop.hh
src/graph/inference/loops/merge_loop.hh
src/graph/inference/overlap/graph_blockmodel_overlap.cc
src/graph/inference/overlap/graph_blockmodel_overlap.hh
src/graph/inference/overlap/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/overlap/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/overlap/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/overlap/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/overlap/graph_blockmodel_overlap_partition.hh
src/graph/inference/overlap/graph_blockmodel_overlap_util.hh
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.cc
src/graph/inference/overlap/graph_blockmodel_overlap_vacate.hh
src/graph/inference/support/cache.cc
src/graph/inference/support/cache.hh
src/graph/inference/support/graph_neighbour_sampler.hh
src/graph/inference/support/graph_state.hh
src/graph/inference/support/int_part.cc
src/graph/inference/support/int_part.hh
src/graph/inference/support/parallel_rng.hh
src/graph/inference/support/spence.cc
src/graph/inference/support/util.hh

commit aeea89f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-20

    Fix compilation issue with clang

src/graph/inference/graph_blockmodel_layers.hh

commit 3d9964ab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-19

    Implement posterior sampling for layered networks
    
    This includes support for sampling from posteriors of layered models
    that are also overlapping and/or with edge covariates.
    
    This fixes issue #325

doc/demos/inference/inference.rst
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_layers_imp.cc
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_layers_util.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit ce270193
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-19

    Small documentation fix

doc/quickstart.rst

commit 36e4c21d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-19

    Ensure that PropertyMaps always belong to the desired graph

src/graph_tool/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/generation/__init__.py

commit a4ad0019
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-02

    Add wrapper for openmp mutex and scoped lock

src/graph/Makefile.am
src/graph/openmp_lock.hh

commit 64ad4686
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-09-02

    Change custom USING_OPENMP to standard _OPENMP

configure.ac
src/graph/clustering/graph_clustering.hh
src/graph/graph_openmp.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/inference/bundled_vacate_loop.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/mcmc_loop.hh
src/graph/inference/merge_loop.hh
src/graph/inference/parallel_rng.hh
src/graph/util/graph_search.hh

commit ee1c9505
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-24

    Fix bug with Graph.get_in_neighbours() and filtered graphs

src/graph/graph_filtered.hh

commit c985e2b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-19

    Add doc/demos to tarball

Makefile.am

commit 74eba3e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-09

    Documentation updates

doc/conf.py
doc/demos/inference/inference.rst
doc/extlinks_fancy.py
doc/gt_theme/static/gt_style.css
src/graph_tool/collection/__init__.py

commit 8a8bb41c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-15

    Makefile.am: Generate ChangeLog from git

Makefile.am

commit e7ab6dae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-15

    configure.ac: Move build auxiliaries to build-aux

configure.ac

commit d01a66e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-10

    graph_draw(): Add support for overriding alpha values of color maps

src/graph_tool/draw/cairo_draw.py

commit 0932e4a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-07

    Add boost/math/special_functions/relative_difference.hpp to boost-workaround
    
    This fixes compilation on boost versions < 1.60.

src/boost-workaround/boost/math/special_functions/relative_difference.hpp

commit 1f4a8092
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-03

    Add workaround for buggy cairomm pkg-config installs
    
    Fixes: #410

configure.ac

commit 1a19aabc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-08-03

    Ensure compatibility with Boost < 1.60
    
    This removes an unnecessary reference to
    <boost/math/special_functions/relative_difference.hpp>.

src/graph/inference/graph_blockmodel_util.hh

commit 8a84e869
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-23

    graph_blockmodel_multiflip_mcmc.hh: Trivial space

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh

commit 67ce58b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-23

    NestedBlockModel.*_sweep(): Enable layers selection

src/graph_tool/inference/nested_blockmodel.py

commit 9d043064
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-23

    graph_draw(): Fix issue with 'text-offset'

src/graph_tool/draw/cairo_draw.py

commit 12ed0c52
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-23

    PropertyMap.get/set_2d_array(): Fix behavior with vector<string>
    
    Resolves: #409

src/graph_tool/__init__.py

commit 45adba93
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-20

    Graph.add_edge_list(): Improve docstring

src/graph_tool/__init__.py

commit 4ffc3827
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-16

    shortest_distance(): Fix typo in docstring

src/graph_tool/topology/__init__.py

commit de13d051
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-16

    shortest_distance(): Return distance array for list of targets

src/graph_tool/topology/__init__.py

commit 263a4f74
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-12

    generate_sbm(): Move sampler query out of the main loop

src/graph/generation/graph_sbm.hh

commit 26671594
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-12

    inference.blockmodel: Small optimizations

src/graph/inference/graph_blockmodel.hh

commit b237feb6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-12

    inference.blockmodel: Fix issue with covariate likelihoods

src/graph/inference/graph_blockmodel_util.hh

commit f9399937
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-09

    graph_draw(): Fix color_coverter typo
    
    This fixes issue #405

src/graph_tool/draw/cairo_draw.py

commit 31ae4357
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-08

    inference.blockmodel: Slight change to signed edge covariate model

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 03b4d2c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-06

    inference.blockmodel: Fix corner case problem with nested SBM + edge covariates

src/graph_tool/inference/nested_blockmodel.py

commit c7d2dfcc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-06

    all_shortest_paths(): Add "epsilon" parameter

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 9f7ea589
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-06

    draw_hierarchy(): Add support for node relative ordering

src/graph/layout/graph_radial.cc
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py

commit c419b2cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-06

    Add constexpr to UnityPropertyMap

src/graph/graph_properties.hh

commit 253a289f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-04

    inference.blockmodel: Fix issue with nested SBM + signed edge covariates

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers_imp.cc
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit dc067716
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-06

    all_shortest_paths(): Fix bug with weighted graphs

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit e64b612d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-03

    inference.blockmodel: Fix issue with testing mode

src/graph_tool/inference/nested_blockmodel.py

commit e739b076
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-03

    inference.blockmodel: Fix issue with state copying

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 17488f9e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-07-03

    inference.blockmodel: Fix precision issue with signed edge covariates

src/graph/inference/graph_blockmodel_util.hh

commit 26404ef4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-30

    shortest_distance(): Allow user-supplied initialization
    
    This adds the parameter "return_reached" so that the user can provide
    and reset the initialization for "dist_map" and "pred_map", to improve
    the performance of multiple searches that do not visit the whole graph.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit bf174831
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-28

    shortest_distance(): Remove redundant initializations

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 2c7cab20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-24

    Add PropertyDict.pop() method

src/graph_tool/__init__.py

commit 29074954
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-19

    Fix deprecation warning with newer numpy

src/graph/numpy_bind.hh

commit b5a4524d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-19

    inference: Fix issue with parallel entropy

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh

commit 823149b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-12

    Add file m4/ax_boost_thread.m4

m4/ax_boost_thread.m4

commit eae50db6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-12

    inference: Fix error in signed_w_lop_P()

src/graph/inference/graph_blockmodel_util.hh

commit 877b2652
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-12

    inference: Update docstrings

src/graph_tool/inference/blockmodel.py

commit 860dfe95
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-12

    inference: Fix problem with directed overlapping SBMs

src/graph/inference/graph_blockmodel_overlap.hh

commit f33cc1e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-12

    inference: Fix problem with layered SBMs

src/graph_tool/inference/layered_blockmodel.py

commit 17410ae1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-09

    configure.ac: Fix CGAL detection

configure.ac
m4/ax_lib_cgal_core.m4

commit 1dc6d7ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-09

    Update doctests

doc/conf.py
doc/demos/inference/inference.rst

commit fe87f75c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-02

    inference: Improve implementation of normal edge covariates

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_imp2.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 5f18fd10
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-02

    inference: Better handling of floating point tests

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 3609230d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-02

    Implement initialization and pickling of Vector_* objects

src/graph_tool/__init__.py

commit ecafce87
Merge: ef74576c cced576d
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2017-06-07

    Merge branch 'patch-4' into 'master'
    
    remove_vertex(): for lists, fix duplicates and property map updates
    
    See merge request !7

commit cced576d
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2017-06-07

    remove_vertex(): for lists, fix duplicates and property map updates

src/graph_tool/__init__.py

commit ef74576c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-06-02

    vertex_percolation(): Fix order of removed edges
    
    This fixes issue #400

src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph_tool/topology/__init__.py

commit cb661c6a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-05-30

    graphviz_draw(): Fix typo in docstring

src/graph_tool/draw/graphviz_draw.py

commit 12caa2f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-05-30

    Fix deepcopy bug in Graph class
    
    This fixes Graph.__deepcopy__() by properly iterating through the
    properties and actually returning the copied graph.

src/graph_tool/__init__.py

commit ab95d46f
Merge: 65a7a009 1a3056c1
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2017-05-27

    Merge branch 'patch-1' into 'master'
    
    Update gtk_draw.py: Fix typo in docstring
    
    See merge request !1

commit 1a3056c1
Author: Aleksandar Trifunovic <akstrfn@gmail.com>
Date:   2017-05-26

    Update gtk_draw.py

src/graph_tool/draw/gtk_draw.py

commit 65a7a009
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-05-23

    inference: Update docstrings

doc/demos/inference/inference.rst

commit ad53db7e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-05-22

    Fix LayeredBlockState.draw()
    
    This fixes issue #393

src/graph_tool/inference/layered_blockmodel.py

commit 47087888
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-05-22

    inference: Decrease memory usage during compilation

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py

commit 17818f1f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-05-19

    inference: add some backward compatibility when unpickling BlockState

src/graph_tool/inference/blockmodel.py

commit b729767d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-20

    Implement weighted hierarchical SBM

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_imp2.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_state.hh
src/graph/inference/util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 3d582a39
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-27

    EMBlockState: Fix typo in e_iter()

src/graph_tool/inference/blockmodel_em.py

commit 1beaa7ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-25

    minimize_blockmodel_dl(): Fix docstring

src/graph_tool/inference/minimize.py

commit 69ecee92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-22

    Update bug template

.gitlab/issue_templates/Bug.md

commit 89a0047c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-21

    graph_blockmodel_overlap.hh: Fix pclabel bug

src/graph/inference/graph_blockmodel_overlap.hh

commit f96aaf0e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-20

    inference: Update docstring

src/graph_tool/inference/overlap_blockmodel.py

commit f4b94a25
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-20

    inference: Improve degree prior for undirected overlapping SBM

src/graph/inference/graph_blockmodel_overlap_util.hh

commit 7fa7f12a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-17

    inference.rst: Update docstrings

doc/demos/inference/inference.rst

commit f6921911
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-17

    Fix syntax error with Python 2.7

src/graph_tool/inference/blockmodel.py

commit 5a17a4b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-12

    graph_blockmodel.hh: Use Bernoulli distribution in sample_block()

src/graph/inference/graph_blockmodel.hh

commit deb80839
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-12

    inference: Fix bug in multiflip_mcmc when c=inf and d > 0

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh

commit 0b59eaac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-11

    nested_blockmodel: Fix bug in couple_state()

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/nested_blockmodel.py

commit cd186a61
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-07

    inference: Refactor multicanonical_sweep based on mcmc_loop.hh

src/graph/inference/Makefile.am
src/graph/inference/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_multicanonical_multiflip.cc
src/graph/inference/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_multicanonical.cc
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_blockmodel_multicanonical_multiflip.cc
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_overlap_multicanonical_multiflip.cc
src/graph/inference/graph_inference.cc
src/graph/inference/mcmc_loop.hh
src/graph/inference/multicanonical_loop.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/overlap_blockmodel.py

commit 87abb56d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-05

    inference: Remove 'dl_beta' parameter

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 69acb919
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-04

    draw_hierarchy(): Add support for 'eorder' parameter

src/graph_tool/draw/cairo_draw.py

commit 14973f45
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-04-04

    draw_hierarchy(): Fix default value for 'empty_branches'

src/graph_tool/draw/cairo_draw.py

commit b626e713
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-28

    inference: Remove Jeffreys prior support

src/graph/inference/graph_blockmodel_util.hh

commit 316f8a3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-28

    inference: Fix segfault in parallel MCMC
    
    This fixes issue #380

src/graph/inference/mcmc_loop.hh

commit 3b1036d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-28

    inference: Implement posterior sampling of nested overlapping SBM

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_imp2.cc
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/overlap_blockmodel.py

commit 0b766917
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-27

    Modify bug report template

.gitlab/issue_templates/Bug.md

commit 1262d6bf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-27

    Add bug report template

.gitlab/issue_templates/Bug.md

commit e514578c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-26

    graphviz_draw(): Fix directed drawing with newer graphviz versions
    
    This fixes issue #386

src/graph_tool/draw/graphviz_draw.py

commit 227c4c87
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-26

    graph_draw(): Fix fit_view behavior
    
    This fixes issue #385

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit 5d160cf0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-22

    shortest_distance: Clip max_dist excess only when it is given

src/graph/topology/graph_distance.cc

commit 7f028b5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-22

    inference: Replace state.B with state.get_nonempty_B() where appropriate

src/graph_tool/inference/bisection.py
src/graph_tool/inference/minimize.py

commit 55b139dc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-22

    overlap_blockmodel: Fix typo in error message

src/graph_tool/inference/overlap_blockmodel.py

commit d82c5981
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-22

    shortest_distance: Change unreached distance to 'inf' if max_dist is given
    
    This fixes issue #383.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 7f7531a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-21

    blockmodel: Fix 'allow_vacate' behavior in multiflip MCMC

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh

commit 0b22f89e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-20

    blockmodel: Implement get/set_rec_params

src/graph_tool/inference/blockmodel.py

commit d709b855
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-19

    Remove some compilation warnings when using clang

src/graph/search/graph_astar.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc

commit b2929128
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-19

    gitlab-ci: Remove inference test from no_sh build

.gitlab-ci.yml

commit 850dfbcf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-19

    inference: Update more docstrings

src/graph_tool/inference/blockmodel.py

commit b554d8a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-19

    inference.rst: Update doctests

doc/demos/inference/inference.rst

commit 316ac849
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-19

    inference: Fix problem with add_block()

src/graph/inference/graph_blockmodel.hh

commit 12fea498
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-19

    Fix edge count update in clear_vertex()
    
    This fixes issue #382

src/graph/graph_adjacency.hh

commit 3a4c81ed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-17

    inference: Add inverse temperature for model priors

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 6e9b45fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-17

    inference: Use palindromic order for deterministic MCMC schedule

src/graph/inference/gibbs_loop.hh
src/graph/inference/mcmc_loop.hh

commit 0b0552cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-17

    inference: Implement 'allow_new_group' in gibbs_sweep()

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit 114998de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-17

    Update test_inference_mcmc.py

doc/test_inference_mcmc.py

commit 9c11f44b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-17

    multiflip_mcmc: Fix problem with detailed balance

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh

commit 10a62bbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-17

    inference: Make size of block graph dynamic to save memory

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py

commit 7b01aff1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-16

    inference: Fix TemperingState with gibbs_sweep()

src/graph_tool/inference/mcmc.py

commit 1b971c0b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-16

    inference: Remove 'block_moves' from mcmc_equilibrate()

src/graph_tool/inference/mcmc.py

commit 0f375326
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-16

    inference: Small improvement to TemperingState

src/graph_tool/inference/mcmc.py

commit 8d81df93
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-16

    inference: Add 'deterministic' docstring

src/graph_tool/inference/blockmodel.py

commit 9cd52015
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-16

    infernece: Revert multiflip algorithm to simpler version

src/graph/inference/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph_tool/inference/blockmodel.py

commit eb99e19a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-12

    multicanonical: Fix out-of-bounds problem

src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/multicanonical_loop.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit cbee5fd8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-11

    multiflip: Implement non-contiguous moves

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph_tool/inference/blockmodel.py

commit f4b5acea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-10

    multiflip: Use bidirectional range

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh

commit 62b54ad2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-09

    blockmodel.py: Fix docstrings

src/graph_tool/inference/blockmodel.py

commit 1ade7acd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-24

    Revamp multiflip mcmc and parametrize single node moves

doc/demos/inference/inference.rst
doc/test_inference_mcmc.py
src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_gibbs.cc
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_imp2.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_layers_gibbs.cc
src/graph/inference/graph_blockmodel_layers_imp.cc
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/graph_blockmodel_overlap_vacate.hh
src/graph/inference/mcmc_loop.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit 04dabc1c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-08

    Remove parallel edges from email-Enron.gt.gz
    
    This fixes issue #379

src/graph_tool/collection/email-Enron.gt.gz

commit aaae585f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-07

    Disambiguate between std::chrono and boost::chrono

src/graph/draw/graph_cairo_draw.cc

commit 8c8fa901
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-06

    NestedBlockState: Fix MCMC bug with filtered graphs
    
    This solves issue #375 (finally).

src/graph_tool/inference/nested_blockmodel.py

commit 0c8548ed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-06

    Fix indentation

src/graph/graph_filtering.cc

commit d791a28a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-06

    Bump minimum Boost version to 1.55

configure.ac

commit cb53ac7a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-03

    configure.ac: Remove outdated template depth flag

configure.ac

commit f24a3fa0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-03

    Bump version to 2.23dev

configure.ac

commit 44bf2b92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-02

    Bump version to 2.22

configure.ac

commit 23815c63
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-02

    configure.ac: Push local includes forward

configure.ac

commit fe0e4a8a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-02

    configure.ac: Move -D flags to CPPFLAGS

configure.ac

commit 49714e7f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-02

    configure.ac: Prevent internal includes to be overridden by CPPFLAGS

configure.ac

commit 51671878
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-02

    inference: split units to improve memory usage during compilation

src/graph/inference/Makefile.am
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel_imp2.cc
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers_imp.cc

commit e1c811ad
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-03-02

    Fix bug in all_edges_range() for directed graphs.
    
    This fixes issue #375

src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_filtered.hh
src/graph/graph_reverse.hh
src/graph/graph_selectors.hh

commit c4ff2303
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-28

    graph_hits.hh: Add line break

src/graph/centrality/graph_hits.hh

commit 1df1da7b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-28

    kcore_decomposition(): Fix behavior for directed graphs

src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph_tool/topology/__init__.py

commit 8237f35f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-28

    Fix problem with all_neighbours_range() selector

src/graph/graph_adaptor.hh
src/graph/graph_filtered.hh
src/graph/graph_reverse.hh
src/graph/graph_selectors.hh

commit 5a4ff166
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-27

    inference.rst: Fix marginal plots

doc/demos/inference/inference.rst

commit c46a1c3f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-27

    Remove compilation warning

src/graph/stats/graph_distance.hh

commit 68fe690f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-27

    Bump version to 2.22dev

configure.ac

commit e5cb2d97
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-26

    Bump version to 2.21

configure.ac

commit 115a4347
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-26

    inference.rst: Update doctests

doc/demos/inference/inference.rst

commit 55d3d90b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-26

    NestedBlockModel: Modify MCMC sweeps to be in random hierarchical order

src/graph_tool/inference/nested_blockmodel.py

commit 9017394c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-26

    blockmodel: Simplify EntrySet operations

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh

commit f4ab27bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-24

    graph_distance_sampled.hh: Fix compilation warning

src/graph/stats/graph_distance_sampled.hh

commit 6e1c0056
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-24

    configure.ac: Fix quotation

configure.ac

commit 5590f887
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-24

    configure.ac: Remove prefix from numpy include

configure.ac

commit 17e38420
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-23

    configure.ac: Tidy up numpy test

configure.ac

commit 61daf01e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-23

    configure.ac: Add cairomm information

configure.ac

commit 92b2d5f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-23

    random_rewire(): Raise warning if edge_probs is not supplied

src/graph_tool/generation/__init__.py

commit 6ba6b6af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-23

    Add descriptor invalidation warning to documentation

src/graph_tool/__init__.py

commit 0e1823c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-23

    blockmodel: Update get_edge_probs()

doc/demos/inference/inference.rst
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit ef15eea7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-22

    blockmodel.py: Store reference to rec_params/wparams

src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit 02067e65
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-22

    Fix bug in graph_union() with filtered graphs

src/graph_tool/generation/__init__.py

commit bfd22685
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-21

    graph_blockmodel.hh: Cosmetic changes

src/graph/inference/graph_blockmodel.hh

commit 64789f16
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-21

    mcmc_equilibrate(): Fix error in docstring

src/graph_tool/inference/mcmc.py

commit dc6d19ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-20

    blockmodel: Fix parameter names of weight distributions and add support for Jeffreys prior

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py

commit 477df9b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-17

    Add "array" parameter to {dfs,bfs,dijkstra,astar}_iterator()

src/graph/numpy_bind.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph_tool/search/__init__.py

commit f327fcb4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-17

    generate_sbm(): fix bug when B=1

src/graph_tool/generation/__init__.py

commit fb37166a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-17

    Add support for iterating over all vertices in {dfs,bfs,dijkstra}_{search,iterator}()

src/graph/graph_bind.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph_tool/__init__.py
src/graph_tool/search/__init__.py

commit 5752f5eb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-17

    Remove HAVE_SCIPY cruft

src/graph/graph_bind.cc

commit 3a76ec81
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-11

    Add OpenMP functions to documentation

doc/graph_tool.rst
src/graph_tool/__init__.py

commit be8922ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-10

    inference.rst: fix doctests

doc/demos/inference/inference.rst

commit 011a2d32
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-10

    inference.rst: reduce display precision of doctests

doc/demos/inference/inference.rst

commit 7ca4f6b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-10

    inference.rst: Fix doctest

doc/demos/inference/inference.rst

commit a2a87884
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-09

    Improve parallelism in motifs()

src/graph/clustering/graph_motifs.hh

commit a5ef466f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-07

    configure.ac: write summary more compactly

configure.ac

commit ada4831b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-06

    configure.ac: Fix warning

configure.ac

commit d37844f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-06

    configure.ac: fix OpenMP flags with clang

configure.ac

commit 8a90c677
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-06

    configure.ac: Deal with dumb or nonexistent terminals

.gitlab-ci.yml
configure.ac

commit 3579cf78
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-06

    Update .gitlab-ci.yml

.gitlab-ci.yml

commit ac509072
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-06

    inference.rst: Fix test results for build without sparsehash

doc/demos/inference/inference.rst

commit ffeaf61c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-05

    configure.ac: Major cleanup and improvements

configure.ac
m4/ax_lib_cgal_core.m4
m4/ax_lib_expat.m4
m4/ax_openmp.m4
src/graph/Makefile.am
src/graph/generation/Makefile.am
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh

commit f1404b20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-05

    configure.ac: honor PYTHON_LIBS
    
    This also removes some cruft, and makes handling of {CXX,LD}FLAGS more
    consistent.

configure.ac

commit 9ff1dd9a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-05

    Slightly better default parameters for minimize_blockmodel_dl()

src/graph_tool/inference/minimize.py

commit 8b5cf600
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-05

    Assorted docstring fixes

doc/demos/animation/animation.rst
doc/demos/animation/animation_zombies.py
doc/demos/inference/inference.rst

commit c86b0856
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-04

    inference: avoid computing move probabilities in greedy mode
    
    This also fixes a potential problem with layered SBMs, where the move
    probabilities would be incorrectly computed.

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_overlap.hh

commit d6c4ad94
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-03

    Implement array-based vertices/edges access interface

doc/graph_tool.rst
doc/quickstart.rst
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 80692ffd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-02-03

    Improve underlying adjacency list implementation
    
    This changes the underlying adjacency matrix implementation to a single
    mixed in + out edge list for each node, instead of separate ones. This
    simplifies the undirected_adaptor<> so that its out-edge iterators
    become trivial, and also faster.

doc/demos/inference/inference.rst
doc/quickstart.rst
src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/reverse_graph_alt.hpp
src/graph/Makefile.am
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/draw/graph_tree_cts.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/generation/graph_triangulation.cc
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_filtered.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_python_interface.cc
src/graph/graph_reverse.hh
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/search/__init__.py
src/graph_tool/topology/__init__.py

commit 7f73bc97
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-28

    Update docstrings

doc/demos/inference/inference.rst
src/graph_tool/inference/blockmodel.py

commit c0c1d44d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-28

    Bump version to 2.21

configure.ac

commit f6ef9990
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-27

    Bump version to 2.20

configure.ac

commit 06035ce3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-23

    mcmc_loop.hh: Shuffle only if sweep is sequential

src/graph/inference/mcmc_loop.hh

commit b1430b32
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-19

    Update autoconf tests for C++14

m4/ax_cxx_compile_stdcxx.m4

commit 01432d60
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-15

    laplacian(): Remove innocuous warning

src/graph_tool/spectral/__init__.py

commit ba7eacbe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-15

    blockmodel.py: Better initialization of q_cache

src/graph_tool/inference/blockmodel.py

commit e63919e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-15

    Disable parallel algorithms for property maps of type python::object
    
    This fixes issue #362.

src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc

commit 7ad89287
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-07

    Implement vertex/edge_percolation()

src/graph/topology/Makefile.am
src/graph/topology/graph_percolation.cc
src/graph/topology/graph_percolation.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit c04533b0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-06

    Fix dlopen() flags problem with Python 3.6

src/graph_tool/dl_import.py

commit 99d8d449
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-02

    demos/inference/inference.rst: Fix doctest

doc/demos/inference/inference.rst

commit 16f65c80
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-02

    PropertyMap.set_value(): Attempt to convert user-supplied value

src/graph_tool/__init__.py

commit 42d89da9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-02

    Fix docstests

doc/conf.py
doc/demos/inference/inference.rst

commit e6374fc4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-01

    Wang-Landau sampling: Tune flatness criterion

src/graph_tool/inference/mcmc.py

commit 5955ae7f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-01

    Fix doctests

src/graph_tool/generation/__init__.py

commit 81eb2b81
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-01

    motif_significance(): Fix default arguments

src/graph_tool/clustering/__init__.py

commit 2e4e4cd6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2017-01-01

    Update copyright information

configure.ac
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/coroutine.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_tool.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/inference/bundled_vacate_loop.hh
src/graph/inference/cache.cc
src/graph/inference/cache.hh
src/graph/inference/exhaustive_loop.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_em.cc
src/graph/inference/graph_blockmodel_em.hh
src/graph/inference/graph_blockmodel_exhaustive.cc
src/graph/inference/graph_blockmodel_exhaustive.hh
src/graph/inference/graph_blockmodel_gibbs.cc
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_imp.cc
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/graph_blockmodel_layers_gibbs.cc
src/graph/inference/graph_blockmodel_layers_mcmc.cc
src/graph/inference/graph_blockmodel_layers_merge.cc
src/graph/inference/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/graph_blockmodel_layers_util.hh
src/graph/inference/graph_blockmodel_marginals.cc
src/graph/inference/graph_blockmodel_mcmc.cc
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_merge.cc
src/graph/inference/graph_blockmodel_merge.hh
src/graph/inference/graph_blockmodel_multicanonical.cc
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_overlap_vacate.cc
src/graph/inference/graph_blockmodel_overlap_vacate.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph/inference/graph_neighbour_sampler.hh
src/graph/inference/graph_state.hh
src/graph/inference/int_part.cc
src/graph/inference/mcmc_loop.hh
src/graph/inference/merge_loop.hh
src/graph/inference/multicanonical_loop.hh
src/graph/inference/parallel_rng.hh
src/graph/inference/spence.cc
src/graph/inference/util.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_planar_layout.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/gt_io.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/modularity.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/util.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 03e7d8d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-26

    Slight improvements to Wang-Landau sampling

src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/multicanonical_loop.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit 18b833e2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-22

    blockmodel.py: Fix get_block_state() with recs

src/graph_tool/inference/blockmodel.py

commit 351e646b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-15

    Remove LaTeX suff from doc config

doc/conf.py

commit 412abc9a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-15

    BlockState.sample_graph(): Use correct probabilities for undirected graphs

src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py

commit d305ec12
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-09

    Add 'epsilon' parameter to hierarchy_minimize()

src/graph_tool/inference/nested_blockmodel.py

commit d1f0958b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-05

    Implement BlockState.sample_graph()

src/graph_tool/inference/blockmodel.py

commit 4974404c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-04

    Slightly refactor random graph generation and add generate_sbm()

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_sbm.cc
src/graph/generation/graph_sbm.hh
src/graph/generation/sampler.hh
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py

commit dd1e9dfa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-02

    overlap_blockmodel.py: Fix bug with edge covariates

src/graph_tool/inference/overlap_blockmodel.py

commit 127dc08e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-12-02

    graph_generation.hh: Fix segfault

src/graph/generation/graph_generation.hh

commit 7561129f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-28

    modularity(): Fix doctest

src/graph_tool/inference/modularity.py

commit 5927ad4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-28

    test_inference.py: Fix some tests using edge covariates

doc/test_inference.py

commit 17cfac1f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    inference.rst: Update doctests

doc/demos/inference/inference.rst
doc/test_inference.py

commit 187b6c04
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    correlation: Fix jacknife variance in assortativity() and scalar_assortativity()

src/graph/correlations/graph_assortativity.hh
src/graph_tool/correlations/__init__.py

commit afd5efeb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    inference: Fix real edge covariates for layered and overlapping SBMs

src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit d4eae9c5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    Fix edge covariate issues with layered SBMs

src/graph/inference/graph_blockmodel_layers.cc
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py

commit bf5e1f9f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    configure.ac: Remove reference to community_old

configure.ac

commit 6d427e04
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    Slightly cleanup assortativity() and scalar_assortativity()

src/graph/correlations/graph_assortativity.hh

commit 28b189f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-27

    Fix bug in assortativity()

src/graph/correlations/graph_assortativity.hh

commit 44183262
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-26

    GML parser: Fix issues with some corner cases

src/graph/gml.hh

commit 146184bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-26

    NestedBlockState.mcmc_sweep(): Fix issue with single-group levels

src/graph_tool/inference/nested_blockmodel.py

commit 18bea80f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-26

    Trivial docstring fix

src/graph_tool/inference/mcmc.py

commit ed204f5e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-26

    Resurrect modularity() function

src/graph/inference/Makefile.am
src/graph/inference/graph_inference.cc
src/graph/inference/graph_modularity.cc
src/graph/inference/graph_modularity.hh
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/modularity.py

commit 98c6c2b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-26

    Remove deprecated community_old sub-module

src/graph/Makefile.am
src/graph/community_old/Makefile.am
src/graph/community_old/graph_blockmodel.cc
src/graph/community_old/graph_blockmodel.hh
src/graph/community_old/graph_blockmodel_covariates.cc
src/graph/community_old/graph_blockmodel_covariates.hh
src/graph/community_old/graph_blockmodel_overlap.cc
src/graph/community_old/graph_blockmodel_overlap.hh
src/graph/community_old/graph_community.cc
src/graph/community_old/graph_community.hh
src/graph/community_old/spence.cc
src/graph_tool/Makefile.am
src/graph_tool/community_old/__init__.py
src/graph_tool/community_old/blockmodel.py
src/graph_tool/community_old/covariate_blockmodel.py
src/graph_tool/community_old/nested_blockmodel.py
src/graph_tool/community_old/overlap_blockmodel.py

commit 0cebc67b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-06

    inference.blockmodel: Implement multiple edge covariates

src/graph/graph_bind.cc
src/graph/graph_selectors.hh
src/graph/inference/cache.cc
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_inference.cc
src/graph/inference/util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 5053de1f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-25

    graph_draw(): Fix issue with directed networks

src/graph/draw/graph_cairo_draw.cc

commit 16b19f7b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-15

    graph_draw(): Fix segfault

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit fc8ac1da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-15

    graph_draw(): Fix bug with interactive drawing

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit a00ea26a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-15

    Fix docstring typo

src/graph_tool/inference/nested_blockmodel.py

commit 76eec1e5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-14

    graph_draw(): Use boost::coroutines for interactive drawing

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit 01f579ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-14

    Bump version to 2.20dev

configure.ac

commit da041f33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-12

    Bump version to 2.19

configure.ac

commit 05d32238
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-12

    blockmodel-example.gt.gz: Fix pickle protocol bug

doc/demos/inference/blockmodel-example.gt.gz

commit 40f2fdf6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-12

    gt_io: Add GT_PICKLE_PROTOCOL module variable

src/graph_tool/gt_io.py

commit e06247f5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-06

    inference: Remove "sequential" parameter from multiflip MCMC

src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph_tool/inference/blockmodel.py

commit 174587ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-05

    inference.rst: Small improvements

doc/demos/inference/inference.rst

commit 9ec47bce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-03

    Fix tests in demos/inference/inference.rst

doc/Makefile
doc/demos/inference/inference.rst

commit 7d66170b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-03

    Revert "Replace some make_tuple instance with brace initializers"
    
    This reverts commit df948de9f22112f2f133f98bdaf346bbf2e6de54.
    
    As it turns out, some slightly older compilers (e.g. GCC 5.6) do not
    like this.
    
    This fixes issue #351

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh

commit 5239342c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-02

    inference: Add multiflip MCMC sweep

doc/test_inference_mcmc.py
src/graph/inference/Makefile.am
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_layers_overlap_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_multiflip_mcmc.cc
src/graph/inference/graph_blockmodel_multiflip_mcmc.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_multiflip_mcmc.cc
src/graph/inference/graph_inference.cc
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 93d7eec3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-02

    inference: Remove ddS from MCMC loop

src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/mcmc_loop.hh

commit 9466363f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    Fix docstrings

doc/demos/inference/inference.rst
src/graph_tool/inference/blockmodel.py

commit f1ac6991
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    graph_draw(): Fix default layout when mplfig is not None
    
    This fixes issue #345

src/graph_tool/draw/cairo_draw.py

commit d8d7bf9e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    inference.rst: Tune testsetup

doc/demos/inference/inference.rst

commit 4f4618c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    football.gt.gz: Improve default node positions

src/graph_tool/collection/football.gt.gz

commit 4e9341e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    inference.rst: Update doctests

doc/demos/inference/inference.rst

commit d30675c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    blockmodel: Set edge hash max load factor to .3

src/graph/inference/graph_blockmodel_util.hh

commit 13d1258a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    blockmodel: Remove unused block edges

src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/nested_blockmodel.py

commit 9ad7b3bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    Better forced inline tuning

src/boost-workaround/boost/graph/filtered_graph.hpp
src/graph/graph_adjacency.hh
src/graph/inference/graph_blockmodel_util.hh

commit cd45a52e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    Use boost::coroutines2 if available (boost >= 1.62)

src/graph/Makefile.am
src/graph/coroutine.hh
src/graph/graph_python_interface.hh
src/graph/inference/graph_blockmodel_exhaustive.cc
src/graph/inference/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/graph_blockmodel_overlap_exhaustive.cc
src/graph/search/graph_astar.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_subgraph_isomorphism.cc

commit 709320ad
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    Fix compilation with Boost 1.62
    
    This fixes issue #347

src/boost-workaround/boost/graph/filtered_graph.hpp
src/graph/inference/graph_blockmodel_marginals.cc

commit 1ac66242
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-11-01

    Avoid global inclusion of std and boost namespaces

src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community_old/graph_blockmodel_covariates.hh
src/graph/graph.hh
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.hh
src/graph/graph_properties_copy.hh
src/graph/graph_python_interface.hh
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/inference/graph_state.hh
src/graph/numpy_bind.hh
src/graph/str_repr.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topology.cc

commit d933fe7e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-31

    Annotate some short important functions with 'flatten' attribute

src/graph/graph_adaptor.hh
src/graph/graph_selectors.hh

commit beefde29
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-31

    blockmodel: Use static neighbour sampler if weighted

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_neighbour_sampler.hh

commit d84dd658
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-30

    blockmodel: Fix test

src/graph/inference/graph_blockmodel.hh

commit 503ec869
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-30

    Fix clang compilation problems with openmp

src/graph/generation/dynamic_sampler.hh
src/graph/generation/sampler.hh
src/graph/layout/graph_arf.hh
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/util/graph_search.hh

commit 8688be7a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-30

    blockmodel: Cleanup get_b(), beop(), etc.

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh

commit 41d98f5c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-29

    blockmodel: Fix minor issue with zero-weight edges

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh

commit 65ea9489
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-28

    nestd_blockmodel.py: Fix copying of NestedBlockState with sampling == True

src/graph_tool/inference/nested_blockmodel.py

commit df948de9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-28

    Replace some make_tuple instance with brace initializers

src/graph/inference/graph_blockmodel.hh

commit c688f9a3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    blockmodel: Refactor neighbour and edge sampling

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_neighbour_sampler.hh

commit d953e5f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    graph_blockmodel.hh: Improve checking

src/graph/inference/graph_blockmodel.hh

commit 3cb74f60
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    graph_blockmodel.hh: Never remove block edges

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh

commit 8b4a7059
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    sampler.hh: Implement access to items

src/graph/generation/sampler.hh

commit 5d891f86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    dynamic_sampler.hh: Keep track of removed items

src/graph/generation/dynamic_sampler.hh

commit 9c58d676
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-21

    Add missing data_ptr() method to edge property maps

src/graph/graph_python_interface_export.cc

commit 52b79792
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-19

    Add perfect forwarding to 'beop' and 'efilt' arguments

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh

commit a83d1c77
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    spence.cc: Include source documentation

src/graph/inference/spence.cc

commit cf79d6b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    graph_blockmodel_util.hh: Improve checking

src/graph/inference/graph_blockmodel_util.hh

commit 859bf4aa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    blockmodel: Add node and edge count checks

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh

commit 407e0bff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    graph_blockmodel.hh: Fix gstate references

src/graph/inference/graph_blockmodel.hh

commit e6183bba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    graph_blockmodel.hh: More checking

src/graph/inference/graph_blockmodel.hh

commit 9d395afb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    blockmodel: Refactor egroup sampling

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_util.hh

commit f7f516e3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    graph_blockmodel.hh: Add beop parameter

src/graph/inference/graph_blockmodel.hh

commit 81d28712
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    blockmodel: Improve weighted degrees

src/graph/inference/graph_blockmodel.cc
src/graph_tool/inference/blockmodel.py

commit 68abf8f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-26

    blockmodel: Refactor mcmc loop

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers_mcmc.cc
src/graph/inference/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/graph_blockmodel_mcmc.cc
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/mcmc_loop.hh

commit 667a4926
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-20

    inference.rst: Remove unnecessary test setups

doc/demos/inference/inference.rst

commit 195526cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-20

    inference.blockmodel: Fix issue with ignore_degrees

src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit 6ad35ea3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-20

    Replace '== None' by 'is None'

src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 1966c234
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-19

    inference: Fix issue when computing description length using pclabel

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 39f0cf57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-19

    inference: Fix issues with rec_type="delta_t"

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_merge.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit bfd485ee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-19

    inference: Remove unnecessary auxiliary functions

src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/util.py

commit 4a5bc229
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-19

    clustering.local_clustering(): Fix bug with directed graphs

src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph_tool/clustering/__init__.py

commit c8d01f45
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-19

    topology.similarity(): Add support for edge weights

src/graph/topology/Makefile.am
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_similarity_imp.cc
src/graph_tool/topology/__init__.py

commit 9668242a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-19

    inference.blockmodel: Avoid clabel overflow
    
    This fixes issue #344

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit aa26ba20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-14

    Fix issue with GraphView composition

doc/quickstart.rst
src/graph_tool/__init__.py

commit 48e68784
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-14

    inference.blockmodel: Improve microstate entropy
    
    This adds an option to store a single partitions instead of all its
    possible permutations.

src/graph/inference/graph_blockmodel_marginals.cc
src/graph_tool/inference/blockmodel.py

commit 7477469e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-13

    Fix problem with and improve BlockState.get_edges_prob()

doc/demos/inference/inference.rst
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 666ccd25
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-13

    Improve Graph.copy_property()
    
    The method no longer temporarily alters the vertex or edge filters.

src/graph_tool/__init__.py

commit e833a522
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-13

    Fix problem with Graph.clear_vertex() when using filtered graphs

src/graph/graph_adjacency.hh
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_util.hh
src/graph_tool/__init__.py

commit 34172d3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-10-10

    Temporarily disable extensive inference testing
    
    It slows downs considerably the automated testing after each
    commit. From now one this should be run at checkpoints before each
    release.

doc/inference.rst

commit c91eb270
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-25

    inference: add support for discrete edge weights

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py

commit 81bcf5c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-22

    random_graph(): improve error message for invalid degrees

src/graph_tool/generation/__init__.py

commit b5545018
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-21

    Fix docstring typo in Graph.set_filters()

src/graph_tool/__init__.py

commit 4e5558a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-19

    NestedBlockState: add nested_partition term

doc/demos/inference/inference.rst
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/nested_blockmodel.py

commit 2a4aa1fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-21

    Fix compilation problem with newer CGAL

src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh

commit 14a128d1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-19

    minimize.py: fix docstring

src/graph_tool/inference/minimize.py

commit ec1a72fa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-10

    bethe_entropy(): fix overflow problem

src/graph/inference/graph_blockmodel_marginals.cc

commit da0ea999
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-06

    inference: modularize neighbour sampling code

src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_generation.cc
src/graph/inference/Makefile.am
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_neighbour_sampler.hh

commit e2e46593
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-05

    shortest_distance(): clarify distance of unconnected vertices in documentation

src/graph_tool/topology/__init__.py

commit 4cdad2f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-09-05

    kcore_decomposition(): fix inconsistency for directed graphs

src/graph_tool/topology/__init__.py

commit 1d2b1fab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-14

    blockmodel: fix bug with vertex movements

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh

commit c9a7fd1d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-09

    blockmodel: fix nested sampling of filtered graphs
    
    This fixes issue #322

src/graph_tool/inference/blockmodel.py

commit 62055e30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-08

    inference.blockmodel: simplify and speedup vertex movements

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh

commit 74cfb8a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-08

    Graph.prune_vertices(): Set correct base for GraphView objects

src/graph_tool/__init__.py

commit 1dad4c00
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-08

    sfdp_layout(): Fix returned property map ownership

src/graph_tool/draw/__init__.py

commit ffab3cfd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-05

    sampler.hh: slightly improve memory usage

src/graph/generation/sampler.hh

commit 559c5bbe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-08-05

    inference.rst: fix typo

doc/demos/inference/inference.rst

commit 5766b181
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-27

    blockmodel: Make sure empty groups' labels are sampled uniformly

doc/demos/inference/inference.rst
src/graph/generation/sampler.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/util.hh
src/graph_tool/inference/nested_blockmodel.py

commit 890aaab5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-26

    Add Vector_*.clear() method

src/graph/graph_bind.cc

commit b0c1d6c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-26

    test_inference_mcmc.py: Change statistics

doc/test_inference_mcmc.py

commit f65645fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-22

    configure.ac: prioritize user-supplied compilation flags

configure.ac

commit a02fd69f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-22

    Bump version to 2.19dev

configure.ac

commit 37996a0a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-21

    Bump version to 2.18

configure.ac

commit 7f03e925
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-21

    Fix another Python 2 compatibility issue

src/graph_tool/__init__.py

commit d38840ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-21

    Fix python 2 compatibility issue

src/graph_tool/__init__.py

commit 825a4a36
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-21

    load_graph_from_csv(): change eprop_titles to eprop_names

src/graph_tool/__init__.py

commit cee71b1e
Merge: 4590f1cc b679e051
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-21

    Merge pull request #14 from verginer/patch-1
    
    Added option to name properties in csv load

commit 4590f1cc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-21

    test_inference_mcmc.py: some tuning

doc/pyenv.py
doc/test_inference_mcmc.py

commit b679e051
Author: Luca Verginer <verginer@users.noreply.github.com>
Date:   2016-07-21

    indenation fixed

src/graph_tool/__init__.py

commit 58f2be1c
Author: Luca Verginer <verginer@users.noreply.github.com>
Date:   2016-07-21

    Added option to name properties in csv load
    
    Added the option to `eprop_titles` to `load_graph_from_csv` to allow the user to specify the names for the properties she would like to use.

src/graph_tool/__init__.py

commit df29e859
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-20

    inference.rst: Fix typo

doc/demos/inference/inference.rst

commit 3ea457d1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-20

    inference.rst: Update examples

doc/demos/inference/inference.rst

commit d0fc4754
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-20

    test_inference_mcmc: Simplify statistics

doc/test_inference_mcmc.py

commit 9566e946
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-20

    test_inference_mcmc: switch to a smaller network

doc/test_inference_mcmc.py

commit c41d1be6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-20

    blockmodel: fix issue with edges having zero weight

src/graph/inference/graph_blockmodel_util.hh

commit 93dbb6c2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    blockmodel: Fix issue with sampling neighbours for degree-zero nodes

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh

commit d510368f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    Fix further Python 2 issues

doc/conf.py
src/graph_tool/__init__.py

commit 70bf7408
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    Fix doctests

doc/Makefile
doc/conf.py
doc/demos/inference/inference.rst

commit 31a16689
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    Fix some Python 2 incompatibilities

src/graph_tool/__init__.py

commit db22b670
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    graph_blockmodel_util.hh: Fix bug with 'waiting times'

src/graph/inference/graph_blockmodel_util.hh

commit 410e8232
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    graph_blockmodel.hh: Fix bug with neighbour sampler
    
    This fixes a bug with isolated nodes that contain only self-loops.

src/graph/generation/sampler.hh
src/graph/inference/graph_blockmodel.hh

commit 34dbc181
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    inference.rst: Update doctest results

doc/demos/inference/inference.rst

commit 4d95c40b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-18

    Fix bug in NestedBlockState.get_edges_prob() when sampling=True

src/graph_tool/inference/nested_blockmodel.py

commit f8b763a5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-17

    NestedBlockState.mcmc_sweep() complement docstring

src/graph_tool/inference/nested_blockmodel.py

commit a014890f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-17

    Fix issue with nested SBM mcmc
    
    This solves a problem when NestedBlockState.mcmc_sweep() is invoked with
    nonstandard values of the parameter 'c'.

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/nested_blockmodel.py

commit 3a609c11
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-11

    Fix superficial build test errors

doc/demos/inference/inference.rst

commit 00b49466
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-10

    demangle.cc: Fix clang compilation issue
    
    This fixes issue #319

src/graph/demangle.cc

commit 3f2a5d5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-10

    Replace python::detail::gcc_demangle by abi::__cxa_demangle
    
    This fixes issue #318

src/graph/Makefile.am
src/graph/demangle.cc
src/graph/demangle.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/graph_bind.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/numpy_bind.hh

commit 14e22f79
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-09

    graph_draw(): Add 'none' vertex shape

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 80d2c864
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-09

    configure.ac: Fix linkage with boost-python

configure.ac

commit 057c9c64
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-09

    Tighten vertex type selection in graph_selectors.hh

src/graph/graph_selectors.hh

commit a739fc15
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-09

    hash_map_wrap.hh: fix issue with libc++

src/graph/hash_map_wrap.hh

commit 0116929e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-09

    Update boost m4 macros

configure.ac
m4/ax_boost_graph.m4
m4/ax_boost_iostreams.m4
m4/ax_boost_regex.m4
m4/ax_cxx_compile_stdcxx.m4
m4/ax_cxx_compile_stdcxx_14.m4

commit 236cc632
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-08

    Fix problems with doctests

doc/conf.py
doc/pyenv.py
doc/test_inference_mcmc.py

commit 78819ad8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Fix issues with doctests

.gitlab-ci.yml
doc/pyenv.py

commit df3de207
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Bump version to 2.18dev

configure.ac

commit 87771cbc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Bump version to 2.17

configure.ac

commit c6dd66a5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Update gitlab tests

.gitlab-ci.yml

commit 7a40f7d9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    inference: add link to cookbook documentation

doc/demos/inference/inference.rst
src/graph_tool/inference/__init__.py

commit 3eded5a8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Increase number of iterations in inference test

doc/test_inference_mcmc.py

commit 39f58776
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Add 'inference' section to cookbook

doc/demos/index.rst
doc/demos/inference/blockmodel-example.gt.gz
doc/demos/inference/inference.rst
doc/demos/inference/nested-diagram.svg
doc/gt_theme/static/gt_style.css
doc/pyenv.py

commit a0d0dd23
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    graph_draw(): Fix issue with vertex/edge categorical colors

src/graph_tool/draw/cairo_draw.py

commit db70b049
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-06

    Fix minor issues with edge prediction and model averaging

src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py

commit 3cd04a82
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-02

    Enable pickling of Vector_* types

src/graph/graph_bind.cc

commit 34735af2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-02

    Implement BlockState.collect_partition_histograms() and microstate_entropy()

src/graph/inference/graph_blockmodel_marginals.cc
src/graph_tool/inference/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 0ba0c262
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-07-01

    Improve memory performance of collect_edge_marginals() and bethe_entropy()

src/graph/inference/Makefile.am
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel_marginals.cc
src/graph/inference/graph_inference.cc
src/graph_tool/inference/blockmodel.py

commit edf3eb7e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-30

    Move mf_entropy() to C++

src/graph/inference/graph_blockmodel.cc
src/graph_tool/inference/blockmodel.py

commit 34ee3d5a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-30

    Fix NestedBlockState.project_level()

src/graph_tool/inference/nested_blockmodel.py

commit 82e496e6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-27

    Fix issue with edge prediction in layered models

src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 9dd4ae83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-26

    Fix Python 2 syntax error

src/graph_tool/inference/mcmc.py

commit ffac9b09
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-25

    NestedBlockState.mcmc_sweep(): add support for different parameters for different levels

src/graph_tool/inference/nested_blockmodel.py

commit 813cf5c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-25

    inference: fix issue with MCMC sampling

src/graph/inference/graph_blockmodel.hh
src/graph/inference/util.hh

commit 2fd39e7b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-25

    Update inference tests

doc/test_inference.py
doc/test_inference_mcmc.py

commit 131553a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-25

    Implement TemperingState

src/graph_tool/inference/__init__.py
src/graph_tool/inference/mcmc.py

commit d88cb044
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-25

    Fix NestedBlockState pickling

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit 677274b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-23

    Add link prediction to layered and nested SBMs

src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit bde826b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-23

    Fix bug with BlockState.merge_sweep()

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_merge.hh

commit 42c81a3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-23

    Fix pickling of NestedBlockState

src/graph_tool/inference/nested_blockmodel.py

commit ff9fdc7d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-23

    Fix compilation error with clang

src/graph/inference/graph_blockmodel_util.hh

commit 46ca49e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-24

    Substantial reorganization and improvement of blockmodel inference
    
    This adds support for exact likelihood calculation, correct posterior
    sampling of models with nonempty groups, much improved "distributed"
    degree-corrected prior, as well as continuous edge covariates.

doc/test_inference.py
doc/test_inference_mcmc.py
src/graph/inference/Makefile.am
src/graph/inference/bundled_vacate_loop.hh
src/graph/inference/cache.cc
src/graph/inference/cache.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_exhaustive.hh
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_imp.cc
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_layers_util.hh
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_merge.hh
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_overlap_vacate.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_state.hh
src/graph/inference/int_part.cc
src/graph/inference/int_part.hh
src/graph/inference/util.hh
src/graph_tool/draw/gtk_draw.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/util.py

commit 0c6e9de7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-14

    Massively simplify PropertyArray class
    
    Now PropertyMap.get_array() will return a simple unchecked numpy.ndarray
    subclass (PropertyArray) that will be invalid if the shape of the graph
    changes. The user is required not to store a copy of this value if the
    graph is to be modified.

src/graph/numpy_bind.hh
src/graph_tool/__init__.py

commit 6092cdaf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-07

    Fix bug with removing last vertex when fast == True
    
    This fixes issue #305

src/graph/graph_adjacency.hh

commit 8dad6746
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-07

    load_graph_from_csv(): Fix default dialect

src/graph_tool/__init__.py

commit d1e2761c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-06-04

    Implement load_graph_from_csv()

doc/graph_tool.rst
src/graph_tool/__init__.py

commit 9b4e7944
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-28

    collection.konect: Fix handling of floating-point edge weights

src/graph_tool/collection/konect.py

commit 1b185bcb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-28

    collection.konect: Fix handling of bipartite graphs

src/graph_tool/collection/konect.py

commit 26e770f5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-24

    Fix bug with edge property sums in condensation_graph()

src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_generation.cc
src/graph_tool/generation/__init__.py

commit 1494f7e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-21

    Disable openmp in clang tests

.gitlab-ci.yml

commit a6340293
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-19

    Fix bug in BlockModel.entropy() with test=True

src/graph_tool/inference/blockmodel.py

commit bf1e07b1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-16

    Properly honor B_min parameter in minimize_blockmodel_dl()

src/graph_tool/inference/minimize.py

commit f772e4e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-13

    Enable openmp in all build tests

.gitlab-ci.yml

commit a934aa6a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-13

    inference.blockmodel.BlockState: add 'allow_empty' option

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/__init__.py
src/graph_tool/inference/blockmodel.py

commit 500878c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-12

    Fix bug with waiting times

src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit 104e09ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-10

    Fix bug introduced in commit 2c877186976

src/graph/community_old/graph_blockmodel_overlap.cc

commit 2c877186
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-10

    Workaround for clang bug

src/graph/community_old/graph_blockmodel_overlap.cc
src/graph/hash_map_wrap.hh

commit eb8deeaa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-10

    inference.BlockModelState: Fix bug with edts

src/graph_tool/inference/blockmodel.py

commit 152ca20b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-09

    Fix compilation errors with clang

src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/merge_loop.hh

commit b946f0f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-09

    Fix bug in shortest_distance() with "directed" parameter
    
    This fixes issue #300

src/graph_tool/topology/__init__.py

commit 0f5c6894
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-03

    inference.blockmodel: implement "waiting times"

src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit 20b48710
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-03

    condensation_graph(): Fix bug with edge property sums

src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_generation.cc
src/graph_tool/generation/__init__.py

commit df42fadc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-02

    inference: fix bug with pickling BlockState
    
    Make sure to preserve "ignore_degrees" even when the values are
    non-Boolean (i.e. 2).

src/graph_tool/inference/blockmodel.py

commit 5b21cc1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-02

    inference: fix blockmodel entropy for weighted graphs

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit f78f5614
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-01

    inference: improve terminology use

src/graph_tool/inference/__init__.py

commit a50e61f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-05-01

    community_old: guarantee symbols from 'inference' module are present
    
    This fixes issue #296.

src/graph_tool/community_old/__init__.py

commit 79d32bcc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-27

    Remove i386 build tests

.gitlab-ci.yml

commit b24556fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-24

    planar_layout(): fix link to BGL documentation

src/graph_tool/draw/__init__.py

commit e2de443b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-22

    Massive OpenMP reorganization
    
    Now algorithms rely more on parallel_{vertex/edge}_loop() and global
    the paralellization threshold is honored.

src/boost-workaround/boost/graph/reverse_graph_alt.hpp
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.hh
src/graph/graph_adjacency.hh
src/graph/graph_copy.cc
src/graph/graph_properties.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_python_interface.cc
src/graph/graph_util.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/mcmc_loop.hh
src/graph/inference/merge_loop.hh
src/graph/layout/graph_arf.hh
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_vertex_similarity.hh
src/graph/util/graph_search.hh
src/graph_tool/__init__.py
src/graph_tool/topology/__init__.py

commit 8783af44
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-21

    Implement all_circuits()
    
    This fixes issue #191

src/graph/topology/Makefile.am
src/graph/topology/graph_all_circuits.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit da47282a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-21

    numpy_bind.hh: some improvements

src/graph/numpy_bind.hh

commit d8bfcd42
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-21

    is_bipartite(): add option 'find_odd_cycle'

src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit eb8e7f10
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-20

    Change default in MulticanonicalState.get_flatness()

src/graph_tool/inference/mcmc.py

commit 3805add7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-20

    Implement draw.planar_layout()

doc/draw.rst
src/graph/layout/Makefile.am
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_planar_layout.cc
src/graph/topology/graph_planar.cc
src/graph_tool/draw/__init__.py
src/graph_tool/topology/__init__.py

commit a3eae6a3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-20

    tsp_tour(): raise exception for directed graphs
    
    This closes issue #293

src/graph_tool/topology/__init__.py

commit 91843211
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-19

    Fix typo bug in mcmc_anneal()

src/graph_tool/inference/mcmc.py

commit 2c1bc95f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-18

    test_inference_mcmc.py: increase equilibration time

doc/test_inference_mcmc.py

commit 7c0c4ac7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-17

    test_inference_mcmc.py: Switch to a smaller network to guarantee speedy equilibration

doc/test_inference_mcmc.py

commit 7b4b5618
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-17

    MulticanonicalState: fix issue with histogram flat

src/graph_tool/inference/mcmc.py

commit 05becca9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-17

    test_inference_mcmc.py: increase statistics

doc/test_inference_mcmc.py

commit 6c3d1149
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-17

    inference: make use of uniform_sample()

src/graph/inference/graph_blockmodel_util.hh

commit 95e1e194
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    test_inference_mcmc.py: decrease probability of false negatives

doc/test_inference_mcmc.py

commit b4e25c3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    test_inference_mcmc.py: include Gibbs sampling

doc/test_inference_mcmc.py

commit e837dcc3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    Bump version to 2.17dev

configure.ac

commit 386af122
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    Bump version to 2.16

configure.ac

commit fc5f379c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    Fix bug in BlockState.{remove/add}_vertex()

src/graph_tool/inference/blockmodel.py

commit 9cc5cb2f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    Documentation and test fixes

doc/test_inference.py
doc/test_inference_mcmc.py
src/graph_tool/inference/blockmodel.py

commit 0dc50885
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-16

    Bump version to 2.15

configure.ac

commit 8122cdcf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-15

    inference: implement extensive detailed balance tests

doc/inference.rst
doc/test_inference.py
doc/test_inference_mcmc.py

commit 2f3b46a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-15

    inference: fix bug in detailed balance enforcement

src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_util.hh

commit 2b0a9da7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-14

    multicanonical_equilibrate(): small improvements

src/graph/inference/multicanonical_loop.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit 2085f45a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-14

    multicanonical_equilibrate(): add "allow_gaps" option

src/graph_tool/inference/mcmc.py

commit 0aee04a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-14

    inference: fix potential issue with get_move_prob()

src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit 952d299b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-13

    Improve docstrings

src/graph_tool/inference/blockmodel.py

commit 1475dc43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-13

    Implement BlockState.exhaustive_sweep()

src/graph/inference/Makefile.am
src/graph/inference/exhaustive_loop.hh
src/graph/inference/graph_blockmodel_exhaustive.cc
src/graph/inference/graph_blockmodel_exhaustive.hh
src/graph/inference/graph_blockmodel_layers_exhaustive.cc
src/graph/inference/graph_blockmodel_layers_overlap_exhaustive.cc
src/graph/inference/graph_blockmodel_overlap_exhaustive.cc
src/graph/inference/graph_inference.cc
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 30e6b8a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-13

    Allow for multiple simultaneous vertex movements in BlockState.move_vertex()

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph_tool/inference/blockmodel.py

commit 2dfe4f33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-13

    Fix python-exposed boost::coroutine iteration
    
    This preserves the synchrony between global states and the iteration
    sequence.

src/graph/graph_python_interface.hh

commit 8037d8d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-12

    inference: implement stricter checking for unexpected keyword arguments

doc/test_inference.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/util.py

commit 8eef438b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-12

    graph_distance_sampled.hh: improve performance

src/graph/stats/graph_distance_sampled.hh
src/graph/topology/graph_all_distances.cc

commit 0c92adbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-12

    Fix bug in GraphAdaptor's in_edges()

src/graph/graph_adaptor.hh

commit 936e7260
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-11

    Improve iteration over out-/in-neighbours

src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/reverse_graph_alt.hpp
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_selectors.hh

commit 9e41e054
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-11

    vertex_similarity(): Small fixes to docstring

src/graph_tool/topology/__init__.py

commit cd8a85bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-11

    draw.random_layout(): Remove Numpy warning

src/graph_tool/draw/__init__.py

commit e173b204
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-11

    Implement topology.vertex_similarity()
    
    This fixes issue #287

src/graph/topology/Makefile.am
src/graph/topology/graph_topology.cc
src/graph/topology/graph_vertex_similarity.cc
src/graph/topology/graph_vertex_similarity.hh
src/graph_tool/topology/__init__.py

commit 058b172a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-10

    Fix MulticanonicalState.get_allowed_energies()

src/graph_tool/inference/mcmc.py

commit 53061723
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-10

    multicanonical_equilibrate(): improve refinement

src/graph/inference/multicanonical_loop.hh
src/graph_tool/inference/mcmc.py

commit 040f4f48
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-10

    multicanonical_equilibrate(): Use both extrema to guarantee histogram flatness

src/graph_tool/inference/mcmc.py

commit 2a058f62
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-10

    Improve initialization speed of BlockState.{mcmc,gibbs,multicanonical}_sweep

src/graph_tool/inference/blockmodel.py

commit c143f91d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-09

    MulticanonicalState: improve flatness criterium

src/graph_tool/inference/mcmc.py

commit 6e6c375c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-09

    blockmodel.py: docstring and test fixes

src/graph_tool/inference/blockmodel.py

commit 8455d1d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-09

    multicanonical_loop.hh: check for out-of-bounds condition

src/graph/inference/multicanonical_loop.hh

commit 2f50ceaf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-08

    Fix bug in BlockState.virtual_vertex_move()

src/graph_tool/inference/blockmodel.py

commit e6361582
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-08

    Fix MulticanonicalState.get_entropy()

src/graph_tool/inference/mcmc.py

commit 864c5f68
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-08

    inference: some improvements to the multicanonical code

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_multicanonical.cc
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_inference.cc
src/graph/inference/multicanonical_loop.hh
src/graph_tool/__init__.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 413c28a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-07

    Implement semi-Bayesian block model inference
    
    This includes code for expectation maximization with belief propagation
    for the stochastic block model.

src/graph/inference/Makefile.am
src/graph/inference/graph_blockmodel_em.cc
src/graph/inference/graph_blockmodel_em.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_state.hh
src/graph_tool/Makefile.am
src/graph_tool/inference/__init__.py
src/graph_tool/inference/blockmodel_em.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py

commit 93b1d393
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-07

    Better default layout for football network

src/graph_tool/collection/football.gt.gz

commit 9aa21c5c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-07

    numpy_bind.hh: change exception name

src/graph/graph_python_interface_imp1.cc
src/graph/numpy_bind.hh

commit 09100295
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-06

    Fix some documentation typos

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit eb1eb083
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-06

    Bump version to 2.15dev

configure.ac

commit 3b5707ca
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-05

    Bump version to 2.14

configure.ac

commit ec7c6e09
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-05

    src/graph/inference/Makefile.am: Add missing files

src/graph/inference/Makefile.am

commit 829c54e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-05

    Fix some documentation typos.

doc/demos/animation/animation.rst
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit af502694
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-05

    Fix bug in BlockState.add_vertex()

src/graph/inference/graph_blockmodel.hh

commit 88496100
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-05

    Remove reference to <boost/graph/reverse_graph.hpp>

src/graph/graph_util.hh

commit 1d7bbba4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    Fix bug in BlockState.get_edges_prob()

src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph_tool/inference/blockmodel.py

commit acfeb0ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    Implement hashing of edge descriptors

src/boost-workaround/boost/graph/reverse_graph_alt.hpp
src/graph/graph_adjacency.hh
src/graph/graph_filtering.hh
src/graph/hash_map_wrap.hh

commit 32a06013
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    Fix boundary issue in NestedBlockState.replace_level()

src/graph_tool/inference/nested_blockmodel.py

commit 520254ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    Fix issue with PropertyArray during pickling

src/graph_tool/__init__.py

commit b20a625e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    nested_blockmodel.py: Fix assertion error

src/graph_tool/inference/nested_blockmodel.py

commit 136db0e2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    blockmodel.py: Fix bug with ignore_degrees

src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph_tool/inference/blockmodel.py

commit d9bcc66f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    Fix bug in graph_draw() with sparsehash enabled
    
    This fixes issue #285

src/graph/draw/graph_cairo_draw.cc

commit d0fb50fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    minimize_nested_blockmodel_dl(): Fix bug with b_max and overlapping state

src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py

commit cb3e6d45
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-04

    Improved consistency checking

src/graph_tool/inference/blockmodel.py

commit 5d2de77b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    minimize(_nested)_blockmodel_dl(): Fix handling of clabel and pclabel

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py

commit 78dcac84
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Implement BlockState.get_edges_prob()

src/graph/inference/graph_blockmodel_layers.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/nested_blockmodel.py

commit c5e1c6a2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    mcmc_equilibrate(): add "block_moves" argument

src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_merge.hh
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/mcmc_loop.hh
src/graph/inference/merge_loop.hh
src/graph/inference/multicanonical_loop.hh
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/mcmc.py

commit 1a33662e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Fix issue with mcmc_gibbs() for weighted block graphs

src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel_gibbs.hh

commit f0bcd76e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Remove spurious assert()

src/graph/inference/graph_blockmodel_gibbs.hh

commit 6f0c58fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Fix bug with perfect_prop_hash()

src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc

commit c2825ffb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Fix Python 2 issues

doc/test_inference.py
src/graph_tool/inference/layered_blockmodel.py

commit f5916cc3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Fix compilation error in debug mode

src/graph/inference/graph_blockmodel_layers.hh

commit 3519b1e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-03

    Fix Python 2 compatibility with test_inference.py

doc/test_inference.py

commit d65bbcf3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    Improve local_clustering()/global_clustering() performance

src/graph/clustering/graph_clustering.hh
src/graph_tool/clustering/__init__.py

commit 69536f1b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    Fix docstring test

src/graph_tool/generation/__init__.py

commit 47843ad6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    Fix syntax error with Python 2

src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py

commit 563c3dde
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    Fix compilation warnings and errors on some compilers

src/graph/centrality/graph_closeness.hh
src/graph/inference/bundled_vacate_loop.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/multicanonical_loop.hh

commit d0bd7f48
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    More docstring test fixes

.gitlab-ci.yml
doc/test_inference.py
src/graph_tool/generation/__init__.py

commit 53933d87
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    Fix test_inference.py

doc/inference.rst
doc/test_inference.py

commit 62a57e77
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-02

    Fix compilation error with clang and openmp
    
    This fixes issue #289

src/graph/community_old/graph_blockmodel.hh
src/graph/community_old/graph_blockmodel_overlap.hh

commit 41471e3c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-15

    Refactor 'community' module and rename to 'inference'
    
    This is a significant refactoring of the statistical inference code,
    with many cleanups and improvements, and is aimed towards future
    extensibility.
    
    The old community module is available as 'community_old' and will be
    completely removed in the near future.

Makefile.am
configure.ac
doc/community.rst
doc/community.xml
doc/graph_tool.rst
doc/inference.rst
doc/test_inference.py
src/boost-workaround/boost/graph/reverse_graph_alt.hpp
src/graph/Makefile.am
src/graph/community_old/Makefile.am
src/graph/community_old/graph_blockmodel.cc
src/graph/community_old/graph_blockmodel.hh
src/graph/community_old/graph_blockmodel_covariates.cc
src/graph/community_old/graph_blockmodel_covariates.hh
src/graph/community_old/graph_blockmodel_overlap.cc
src/graph/community_old/graph_blockmodel_overlap.hh
src/graph/community_old/graph_community.cc
src/graph/community_old/graph_community.hh
src/graph/community_old/spence.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/generation/Makefile.am
src/graph/generation/graph_community_network.cc
src/graph/generation/graph_community_network.hh
src/graph/generation/graph_community_network_eavg.cc
src/graph/generation/graph_community_network_eavg_imp1.cc
src/graph/generation/graph_community_network_edges.cc
src/graph/generation/graph_community_network_vavg.cc
src/graph/generation/graph_generation.cc
src/graph/generation/sampler.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.hh
src/graph/inference/Makefile.am
src/graph/inference/bundled_vacate_loop.hh
src/graph/inference/cache.cc
src/graph/inference/cache.hh
src/graph/inference/gibbs_loop.hh
src/graph/inference/graph_blockmodel.cc
src/graph/inference/graph_blockmodel.hh
src/graph/inference/graph_blockmodel_gibbs.cc
src/graph/inference/graph_blockmodel_gibbs.hh
src/graph/inference/graph_blockmodel_layers.cc
src/graph/inference/graph_blockmodel_layers.hh
src/graph/inference/graph_blockmodel_layers_gibbs.cc
src/graph/inference/graph_blockmodel_layers_mcmc.cc
src/graph/inference/graph_blockmodel_layers_merge.cc
src/graph/inference/graph_blockmodel_layers_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_overlap.cc
src/graph/inference/graph_blockmodel_layers_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_layers_overlap_mcmc.cc
src/graph/inference/graph_blockmodel_layers_overlap_mcmc_bundled.cc
src/graph/inference/graph_blockmodel_layers_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_layers_overlap_vacate.cc
src/graph/inference/graph_blockmodel_layers_util.hh
src/graph/inference/graph_blockmodel_mcmc.cc
src/graph/inference/graph_blockmodel_mcmc.hh
src/graph/inference/graph_blockmodel_merge.cc
src/graph/inference/graph_blockmodel_merge.hh
src/graph/inference/graph_blockmodel_multicanonical.cc
src/graph/inference/graph_blockmodel_multicanonical.hh
src/graph/inference/graph_blockmodel_overlap.cc
src/graph/inference/graph_blockmodel_overlap.hh
src/graph/inference/graph_blockmodel_overlap_gibbs.cc
src/graph/inference/graph_blockmodel_overlap_mcmc.cc
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.cc
src/graph/inference/graph_blockmodel_overlap_mcmc_bundled.hh
src/graph/inference/graph_blockmodel_overlap_multicanonical.cc
src/graph/inference/graph_blockmodel_overlap_util.hh
src/graph/inference/graph_blockmodel_overlap_vacate.cc
src/graph/inference/graph_blockmodel_overlap_vacate.hh
src/graph/inference/graph_blockmodel_util.hh
src/graph/inference/graph_inference.cc
src/graph/inference/graph_state.hh
src/graph/inference/mcmc_loop.hh
src/graph/inference/merge_loop.hh
src/graph/inference/multicanonical_loop.hh
src/graph/inference/parallel_rng.hh
src/graph/inference/spence.cc
src/graph/inference/util.hh
src/graph_tool/Makefile.am
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/community_old/__init__.py
src/graph_tool/community_old/blockmodel.py
src/graph_tool/community_old/covariate_blockmodel.py
src/graph_tool/community_old/nested_blockmodel.py
src/graph_tool/community_old/overlap_blockmodel.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/generation/__init__.py
src/graph_tool/inference/__init__.py
src/graph_tool/inference/bisection.py
src/graph_tool/inference/blockmodel.py
src/graph_tool/inference/layered_blockmodel.py
src/graph_tool/inference/mcmc.py
src/graph_tool/inference/minimize.py
src/graph_tool/inference/nested_blockmodel.py
src/graph_tool/inference/overlap_blockmodel.py
src/graph_tool/inference/util.py

commit 4843cf1a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-01

    Make PropertyMap objects iterable
    
    This fixes issue #286

src/graph_tool/__init__.py

commit 9fcc539d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-04-01

    Fix some docstring typos

src/graph_tool/topology/__init__.py

commit 252f3583
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-31

    Fix deep copy of property maps

src/graph_tool/__init__.py

commit 0dde437d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-31

    graph_motifs.hh: Use range-based iteration

src/graph/clustering/graph_motifs.hh

commit 13d4477a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-15

    Fix bug with repeated vertices in all_paths()

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 3fde5e74
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-15

    Fix bug all_paths() with parallel edges

src/graph/topology/graph_distance.cc

commit f2c93fc6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-11

    Fix bug in find_edge_range()
    
    This fixes issue #281.

src/graph_tool/util/__init__.py

commit 31137b5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-10

    Fix bug with edge filtering when inversion changes
    
    This fixes issue #279.

src/graph/graph_filtering.cc
src/graph/graph_filtering.hh

commit df06590b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-10

    all_paths(): fix test in docstring

src/graph_tool/topology/__init__.py

commit a4abd055
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-10

    Implement all_paths()
    
    This fixes issue #278.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 1989b4b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-09

    eigenvector(): prevent getting stuck in iteration
    
    This aborts the iteration if no progress is being made. This fixes issue #276.

src/graph/centrality/graph_eigenvector.hh

commit 763a0871
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-06

    Fix typo in GraphWindow's docstring
    
    This fixes issue #275.

src/graph_tool/draw/gtk_draw.py

commit 4ebc5a3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-06

    Fix typo in GraphWidget's docstring
    
    This fixes issue #275.

src/graph_tool/draw/gtk_draw.py

commit 257f80df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-03

    Fix i386 builds

.gitlab-ci.yml

commit bc7495ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-02

    Rename io.py to gt_io.py
    
    This avoids confusion with the standard 'io' module.

src/graph_tool/Makefile.am
src/graph_tool/__init__.py
src/graph_tool/gt_io.py

commit 1c5bc9ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-02

    Up minimum GCC requirement to version 5

README.md

commit fd65d1e6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-02

    Bump version to 2.14dev

configure.ac

commit c15ecea6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-03-01

    Bump version to 2.13

configure.ac

commit 8b1b7c83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-08

    Allow pkgconfigdir to be set when running configure
    
    This also makes autogen.sh compatible with older versions of autotools +
    pkg-config.

Makefile.am
configure.ac

commit 3399e323
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Fix compilation error in graph_pagerank.hh

src/graph/centrality/graph_pagerank.hh

commit 0f2d575e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Cosmetic change to checked_vector_property_map

src/graph/fast_vector_property_map.hh

commit b50b31da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Add never_filtered_never_reversed to list of graph_views

src/graph/graph_filtering.hh

commit cf6905e8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Implement naked nested_for_each()

src/graph/mpl_nested_loop.hh

commit 31999eb5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Implement convenience metafunctions to get property map types

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/draw/graph_tree_cts.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/graph.hh
src/graph/graph_filtering.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.cc

commit a19d4056
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Replace some explicit parallel loops by implicit ones

src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/graph_copy.cc
src/graph/stats/graph_parallel.hh

commit 8a608cb9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-07

    Implement parallel loop convenience functions

configure.ac
src/graph/graph_util.hh

commit e6ee882b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-05

    README.md: Remove redundant build status and update minimum GCC version

README.md

commit 2881e360
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-05

    Fix drawing of graphs with no edges
    
    This fixes issue #269

src/graph_tool/draw/cairo_draw.py

commit 441463ed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-04

    Fix bug in init_nested_state() with overlapping states

src/graph_tool/community/nested_blockmodel.py

commit 17f3d190
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-03

    Fix a problem with B_min in minimize_nested_blockmodel_dl()

src/graph_tool/community/nested_blockmodel.py

commit ecee9d6f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-03

    Fix problem with B_max in minimize_nested_blockmodel_dl()
    
    This also removes (Nested)MinimizeState and checkpoints, in order to
    simplify the code.

doc/community.rst
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit a9bc162f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-02-02

    Trivial indentation/space fix

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/community/blockmodel.py

commit 26b147db
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-28

    minimize_(nested_)blockmodel_dl(): Add random_bisection optional parameter

src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit 64471e25
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-28

    minimize_nested_blockmodel_dl(): Fix bug with max_B parameter

src/graph_tool/community/nested_blockmodel.py

commit 3de2946d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-25

    Fix bug in sampled distance histogram

src/graph/stats/graph_distance_sampled.hh
src/graph_tool/stats/__init__.py

commit d7f9030b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-25

    Fix some docstring tests

src/graph_tool/clustering/__init__.py
src/graph_tool/community/blockmodel.py

commit 0cb5e19d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-24

    graph_blockmodel.hh: Some trivial cosmetic changes

src/graph/community/graph_blockmodel.hh

commit e8393974
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-24

    Simplify sparsehash autoconf section

configure.ac

commit 4ccc3789
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-24

    Select correct pycairo header according to Python version
    
    This fixes issue #262.

configure.ac
src/graph/draw/graph_cairo_draw.cc

commit 3446c01d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-22

    Force inline of key wrapper functions

src/boost-workaround/boost/graph/filtered_graph.hpp
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_selectors.hh

commit f74932df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-20

    Fix compilation error in clang

src/graph/graph_adjacency.hh

commit 9d0006a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-20

    cairo_draw(): Check if vorder is of scalar type
    
    This fixes issue #264

src/graph_tool/draw/cairo_draw.py

commit a6a09e6b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-19

    Fix motifs() for undirected graphs
    
    This fixes a bug where the isomorphism class for undirected subgraphs
    was wrongly computed using their directed view.

src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh

commit dcfbada3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-19

    graph_adjacency.hh: Simplify out/in-edge iterators

src/graph/graph_adjacency.hh

commit 9469b538
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-18

    Inline central simple functions in boost's filtered_graph.hpp

src/boost-workaround/boost/graph/filtered_graph.hpp
src/graph/Makefile.am

commit 5cd8d5c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-18

    Avoid unnecessary testing for valid vertices in unfiltered graphs in parallel loops

src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/generation/graph_geometric.hh
src/graph/graph.cc
src/graph/graph_adjacency.hh
src/graph/graph_copy.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_python_interface.cc
src/graph/graph_selectors.hh
src/graph/layout/graph_arf.hh
src/graph/layout/graph_sfdp.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/util/graph_search.hh

commit 8c8323af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-13

    graph_blockmodel_covariates.cc: Fix bad_any_cast bug

src/graph/community/graph_blockmodel_covariates.cc

commit 3dfbb30d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-13

    nested_for_each(): isolate boost::any_cast<>

src/graph/mpl_nested_loop.hh

commit 4fa837b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-12

    Change graph_tool::detail::all_graph_views to graph_tool::all_graph_views

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/topology/graph_components.cc

commit 9bb015d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-06

    graph_draw(): Improve flipping of y-direction when mplfig is being used
    
    This fixes issue #261

src/graph_tool/draw/cairo_draw.py

commit ca0d64e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-04

    sfdp_layout(): Prevent Barnes-Hut tree from becoming unnecessarily dense

src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 65c9d1a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-04

    Small improvements to sfdp_layout()

src/graph/layout/graph_sfdp.hh

commit 39089ded
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    Add "graph_tool.hh" convenience include file

src/graph/Makefile.am
src/graph/graph_tool.hh

commit 7ab12601
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    Fix path in animation demos

doc/demos/animation/animation.rst
doc/demos/animation/animation_dancing.py

commit bd5b8ab3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    Fix bug with vector<short> properties in graphml IO

src/boost-workaround/boost/graph/graphml.hpp
src/graph/graphml.cpp

commit b1cf2546
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    Move animation demos to a subdirectory

doc/demos/animation/animation.rst
doc/demos/animation/animation_dancing.py
doc/demos/animation/animation_sirs.py
doc/demos/animation/animation_zombies.py
doc/demos/animation/face-grin.png
doc/demos/animation/face-surprise.png
doc/demos/animation/interactive_bst.py
doc/demos/animation/zombie.png
doc/demos/index.rst

commit c114f861
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    kcore_decomposition(): Stylistic changes

src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh

commit e92b8eaa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    Replace shared_ptr by weak_ptr in Python descriptors and iterators

src/graph/graph_bind.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/util/graph_search.hh

commit b7785f2d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    name_demangle(): Fallback if demangling fails

src/graph/graph_filtering.cc

commit a54b52eb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-03

    nested_for_each(): Keep pointers instead of copies

src/graph/mpl_nested_loop.hh

commit b9d9bd3b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2016-01-01

    Update copyright date

configure.ac
doc/conf.py
src/graph/base64.cc
src/graph/base64.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/community/spence.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_python_interface_imp1.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/hash_map_wrap.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/konect.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 60b69009
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-30

    Remove PACKAGE_SOURCE_DIR definition from configure.ac

configure.ac

commit d6aaa556
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-26

    Replace ConstantPropertyMap by UnityPropertyMap whenever appropriate

src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_pagerank.cc
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/graph.hh
src/graph/graph_properties.hh
src/graph/graph_selectors.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_sfdp.cc
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_tsp.cc

commit 27f82a7d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-26

    shortest_distance(): Optimize all-pairs distances for unweighted graphs
    
    This fixes issue #260.

src/graph/topology/graph_all_distances.cc

commit 99440ef3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-26

    Change sphinx build test in amd64

.gitlab-ci.yml

commit ca9c8318
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-26

    Fix bug in ActionNotFound exception handling

configure.ac
src/graph/graph_bind.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh

commit 61421243
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-25

    Refactor run_action<> and implement the more general gt_dispatch<>

doc/graph_tool.rst
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/correlations/graph_assortativity.cc
src/graph/draw/graph_tree_cts.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_python_interface_export.cc
src/graph/layout/graph_sfdp.cc
src/graph/mpl_nested_loop.hh
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph_tool/__init__.py
src/graph_tool/community/blockmodel.py

commit b57dcbd5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-25

    Implement UnityPropertyMap

src/graph/graph_properties.hh
src/graph/graph_selectors.hh

commit 248b0861
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-24

    Fix std::placeholder vs. boost::placeholder ambiguity in boost 1.60

src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_pagerank.cc
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/correlations/graph_assortativity.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/graph.cc
src/graph/graph_properties.hh
src/graph/graph_properties_group.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values_imp1.cc
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface_imp1.cc
src/graph/layout/graph_arf.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_parallel.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/util/graph_search.cc

commit ee3b35bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-23

    graph_draw(): Flip y-direction when mplfig is given

src/graph_tool/draw/cairo_draw.py

commit 1c47cb6f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-23

    Handle foreign cairocffi.Context objects

src/graph_tool/draw/cairo_draw.py

commit 4b6ba22a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-23

    Add in/out/total_degreeS selectors with constant weights

src/graph/graph_properties.hh
src/graph/graph_selectors.hh

commit 2f5cdc0d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-22

    Remove unnecessary pkgconfigdir from Makefile.am

Makefile.am

commit 76d05e6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-22

    Include pkgconfigdir in Makefile.am for backward compatibility

Makefile.am

commit 51f34e07
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-21

    Update python/boost/c++ autoconf m4 macros

m4/ax_boost_base.m4
m4/ax_boost_python.m4
m4/ax_cxx_compile_stdcxx.m4
m4/ax_cxx_compile_stdcxx_14.m4
m4/ax_python_devel.m4
m4/ax_python_module.m4

commit c1d8a409
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-21

    Fix bug in find_vertex() with prop in ["in", "out", "total"]
    
    This fixes issue #258.

src/graph_tool/util/__init__.py

commit ce514489
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-17

    Fix self-loop bug in graph_draw()

src/graph/draw/graph_cairo_draw.cc

commit 615a8925
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-12-17

    Implement all_shortest_paths()

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit c49a9dd6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-25

    Add int16_t type to property map checks

src/graph_tool/__init__.py

commit 998fd1d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-25

    Accept non-scalar value types for partition property in modularity()
    
    This fixes issue #57 (again).

src/graph_tool/community/__init__.py

commit 5ce0259d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-22

    Improve performance in local/global_clustering()

src/graph/clustering/graph_clustering.hh

commit 5f7002dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-22

    Trivial simplification in adj_list<>::reindex_edges()

src/graph/graph_adjacency.hh

commit 95ed1e9d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-20

    Slightly simplify kcore_decompostion()

src/graph/topology/graph_kcore.hh

commit 6f28389f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-20

    Implement Vector_<type>_t.resize() and related members

src/graph/graph_bind.cc

commit 3fc7f752
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-20

    Remove no-op line

src/graph_tool/community/blockmodel.py

commit 1d6da511
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-20

    graph_motifs.hh: Clean openmp locking

src/graph/clustering/graph_motifs.hh

commit 6f31e429
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-14

    Change default edge/node label type in subgraph_isomorphism()
    
    Use int64_t instead of int32_t as the default label type.

src/graph/topology/graph_subgraph_isomorphism.cc
src/graph_tool/topology/__init__.py

commit 24a16870
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-14

    Do not mix yield and return in subgraph_isomorphism()

src/graph_tool/topology/__init__.py

commit ca2b8d11
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-13

    Implement "generator" option for subgraph_isomorphism()
    
    This introduces support for returning a generator in
    subgraph_isomorphism(), so that all matches do not need to be kept on
    memory simultaneously.
    
    This fixes issue #255.

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 8d57975d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-10

    Add pkg-config support
    
    This facilitates the development of C++ extensions to graph-tool.

Makefile.am
configure.ac
m4/ax_create_pkgconfig_info.m4

commit 6a4646f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-08

    GraphWidget: Implement smooth scrolling

src/graph_tool/draw/gtk_draw.py

commit 3c3907e3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-07

    Bump version to 2.13dev

configure.ac

commit 1d6bf978
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-06

    Bump version to 2.12

configure.ac

commit b54e1a83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-06

    Replace 'N' by 'V' in docstrings, when referring to number of nodes
    
    This improves the consistency in the documentation.

src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/generation/__init__.py

commit a5fd88ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-06

    graph_tree_cts.cc: More range-based loops

src/graph/draw/graph_tree_cts.cc

commit 6625a8ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-06

    _prop(): guarantee that property map always has sufficient size

src/graph_tool/__init__.py
src/graph_tool/draw/cairo_draw.py

commit ce197588
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-06

    graph_blockmodel.hh: pre-init function cache to prevent race condition if parallel=True
    
    This fixes issue #252.

src/graph/community/graph_blockmodel.hh

commit b456f304
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-05

    Make boost::coroutine test fail for boost < 1.55

m4/ax_boost_coroutine.m4

commit 1406c4c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-05

    Drop strict dependency on Boost 1.55
    
    This revers the dependency to 1.54. This can be done since
    boost::coroutines has been made optional.

configure.ac

commit f74de6f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-11-05

    Change Graph.max_edge_index to Graph.edge_index_range

src/graph/centrality/graph_betweenness.cc
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_rewiring.cc
src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties_imp1.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph_tool/__init__.py

commit 5c872d16
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-27

    Fix doctest in min_spanning_tree()

src/graph_tool/topology/__init__.py

commit 13d0ae0a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-27

    Bump version to 2.12dev

configure.ac

commit b6b2152c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-26

    Bump version to 2.11

configure.ac

commit 1a6f6c41
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-27

    Fix detection of boost::coroutine
    
    This causes the test to fail when only static variables are available.

configure.ac
m4/ax_boost_coroutine.m4

commit add3d518
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-27

    Remove any mention of boost::coroutine if HAVE_BOOST_COROUTINE is not defined

src/graph/search/graph_astar.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc

commit 1e051953
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-26

    Fix compilation error in action_wrap

src/graph/graph_filtering.hh

commit 051c267f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-26

    Remove more recursions in nested_for_each()
    
    This reduces even more compilation time and memory use.

src/graph/graph_filtering.hh
src/graph/mpl_nested_loop.hh

commit 09db85b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-26

    Fix PropertyDict.has_key() in Python 2

src/graph_tool/__init__.py

commit f6c1f995
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-25

    Fix bug in astar_iterator()

src/graph/search/graph_astar.cc

commit 0a0d95c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-25

    Remove search_module.rst from i386 tests due to Debian bug

.gitlab-ci.yml

commit d5f311ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-25

    Disable astar_iterator() if boost::coroutine is unavailable

src/graph/search/graph_astar.cc

commit 5dbe3935
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-25

    Re-organize compilation units to reduce compile-time memory usage

src/graph/Makefile.am
src/graph/graph_copy.cc
src/graph/graph_copy_imp1.cc
src/graph/graph_properties.cc
src/graph/graph_properties_copy.cc
src/graph/graph_properties_copy.hh
src/graph/graph_properties_copy_imp1.cc
src/graph/graph_properties_imp3.cc
src/graph/graph_properties_imp4.cc
src/graph/graph_properties_map_values.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface_imp1.cc

commit 322a4f4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-25

    Make boost::coroutine optional
    
    This is essentially because of a Debian bug, where no boost::coroutine
    shared libraries are available.

configure.ac
src/graph/search/graph_astar.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc

commit a875e876
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-25

    Get rid of clang++ warning

src/graph/mpl_nested_loop.hh

commit e809a910
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-24

    Add "label" parameter to label_out_component()

src/graph_tool/topology/__init__.py

commit 7bddacff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-24

    Split large compilation unites into smaller ones
    
    This saves memory during compilation.

src/graph/Makefile.am
src/graph/graph_copy_imp1.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values_imp1.cc

commit 0841edbb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-24

    Simplify mpl::nested_for_each()
    
    This modification provides a significant compile-time memory reduction.

src/graph/graph_filtering.hh
src/graph/graph_properties.hh
src/graph/graph_selectors.hh
src/graph/mpl_nested_loop.hh

commit 5b665fcc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-21

    More corrections to random_spanning_tree()'s docstring.

src/graph_tool/topology/__init__.py

commit c8b9f071
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-21

    Fix random_spanning_tree()'s docstring

src/graph_tool/topology/__init__.py

commit bfc59c37
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-21

    Remove tabs from ax_boost_coroutine.m4

m4/ax_boost_coroutine.m4

commit 45565cd1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-20

    Implement dfs/bfs/dijkstra/astar_iterator()

configure.ac
m4/ax_boost_coroutine.m4
src/graph/Makefile.am
src/graph/centrality/Makefile.am
src/graph/community/Makefile.am
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/search/Makefile.am
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/topology/Makefile.am
src/graph_tool/search/__init__.py

commit c68fd018
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-17

    Include test for specific C++14 features in ax_cxx_compile_stdcxx_14.m4

m4/ax_cxx_compile_stdcxx_14.m4

commit 78337816
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-15

    Fix bug in graph_draw() with new numpy

src/graph_tool/draw/cairo_draw.py

commit 19c9b394
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-15

    More "auto" and range-based loops

src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_hits.hh

commit af2fda8f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-15

    Cosmetic docstring cleanups

src/graph_tool/__init__.py

commit 59427bf3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-14

    Improve performance of Graph.edge(s,t) when the degrees of the vertices are unbalanced

src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 8caa6fa4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-13

    Bump version to 2.11dev

configure.ac

commit 547c17df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-13

    Bump version to 2.10

configure.ac

commit 2d105b70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-12

    More perfect reference forwarding in graph_selectors.hh

src/graph/graph_selectors.hh

commit e908d34a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-11

    Implement full parallelization of betweenness()

src/boost-workaround/boost/graph/betweenness_centrality.hpp

commit 0313ff37
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-11

    Implement "negative_weights" in shortest_distance/path()

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 441495fa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-11

    Use range-based iteration in centrality algorithms

src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh

commit 6daae30b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-11

    graph_adaptor.hh: Simplify joined_edge_iterator

src/graph/graph_adaptor.hh

commit 9f487e46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-11

    Enforce reverence/rvalue propagation in mk_range()

src/graph/graph_selectors.hh

commit 293c8a36
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-11

    Simplify edges(adj_list<Vertex>)

src/graph/graph_adjacency.hh

commit 30beecf7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-10

    graph_blockmodel.hh: use range-based for loop

src/graph/community/graph_blockmodel.hh

commit dde178cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-09

    Ensure GTK+ version 3 is imported in cairo_draw.py

src/graph_tool/draw/cairo_draw.py

commit 414a83c1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-09

    Fix formatting error in graph_draw()'s docstring

src/graph_tool/draw/cairo_draw.py

commit 5c4d2d92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-09

    Fix edge highlight in graph_draw()

src/graph_tool/draw/gtk_draw.py

commit 35341c80
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-08

    Add missing conversion protection in CovariateBlockState.__setstate__()

src/graph_tool/community/covariate_blockmodel.py

commit 577958b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-08

    No longer compress pickled graphs and fix unpickling of Python 2 states in Python 3
    
    This preserves backwards compatibility.

src/graph_tool/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit be3f8c07
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-08

    Make "propagate_clabel=True" default in minimize_nested_blockmodel_dl()

src/graph_tool/community/nested_blockmodel.py

commit be3df2bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Fix bug in Graph.copy() for filtered graphs

src/graph/graph_copy.cc

commit d5e5cfa7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Fix bug in PropertyMap.copy() and Graph.copy_property()

src/graph_tool/__init__.py

commit c2227dee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Implement "full" parameter in PropertyMap.copy() and Graph.copy_property()

src/graph_tool/__init__.py

commit e3fe062b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Simply GraphView.__init__()

src/graph_tool/__init__.py

commit 802a82dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Replace reserve() by resize() in PropertyMap.get_array()
    
    This ensures that the array is always of the correct size.

src/graph/graph_python_interface.hh

commit 65e954ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Remove dead code

src/graph/graph_copy.cc

commit e6dc5d63
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-07

    Fix pickling of NestedBlockState when layers == True

src/graph_tool/community/nested_blockmodel.py

commit 27552584
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-06

    Fix bug in Graph.remove_vertex(vs) when vs is an iterable

src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 0da3e441
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-06

    Fix bug when pickling PropertyMap objects that belong to filtered graphs

src/graph_tool/__init__.py

commit a18ba05a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-06

    Fix bug when saving filtered graphs

src/graph_tool/__init__.py

commit 78c7df83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-05

    Move Graph.clear_vertex() fully into C++

src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 7e033535
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-05

    Fix bugs in remove_vertex() and rebuild_epos()

src/graph/graph_adjacency.hh

commit b7b68451
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Implement PropertyMap.shrink_to_fit()

src/graph/fast_vector_property_map.hh
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph_tool/__init__.py

commit 6c264a5c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Add new function: Graph.shrink_to_fit()

doc/graph_tool.rst
src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph_tool/__init__.py

commit 70f17f21
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Improve speed of remove_vertex_fast() when edge positions are being kept

src/graph/graph_adjacency.hh

commit 6a62c314
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Remove redundancy in clear_vertex(), remove_vertex() and remove_edge()

src/graph/graph_adjacency.hh

commit 002d6d2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Use std::remove_if() in clear_vertex() and employ range loops

src/graph/graph_adjacency.hh

commit 84ded33e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Use std::find_if() in remove_edge(s, t, g)

src/graph/graph_adjacency.hh

commit f3412e57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-04

    Fix bug in remove_edge()

src/graph/graph_adjacency.hh

commit 2536f2a5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-03

    Removed forced inlines and add some C++14 mannerisms

src/graph/fast_vector_property_map.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_filtering.hh
src/graph/graph_selectors.hh

commit 423177ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-03

    graph_blockmodel.hh: trivial whitespace change

src/graph/community/graph_blockmodel.hh

commit 4488a86d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-03

    graph_adjacency.hh: small C++14-oriented modifications

src/graph/graph_adjacency.hh

commit 819cb692
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-02

    Revert "graph_adjacency.hh: change check to assertion in remove_edge()"
    
    This reverts commit cf1222272559248984ddb48343ff980c2c710e1e.

src/graph/graph_adjacency.hh

commit a3120754
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-02

    decorators.py: Add newline to end of file

src/graph_tool/decorators.py

commit f80d403b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-02

    graph_blockmodel_overlap.hh: remove redundancy in constructor

src/graph/community/graph_blockmodel_overlap.hh

commit cf122227
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-02

    graph_adjacency.hh: change check to assertion in remove_edge()

src/graph/graph_adjacency.hh

commit 7a3620b2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-02

    Add short aliases to Graph.new_vertex/edge/graph_property()

doc/graph_tool.rst
src/graph_tool/__init__.py
src/graph_tool/decorators.py

commit 31013589
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-10-01

    Fix bug in value conversion for property maps of type "string"

src/graph_tool/__init__.py

commit 6d4b6bb3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-30

    Fix bug in find_vertex_range()

src/graph_tool/util/__init__.py

commit f8c7a320
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-28

    Fix compilation issue with clang-3.7
    
    This closes #246

src/boost-workaround/boost/graph/betweenness_centrality.hpp

commit c4659b68
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-28

    Bump version to 2.10dev

configure.ac

commit b697ad98
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-28

    Bump version to 2.9

configure.ac

commit 7d272021
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-28

    Fix bug in Graph.copy_property() for filtered/reversed graphs

src/graph/graph_properties_copy.cc

commit f52c11d3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-27

    Include build tests without sparsehash

.gitlab-ci.yml

commit b35af122
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-27

    Bump version to 2.9dev

configure.ac

commit a4d26ca7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-27

    Simply build tests

.gitlab-ci.yml

commit e523cea5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-27

    Bump version to 2.8

configure.ac

commit 491b66ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-27

    Trivial docstring improvement

src/graph_tool/__init__.py

commit d5524e8f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    Mention C++14 requirement in README.md

README.md

commit 56224f3f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    Fix "infinite vertex" bug in triangulation() with type="delaunay"

src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/graph_util.hh

commit c9ef724b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    graph_blockmodel.hh:: Fix issue with duplicate setting of empty key in sparse_hash

src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.hh

commit 5486e6d8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    Remove check for scipy.weave

configure.ac

commit 35bd34a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    Remove more compiler warnings with clang

src/boost-workaround/boost/graph/metric_tsp_approx.hpp
src/graph/spectral/graph_laplacian.hh

commit 0507fe70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    Fix remaining incompatibility issues with Python 2

doc/pyenv.py
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/topology/__init__.py

commit ce5f96f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-26

    Remove unused variable in random_rewire.hh

src/graph/generation/graph_rewiring.hh

commit 334becf6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Remove unused member function definition in GraphInterface

src/graph/graph.hh

commit 66cf8d87
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Fix some compatibility problems with Python 2

doc/gt_format.rst
src/graph_tool/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/generation/__init__.py

commit 4c4ff110
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    price.py: Improve output compatibility with python 2

doc/price.py

commit 3e02ed34
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Include MAKEOPTS in build tests

.gitlab-ci.yml

commit 2736fecc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Move to C++14

configure.ac
m4/ax_cxx_compile_stdcxx_14.m4

commit 077b32e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Replace shared_ptr<T>(new T()) by make_shared<T>()

src/graph/graph.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.hh

commit a35440a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Appease clang, and suppress some harmless warnings

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh

commit 66f3d525
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-25

    Fix python2 doctest discrepancy

doc/price.py

commit 1a6ec639
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-24

    Cosmetic c++11 cleanups

src/graph/community/graph_blockmodel.hh

commit 7f3fd7e6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-24

    Protect modularity() against malformed (i.e. negative) spin values

src/graph/community/graph_community.hh

commit 461ec345
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-24

    Fix bug in community_structure()

src/graph/community/graph_community.hh

commit 5e66f348
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-24

    Simply graph augmentation for flow algorithms

src/graph/flow/graph_augment.hh

commit 65566f44
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-23

    Fix build tests

.gitlab-ci.yml

commit c565ae57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-23

    Split build tests into i386 and amd64 tags

.gitlab-ci.yml

commit f231f648
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Fix status badge link

README.md

commit a4c7e63e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Update build status badge

README.md

commit 91ffeb2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    gt_format.rst: create temporary directories

doc/gt_format.rst

commit 5c4c7238
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Allow boost::python to bind to std::functions

src/graph/graph_bind.cc
src/graph/graph_python_interface.cc
src/graph/graph_util.hh

commit 3673202b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Implement __hash__() for vector<> types

src/graph/graph_bind.cc

commit 396e4828
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Fix docstring in graph_tool.stats

src/graph_tool/stats/__init__.py

commit e09a1150
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Fix pickling of PropertyMap

src/graph_tool/__init__.py

commit d8c66e54
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Remove assortativity computation from generation test

src/graph_tool/generation/__init__.py

commit 5cb29877
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Re-structure graph_tool.correlations tests

src/graph_tool/correlations/__init__.py

commit feb1701c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Graph.list_properties(): Sort output in lexicographic order

src/graph_tool/__init__.py

commit 0e9a75e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    edge_endpoint_proprty(): Fix bug for 32bit architectures

src/graph_tool/__init__.py

commit 42a3751a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Make gt_format.rst test deterministic

doc/gt_format.rst

commit c7ae30cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Remove reference to run_action

doc/graph_tool.rst

commit 36e34622
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    Simple test changes to gt_format.rst

doc/gt_format.rst

commit e2b96ff6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-22

    incident_edges_op(): Fix issue in 32bit architectures

src/graph_tool/__init__.py

commit b08d153c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-21

    Fix simple test failures for 32bit architectures

doc/gt_format.rst
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py

commit 3cb868e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-21

    Add missing documentation file

doc/mincut-st-example.xml.gz

commit 7ecacef5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-20

    Fix issue with terminal_size() when no tty is available

src/graph_tool/__init__.py

commit a61b5182
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-20

    More doctest fixes

src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py

commit 26cf7433
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-20

    Include tests in .gitlab-ci.yml

.gitlab-ci.yml

commit d7de874d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-20

    Fix small docstring issues

doc/gt_format.rst
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit f74ec353
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-20

    Fix API issue with graphviz_draw()

src/graph_tool/draw/graphviz_draw.py

commit 429eeb8c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-19

    Remove deprecated run_action module

Makefile.am
doc/run_action.rst
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_support.hh
src/graph_tool/run_action/run_action_template.hh

commit e9ab02cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-19

    Unify ccache in .gitlab-ci.yml

.gitlab-ci.yml

commit fbf28f6e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-19

    Simplify .gitlab-ci.yml

.gitlab-ci.yml

commit 94ac6883
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-19

    Move COPYING to LICENSE

LICENSE
Makefile.am
README.md
configure.ac

commit 0b2bd004
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-19

    Add build status badge

README.md

commit 9b846e0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-19

    Add gitlab-ci.yml

.gitlab-ci.yml

commit d9ee9b1d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-18

    Include upstream corrections to football dataset

src/graph_tool/collection/football.gt.gz

commit e92c953e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-18

    Bump version to 2.8dev

configure.ac

commit ebd75c28
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    Bump version to 2.7

configure.ac

commit 4119cf8c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    Add default constructors in search comparison functors

src/graph/search/graph_astar.hh
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_dijkstra.cc

commit 2e1969c1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    Fix issue with filtered graphs in draw_hierarchy()

src/graph_tool/draw/cairo_draw.py

commit bd767417
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    Bump version to 2.7dev

configure.ac

commit 575c0044
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    Bump version to 2.6

configure.ac

commit 94a72423
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    Purge typeof() in favor or decltype() or auto

src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.hh
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.hh
src/graph/graph_adaptor.hh
src/graph/graph_filtering.cc
src/graph/graph_io.cc
src/graph/histogram.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_dijkstra.cc
src/graph/shared_map.hh

commit 69885931
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-17

    minimize_nested_blockmodel_dl(): Fix issue with propagate_clabel=True

src/graph_tool/community/nested_blockmodel.py

commit 8b2d4b66
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Fix test in minimize_nested_blockmodel_dl()

src/graph_tool/community/nested_blockmodel.py

commit 44d44d06
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Bump version to 2.6dev

configure.ac

commit 28c4b6dc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Bump version to 2.5

configure.ac

commit 1abd6bdc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    minimize_nested_blockmodel_dl(): Add "propagate_clabel" parameter

src/graph_tool/community/nested_blockmodel.py

commit 97909eac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Fix more compatibility bugs with python 2

src/graph_tool/__init__.py
src/graph_tool/collection/konect.py

commit fdf387eb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Bump version to 2.5dev

configure.ac

commit 95a44eda
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Bump version to 2.4

configure.ac

commit 913d42f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Fix compatibility issue with python 2

src/graph_tool/__init__.py
src/graph_tool/collection/konect.py

commit 857bdaac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-16

    Fix edge placement in animation_zombies.py

doc/demos/animation_zombies.py

commit 5c5972ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-15

    Bump version to 2.3

configure.ac

commit 28e20607
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-15

    Speed up unpicking of PropertyMaps

src/graph_tool/__init__.py

commit c998861d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-15

    draw_hierarchy(): Implement "bip_aspect" parameter

src/graph_tool/draw/cairo_draw.py

commit 4f1ac5ad
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-14

    Improve performance of get_hierarchy_tree()

src/graph_tool/community/nested_blockmodel.py

commit 91872c4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-14

    Improve performance of Graph.add_vertex() and Graph.add_edge()

src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph_tool/__init__.py

commit f7020a22
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-13

    betweenness(): Remove property map checking

src/boost-workaround/boost/graph/betweenness_centrality.hpp

commit 9dc8c691
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-13

    Get rid of inconsistent CamelCase in GraphInterface methods

src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_trust_transitivity.cc
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_covariates.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.hh
src/graph/draw/graph_tree_cts.cc
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_complete.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties_copy.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/histogram.hh
src/graph/layout/graph_sfdp.cc
src/graph/search/graph_dfs.cc
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/util/graph_search.cc
src/graph_tool/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/inline.py

commit fa6816e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-13

    Remove "permissions" control in Graph class

src/graph_tool/__init__.py
src/graph_tool/search/__init__.py

commit 26553a42
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-13

    Fix bug in cairo_draw() with vertex_index as attribute

src/graph_tool/draw/cairo_draw.py

commit afae7aa1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-12

    Significantly improve speed of vertex/edge iterators and descriptors in python interface

src/graph/graph.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph_tool/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/util/__init__.py

commit 973d73cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-12

    draw_hieararchy() and radial_tree_layout(): Add "node_weight" parameter

src/graph/layout/graph_radial.cc
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py

commit c84e5eeb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-11

    Fix bug in PropertyDict.keys()

src/graph_tool/__init__.py

commit 3d74d3c5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-10

    graph_draw(): implement option "vertex_rotation"

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 4a4cebb7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-08

    Cosmetic blockmodel.py fixes

src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py

commit ee978e1d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-08

    Documentation fixes

doc/graph_tool.rst
src/graph_tool/__init__.py

commit d6992aa4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-08

    Fix conversion of python iterators (generators, etc) to std::vector<T>

src/graph/graph_bind.cc

commit 4914c902
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-31

    Implement neighbourhood highlight in interactive graph_draw()

src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/graph_properties_copy.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit ecd308f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-31

    Improve performance of graph_draw() and draw_hierarchy()

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit 83186f00
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-06

    Implement support for edge properties in Graph.add_edge_list()

src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py
src/graph_tool/util/__init__.py

commit 2bc9ddf4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-05

    Fix issue in Graph.add_edge_list()

src/graph_tool/__init__.py

commit 6957f8ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-05

    Implement PropertyMap.set_value()

src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit bc126545
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-09-05

    Implement options "hashed" and "string_vals" in Graph.add_edge_list()

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/numpy_bind.hh
src/graph_tool/__init__.py

commit bc1feb23
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-29

    Implement map_property_values()

src/graph/Makefile.am
src/graph/graph_bind.cc
src/graph/graph_properties_map_values.cc
src/graph/graph_properties_map_values.hh
src/graph_tool/__init__.py

commit 40aaa59c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-29

    Fix issue in GraphView with edge filter composition

src/graph_tool/__init__.py

commit 16bdbf15
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-26

    minimize_nested_blockmodel_dl(): Fix issues with clabel for graphs with filtered vertices

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit fe27ada4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-25

    Fix issue in Overlap/Covariate/BlockState.__check_clabel()

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit 5908da56
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-25

    Implement "block_list" parameter in mcmc_sweep()

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit dfd68d0d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-24

    Fix BlockState.__check_clabel() for filtered graphs

src/graph_tool/community/blockmodel.py

commit ac0c1325
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-24

    Add 'Allocator' template parameter to vector template specializations

src/graph/graph_util.hh
src/graph/hash_map_wrap.hh

commit 1e5a0f49
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-24

    Fix possible infinite loop in Overlap/Covariate/BlockState.copy()

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit b65db1f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-23

    draw_hierarchy(): Improve efficiency of "hshortcuts" option

src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph_tool/draw/cairo_draw.py

commit 61c4bfed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-21

    draw_hierarchy(): Implement layout == "bipartite"

src/graph_tool/draw/cairo_draw.py

commit 4dbdc276
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-21

    draw_hierarchy(): Implement "hshortcuts" and "hide" parameters

src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/draw/cairo_draw.py

commit acedc700
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-21

    graph_blockmodel.hh: Return const references in egroup sampling

src/graph/community/graph_blockmodel.hh

commit 8d806b4e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-21

    dynamic_sampler.hh: Impose const correctness

src/graph/generation/dynamic_sampler.hh

commit d2e7d4f9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-21

    BlockState: Remove instance counting

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit d0709299
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-20

    covariate_blockmodel.py: Fix initialization bug in CovariatBlockState

src/graph_tool/community/covariate_blockmodel.py

commit a27a87af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-20

    graph_blockmodel_overlap.hh: Fix description length delta computation

src/graph/community/graph_blockmodel_overlap.hh

commit bdfa296b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-20

    blockmodel.py: Improve hash performance via edge lookup cache

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.hh
src/graph/generation/sampler.hh
src/graph_tool/community/blockmodel.py

commit 9a702f44
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-19

    Improve Graph.vertex/edge/graph_properties to avoid circular references

src/graph_tool/__init__.py

commit 9b659850
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-19

    (*)_blockmodel.py: Improve memory usage by clearing cache more frequently

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit f44436b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-19

    Implement __copy__ and __deepcopy__ for Nested/Overlap/Covariate/BlockState

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit da569528
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-19

    Implement __copy__ and __deepcopy__ for Graph and PropertyMap

src/graph_tool/__init__.py

commit f2acf0b1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-19

    blockmodel.py: Fix pmap() and reverse_map() for filtered property maps

src/graph_tool/community/blockmodel.py

commit 212f2f2f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-19

    transition(): Fix matrix transposition

src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph_tool/spectral/__init__.py

commit 33b9efb0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-15

    graph_blockmodel.hh: Improve log/gamma cache memory use and improve edge lookup performance

src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit f05c11df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-14

    (Nested)BlockState: fix preservation of "ignored_degrees" when copying and pickling

src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit f2c64271
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-13

    Add missing file konect.py

src/graph_tool/collection/konect.py

commit e4b5ee4c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-13

    graph_blockmodel.hh: Update "ignored_degrees" semantics for directed graphs

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh

commit b0ac0d96
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-13

    Remove redundant setting of empty key.

src/graph/community/graph_blockmodel.cc

commit 396578de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-04

    collection.py: Add support for automatic downloading and parsing from the KONECT database

src/graph_tool/Makefile.am
src/graph_tool/collection/__init__.py

commit eed1f09e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-04

    graph_blockmodel.hh: Use const reference in get_me()

src/graph/community/graph_blockmodel.hh

commit a3a8805a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-03

    condensation_graph(): Fix edge averages if parallel_edges=True

src/graph/community/graph_community_network.hh

commit acc0c10a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-03

    Fix compilation warning

src/graph/generation/graph_predecessor.hh

commit d3411dcf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-01

    (overlap_)blockmodel.py: Convert clabel to "int" type

src/graph_tool/community/blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit ab0da1a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-08-01

    graph_blockmodel(_overlap).hh: Removed forced inline and slightly reorganize

src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.hh

commit cd488ae1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-31

    Use AX_CXX_COMPILE_STDCXX_11() to detect/enforce c++11 compiler

configure.ac
m4/ax_cxx_compile_stdcxx_11.m4

commit fdd6f387
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-27

    Add eweight and vweight parameters to Nested/Covariate/Overlap/BlockState.copy()

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit d6716457
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-23

    Add "g" parameter to Nested/Overlap/CovariateBlockState.copy()

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit 60a97dff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-22

    Attempt to properly convert PropertyMap keys to vertex or edge descriptors

src/graph_tool/__init__.py

commit 36514eb1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-22

    Fix bug in BlockState.entropy() when deg_corr=True and edge weights are being used
    
    This also adds the 'ignore_degrees' parameter.

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit 254b7f3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-22

    Accept also iterables as filters in GraphView

src/graph_tool/__init__.py

commit 2bbbdf08
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-20

    Fix problem with vertex colors in draw_hierarchy()
    
    This closes #238

src/graph_tool/draw/cairo_draw.py

commit a240d1e2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-20

    Always copy entire property map in Graph.copy_property() when graph is filtered

src/graph_tool/__init__.py

commit 8d512bb3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-20

    Fix issues with filtered graphs in blockmodel.py

src/graph_tool/community/blockmodel.py

commit f2e8082e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-19

    Fix cumulative filtering with GraphView

src/graph_tool/__init__.py

commit 6db830a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-19

    Replace float("inf") by numpy.inf

src/graph_tool/community/blockmodel.py
src/graph_tool/community/overlap_blockmodel.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py

commit 19ccc559
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-19

    Fix possible infinite loop in minimize_blockmodel_dl()

src/graph_tool/community/blockmodel.py

commit e24f60db
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-18

    Fix a performance issue with filtered graphs
    
    This avoids unnecessary copying of the filter property map, which
    although being O(1), does end up consuming a measurable time.

src/graph/graph_filtering.hh

commit 00a0e7ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-18

    Fix draw_hierarchy() for filtered graphs

src/graph/draw/graph_tree_cts.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/layout/graph_radial.cc
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/draw/cairo_draw.py

commit 2291b947
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-17

    Fix bug in CovariateBlockState with filtered graphs

src/graph/community/graph_blockmodel_covariates.cc
src/graph_tool/community/covariate_blockmodel.py

commit c592d964
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-16

    Fix bug in overlap_partition_stats_t

src/graph/community/graph_blockmodel_overlap.hh

commit 41e8c3fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-16

    Replace gt_hash_map by unordered_map for std::string and other generic keys

src/graph/community/graph_blockmodel_covariates.hh
src/graph/community/graph_community_network.hh
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.hh
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/hash_map_wrap.hh
src/graph/topology/graph_similarity.hh

commit b8fe4467
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-16

    Fix issue with vector<tuple<...>> in gt_hash_map/set
    
    This also transforms a run-time exception into a static_assert, in case
    there is no available default empty or deleted key of the specified type.

src/graph/hash_map_wrap.hh

commit b16c2341
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-16

    Fix bug in graph_union() when copying property maps

src/graph_tool/generation/__init__.py

commit a3635d0b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-16

    Include gt_hash_map::resize if sparsehash is disabled

src/graph/hash_map_wrap.hh

commit 11c15b0b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-16

    Replace unordered_map/set for gt_hash_map/set whenever possible

src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community.hh
src/graph/correlations/graph_assortativity.hh
src/graph/generation/graph_generation.hh
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.hh
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/layout/graph_sfdp.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/topology/graph_distance.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/util/graph_search.hh

commit a6667db7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-15

    Remove dense_hash_map/set cruft
    
    This implements a general wrapper for dense_hash_map and dense_hash_set,
    that falls back to unordered_map and unordered_set, if sparsehash is not
    enabled.

src/graph/Makefile.am
src/graph/clustering/graph_clustering.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.hh
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community_network.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/generation/graph_rewiring.hh
src/graph/hash_map_wrap.hh
src/graph/stats/graph_parallel.hh

commit 9774522c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-08

    Fix typo in mcmc_sweep()

src/graph_tool/community/blockmodel.py

commit c9227dee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-08

    graph_draw(): Honor option output_size, even when output=None

src/graph_tool/draw/cairo_draw.py

commit 44a65959
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-06

    Add support for "target_blocks" in mcmc_sweep()

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph_tool/community/blockmodel.py

commit 3a1dec89
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-06

    Drop support for numpy < 1.7

configure.ac
src/graph/Makefile.am
src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh

commit 22d1675a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-03

    Bump version to 2.2.45dev

configure.ac

commit 178add3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-02

    Bump version to 2.2.44

configure.ac

commit 92c1739f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-02

    Update animation demos

doc/demos/animation_dancing.py
doc/demos/animation_sirs.py
doc/demos/animation_zombies.py
doc/demos/interactive_bst.py

commit aab34c1b
Author: Tiago Peixoto <tiago@skewed.de>
Date:   2015-07-01

    Update README.md

README.md

commit c64c88ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-02

    Update README and remove outdated crud (ChangeLog, TODO, etc)

ChangeLog
Makefile.am
NEWS
README
README.md
TODO

commit 4eca7b1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-02

    Fix problem with initial bracketing in minimize_blockmodel_dl()

src/graph_tool/community/blockmodel.py

commit 5dfd641b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-02

    Fix unweighted_merge semantics in mcmc_sweep()

src/graph_tool/community/blockmodel.py

commit ed3cf9f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-07-02

    Fix verbose="full" option in minimize_nested_blockmodel_dl()

src/graph_tool/community/nested_blockmodel.py

commit 7b8b158c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-25

    Fix bug in edge_endpoint_property()

src/graph/graph_properties_imp1.cc

commit 449fca9e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-22

    Fix example in quickstart.rst

doc/quickstart.rst

commit 85f11ae8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-18

    configure.ac: Fix indentation issues

configure.ac

commit 7c40bdcd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-18

    graph_draw(): Improve performance of X11 interactive drawing

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit fdc1c377
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-16

    PropertyMap: assure that filtered arrays (fa) have always the correct size
    
    This closes issue #228

src/graph_tool/__init__.py
src/graph_tool/draw/cairo_draw.py

commit 06157bcc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-16

    graph_draw(): draw edge markers only if larger than minimum resolution

src/graph/draw/graph_cairo_draw.cc

commit 588cd181
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-16

    GraphWidget: implement touch gestures

src/graph_tool/draw/gtk_draw.py

commit 04572376
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-15

    GraphWidget: Implement progressive drawing to improve interactive responsiveness

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit 406d7c4a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-15

    gtk_draw(): Fix re-drawing after panning

src/graph_tool/draw/gtk_draw.py

commit 627015f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-14

    graph_draw(): honor float values passed to 'fit_view' as described in documentation

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit 8664f7f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-13

    Fix handling of property maps with python::object values with dot and gml formats

src/boost-workaround/boost/graph/graphml.hpp
src/graph/Makefile.am
src/graph/base64.cc
src/graph/base64.hh
src/graph/gml.hh
src/graph/graph_io.cc
src/graph/graphml.cpp

commit 8141f5f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-12

    Add support for nested lists in gml.hh

src/graph/gml.hh
src/graph/graph_io.cc

commit c6dc8cf7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-08

    Simple documentation fixes

doc/conf.py
doc/draw.rst
doc/graph_tool.rst
src/graph_tool/collection/__init__.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/draw/gtk_draw.py

commit ef2fae83
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-08

    Trivial change in graph_blockmodel.hh

src/graph/community/graph_blockmodel.hh

commit b548dead
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-07

    Change default to nonoverlap_init=False in minimize_nested_blockmodel_dl()

src/graph_tool/community/nested_blockmodel.py

commit ee9eb8fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-07

    Fix typo in graph_draw() docstring

src/graph_tool/draw/cairo_draw.py

commit b5e3ee50
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-07

    Bump version to 2.2.44dev

configure.ac

commit f23f19e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-06

    Bump version to 2.2.43

configure.ac

commit 99dd817e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-06

    Fix typo in quickstart.rst

doc/quickstart.rst

commit d4980abf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-05

    Move Graph.edge() implementation to C++

src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 92d0c0b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-05

    Fix memory usage issue in graph_blockmodel.cc

src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py

commit 0fdb192b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-04

    Remove outdated and no longer necessary configure.ac libtool hack

configure.ac

commit 96127341
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-03

    Fix bug with parallel edges when deg_corr=True and dl=True in minimize_blockmodel_dl()
    
    This closes #225

src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.hh

commit 65b8425e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-06-01

    Change semantics of Graph.vertex() and Graph.add_edge()
    
    This adds an "add_missing" option to allow the automatic addition of
    vertices if they do not exist in the graph.
    
    This also changes the parameter "new" in Graph.edge() to "add_missing".

src/graph_tool/__init__.py

commit 25f565d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-31

    Clarify documentation for adjacency()

src/graph_tool/spectral/__init__.py

commit 7ddae8ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-31

    draw_hierarchy(): Propagate tree properties unchanged

src/graph_tool/draw/cairo_draw.py

commit 8bd9024a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-31

    Fix PropertyMap.set/get_2d_array() for "string"-valued property maps with filtered graphs
    
    This closes #226

src/graph_tool/__init__.py

commit b681cbc3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-26

    Implement attribute access to PropertyDict

doc/quickstart.rst
src/graph_tool/__init__.py

commit b98a11db
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-15

    Always use layers=True for upper layers of OverlapBlockState()

src/graph_tool/community/covariate_blockmodel.py

commit d1c285d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-08

    Improve slightly the performance of shortest_distance() with multiple targets and revert shortest_path() to single-target-only

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 2131b6f0
Merge: 2a97cab1 58987030
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-08

    Merge pull request #13 from Fkawala/master
    
    update: topology.shortest_distance and topology.shortest_path to sear…

commit 58987030
Author: Francois <francois@karos.fr>
Date:   2015-05-08

    update: topology.shortest_distance and topology.shortest_path to search more than one target.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 2a97cab1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-04

    Improve documentation for astar_search()
    
    This closes #222 and #223.

src/graph_tool/search/__init__.py

commit 0e7a05fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-05-01

    Fix numerical issue in OverlapBlockState.entropy() with excessive overlaps

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.hh
src/graph_tool/community/blockmodel.py

commit bc21f238
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-30

    Fix issue with CovariateBlockState.merge_layers() when layers == True

src/graph_tool/community/covariate_blockmodel.py

commit c6814980
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-30

    Fix error in gt format specification in the documentation
    
    This fixes #221

doc/gt_format.rst

commit 5e7cf6dc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-30

    Fix typo in gt_format.rst
    
    This fixes issue #220

doc/gt_format.rst

commit 1eb7786d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-30

    Correct documentation for purge_vertices()/edges()

doc/graph_tool.rst
src/graph_tool/__init__.py

commit 097bb6f5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-27

    Enable vector types and python::object in vertex/edge_average()

src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph_tool/stats/__init__.py

commit 90cda9bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-27

    Fix bug with CovariateBlockState.merge_layers()

src/graph/community/graph_blockmodel_covariates.cc
src/graph_tool/community/covariate_blockmodel.py

commit a9b02d3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-23

    Fix binding error in graph_community.cc

src/graph/community/graph_community.cc

commit 8be3461d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-23

    Fix compilation warnings

src/graph/graph_properties_copy.cc
src/graph/read_graphviz_new.cpp

commit 1a49d458
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-23

     Fix bug in CovariateBlockState.merge_layers() with non-overlapping groups

src/graph_tool/community/covariate_blockmodel.py

commit c72bb4c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-23

    Enable (and clear) more strict warnings during compilation

configure.ac
src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/boost-workaround/boost/graph/metric_tsp_approx.hpp
src/boost-workaround/boost/graph/stoer_wagner_min_cut.hpp
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_rewiring.hh
src/graph/graph_bind.cc
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_properties_imp2.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_util.hh
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/search/graph_astar.hh
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_maximal_vertex_set.cc
src/graph_tool/community/blockmodel.py
src/graph_tool/community/overlap_blockmodel.py
src/graph_tool/stats/__init__.py

commit e0db25e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-22

    Fix bug in CovariateBlockState.merge_layers() with overlapping groups

src/graph_tool/community/covariate_blockmodel.py

commit 211e1a92
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-23

    Bump version to 2.2.43dev

configure.ac

commit 35e808bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-21

    Bump version to 2.2.42

configure.ac

commit 0fe23164
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-21

    Fix bug in covariate_blockmodel.py with the overlapping case

src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py

commit 798d3cd9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-21

    Fix some docstring errors

doc/quickstart.rst
src/graph_tool/draw/cairo_draw.py

commit af98d1df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-21

    Bump version to 2.2.41

configure.ac

commit 63e23b1d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-21

    Fix bug with model selection in nested_blockmodel.py

src/graph_tool/community/nested_blockmodel.py

commit 3ad8fbf8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-21

    Remove dead code/comments from nested_blockmodel.py

src/graph_tool/community/nested_blockmodel.py

commit d00af0dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-19

    Fix compilation bug when sparse_hash is not enabled

src/graph/community/graph_blockmodel_covariates.cc

commit c8f99e7c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-18

    Fix import error when pycairo or Gtk+ are not available

src/graph_tool/draw/__init__.py

commit e0edd448
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-17

    Fix bug in OverlapBlockState.get_edge_blocks() with multigraphs

src/graph/community/graph_blockmodel_overlap.cc

commit 4b3e3a57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-17

    Fix small docstring typo.

src/graph_tool/community/blockmodel.py

commit 7ec9e319
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-13

    Fix problems with interactive drawing of empty graphs

src/graph_tool/draw/gtk_draw.py

commit 2632b39d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-13

    Bump version to 2.2.41dev

configure.ac

commit 7f05702f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-12

    Bump version to 2.2.40

configure.ac

commit 7cf34d58
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-12

    Fix syntax error with python 2 in covariate_blockmodel.py
    
    This fixes #215.

src/graph_tool/community/covariate_blockmodel.py

commit 76dbca5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-12

    Fix drawing of empty graphs
    
    This fixes #209

src/graph_tool/draw/cairo_draw.py

commit 7d1b0536
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-12

    Remove compilation warnings in graph_line_graph.cc

src/graph/generation/graph_line_graph.cc

commit 37aaaf33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-12

    Bump version to 2.2.40dev

configure.ac

commit d0372fb3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Bump version to 2.2.39

configure.ac

commit 4e580605
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Add missing graph_blockmodel_covariates.hh to Makefile.am

src/graph/community/Makefile.am

commit 5b4b14ca
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Include interactive_bst.py demo into repository

doc/demos/interactive_bst.py

commit 9f6be6f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Replace linkcode by viewcode in docs

doc/conf.py

commit b8446f7b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Small docstring fixes

doc/quickstart.rst
src/graph_tool/community/blockmodel.py

commit 275ff70b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Cleanup doc Makefile

doc/Makefile

commit 1f037fb4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-11

    Fix placement of spline anchors in graph_draw()

src/graph/draw/graph_cairo_draw.cc

commit a5574175
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Implement SBM inference with layers and edge covariates

doc/community.rst
doc/draw.rst
src/graph/community/Makefile.am
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_covariates.cc
src/graph/community/graph_blockmodel_covariates.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_edges.cc
src/graph/generation/dynamic_sampler.hh
src/graph/layout/graph_sfdp.cc
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/covariate_blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit 5075e605
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-17

    Improve fit_view parameter to graph_draw(), allowing for a specific viewport

src/graph_tool/draw/cairo_draw.py

commit 92eaff23
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-05

    Significant improvement of edge splines in graph_draw()

src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph_tool/draw/cairo_draw.py

commit 66d10524
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-29

    Pass widget to user callback functions in graph_draw()

src/graph_tool/draw/gtk_draw.py

commit db9640c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-27

    Implement vertex_text_position == "centered"

src/graph_tool/draw/cairo_draw.py

commit dc837983
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-27

    Slightly more user-friendly color handling in graph_draw()

src/graph/draw/graph_cairo_draw.cc

commit b46a8656
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-11-06

    Better error diagnostics in graph_draw()

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/gtk_draw.py

commit 8e851554
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-08

    Replace average by sum in condensation_graph()

src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_vavg.cc
src/graph_tool/community/blockmodel.py

commit 3c962eab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-08

    Fig Graph.edge() behavior with new=True and all_edges=False

src/graph_tool/__init__.py

commit eca90cc4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-08

    Fix bug in graph_union() when an intersection is given

src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph_tool/generation/__init__.py

commit 01ddad4f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-07

    Fix bug in similarity() when graphs have a different number of vertices

src/graph/topology/graph_similarity.hh

commit 800ab682
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-04-07

    Bump version to 2.2.39dev

configure.ac

commit 136d9c23
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-23

    Bump version to 2.2.38

configure.ac

commit 141785e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-23

    Properly export Vector_size_t if size_t is something other than uint64_t

src/graph/graph_bind.cc

commit 6f49ca43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-20

    Fix compilation issue with clang

src/graph/graph_properties_imp2.cc

commit 424eacfd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-18

    Bump version to 2.2.38dev

configure.ac

commit dd4d088e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-18

    Bump version to 2.2.37

configure.ac

commit 2ce3765f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-18

    Fix bug in Vertex.in_degree() with weights

src/graph/graph_python_interface.cc

commit 5bbb1aad
Merge: 49376c0c 0e4a6db6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-15

    Merge pull request #11 from joernhees/master
    
    fix docstring copy paste error (util.find_edge*)

commit 0e4a6db6
Author: Joern Hees <dev@joernhees.de>
Date:   2015-03-15

    fix docstring copy paste error (util.find_edge*)

src/graph_tool/util/__init__.py

commit 49376c0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-11

    Normalize the hub centrality values returned by hits()
    
    This fixes issue #205

src/graph/centrality/graph_hits.hh

commit 51c87908
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-09

    Cosmetic changes to graph_copy.cc

src/graph/graph_copy.cc

commit ab5055aa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-09

    Improve performance of property map copying when no conversion is required

src/graph/graph_properties_copy.cc

commit f4edaefc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-03-05

    Add 'new' optional parameter to Graph.edge() for automatic edge creation

src/graph_tool/__init__.py

commit ed9fa3ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-02-24

    Include No-Op specialization of property map converter

src/graph/graph_properties.hh

commit 2b25ac58
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-02-22

    Refactor incident_edges_sum() into more general incident_edges_op()

src/graph/graph_bind.cc
src/graph/graph_properties_imp2.cc
src/graph_tool/__init__.py

commit 126f2179
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-02-22

    Implement incident_edges_sum()

src/graph/Makefile.am
src/graph/graph_bind.cc
src/graph/graph_properties_imp1.cc
src/graph/graph_properties_imp2.cc
src/graph_tool/__init__.py

commit 010afe9b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-11-06

    Export Vector_size_t and std::type_info to Python

src/graph/graph_bind.cc
src/graph_tool/__init__.py

commit bd96105e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-02-05

    Include support for removal of vertex sequences
    
    This fixes #189

doc/quickstart.rst
src/graph/graph.hh
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 0bc62ada
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-28

    Remove references to tr1::hash<> and boost::hash<> in favor of std::hash<>

src/graph/clustering/graph_clustering.hh
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_rewiring.hh
src/graph/graph_properties.cc
src/graph/layout/graph_sfdp.cc
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_similarity.hh

commit 2092c3c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-24

    Include interactive visualization demo

doc/demos/animation.rst
src/graph_tool/draw/gtk_draw.py

commit c9fca17b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-17

    Replace edge_difference() by the more general edge_endpoint_property()

src/graph/Makefile.am
src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph/graph_properties_imp1.cc
src/graph_tool/__init__.py

commit 201879ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-09

    Bump version to 2.2.37dev

configure.ac

commit e3865108
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-08

    Bump version to 2.2.36

configure.ac

commit ace2539f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-08

    Fix docstring issues

src/graph_tool/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/topology/__init__.py

commit da2167f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-08

    Fix typo bug in nested_mcmc_sweep()

src/graph_tool/community/nested_blockmodel.py

commit adf14b20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-08

    Update copyright information

doc/conf.py
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/community/spence.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_support.hh
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit f7cb33ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-11-04

    Remove useless function from graph_adjacency.hh

src/graph/graph_adjacency.hh

commit 2009aa5d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-01

    Change topological_sort() to conventional ordering
    
    This fixes #192

src/graph_tool/topology/__init__.py

commit f87c1e11
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2015-01-01

    Improve speed of Graph.remove_vertex()

src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit 1b6f5ae1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-20

    Add -DNDEBUG to CXXFLAGS to disable assert() when --enable-debug is not being used

configure.ac

commit 53e686e5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-19

    Improve the performance of Graph.vertex() when filtering is disabled or use_index = False
    
    This fixes issue #197

src/graph_tool/__init__.py

commit 67e10f3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-18

    Property map creation docstring fix

src/graph_tool/__init__.py

commit 6761eebc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-18

    Throw appropriate exception when file is not found in Graph.load()

src/graph_tool/__init__.py

commit 6c20965e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-17

    Fix pickle bug in Python 2

src/graph_tool/__init__.py

commit 86677466
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-08

    Fix automatic detection of numpy C API include path

configure.ac
src/graph/numpy_bind.hh

commit 50cbd928
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-08

    Change python install path to the platform-specific directory

m4/ax_python_devel.m4

commit 7c559195
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-01

    Add optional 'vals' parameter to Graph.new_vertex_property()/Graph.new_edge_property()

src/graph_tool/__init__.py

commit 98674cb9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-12-01

    Remove critical section from fast_vector_property_map

src/graph/fast_vector_property_map.hh

commit b2cce016
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-22

    Fix uniform_sample() to return a const reference

src/graph/generation/sampler.hh

commit a65ce3df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-25

    Fix SBM entropy with parallel edges and directed graphs

src/graph/community/graph_blockmodel.hh

commit 66e5720f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-16

    Update edge filter after purging vertices

src/graph_tool/__init__.py

commit 314d647b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-16

    Fix pickle compatibility issue between python 2 and 3

src/graph_tool/io.py

commit d529c67e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-16

    Improve display of property maps

src/graph_tool/__init__.py

commit 26f7d07b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-16

    Fix and improve Edge/Vertex ordering and comparisons
    
    This fixes a bug where equal edge descriptors would be considered
    unequal. Additionally, now Vertex and Edges can be ordered (via >, <,
    >=, <=).

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph_tool/__init__.py

commit 247d3c9f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-09

    Fix Graph pickling in python 2
    
    This fixes issue #190

src/graph_tool/__init__.py

commit d1d92728
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-02

    Enable linkcode sphinx extension in documentation

doc/conf.py
doc/draw.rst
doc/gt_theme/static/gt_style.css

commit cd28dbb3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-02

    Partial fix to missing docstring of GraphWidget and GraphWindow

src/graph_tool/draw/gtk_draw.py

commit 8a6f986e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-10-02

    Add support for weighted in/out-degrees via weight parameter to Vertex.in/out_degree()

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph_tool/__init__.py

commit d1d660cc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Enable in-place calculation in get_hierarchy_control_points()

src/graph_tool/draw/cairo_draw.py

commit f38ef846
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Fix documentation typos in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit 50f93c5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Fix bug in parsing vertex/edge shapes in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit d2e836fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Implement 'no_main' option in graph_draw() to enable parallel drawings

src/graph_tool/draw/gtk_draw.py

commit 79dcee41
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Fix documentation typo in community_structure()

src/graph_tool/community/__init__.py

commit 53af7627
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Fix destructor bug in BlockState

src/graph_tool/community/blockmodel.py

commit e46ea311
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Include support for user-supplied callbacks in GraphWidget

src/graph_tool/draw/gtk_draw.py

commit c2c359ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Include support for relative ordering of nodes in radial_layout()

src/graph/layout/graph_radial.cc
src/graph_tool/draw/__init__.py

commit 618b019e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-29

    Throw exception if edge block labels are invalid in OverlapBlockState

src/graph/community/graph_blockmodel_overlap.cc

commit 0b7e420e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-28

    Add property map type alias from "unsigned long" to "int64_t"

src/graph_tool/__init__.py

commit 88b485d3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-23

    Properly place graph layout in matplotlib figure in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit f93b833f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-23

    Add "bg_color" to graph_draw()'s documentation

src/graph_tool/draw/cairo_draw.py

commit dcc3a3f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-19

    Fix weighted shortest_distance() when a target is given
    
    This fixes #188

src/graph/topology/graph_distance.cc

commit 5229271f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-17

    Fix BlockState destructor

src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit 39963df0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-17

    Fix parsing of boolean property maps in graphml.hpp
    
    This fixes #186

src/boost-workaround/boost/graph/graphml.hpp

commit 26150b75
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-12

    Fix inconsistency issue with minimize_nested_blockmodel_dl() when clabel is used with overlap=True

src/graph/community/graph_blockmodel.cc
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit 0254683d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-13

    OverlapBlockState documentation improvements

src/graph_tool/community/overlap_blockmodel.py

commit 38e2952a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-13

    Keep track of (Overlap)BlockState instances to free cache resources when possible

src/graph_tool/community/blockmodel.py
src/graph_tool/community/overlap_blockmodel.py

commit 149e15c1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-16

    Prevent eigenvector() from getting stuck on graphs with a small spectral gap

src/graph/centrality/graph_eigenvector.hh

commit becec30e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-12

    Configure option --with-boost-python must take precedence

m4/ax_boost_python.m4

commit 70c7210e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-12

    Fix clabel propagation in minimize_nested_blockmodel_dl()

src/graph_tool/community/nested_blockmodel.py

commit af5b93da
Author: Joel Moberg <joel.moberg@gmail.com>
Date:   2014-09-10

    Add ability to grap_draw for drawing onto matplotlib figure

src/graph_tool/draw/cairo_draw.py

commit 61a4ec32
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-12

    Bump version to 2.2.36dev

configure.ac

commit c32ffd6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Bump version to 2.2.35

configure.ac

commit 5d4b96c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Fix additional issues with std::hash<> specializations

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/graph_util.hh

commit 4d8ac23d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Fix issue with python 3 in some platforms

src/graph_tool/run_action/inline.py

commit c006c64a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Fix compilation warning

src/graph/topology/graph_distance.cc

commit 412aa6f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Update references in blockmodel code

src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit 1522bd8c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Include citation information to FAQ

doc/faq.rst
doc/index.rst

commit 1f28c53e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Bump version to 2.2.35dev

configure.ac

commit 21b695d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Bump version to 2.2.34

configure.ac

commit 1ec70e71
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Force default construction of value type in ConstantPropertyMap

src/graph/graph_properties.hh

commit 5401018a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Simplify std::hash<> specializations

src/graph/community/graph_blockmodel.hh

commit 4077f90b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Fix bug with uninitialized value in graph_binary_io.hh

src/graph/graph_io_binary.hh

commit dc350dc1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-11

    Change c-type casts to reinterpret_cast<> in graph_binary_io.hh

src/graph/graph_io_binary.hh

commit 875144da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Fix compilation error with clang

src/graph/graph_io_binary.hh

commit a368a267
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Bump version to 2.2.33dev

configure.ac

commit ef4e5763
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Bump version to 2.2.33

configure.ac

commit 6c51a824
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Fix compilation errors with clang

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/graph.hh
src/graph/graph_properties.hh
src/graph/mpl_nested_loop.hh

commit e7a63ff2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Update autoconf macros for boost::python and python

m4/ax_boost_python.m4
m4/ax_python_devel.m4

commit d7a3c85d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Fix compilation issue with gcc 4.8 and openmp

src/graph/topology/graph_similarity.hh

commit 287b0e44
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-10

    Fix issue building numpy bindings on 32-bit architectures

src/graph/numpy_bind.hh

commit f7f1865e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Bump version to 2.2.32

configure.ac

commit be08cb93
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Add font-awesome to the documentation

doc/gt_theme/static/font-awesome-4.2.0/css/font-awesome.css
doc/gt_theme/static/font-awesome-4.2.0/css/font-awesome.min.css
doc/gt_theme/static/font-awesome-4.2.0/fonts/FontAwesome.otf
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.eot
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.svg
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.ttf
doc/gt_theme/static/font-awesome-4.2.0/fonts/fontawesome-webfont.woff
doc/gt_theme/static/font-awesome-4.2.0/less/bordered-pulled.less
doc/gt_theme/static/font-awesome-4.2.0/less/core.less
doc/gt_theme/static/font-awesome-4.2.0/less/fixed-width.less
doc/gt_theme/static/font-awesome-4.2.0/less/font-awesome.less
doc/gt_theme/static/font-awesome-4.2.0/less/icons.less
doc/gt_theme/static/font-awesome-4.2.0/less/larger.less
doc/gt_theme/static/font-awesome-4.2.0/less/list.less
doc/gt_theme/static/font-awesome-4.2.0/less/mixins.less
doc/gt_theme/static/font-awesome-4.2.0/less/path.less
doc/gt_theme/static/font-awesome-4.2.0/less/rotated-flipped.less
doc/gt_theme/static/font-awesome-4.2.0/less/spinning.less
doc/gt_theme/static/font-awesome-4.2.0/less/stacked.less
doc/gt_theme/static/font-awesome-4.2.0/less/variables.less
doc/gt_theme/static/font-awesome-4.2.0/scss/_bordered-pulled.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_core.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_fixed-width.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_icons.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_larger.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_list.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_mixins.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_path.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_rotated-flipped.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_spinning.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_stacked.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/_variables.scss
doc/gt_theme/static/font-awesome-4.2.0/scss/font-awesome.scss

commit 14c0e36f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Modify docstring tests after RNG update

src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 0f5d1a99
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Small performance improvement to sfdp_layout()

src/graph/layout/graph_sfdp.hh

commit ab6bef60
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-21

    Refactor SBM code and implement overlapping model

doc/community.rst
src/graph/community/Makefile.am
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_blockmodel_overlap.cc
src/graph/community/graph_blockmodel_overlap.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.hh
src/graph/community/spence.cc
src/graph/generation/sampler.hh
src/graph_tool/Makefile.am
src/graph_tool/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/community/overlap_blockmodel.py
src/graph_tool/draw/cairo_draw.py

commit 2905fe8c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Modify automatic text color selection heuristic

src/graph_tool/draw/cairo_draw.py

commit 0380bdf5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Change default colors in draw.cairo_draw

src/graph_tool/draw/cairo_draw.py

commit 124bbe06
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Change default colormap

src/graph_tool/centrality/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py

commit 9b147c0d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-09

    Stylistic changes to the documentation

doc/gt_theme/static/flasky.css
doc/gt_theme/static/gt_style.css
doc/pyenv.py
doc/quickstart.rst
src/graph_tool/generation/__init__.py

commit dccf2873
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-08

    Default intersphinx version to python 3

doc/conf.py

commit 3110f96f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-08

    Include documentation for the 'gt' format

doc/gt_format.rst
doc/index.rst
doc/quickstart.rst

commit 3fb664a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-05

    Change default colormap in draw module

src/graph_tool/draw/cairo_draw.py

commit 9b58ad6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-05

    Convert internally-stored networks in the collection module to new 'gt' format

src/graph_tool/Makefile.am
src/graph_tool/collection/__init__.py
src/graph_tool/collection/adjnoun.gt.gz
src/graph_tool/collection/adjnoun.xml.gz
src/graph_tool/collection/as-22july06.gt.gz
src/graph_tool/collection/as-22july06.xml.gz
src/graph_tool/collection/astro-ph.gt.gz
src/graph_tool/collection/astro-ph.xml.gz
src/graph_tool/collection/celegansneural.gt.gz
src/graph_tool/collection/celegansneural.xml.gz
src/graph_tool/collection/cond-mat-2003.gt.gz
src/graph_tool/collection/cond-mat-2003.xml.gz
src/graph_tool/collection/cond-mat-2005.gt.gz
src/graph_tool/collection/cond-mat-2005.xml.gz
src/graph_tool/collection/cond-mat.gt.gz
src/graph_tool/collection/cond-mat.xml.gz
src/graph_tool/collection/dolphins.gt.gz
src/graph_tool/collection/dolphins.xml.gz
src/graph_tool/collection/email-Enron.gt.gz
src/graph_tool/collection/email-Enron.xml.gz
src/graph_tool/collection/football.gt.gz
src/graph_tool/collection/football.xml.gz
src/graph_tool/collection/hep-th.gt.gz
src/graph_tool/collection/hep-th.xml.gz
src/graph_tool/collection/karate.gt.gz
src/graph_tool/collection/karate.xml.gz
src/graph_tool/collection/lesmis.gt.gz
src/graph_tool/collection/lesmis.xml.gz
src/graph_tool/collection/netscience.gt.gz
src/graph_tool/collection/netscience.xml.gz
src/graph_tool/collection/pgp-strong-2009.gt.gz
src/graph_tool/collection/pgp-strong-2009.xml.gz
src/graph_tool/collection/polblogs.gt.gz
src/graph_tool/collection/polblogs.xml.gz
src/graph_tool/collection/polbooks.gt.gz
src/graph_tool/collection/polbooks.xml.gz
src/graph_tool/collection/power.gt.gz
src/graph_tool/collection/power.xml.gz
src/graph_tool/collection/serengeti-foodweb.gt.gz
src/graph_tool/collection/serengeti-foodweb.xml.gz

commit 1b9b952d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-03

    Include support for vertex invariants in isomorphism()
    
    This also properly handles self-loops and thus fixes #180.

src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 8d7af911
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-03

    Raise ValueError if non-bool properties are passed to Graph.set_vertex/edge_filter()

src/graph_tool/__init__.py

commit ab15e6b2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-03

    Fix bug in graph_io_binary.hh with vector<string> property maps

src/graph/graph_io.cc
src/graph/graph_io_binary.hh

commit 6e537ef0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-02

    Fall back to 'xml' format when unpickling graph in old format

src/graph_tool/__init__.py

commit 5f9e350b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-02

    Change doc matplotlib backend to Cairo

doc/pyenv.py

commit 22557076
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-02

    Set default pickle format to "gt"

src/graph_tool/__init__.py

commit 6ab9c6f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-02

    Include support for lzma compression in Graph.load()/save()

src/graph_tool/__init__.py

commit d0d247ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-02

    Implement new binary graph format "gt"
    
    The new format fully supports all property map types present in
    graph-tool and should be much faster and produce smaller files than the
    other text-based formats.

doc/quickstart.rst
src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/graphml.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/graph/Makefile.am
src/graph/gml.hh
src/graph/graph_io.cc
src/graph/graph_io_binary.hh
src/graph/graph_python_interface.hh
src/graph/graph_util.hh
src/graph/graphml.cpp
src/graph_tool/__init__.py
src/graph_tool/io.py

commit 531add6b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-09-02

    Fix bug in similarity()

src/graph/topology/graph_similarity.hh
src/graph_tool/topology/__init__.py

commit e8fa7fbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-20

    Fix bug in PropertyMap.get_2d_array() with vector-valued maps

src/graph_tool/__init__.py

commit 7c536b02
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-19

    Fix bug with memory handling in numpy_bind.hh

src/graph/graph_python_interface.cc
src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh

commit 1531aed5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-18

    Call vf2_subgraph_mono() in subgraph_isomorphism() when induced=False
    
    This fixes #178.

src/graph/topology/graph_subgraph_isomorphism.cc

commit 117b0a0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-18

    Fix typo in bug report instructions

src/graph/graph_filtering.cc

commit 4d744b5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-18

    Fix bug with edge labels in subgraph_isomorphism()

src/graph/topology/graph_subgraph_isomorphism.cc

commit af3ce488
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-18

    Fix bug with undirected graphs in subgraph_isomorphism()
    
    This fixes #177.

src/graph_tool/__init__.py

commit 4e09ea38
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-18

    Import perfect_prop_hash from .. in topology/__init__.py
    
    This fixes #176.

src/graph_tool/topology/__init__.py

commit 7557026b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-18

    Bump Boost version requirement to 1.53
    
    This fixes issue #175.

configure.ac

commit a49b19f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-15

    Improve performance of PropertyMap.__get_data() and raise exceptions array cannot be obtained

src/graph/graph.cc
src/graph/graph.hh
src/graph_tool/__init__.py

commit 19843f96
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-12

    Check if a vertex has a 2D position before placing it in cairo_draw()
    
    This fixes #171

src/graph/draw/graph_cairo_draw.cc

commit 0d238dd3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-11

    Fix documentation for GraphWidget and GraphWindow
    
    This fixes issue #171

src/graph_tool/draw/gtk_draw.py

commit 8d8cf709
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-08

    Refuse to return vertex and edge descriptors to filtered vertices or edges
    
    This fixes #170

src/graph_tool/__init__.py

commit 08e5aa7b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-07

    Allow for simultaneous propagation of internal and external properties in graph_union()
    
    This fixes #163

src/graph_tool/generation/__init__.py

commit aff1496f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-08-07

    Avoid excessive checking during iteration and creation of vertex and edge descriptors

src/graph/graph_python_interface.hh

commit a5f87638
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-28

    Remove test code from subgraph_isomorphism()

src/graph/topology/graph_subgraph_isomorphism.cc

commit 65f4f8c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-28

    Implement VF2 subgraph isomorphism from BGL
    
    This replaces a custom implementation of Ullmann's code.

src/graph/graph_adjacency.hh
src/graph/topology/Makefile.am
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 3ad70d15
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-28

    Make reverse_graph conform to AdjacencyMatrix

src/boost-workaround/boost/graph/reverse_graph_alt.hpp

commit 51c0fc29
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-28

    Implement perfect_prop_hash()

src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit 9da39d0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-28

    Make UndirectedAdaptor conform to BidirectionalGraph concept

src/graph/graph_adaptor.hh

commit 44f2c151
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-28

    Make adj_list<> conform to AdjacencyMatrix concept

src/graph/graph_adjacency.hh

commit 835aa308
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-27

    Remove unnecessary warnings in graph_draw() with inline=True

src/graph_tool/draw/cairo_draw.py

commit 0f58db6d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-27

    Fix DrawingArea origin offsets in GraphWidget()

src/graph_tool/draw/gtk_draw.py

commit e97f5ee1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-27

    Fix bug in vertex/edge filter initialization in Graph.__init__()

src/graph/graph_filtering.cc
src/graph_tool/__init__.py

commit aad493dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-26

    Force inline in some key wrapper functions

src/graph/graph_adjacency.hh
src/graph/graph_selectors.hh

commit 96f0f7c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-24

    Improve RNG seeding

src/graph/random.cc

commit cd4cef2b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-23

    Modify default constructor of adj_list<>::edge_descriptor
    
    Now default constructed edge descriptors are impossible to occur in
    regular graphs.

src/graph/graph_adjacency.hh

commit e89b2d90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-19

    Include 'graphml' as synonym for 'xml' file format in graph IO functions
    
    This also clarifies the relevant documentation.

src/graph_tool/__init__.py

commit baf6c4cc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-19

    Fix bug in graph_union() when using filtered graphs

src/graph_tool/generation/__init__.py

commit 3c64c67b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-18

    Fix bug in graphml.cpp with non-canonical edge ids

src/graph/graph_io.cc
src/graph/graphml.cpp

commit 21c38be9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-09

    Return trivial partition in is_bipartite() if graph is not bipartite

src/graph_tool/topology/__init__.py

commit 0c9b33c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-14

    Fix stopping condition for shortest_distance() when maximum distance is given

src/graph/topology/graph_distance.cc

commit 8a5b5c24
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-07-14

    Fix ordering of motif vertex maps in motifs()

src/graph_tool/clustering/__init__.py

commit 9b31eeae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-30

    Small cleanups in line_graph() code

src/graph/generation/graph_line_graph.cc

commit f427e412
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-30

    Fix bug in edge_descriptor comparison
    
    This switches the edge_descriptor type in adj_list<> from std::tuple to
    a custom struct.

src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh

commit 09139678
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-29

    Simplify undirected adaptor so that edge descriptors are unmodified

src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh

commit 07f3897c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-17

    Avoid unnecessary copying of property map in in/out_edges()

src/graph/graph_selectors.hh

commit ef5d354a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-26

    Use provided vertex colormap to choose vertex pie colors

src/graph_tool/draw/cairo_draw.py

commit ed3ed342
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-17

    Improve docstring of Graph.degree_property_map()

src/graph_tool/__init__.py

commit e2e64883
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-17

    Fix compilation error when openmp is not enabled

src/graph/graph_openmp.cc

commit 1277a9d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-09

    Switch default OpenMP schedule to 'runtime'
    
    This also implements direct manipulation of OpenMP settings (schedule
    and number of threads) via python.

src/graph/Makefile.am
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_openmp.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/util/graph_search.hh
src/graph_tool/__init__.py

commit d6899abe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-06-07

    Fix similarity() to accept non-integer properties

src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph_tool/topology/__init__.py

commit 3d2ea9f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-31

    Force simultaneous filtering of vertex and edges
    
    Now, if either vertex or edge filtering is enabled, simultaneous
    filtering is activated. By not considering vertex or edge filtering in
    completely independent fashion, the compile time memory requirements
    reduced to about 50%.

doc/graph_tool.rst
src/graph/clustering/graph_motifs.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_geometric.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/layout/graph_radial.cc
src/graph/topology/graph_distance.cc
src/graph_tool/__init__.py

commit 7a84d0f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-31

    Switch to variadic template implementation of mpl_nested_loop() and run_action()

src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/graph.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/mpl_nested_loop.hh

commit c212db96
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-29

    Fix graph IO to properly address unicode strings

src/graph/graph_io.cc
src/graph_tool/__init__.py

commit 4a171495
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-28

    Implement pickling of PropertyMap objects

src/graph_tool/__init__.py

commit 661ffc73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-24

    Fix some trivial compilation warnings

src/graph/generation/graph_complete.hh
src/graph/layout/graph_radial.cc
src/graph/numpy_bind.hh

commit 2ffa62b1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-24

    Use std::shared_ptr instead of boost::shared_ptr in property maps

src/graph/fast_vector_property_map.hh

commit f9ed3a8c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-24

    Force inlining of range iterator selectors

src/graph/graph_selectors.hh

commit ea3cc760
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-24

    Force inlining of simple UndirectedAdaptor functions

src/graph/graph_adaptor.hh

commit a993433c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-21

    Improve documentation of subgraph_isomorphism() and motifs()

src/graph_tool/clustering/__init__.py
src/graph_tool/topology/__init__.py

commit 6fcf0f1b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-05-16

    Fix generation of adjacency, laplacian and adjacency matrices when there are no edges.

src/graph_tool/spectral/__init__.py

commit d0871cee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-30

    Fix bug in label_largest_component() with filtered graphs

src/graph_tool/topology/__init__.py

commit b88b299a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-30

    Ignore unwritable property maps in purge_vertices() with in_place==True

src/graph_tool/__init__.py

commit 4ca52e7c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-29

    Fix copying of graphs with internal unwritable properties

src/graph_tool/__init__.py

commit 4d0809f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-28

    Use range iterators in spectral functions

src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_transition.hh

commit cfb7809f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-28

    Fix transition() matrix for weighted graphs

src/graph/spectral/graph_transition.hh

commit 0fa8cbfb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-24

    Properly initialize PageRank and eigenvector centralities for filtered graphs

src/graph_tool/centrality/__init__.py

commit 29970a2f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-23

    Fix issue in sfdp_layout() with vertices with self-loops

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 7b263944
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-23

    Fix range selector for adjacent vertices

src/graph/graph_selectors.hh

commit 16fba789
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-21

    Fix issue with missing geometry in the Cairo surface created with Quartz

src/graph_tool/draw/gtk_draw.py

commit b7552219
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-19

    Implement correct behavior for min_st_cut()
    
    This fixes ticket #167

src/graph/flow/graph_augment.hh
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_minimum_cut.cc
src/graph_tool/flow/__init__.py

commit 31373d8f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-19

    Fix Graph.clear() and Graph.clear_edges() behavior for filtered graphs

src/graph/graph.cc
src/graph/graph_adaptor.hh
src/graph/graph_util.hh

commit eb743ada
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-16

    Add adaptor of iterator pairs to c++11 range-based for loops

src/graph/graph_selectors.hh

commit 4912769e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-16

    Fix conversion bug in boost::edge() for reversed graphs

src/boost-workaround/boost/graph/reverse_graph_alt.hpp

commit 38d63b74
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-03

    Complete Numpy type table in numpy_bind.hh

src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh

commit 635e475b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-04-03

    Properly propagate ndarray strides into multi_array_ref in numpy_bind.hh
    
    This fixes problems with transposed arrays, or arrays with arbitrary strides.

src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh

commit 7d0eda91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-27

    Bump version to 2.2.32dev

configure.ac

commit 245d1e2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-27

    Bump version to 2.2.31

configure.ac

commit 5077b209
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-27

    Update package URL and TARNAME

configure.ac

commit 65fced62
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-27

    Fix typo bug in cairo_draw.py

src/graph_tool/draw/cairo_draw.py

commit 8cb0c10c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-27

    Bump version to 2.2.31dev

configure.ac

commit 8ff4701a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-25

    Bump version to 2.2.30

configure.ac

commit 260be9b0
Author: Pietro Battiston <me@pietrobattiston.it>
Date:   2014-03-21

    Surface must be ("del"eted, or) finished before sending it to ipython

src/graph_tool/draw/cairo_draw.py

commit c1ef302d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-25

    Temporarily disable option to turn off graph-filtering during compilation

configure.ac

commit 5da07034
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-25

    Include automatic copying of internal property maps in graph_union()

src/graph_tool/generation/__init__.py

commit 4546c908
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-25

    Documentation updates

doc/conf.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit fbb9adfb
Author: Joel Moberg <joel.moberg@gmail.com>
Date:   2014-03-21

    Set up default for parameter inline in grap_draw()

src/graph_tool/draw/cairo_draw.py

commit de6fbcc5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-21

    Display inline images in graph_draw() instead of simply returning them
    
    Now, as usual, the position values are returned, instead of the inline
    image object.

src/graph_tool/draw/cairo_draw.py

commit c7d42eca
Author: Pietro Battiston <me@pietrobattiston.it>
Date:   2014-03-21

    Fixed indentation

src/graph_tool/draw/cairo_draw.py

commit 9d30effe
Author: Pietro Battiston <me@pietrobattiston.it>
Date:   2014-03-21

    Allow inline images even if an unsuitable format is requested

src/graph_tool/draw/cairo_draw.py

commit d23a2e21
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-20

    Don't ignore output parameter in graph_draw() when inline == True

src/graph_tool/draw/cairo_draw.py

commit 4bc34c3b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-20

    Implement Graph.add_edge_list() for fast insertion of multiple edges

doc/graph_tool.rst
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 13a6b871
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-16

    Fix incompatibility bug with python 2.7 in nested_blockmodel.py

src/graph_tool/community/nested_blockmodel.py

commit e0ff2756
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-14

    Implement inline drawing option for graph_draw() with IPython notebooks

src/graph_tool/draw/cairo_draw.py

commit d073ff2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-24

    Convert graph attributes in graph_draw() before passing them to interative_window()
    
    This improves per formance, since the conversion is not performed at
    every drawing operation.

src/graph_tool/draw/cairo_draw.py

commit 1d2ac65c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-24

    Fix handling of "pie" vertex shape properties

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit c7689e67
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-13

    Fix bug in vertex removal

src/graph/graph_adjacency.hh

commit 4b753363
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-21

    Properly reflect include file tree in the install include path

src/graph/centrality/Makefile.am
src/graph/clustering/Makefile.am
src/graph/community/Makefile.am
src/graph/correlations/Makefile.am
src/graph/draw/Makefile.am
src/graph/flow/Makefile.am
src/graph/generation/Makefile.am
src/graph/layout/Makefile.am
src/graph/search/Makefile.am
src/graph/spectral/Makefile.am
src/graph/stats/Makefile.am
src/graph/topology/Makefile.am
src/graph/util/Makefile.am

commit 7573f57e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-17

    Only initialize non-filtered properties in BlockState.__init_()

src/graph_tool/community/blockmodel.py

commit 9d541760
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-17

    Make PropertyMap.fa properly handle graphs with non-contiguous edge indexes

src/graph_tool/__init__.py

commit 8aefa447
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-17

    Include support for keeping certain edges "pinned down" in random_rewire()

configure.ac
src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit 9f0de17f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-13

    Fix bug with run_action.inline() and c++11

src/graph_tool/run_action/run_action_support.hh

commit 1111c959
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-03-14

    Bump version to 2.2.30dev

configure.ac

commit fa67d75c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-07

    Bump version to 2.2.29.1

configure.ac

commit a6ccdb26
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-07

    Fix compatibility bug with Python 3.2

src/graph_tool/community/blockmodel.py

commit 34b34b06
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-06

    Improve autoconf detection of boost::python and sparsehash

configure.ac
m4/ax_boost_python.m4

commit b0e68cc3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-06

    Bump version to 2.2.30dev

configure.ac

commit a4866781
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-04

    Bump version to 2.2.29

configure.ac

commit 07a7d556
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-04

    Fix bug in sfpd_layout() which causes positional artifacts

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 28de6290
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-04

    Update citation information in docstrings

src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit 8ff5bbd4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-04

    Docstring correction

src/graph_tool/generation/__init__.py

commit 5d66e191
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-03

    Remove redundant get_weight() method in BlockState and update get_ers() docstring

src/graph_tool/community/blockmodel.py

commit ed54390f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-02-02

    Change default value for parameter 'c' in multilevel_minimize()

src/graph_tool/community/blockmodel.py

commit 0e21f9a5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-27

    Improve speed of random_rewire() when parallel edges are not allowed
    
    This also changes the semantics of random_rewire() when parallel edges
    / self loops are forbidden, but the initial graph contains them. Now,
    instead of throwing an exception, the rewiring is attempted, with no
    new parallel edges / self-loops being created. Under some
    circumstances, if the degree sequence is graphical, eventually the
    graph can become simple after sufficiently many sweeps.

src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit 2e1d1a07
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-22

    Ignore self-loops when merging nodes in block graph

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py

commit a7c6527b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-15

    Cosmetic docstring example improvements

doc/quickstart.rst
src/graph_tool/generation/__init__.py

commit 28610ba6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-15

    Remove redundant random_move parameter from mcmc_sweep() and related functions
    
    To specify fully random moves, one should set the parameter "c" to
    "float(inf)", as explained in the docstring.

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit 0abe5a7c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-14

    Randomize sweep order in sfdp_layout()
    
    This fixes some strange bugs where deterministic position updates lead
    to strange artifacts.

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 566d6dd8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-13

    Fix vertex/edge search with python::object properties

src/graph/util/graph_search.hh
src/graph_tool/__init__.py

commit 2806a95d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-08

    Fix degree-corrected entropy computation in NestedBlockState

src/graph_tool/community/nested_blockmodel.py

commit 51c50231
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-04

    Change default options to sfdp_layout()

src/graph_tool/draw/__init__.py

commit c6e30b6e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-04

    Bump version to 2.2.29dev

configure.ac

commit 6aa46d31
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-03

    Bump version to 2.2.28

configure.ac

commit dbc89569
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-03

    Reduce memory usage during compilation for graph_community_network_*.cc

src/graph/community/Makefile.am
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_eavg_imp1.cc
src/graph/community/graph_community_network_vavg.cc
src/graph_tool/community/blockmodel.py

commit c3cdcdd9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-03

    Improve inclusion of sparsehash when directory prefix is nonstandard

configure.ac
src/graph/clustering/graph_clustering.hh
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community_network.hh
src/graph/generation/graph_rewiring.hh
src/graph/stats/graph_parallel.hh

commit 4323e370
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-03

    Small optimization in sfdp_layout() and change of default cooling_step parameter.

src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 448a914b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-03

    More documentation fixes.

doc/draw.rst
doc/search_example.xml
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/search/__init__.py

commit 61d8cebd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-02

    Assorted docstring fixes

src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/topology/__init__.py

commit 22cf7c5a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2014-01-02

    Update copyright information

configure.ac
doc/conf.py
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_edges.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/str_repr.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/transform_iterator.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_support.hh
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 959b5fd9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-28

    Improve performance and memory usage of blockmodel inference code

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/generation/Makefile.am
src/graph/generation/dynamic_sampler.hh
src/graph/generation/graph_generation.cc
src/graph/generation/sampler.hh
src/graph_tool/community/blockmodel.py
src/graph_tool/generation/__init__.py

commit a4834bf7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-26

    Fix typo bug in BlockState.get_er()

src/graph_tool/community/blockmodel.py

commit 698e6763
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-24

    Fix pickling of GraphView objects

src/graph_tool/__init__.py

commit 1cc26bed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-24

    Always use fast edge removal in random_graph()

src/graph_tool/generation/__init__.py

commit da179ff0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-05

    Fix sampling of stochastic blockmodel to guarantee correct asymptotic probability

src/graph/community/graph_blockmodel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/sampler.hh
src/graph_tool/community/blockmodel.py
src/graph_tool/generation/__init__.py

commit ca503515
Author: Xin Sun <Sun.Simpson@gmail.com>
Date:   2013-12-21

    Uses pkg-config when configuring google sparse hash.
    In case google sparsehash uses a non-standard prefix, e.g., in Homebrew.

configure.ac
src/graph/clustering/graph_clustering.hh
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community_network.hh
src/graph/stats/graph_parallel.hh

commit cfc04311
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-17

    Trivial whitespace fix

src/graph/graph_adjacency.hh

commit 6cccd783
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-06

    Correct degree sequence description length in blockmodel.py

src/graph_tool/community/blockmodel.py

commit 2d574cb3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-06

    Small docstring fix in BlockState.get_matrix()

src/graph_tool/community/blockmodel.py

commit 67f2bb5c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-04

    Fix remaining incompatibilities with graphviz > 2.30

src/graph_tool/draw/graphviz_draw.py

commit 995c8809
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-01

    Fix bug in eigenvector()
    
    The routine wrongly returned 1/lambda instead of lambda, as the leading
    eigenvalue of the adjacency matrix.

src/graph/centrality/graph_eigenvector.hh

commit ca3c49f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-01

    Fix segfault in sfdp_layout()

src/graph/layout/graph_sfdp.cc

commit 58b73413
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-12-01

    Include support for new graphviz API (>= 2.30) in graphviz_draw()

src/graph_tool/draw/graphviz_draw.py

commit 392b1150
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-27

    Fix small error in partition_entropy()

src/graph_tool/community/blockmodel.py

commit 886b377c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-27

    Update reference in kcore_decomposition()'s docstring

src/graph_tool/topology/__init__.py

commit 0dcf00ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-21

    Fix race condition in betweenness() with openmp enabled

src/boost-workaround/boost/graph/betweenness_centrality.hpp

commit 90b1e76d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-19

    Bump version to 2.2.28dev

configure.ac

commit 08d00ed9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-17

    Bump version to 2.2.27

configure.ac

commit bd0f7fd5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-17

    Fix compilation errors with older numpy versions

src/graph/numpy_bind_old.hh

commit 9384b6e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-17

    Enable c++11 mode for older GCC versions

configure.ac

commit dd390b86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-16

    Split graph_community_network.cc into two compilation units
    
    This reduces memory use during compilation.

src/graph/community/Makefile.am
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network_edges.cc

commit 45f28a19
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-15

    Update docstrings

src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/topology/__init__.py

commit 26cdde1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-11

    Fix segfault in graph_blockmodel.hh

src/graph/community/graph_blockmodel.hh

commit c3bd7666
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-11

    Fix compilation issues with boost 1.54

src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/graph_bind.cc
src/graph/graph_copy.cc

commit e11f3535
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-10

    Improve deletion of edges from python interface
    
    This makes edge deletion O(1) if fast edge deletion is enabled for the
    graph.

src/graph/graph_adjacency.hh
src/graph/graph_python_interface.cc

commit d6f00e98
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-10

    Include transition() and modularity_matrix() in spectral module

src/graph/spectral/Makefile.am
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_transition.cc
src/graph/spectral/graph_transition.hh
src/graph_tool/spectral/__init__.py

commit fe42f743
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-01

    Port to c++11

configure.ac
src/boost-workaround/boost/graph/graphml.hpp
src/boost-workaround/boost/graph/isomorphism.hpp
src/graph/Makefile.am
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_radial.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/shared_map.hh
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_norm_laplacian.cc
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph/tr1_include.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh

commit 0d2a562a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-07

    Fix compilation error with Boost 1.46

src/graph/graph_io.cc
src/graph/str_repr.hh

commit 2d315d45
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-03

    Forbid creation of empty blocks in mcmc_sweep()

src/graph/community/graph_blockmodel.hh

commit 1441551e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-11-02

    Improve performance of global/local_clustering()

src/graph/clustering/graph_clustering.hh
src/graph_tool/clustering/__init__.py

commit 4d7eb88e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-28

    Fix bug in katz() and introduce optional normalization

src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph_tool/centrality/__init__.py

commit 5c45cb3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-24

    Remove references to 'typename' outside of templates

src/graph/graph_python_interface.cc
src/graph/topology/graph_subgraph_isomorphism.cc

commit 101b2e32
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-22

    Fix unicode issue with python 2.7

src/graph_tool/run_action/inline.py

commit fc0eb37f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-22

    Fix size of figures in documentation

doc/pyenv.py

commit 801be366
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-22

    Bump version to 2.2.27

configure.ac

commit cd03385c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-20

    Bump version to 2.2.26

configure.ac

commit 892a658d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-20

    Simple documentation fixes

doc/graph_tool.rst
src/graph_tool/community/nested_blockmodel.py

commit e2ef6e01
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-20

    Keep backwards compatibility with numpy < 1.7

src/graph/Makefile.am
src/graph/numpy_bind.hh
src/graph/numpy_bind_old.hh

commit 99573742
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-20

    Fix matplotlib deprecation warning

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py

commit 87bccc0e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-20

    Add generic from_python scalar converters
    
    This enables the acceptance of numpy types such as numpy.int64 as
    parameters to functions taking C++ integers or floats.

src/graph/graph_bind.cc

commit 9e0367b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-19

    Improve mid_marker placement with bezier curves
    
    This also includes a "mid_marker_pos" edge attribute which allows a
    relative placement of the mid marker along the edge.

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 57e4e54c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-19

    Fix drawing of self-loops with edge markers

src/graph/draw/graph_cairo_draw.cc

commit 6508fba3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-18

    Sphinx documentation configuration change

doc/conf.py
doc/graph_tool.rst

commit 00ea6536
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-12

    Performance improvement to condensation_graph()
    
    Avoid hash of pair<vertex_t, vertex_t> types.

src/graph/community/graph_community_network.hh

commit 50fb2c31
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-27

    Refactor stochastic blockmodel inference
    
    This greatly improves the performance of the previous algorithm, and
    includes support for hierarchical models.

doc/community.rst
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community_network.hh
src/graph_tool/Makefile.am
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/community/nested_blockmodel.py

commit ae9857c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-18

    Implement radial_tree_layout()

doc/draw.rst
src/graph/layout/Makefile.am
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_radial.cc
src/graph_tool/draw/__init__.py

commit 30dee452
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-17

    Modify semantics of prop.fa attribute for edge properties
    
    The filtered array returned now also reflects the vertex filtering, so that
    it corresponds only to actually visible edges in the graph, not only
    those explicitly selected via an edge filter.

src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit dba90964
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-10-13

    Improve modularity() computation

src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph_tool/community/__init__.py

commit c61bda50
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-30

    Improve self-loop drawing in cairo_draw()

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit ea88db33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-21

    Improve edge label drawing

src/graph/draw/graph_cairo_draw.cc

commit 6cb45f26
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-19

    Implement get_hierarchy_control_points()

doc/draw.rst
src/graph/draw/Makefile.am
src/graph/draw/graph_cairo_draw.cc
src/graph/draw/graph_tree_cts.cc
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py

commit ed228c88
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-18

    Fix issue with graph_union() and filtered graphs

src/graph_tool/generation/__init__.py

commit c249846a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-17

    Implement edge gradients

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 965dd32e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-16

    Allow empty property maps in graph_union()

src/graph_tool/generation/__init__.py

commit be1b95da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-16

    Improve vertex text positioning in graph_draw()
    
    This also includes the new text_rotation, and text_offset properties.

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 223f48af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-09

    Update website in README file

README

commit 91a9345c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-06

    Fix compilation issue on MacOSX with clang

src/graph/graph_adaptor.hh
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh

commit 73d5b286
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-02

    Small changes to documentation layout to match new website

doc/.templates/layout.html
doc/gt_theme/static/flasky.css

commit ea5e0352
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-02

    Bump version to 2.2.26dev

configure.ac

commit feec13d9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-02

    Bump version to 2.2.25

configure.ac

commit d08bd85a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-01

    Assorted documentation fixes

doc/Makefile
doc/conf.py
doc/graph_tool.rst
doc/price.py
doc/quickstart.rst
src/graph_tool/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/topology/__init__.py

commit 1d0b48de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-01

    Fix initialization bug in adj_list<>

src/graph/graph_adjacency.hh

commit 444be204
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-09-01

    Enable drawing to file-like object

src/graph_tool/draw/cairo_draw.py

commit 0c932865
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-08-13

    Enable optional debugging with valgrind by disabling CGAL's rounding tests

configure.ac

commit 74783c94
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-08-11

    Improve docstring for Graph.own_property()

src/graph_tool/__init__.py

commit cefe49d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-29

    Include support for arbitrary multilevel structure in sfdp_layout

src/graph/layout/graph_sfdp.cc
src/graph_tool/draw/__init__.py

commit d2b60b99
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-25

    Disable conversion of 'zero' and 'infinity' values in search functions when the distance type is 'python::object'

src/graph_tool/search/__init__.py

commit 280d24ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-24

    Improve speed of condensation_graph()

src/graph/community/graph_community_network.hh

commit ac45a275
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-24

    Improve speed of label_parallel_edges()

src/graph/stats/graph_parallel.hh

commit 18723245
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-24

    Fix edge property map query in reverse_graph

src/boost-workaround/boost/graph/reverse_graph_alt.hpp

commit 78d42c38
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-22

    Faster Graph copying if filter state is identical

src/graph/graph_copy.cc
src/graph_tool/__init__.py

commit 27d059c2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-22

    Change default OpenMP parameters to: schedule(static) if (N > 100)

src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.hh
src/graph/graph_python_interface.cc
src/graph/layout/graph_sfdp.hh
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/util/graph_search.hh

commit 29f9f248
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-21

    Fix copying of filtered graphs

src/graph_tool/__init__.py

commit 137eb9fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-19

    Fix clear_vertex() and remove_edge(s, t, g) in adj_list<>

src/graph/graph_adjacency.hh

commit 44739a41
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-19

    Fix edge(s, t, g) return type in revese_graph

src/boost-workaround/boost/graph/reverse_graph_alt.hpp

commit fe8e0085
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-16

    Fix behaviour of Graph.add_vertex(n) for n == 0

src/graph_tool/__init__.py

commit 8a44eee1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-16

    Small optimization in sfdp_layout()

src/graph/layout/graph_sfdp.hh

commit 401408f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-15

    Change OpenMP schedule directive to 'static' instead of 'dynamic'
    
    Use schedule(static, 100), to reduce overhead with small graphs in the
    majority of cases.

src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_closeness.hh
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_corr_hist.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.hh
src/graph/graph_python_interface.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/util/graph_search.hh

commit a00ca7fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-12

    Make alias Sampler default-constructible

src/graph/generation/sampler.hh

commit 4296b96e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-10

    Implement optional faster O(1) removal of edges

src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph_tool/__init__.py

commit e16c781f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-09

    Fix edge() function in adj_list class

src/graph/graph_adjacency.hh

commit f54492ca
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-04

    Remove old documentation from filter stash operations

doc/graph_tool.rst

commit 38276b9f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-02

    Get rid of the filter stash in Graph class
    
    Fully remove the filter stash and associated functions in the Graph
    class, in favor of using GraphView uniquely.

src/graph_tool/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py

commit 1f6f566f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-02

    Do not use filter stash internally, in favour of graph views

src/graph_tool/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 7a401052
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-02

    Implement weighted degree property maps and weighted degree selectors

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_python_interface.cc
src/graph/graph_selectors.hh
src/graph_tool/__init__.py

commit 0c4b511c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-02

    Implemet __copy__ in Graph and PropertyMap

src/graph_tool/__init__.py

commit 808318a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-07-02

    Implement vertex reordering during graph copy

src/graph/graph.hh
src/graph/graph_copy.cc
src/graph_tool/__init__.py

commit cbc77236
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-27

    Fix bug in run_action.inline()
    
    This removes old dependency on an outdated graph wrapper which did edge
    index housekeeping.

src/graph/Makefile.am
src/graph/graph_wrap.hh
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_support.hh

commit e8d3c604
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-22

    Trivial docstring fix

src/graph_tool/clustering/__init__.py

commit c040f44d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-22

    Return _really_ at most n_max subgraphs in subgraph_isomorphism()

src/graph/topology/graph_subgraph_isomorphism.hh

commit 5781125c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-22

    Enable vertex/edge label matching in subgraph_isomorphism

src/graph/topology/graph_subgraph_isomorphism.cc
src/graph_tool/topology/__init__.py

commit 3a95582f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-12

    Implement `return_maps` option in motifs()
    
    This returns an optional list of locations of the motifs found in the
    main graph.

src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph_tool/clustering/__init__.py

commit 1e2702b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-07

    Include 'epsilon' parameter in minimize_blockmodel_dl()

src/graph_tool/community/blockmodel.py

commit 6c624cac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-02

    Improve bounding box calculation in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit c423f60f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-06-02

    Fix typo in quickstart guide

doc/quickstart.rst

commit 9f30098b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-24

    Update numpy bindings to comply with upcoming API deprecation

src/graph/numpy_bind.hh

commit a5990d2a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-22

    Remove some useless compiler warnings

configure.ac

commit 733ae662
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-22

    Ensure in/out_edge/adjacency_iterator and associated are random access in adj_ist<> and UndirectedAdaptor<>

src/graph/Makefile.am
src/graph/graph_adaptor.hh
src/graph/graph_adjacency.hh
src/graph/transform_iterator.hh

commit 86861179
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-21

    Small performance improvements to graph_blockmodel.hh

src/graph/community/graph_blockmodel.hh

commit 2d799f30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-21

    Remove C++ signature cruft from documentation

doc/conf.py
doc/gt_theme/static/gt_style.css

commit bd375efd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-21

    Improve checkpointing in blockmodel.py

src/graph_tool/community/blockmodel.py

commit bc4b3707
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-21

    Implement fully random moves in blockmodel.py

src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py

commit 3af0783d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-07

    Better error reporting in numpy_bind.hh

src/graph/numpy_bind.hh

commit 3b911079
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-07

    Bump version to 2.2.25dev

configure.ac

commit 0bcfb12d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-05

    Bump version to 2.2.24

configure.ac

commit 6ecafc45
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-02

    Implement halo size option in graph_draw()

doc/demos/animation_zombies.py
src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit c8c4518d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-02

    Docstring tests update

src/graph_tool/community/blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit bb2e8bf4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-02

    Implement get/set_2d_array() in PropertyMap
    
    This implements indirect array access to property maps with vector
    values.

src/graph_tool/__init__.py

commit 64873588
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-02

    Fix drawing when the layout has zero width or height

src/graph_tool/draw/cairo_draw.py

commit 0e3893f2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-02

    Fix help for --with-python-module-path option in configure script

configure.ac

commit 7a49155d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-05-01

    Docstring fixes in the generation module

src/graph_tool/generation/__init__.py

commit 36de5a80
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-30

    Fix graph unpickling bug with Python 2

src/graph/graph_io.cc

commit 6b9f07b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-30

    Fix animation demo problem with newer gobject

doc/demos/animation_dancing.py
doc/demos/animation_sirs.py
doc/demos/animation_zombies.py

commit 36f45f5e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-30

    Fix bug with visitor wrappers in search module
    
    This changes the way search visitors are wrapped, such that the original
    class remains unmodified. With the previous code, the original classes
    would be repeatedly modified, adding unnecessary overhead, and even
    possibly causing the number of nested calls to exceed the maximum
    threshold.

src/graph_tool/search/__init__.py

commit 0c34c720
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-25

    Add fast "traditional" blockmodel sampling to random_graph/rewire
    
    This also improves some of the existing shuffling strategies with a fast
    alias sampling. The parameter names of the random_graph() and
    random_rewire() functions have been made more consistent.

src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/sampler.hh
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py

commit ffc3eaae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-23

    Trivial typo in random_graph() docstring

src/graph_tool/generation/__init__.py

commit ce741734
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-23

    Implement spectral functions in C++

configure.ac
src/graph/Makefile.am
src/graph/graph_selectors.hh
src/graph/spectral/Makefile.am
src/graph/spectral/graph_adjacency.cc
src/graph/spectral/graph_adjacency.hh
src/graph/spectral/graph_incidence.cc
src/graph/spectral/graph_incidence.hh
src/graph/spectral/graph_laplacian.cc
src/graph/spectral/graph_laplacian.hh
src/graph/spectral/graph_matrix.cc
src/graph/spectral/graph_norm_laplacian.cc
src/graph_tool/spectral/__init__.py

commit 491d21a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-13

    Implement circular_graph()

src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph_tool/generation/__init__.py

commit 203d04bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-13

    Fix compilation warning

src/graph/graph_util.hh

commit 945ca547
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-13

    Implement complete_graph()

src/graph/generation/Makefile.am
src/graph/generation/graph_complete.cc
src/graph/generation/graph_complete.hh
src/graph/generation/graph_generation.cc
src/graph_tool/generation/__init__.py

commit 98795441
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-11

    Fix import issue with newer gobject-introspection

src/graph_tool/draw/cairo_draw.py

commit 265f792d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-04-05

    Update citation information in blockmodel.py

src/graph_tool/community/blockmodel.py

commit 2583f906
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-25

    Improve memory usage of graphml reader and include support for ignoring properties
    
    The graphml reader no longer builds a list of edges/vertices during
    parsing, whenever the graph uses canonical names.

src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/graphml.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/graph/gml.hh
src/graph/graph.hh
src/graph/graph_io.cc
src/graph/graphml.cpp
src/graph_tool/__init__.py

commit 655107df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-25

    Raise exception in random_spanning_tree() if the graph is not connected

src/graph_tool/topology/__init__.py

commit 6d3b293c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-25

    Implement PropertyDict.clear()

src/graph_tool/__init__.py

commit dc7f9f73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-25

    Bump version to 2.2.24dev

configure.ac

commit 66e8c6a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-20

    Bump version to 2.2.23

configure.ac

commit 67eff378
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-20

    Fix initialization of distance values in shortest_distance()

src/graph/topology/graph_distance.cc

commit f90c6c2b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-20

    Cosmetic documentation fix

src/graph_tool/__init__.py
src/graph_tool/topology/__init__.py

commit b69fdece
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-20

    Remove 'remove_vertex_if()' and 'remove_edge_if()'
    
    These are redundant functions which can be trivially implemented as
    loops.

doc/graph_tool.rst
src/graph_tool/__init__.py

commit a8481771
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-20

    Add 'target' parameter to shortest_distances()

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit e5a1861d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-20

    Fix bug with remove_vertex() and include 'fast' option
    
    This fixes ticket #131, and includes a 'fast' O(k) option, which
    changes the vertex index ordering.

src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit e9cbea5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-04

    Avoid visiting all vertices in dfs_search()
    
    This is done by default in depth_first_search() in BGL, so we switch to
    depth_first_visit().

src/graph/search/graph_dfs.cc

commit 84615544
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-03

    Modify google analytics code in documentation

doc/.templates/layout.html

commit 020c0a33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-03

    Fix issue with edge_difference() and directed edges

src/graph_tool/__init__.py

commit 6cfd05c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-03-03

    Fix closeness() when source option is given

src/graph_tool/centrality/__init__.py

commit 095668c8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-28

    Implement closeness centrality

src/graph/centrality/Makefile.am
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_closeness.cc
src/graph/centrality/graph_closeness.hh
src/graph_tool/centrality/__init__.py

commit 23fa373d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-28

    Fix potential bug in graph_distance.hh

src/graph/stats/graph_distance.hh

commit fdf7b485
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-28

    Remove compilation warnings in graph_components.hh

src/graph/topology/graph_components.hh

commit 2a21ab19
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-28

    Implement k-core decomposition

src/graph/topology/Makefile.am
src/graph/topology/graph_kcore.cc
src/graph/topology/graph_kcore.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 072781c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-27

    Modify outdated copyright information

src/graph/flow/graph_augment.hh
src/graph/flow/graph_flow_bind.cc
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/run_action/run_action_support.hh

commit 472aaece
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-27

    Implement "attractors" option in label_components()

src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph_tool/topology/__init__.py

commit 33c66543
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-27

    Add bool to the list of supported numpy types

src/graph/numpy_bind.hh

commit d864ef87
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-24

    Implement edge text labels in graph_draw()

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit e1fa3a90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-23

    Fix mcmc_sweep() bug with filtered graphs

src/graph_tool/community/blockmodel.py

commit bcf73e28
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-23

    Update docs to newer version of MathJax

doc/conf.py

commit febb28fa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-23

    Bump version to 2.2.23dev

configure.ac

commit 8c1a8f04
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-21

    Bump version to 2.2.22

configure.ac

commit f6db1821
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-21

    Workaround for adj_list<> with older boost versions

src/graph/graph_adjacency.hh

commit d1621047
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-21

    Reduce bitrate of animation example

doc/demos/animation.rst

commit 2d0b22b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-21

    Update documentation to Graph.edge_index/Graph.vertex_index.

src/graph_tool/__init__.py

commit cdb24426
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-17

    Fix graphviz_draw() errors with python3

src/graph_tool/draw/graphviz_draw.py

commit a5af9c2f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-15

    Install graph_adjacency.hh in include dir

src/graph/Makefile.am

commit fa67d1de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-15

    Avoid tr1 from libsdtc++ 4.2 and below, not 4.5 and above

src/graph/tr1_include.hh

commit 6d45ef4c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-14

    Disable use of tr1 for libstc++ older than GCC 4.5

src/graph/tr1_include.hh

commit bfb8db48
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-14

    Include option to disable the use of google sparsehash

configure.ac
src/graph/community/graph_blockmodel.hh

commit 3a7350b5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-12

    Fix issue with boost::xpressive and some macros in Python headers

src/graph/graph_io.cc

commit ca651e2d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-12

    Invert order of compiler warning flags so they can be overridden

configure.ac

commit 2850c93f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-12

    Force use of boost::tuple when using boost::tr1
    
    This avoids a conflict with the overloaded tie() function.

src/graph/tr1_include.hh

commit 023b5e95
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-11

    Add licence information to graph_adjacency.hh

src/graph/graph_adjacency.hh

commit cc253798
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-11

    Enable -Wextra by default during compilation.

configure.ac

commit f74098a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-11

    Fix output of docstring tests.

src/graph_tool/clustering/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit ddd84961
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-11

    Fix BlockState.min_dist()

src/graph_tool/community/blockmodel.py

commit 4d212c1b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-02-11

    Switch from boost::adjacency_list<> to custom made and lightweight adj_list<>
    
    Dumping boost::adjacency_list<> improves memory usage by a factor of
    two, and also slightly improves performance in some cases.

src/boost-workaround/boost/graph/isomorphism.hpp
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_union.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adjacency.hh
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties_group.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_util.hh
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/mpl_nested_loop.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_components.hh
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_transitive_closure.cc
src/graph_tool/__init__.py

commit 5b67db19
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-29

    Fix computation of normalized Laplacian matrix

src/graph_tool/spectral/__init__.py

commit fc732cfa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-27

    Fix remaining issues with pickling in Python 3

src/graph/graph_io.cc
src/graph_tool/__init__.py

commit b2ed6f34
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-23

    Fixes bug when edge/vertex_hist are called for non-scalar types

src/graph/stats/graph_histograms.cc

commit 14055716
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-23

    Fix docstring in minimize_blockmodel_dl()

src/graph_tool/community/blockmodel.py

commit 0bd803e9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-16

    Implement Graph.purge_vertices() via graph copying in O(V + E) time

src/graph_tool/__init__.py

commit 6f91e1ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-10

    Remove unused variable from blockmodel.hh

src/graph/community/graph_blockmodel.hh

commit 1efd1c06
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-10

    Unify inclusion of tr1 headers based on libstdc++ version
    
    This enables the inclusion of the non-boost tr1 headers if a recent
    enough version of libstdc++ is detected. This als fixes a bug with
    clang when sparsehash pulls unwanted tr1 headers.

src/graph/Makefile.am
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.hh
src/graph/gml.hh
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/layout/graph_arf.hh
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/random.hh
src/graph/shared_map.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/tr1_include.hh
src/graph/util/graph_search.hh

commit a7f57fbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-09

    Complete docstring for condensation_graph()

src/graph_tool/community/blockmodel.py

commit 717ef0f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-09

    Fix bug in pseudo_diameter() when using filtered graphs

src/graph_tool/topology/__init__.py

commit 69c011b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-09

    Fix typo and inconsistency in animation_dancing.py

doc/demos/animation_dancing.py

commit 73e23eaa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-09

    Bump version to 2.2.22dev

configure.ac

commit 9ce45576
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-08

    Bump version to 2.2.21

configure.ac

commit 5d08ef67
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-08

    Install shared objects in the correct path

src/graph/Makefile.am
src/graph/clustering/Makefile.am
src/graph/community/Makefile.am
src/graph/correlations/Makefile.am
src/graph/draw/Makefile.am
src/graph/flow/Makefile.am
src/graph/generation/Makefile.am
src/graph/layout/Makefile.am
src/graph/stats/Makefile.am
src/graph/util/Makefile.am

commit 93304aa7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-06

    Bump version to 2.2.20

configure.ac

commit 32183e5d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-07

    Fix compilation issue with boost < 1.50

src/boost-workaround/boost/graph/isomorphism.hpp
src/boost-workaround/boost/graph/named_function_params-alt.hpp
src/graph/Makefile.am

commit 1c6cd9c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-06

    Implement --with-python-module-path in configure.ac
    
    This allows ones to specify exactly where the module will be installed.

configure.ac

commit 9a589107
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-06

    Update copyright information

configure.ac
doc/conf.py
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_minimum_cut.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/random.cc
src/graph/random.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/str_repr.hh
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/topology/graph_tsp.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/collection/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 7544ddb8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-06

    Fix wrong handling of docdir in configure.ac

configure.ac

commit d15a535e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-04

    Further fixes to boost's isomorphism.hpp with filtered graphs

src/boost-workaround/boost/graph/isomorphism.hpp

commit b8d0dd73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-04

    Fix bug in BlockState.entropy()

src/graph_tool/community/blockmodel.py

commit 29d46748
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-04

    Include corrections to the American football network
    
    This includes some corrections to the conference assignments made by
    T. S. Evans.

src/graph_tool/collection/__init__.py
src/graph_tool/collection/football.xml.gz

commit 8f27ef86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-04

    Fix bug in isomorphism when using filtered graphs
    
    This also synchronizes the code with the most recent boost version
    (1.52).

src/boost-workaround/boost/graph/isomorphism.hpp
src/graph/clustering/graph_motifs.hh

commit 971de369
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-04

    Safeguard for empty graphs in subgraph_isomorphism()

src/graph_tool/topology/__init__.py

commit b0d238d2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-03

    Correct typo in dosctring

src/graph_tool/community/blockmodel.py

commit 8bf19c02
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-03

    Include cookbook documentation on animations

doc/demos/animation.rst
doc/demos/animation_dancing.py
doc/demos/animation_sirs.py
doc/demos/animation_zombies.py
doc/demos/face-grin.png
doc/demos/face-surprise.png
doc/demos/index.rst
doc/demos/zombie.png
doc/index.rst

commit 7a015e02
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2013-01-03

    Improve drawing of vertex surface and include the `anchor` vertex property

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 8844ca44
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-30

    Fix issue in BlockState with python2

src/graph_tool/community/blockmodel.py

commit 3424a562
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-30

    Fix issue with pickling and python3

src/graph_tool/io.py

commit aa341e2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-29

    Fix typo in blockmodel documentation.

src/graph_tool/community/blockmodel.py

commit dffb8bd5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-29

    Improve performance of mcmc_sweep() when beta == inf.

src/graph/community/graph_blockmodel.hh
src/graph_tool/community/blockmodel.py

commit 52918e82
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-29

    Implement optional simulated annealing in minimize_blockmodel_dl()

src/graph_tool/community/blockmodel.py

commit 7d221334
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-29

    Bump version to 2.2.20dev

configure.ac

commit 296855b0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-28

    Include documentation for the "pie" vertex shape in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit 9ecface6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Bump version to 2.2.19

configure.ac

commit 50c22261
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-27

    Include autoconf test for google's sparsehash

configure.ac
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh

commit f444def1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Add collection files to tarball

src/graph_tool/Makefile.am

commit 1db5c5a6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Fix issue with hashing in run_action

src/graph_tool/run_action/inline.py

commit 3c5c01e8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Documentation typo fixes

src/graph_tool/__init__.py
src/graph_tool/spectral/__init__.py

commit 8cc36394
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Use ${docdir} in configure.ac

configure.ac

commit a9c68daa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Fix trust_transitivity() with filtered graphs

src/graph/centrality/graph_trust_transitivity.hh

commit 2ebe821e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Fix pickling with python3

src/graph_tool/io.py

commit 5d76bbb1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-26

    Assorted fixes to the documentation

doc/conf.py
doc/draw.rst
doc/graph_tool.rst
doc/price.py
doc/quickstart.rst
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/blockmodel.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit b487971b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-25

    Fix bug with computation of bounding box in graph_draw() when self-loops are present

src/graph_tool/draw/cairo_draw.py

commit 65860700
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-25

    Fix bug with python3 and xrange

src/graph_tool/__init__.py
src/graph_tool/search/__init__.py

commit 6e3cce61
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-25

    Update sphinx/documentation files for python3 conformance

doc/Makefile
doc/gt_theme/static/flasky.css
doc/pyenv.py
doc/sphinxext/linkcode.py
doc/sphinxext/plot_directive.py

commit d7876c80
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-25

    Implement blockmodel inference in community module

doc/community.rst
src/graph/community/Makefile.am
src/graph/community/graph_blockmodel.cc
src/graph/community/graph_blockmodel.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/community/graph_community_network_eavg.cc
src/graph/community/graph_community_network_vavg.cc
src/graph/graph_bind.cc
src/graph_tool/Makefile.am
src/graph_tool/community/__init__.py
src/graph_tool/community/blockmodel.py

commit f4234551
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-25

    Unify all random number generators into a single module-wise instance
    
    The object may be globally reset via the seed_rng() function.

src/graph/Makefile.am
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.hh
src/graph/generation/sampler.hh
src/graph/graph_bind.cc
src/graph/layout/graph_sfdp.cc
src/graph/random.cc
src/graph/random.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topology.cc
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 2e0b08d3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-22

    Implement "pie" (i.e. pie chart) vertex shape

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit d284760a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-22

    Fix artifacts when drawing using the PDF backend

src/graph/draw/graph_cairo_draw.cc

commit 6a5cf429
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-21

    Update sphinx files to python3

doc/conf.py
doc/pyenv.py
doc/sphinxext/LICENSE.txt
doc/sphinxext/__init__.py
doc/sphinxext/comment_eater.py
doc/sphinxext/compiler_unparse.py
doc/sphinxext/docscrape.py
doc/sphinxext/docscrape_sphinx.py
doc/sphinxext/numpydoc.py
doc/sphinxext/phantom_import.py
doc/sphinxext/setup.py
doc/sphinxext/traitsdoc.py

commit e29e4ce5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-21

    Add collection modules which contains an assortment of useful networks

doc/collection.rst
doc/graph_tool.rst
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/collection/__init__.py
src/graph_tool/collection/adjnoun.xml.gz
src/graph_tool/collection/as-22july06.xml.gz
src/graph_tool/collection/astro-ph.xml.gz
src/graph_tool/collection/celegansneural.xml.gz
src/graph_tool/collection/cond-mat-2003.xml.gz
src/graph_tool/collection/cond-mat-2005.xml.gz
src/graph_tool/collection/cond-mat.xml.gz
src/graph_tool/collection/dolphins.xml.gz
src/graph_tool/collection/email-Enron.xml.gz
src/graph_tool/collection/football.xml.gz
src/graph_tool/collection/hep-th.xml.gz
src/graph_tool/collection/karate.xml.gz
src/graph_tool/collection/lesmis.xml.gz
src/graph_tool/collection/netscience.xml.gz
src/graph_tool/collection/pgp-strong-2009.xml.gz
src/graph_tool/collection/polblogs.xml.gz
src/graph_tool/collection/polbooks.xml.gz
src/graph_tool/collection/power.xml.gz
src/graph_tool/collection/serengeti-foodweb.xml.gz

commit 8108a52a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-18

    Fix typo in docstring of max_cardinality_matching()

src/graph_tool/topology/__init__.py

commit 25408915
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-18

    Get rid of cPickle module since it has been removed in python3

src/graph_tool/io.py

commit d839faf9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-09

    Fix bug when vertex_font_size is a property map

src/graph_tool/draw/cairo_draw.py

commit b974e3c5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-09

    Improve performance and quality of edge drawing in absence of transparency

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 003d8792
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-06

    Fix typo in docstring

src/graph_tool/draw/gtk_draw.py

commit fee7b2c9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-06

    Refined positioning of vertex text labels

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 6b2f501a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-06

    Fix Graph.ep shortcut

src/graph_tool/__init__.py

commit 7bf34e3f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-06

    Refactor UndirectedAdaptor edge iterators
    
    The edge and adjacency iterators of UndirectedAdaptor are now
    implemented using Boost.Iterators and Boost.Range. Among other things,
    this preserves underlying properties of the original iterators, such as
    random access.

src/graph/graph_adaptor.hh
src/graph/graph_selectors.cc

commit 6df1466c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-12-02

    Implement easy copying of checked/unchecked_vector_property_map

src/graph/fast_vector_property_map.hh

commit fd883479
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-28

    Fix copying of internal property maps during graph pruning

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_python_interface.hh
src/graph_tool/__init__.py

commit 0072e255
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-28

    Fix segfault when purging vertices with self-loops

src/graph/graph_filtering.cc

commit d9d99c0d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-26

    Fix vertex_surface conversion in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit 63ab770f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-25

    Accept integers as vertices in certain functions

src/graph_tool/__init__.py

commit be9f0a3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-25

    Implement faster addition of many vertices

doc/quickstart.rst
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit 254721ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-25

    Update graph IO to preserve the graph filtering state

src/graph_tool/__init__.py

commit 14b91f60
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-25

    Include {vertex,edge,graph}_properties aliases: vp, ep, gp
    
    This also modifies the behaviour of the graph_properties dict, which now
    return the property values directly, instead of the map objects.

doc/graph_tool.rst
doc/quickstart.rst
src/graph_tool/__init__.py

commit d2d47234
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-21

    Introduce new property type: int16_t (short)

doc/quickstart.rst
src/boost-workaround/boost/graph/graphml.hpp
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/numpy_bind.hh
src/graph_tool/__init__.py

commit 01d9c519
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-19

    Cleanup pickler/unpickler objects in io.py
    
    This is to avoid strange segfaults in atexit functions defined by
    boost::python.

src/graph_tool/io.py

commit 440abbdb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-19

    Bump version to 2.2.19dev

configure.ac

commit 83bb8a49
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-13

    Bump version to 2.2.18

configure.ac

commit 444651a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-13

    Fix make_maximal_planar()

src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 2a05bb3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-12

    Guarantee inlining of some important functions

src/graph/fast_vector_property_map.hh
src/graph/graph_filtering.hh

commit c9afd8cc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-03

    Fix bug in graph_copy()

src/graph/clustering/graph_motifs.cc
src/graph/graph_util.hh
src/graph_tool/clustering/__init__.py

commit e9ebd2f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-11-01

    Get rid of compilation warning due to <Python.h>

src/graph/generation/graph_triangulation.cc
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_copy.cc
src/graph/graph_filtering.hh
src/graph/graph_properties_copy.cc
src/graph/graph_selectors.cc
src/graph/graphml.cpp
src/graph/topology/graph_transitive_closure.cc

commit 8e046d6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-31

    Implement make_maximal_planar()

src/graph/topology/Makefile.am
src/graph/topology/graph_maximal_planar.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit a7a1a83b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-31

    Fix transposed correlation plots in the documentation

src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py

commit 26fdc3b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-31

    Fix automatic text-color computation

src/graph_tool/draw/cairo_draw.py

commit b55261c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-31

    Include __repr__ member for vector<string> classes

src/graph_tool/__init__.py

commit 40d467ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-29

    Fix compilation issues with clang

src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/graph_wrap.hh
src/graph/layout/graph_sfdp.hh
src/graph/topology/graph_components.cc

commit 2c18c898
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-29

    Fix dependency on gobject

src/graph_tool/draw/cairo_draw.py

commit 4f894336
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-28

    Fix compilation issues with Boost 1.51

src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_rewiring.cc
src/graph/graph_adaptor.hh
src/graph/graph_copy.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_util.hh

commit 8961b6ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-27

    Add prop_to_size() convenience function

src/graph_tool/draw/__init__.py

commit f84f49af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-27

    Improve automatic color handling in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit 78399c2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-27

    Add edge() function to undirected adaptor

src/graph/graph_adaptor.hh

commit b0f284a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-27

    Include support for intra/iter-group attraction/repulsive forces in sfdp_layout()

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 8d5b50b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-06

    Fix compilation of graph_hits.cc with openmp

src/graph/centrality/graph_hits.hh

commit 4f485b9b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-03

    Fix bug in __getitem__ in PropertyDict

src/graph_tool/__init__.py

commit 11dbcdf0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-01

    Fix issue with adjacency() and multiple edges + self_loops

src/graph_tool/spectral/__init__.py

commit 527ae0ee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-01

    Fix another typo in the Katz docstring.

src/graph_tool/centrality/__init__.py

commit f6c7f010
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-01

    Fix Katz centrality docstring

src/graph_tool/centrality/__init__.py

commit 50f53515
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-01

    Slightly modify and clarify the one-way proxy behavior of internal property dictionaries
    
    This fixes ticket #110

doc/graph_tool.rst
src/graph_tool/__init__.py

commit ae2b9c4f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-10-01

    Fix bug with edge indexes in transitive_closure()
    
    This fixes ticket #111

src/graph/topology/graph_transitive_closure.cc

commit be0a81d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-09-30

    Make initialization of eigenvector() and pagerank() optional

src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_pagerank.hh
src/graph_tool/centrality/__init__.py

commit 4938eb8b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-09-30

    Implement Katz centrality

src/graph/centrality/Makefile.am
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_katz.cc
src/graph/centrality/graph_katz.hh
src/graph_tool/centrality/__init__.py

commit 24a2a628
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-09-30

    Implement HITS centrality (aka hubs and authorities)

src/graph/centrality/Makefile.am
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_hits.cc
src/graph/centrality/graph_hits.hh
src/graph_tool/centrality/__init__.py

commit 7d08675e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-09-30

    Fix bug in eigenvector centrality for weighted graphs

src/graph/centrality/graph_eigenvector.cc

commit 1c796549
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-09-29

    Fix bug in eigenvector(), pagerank() and eigentrust() with undirected graphs

src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_pagerank.hh

commit 08a4a117
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-09-25

    Fix bug when reading floating point values in graphml with comma-using locales

src/boost-workaround/boost/graph/graphml.hpp

commit 1b433d91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-08-03

    Fix double counting of undirected edges in condensation_graph()

src/graph/community/graph_community_network.hh

commit 94c09da9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-08-01

    Fix bug in GraphWrap with edge removal

src/graph/graph_wrap.hh

commit 83087948
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-08-01

    Speed up removal of edges
    
    An attempt no longer is made to reuse edge indexes in a contiguous
    fashion.

src/graph/graph_python_interface.cc

commit edb9e873
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-08-01

    Push is_adjacent() to graph_util.hh

src/graph/generation/graph_generation.hh
src/graph/generation/graph_rewiring.hh
src/graph/graph_util.hh

commit 3721923c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-20

    Improve pickling of very large graphs
    
    The string representation is now compressed, to avoid strings of huge
    length, which makes pickle.dump() bork.

src/graph_tool/__init__.py

commit a35c4622
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-18

    Fix open_file() in cairo_draw.py

src/graph_tool/draw/cairo_draw.py

commit e8208c35
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-18

    Fix pickle error with StringIO

src/graph_tool/__init__.py

commit 8e9cb218
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-18

    Fix clear_vertex() in graph_wrap.hh when there are self-loops in directed graphs

src/graph/graph_wrap.hh

commit 016d8244
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-12

    Fix problem in search functions when 'zero' and 'infinity' values cannot be cleanly converted to property type

src/graph_tool/search/__init__.py

commit 91de09bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-09

    Docstring fix

src/graph_tool/topology/__init__.py

commit 0285f00a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-09

    Check for vector property type in graph_draw()

src/graph_tool/draw/cairo_draw.py

commit 03248ef2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-09

    Fix to the GraphWrap class
    
    Removal of vertices now compiles and works properly.

src/graph/graph_wrap.hh

commit 5dc8d45a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-09

    Optimize validation of edge descriptors.

src/graph/graph_python_interface.hh

commit 6d61075d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-07-09

    Fix bug in find_vertex/edge functions in util modules
    
    This catches up to a previous modification where vertex/edge descriptors
    need to receive a weakref to the graph class.

src/graph/util/graph_search.cc

commit 6170c9a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-29

    Use cPickle instead of pickle in io.py

src/graph_tool/io.py

commit 0810ef0b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-29

    Bump version to 2.2.18dev

configure.ac

commit f29ff272
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-29

    Replace StringIO by BytesIO in io.py
    
    This fixes a problem with pickling python::object property maps.

src/graph_tool/io.py

commit d058ad14
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-19

    Bump version to 2.2.17

configure.ac

commit 0c4cab37
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-22

    Include stoer_wagner_min_cut boost header to keep compatibility with older boost versions

src/boost-workaround/boost/graph/stoer_wagner_min_cut.hpp
src/graph/Makefile.am

commit 3a7b665f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-21

    Include missing file in Makefile.am

src/graph/Makefile.am

commit 0adf28d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-18

    Some doctest fixes

doc/quickstart.rst
src/graph_tool/flow/__init__.py
src/graph_tool/topology/__init__.py

commit 609462cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-18

    Implement fit_view option in cairo_draw()

src/graph_tool/draw/cairo_draw.py

commit 26c87a90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-18

    Fix graph_draw() documentation

src/graph_tool/draw/cairo_draw.py

commit 4fb60b70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-18

    Fix bug when drawing empty graphs.

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit a0f67bbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-18

    Simplify vertex surface drawing and support arbitrary image types

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit 502c383c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-17

    Fix bug with apply_transforms() in gtk_draw.py

src/graph_tool/draw/gtk_draw.py

commit 837fc641
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-17

    Implement arbitrary surface vertex drawing, vertex aspect ratio and edge dashes

src/graph/draw/graph_cairo_draw.cc
src/graph_tool/draw/cairo_draw.py

commit ea0ce086
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-17

    Implement is_DAG()

src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 979e9680
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-17

    Implement sequential_vertex_coloring()

src/graph/topology/Makefile.am
src/graph/topology/graph_sequential_color.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 3a7ae957
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-17

    Implement tsp_tour()

src/boost-workaround/boost/graph/metric_tsp_approx.hpp
src/graph/topology/Makefile.am
src/graph/topology/graph_tsp.cc
src/graph_tool/topology/__init__.py

commit 40bac497
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-04

    Allow setting of property array from value of different size.

src/graph_tool/__init__.py

commit ebc00aa1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-04

    Implement min_st_cut() and min_cut()

doc/mincut-example.xml.gz
src/graph/flow/Makefile.am
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_minimum_cut.cc
src/graph_tool/flow/__init__.py
src/graph_tool/topology/__init__.py

commit 2ca0c3dd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-04

    Implement random_spanning_tree() and label_out_component()

src/graph/topology/Makefile.am
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_random_spanning_tree.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit fa8ca4ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-04

    Implement topology.is_bipartite()

src/graph/topology/Makefile.am
src/graph/topology/graph_bipartite.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit e43e4e8b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-04

    Fix some remaining issues with the clang compiler in MacOS X

src/graph/graph_properties.hh
src/graph/layout/graph_sfdp.hh

commit 70a2ce29
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-06-03

    Fix some compilation issues and warnings with clang

src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/boost-workaround/boost/graph/isomorphism.hpp
src/graph/Makefile.am
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_correlations.hh
src/graph/fast_vector_property_map.hh
src/graph/graph_exceptions.cc
src/graph/graph_exceptions.hh
src/graph/graph_properties.hh
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/histogram.hh
src/graph/layout/graph_sfdp.hh
src/graph_tool/community/__init__.py

commit b2b27965
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-29

    Fix trivial matplotlib import bug

src/graph_tool/draw/cairo_draw.py

commit cba9cf2d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-29

    Fix problem with sfdp_layout() and the clang compiler

src/graph/layout/graph_sfdp.cc
src/graph_tool/draw/__init__.py

commit de6e73a2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-28

    Fix compilation issues with clang++

configure.ac
src/graph/correlations/graph_assortativity.hh
src/graph/draw/graph_cairo_draw.cc
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/gml.hh
src/graph/graph.hh
src/graph/str_repr.hh
src/graph/topology/graph_components.hh
src/graph/topology/graph_transitive_closure.cc

commit 01fd54e2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-27

    Implement compatibility with python 3

src/graph/graph_bind.cc
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/draw/gtk_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit cc1b6517
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-27

    Improve and cleanup python detection

Makefile.am
autogen.sh
configure.ac
m4/ax_boost_python.m4
m4/ax_python.m4
m4/ax_python_devel.m4
m4/ax_python_module.m4

commit f6aa2b20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-27

    Update copyright info

src/graph_tool/__init__.py

commit 4424f6c8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-26

    Fix bug when drawing graphs without edges

src/graph_tool/draw/cairo_draw.py

commit 1c2b3791
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-26

    Bump version to 2.2.17dev

configure.ac

commit a6e03810
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-23

    Bump version to 2.2.16.2

configure.ac

commit 03c7c8cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-23

    Fix bug when drawing coarse-grained graphs interactively

src/graph_tool/draw/gtk_draw.py

commit ac8d5f3c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-23

    Fix bounding-box error with SFDP layout
    
    This fixes some layout glitches with smaller graphs, and also
    improves the convergence speed.

src/graph/layout/graph_sfdp.hh

commit 0816f566
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-21

    Bump version to 2.2.16.1

configure.ac

commit 46d7b30a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-21

    Cosmetic documentation improvements

src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/topology/__init__.py

commit 82b9ccc0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-21

    Improve import warnings in graphviz_draw()

src/graph_tool/draw/graphviz_draw.py

commit 7ea3821e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-21

    Slightly refactor draw module to only optionally depend on GTK+
    
    This implements a graceful fallback in case GTK cannot be loaded, which
    can (currently) happen simply by not having a environment DISPLAY
    variable.

src/graph_tool/Makefile.am
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/gtk_draw.py

commit fbf26825
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-08

    Bump version to 2.2.16

configure.ac

commit fea04db6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-12

    Fix compilation with older GCC versions.

src/graph/community/graph_community_network.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/layout/graph_sfdp.cc

commit 46c480da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-09

    Add missing distribution files

Makefile.am
doc/.static/graph-icon.png
src/graph_tool/Makefile.am

commit 831eb93f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-08

    Add missing sphinxext files

doc/sphinxext/MANIFEST.in
doc/sphinxext/README.txt
doc/sphinxext/setup.py

commit 874d6fee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-08

    Make sure the string representation of floating point values is locale independent

src/graph/str_repr.hh

commit 3f1e0fd9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-08

    Small documentation fixes.

src/graph_tool/generation/__init__.py

commit 7f6d3aee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-07

    Add autogen.sh to tarball

Makefile.am

commit 4453f7e0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-06

    Implement edge_reciprocity()
    
    Ressurect old edge_reciprocity code.

src/graph/topology/Makefile.am
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 71ac2f59
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-06

    Add documentation to tarball

Makefile.am

commit 461ed63c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-06

    Fix bug with run_action()
    
    This install the boost workaround headers together with graph_tool's
    header files.

src/graph/Makefile.am
src/graph_tool/run_action/inline.py

commit 807fc3ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-06

    Fix some compilation issues with GCC 4.7

src/graph/community/graph_community.hh
src/graph/fast_vector_property_map.hh
src/graph/histogram.hh
src/graph/stats/graph_distance_sampled.hh

commit 03d646d3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-03

    Include test for pycairo.h header in configure.ac

configure.ac
src/graph/draw/graph_cairo_draw.cc

commit 6b959e20
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-05-02

    Update copyright information

src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/draw/graph_cairo_draw.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/gml.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_exceptions.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/str_repr.hh
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 3eaf7009
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-30

    Fix loading of libgv in certain environments
    
    This resolves ticket #100

src/graph_tool/draw/graphviz_draw.py

commit 2301bff2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-30

    Documentation fixups

doc/price.py
doc/quickstart.rst
src/graph_tool/search/__init__.py
src/graph_tool/topology/__init__.py

commit 13a0fce4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-29

    Use bash instead of default shell in autogen.sh

autogen.sh

commit 371d3b75
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-21

    Fix initial placement of arf_layout()

src/graph_tool/draw/__init__.py

commit cc6a4ca2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-15

    Enable generation of self_loops in condensation_graph()

src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph_tool/community/__init__.py

commit 07911562
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-15

    Allow the disabling of probability caching in random_rewire()
    
    This makes the code more efficient if the input parameter combinations
    are much larger than the graph itself.

src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit 7b2aa166
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-13

    Implement vertex intersection in graph_union()

src/graph/generation/graph_generation.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph_tool/generation/__init__.py

commit ee4d43cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Improve automatic detection of scipy/numpy include paths

configure.ac

commit cb0e04d1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Improve autoconf checking of boost_python

m4/ax_boost_python.m4

commit e35f6b0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Avoid unecessary namespace pollution from numpy

src/graph_tool/draw/graphviz_draw.py

commit 1845dd07
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Improve label_self_loops()

src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph_tool/stats/__init__.py

commit f2bdc674
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Improve label_parallel_edges()

src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph_tool/stats/__init__.py

commit fa2b7b99
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Simplify internal filtering composition rules for GraphView

src/graph_tool/__init__.py

commit 479daa91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Make PropertyMap instancess callable
    
    This allows them to be modified and passed forward in one expression.

src/graph_tool/__init__.py

commit 88cf9f15
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Implement edge weight parameter in condensation_graph()

src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph_tool/community/__init__.py

commit 33b91262
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Fix action_wrap bug for larger number of parameters

src/graph/graph_filtering.hh

commit 88ab00bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Trivial whitespace fixups

src/graph/generation/graph_rewiring.hh
src/graph/graph.hh
src/graph/layout/graph_arf.cc
src/graph/topology/graph_similarity.hh

commit 48f1b2e9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Move random_permutation_interator to graph_util.hh

src/graph/generation/graph_rewiring.hh
src/graph/graph_util.hh

commit 1fd8cd95
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-29

    Fix sfdp_layout() implementation for unconnected graphs

src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 11e2b682
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-21

    Documentation update, following new graph_draw() function

doc/Makefile
doc/community.xml
doc/conf.py
doc/draw.rst
doc/gt_theme/static/gt_style.css
doc/price.py
doc/pyenv.py
doc/quickstart.rst
doc/sphinxext/plot_directive.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graphviz_draw.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/topology/__init__.py

commit 7ae9a870
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Implement cairo_draw()

configure.ac
src/graph/Makefile.am
src/graph/draw/Makefile.am
src/graph/draw/graph_cairo_draw.cc
src/graph_tool/Makefile.am
src/graph_tool/draw/__init__.py
src/graph_tool/draw/cairo_draw.py
src/graph_tool/draw/graph-tool-logo.svg
src/graph_tool/draw/graphviz_draw.py

commit fc8437b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Implement sfdp_layout

src/graph/layout/Makefile.am
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_sfdp.cc
src/graph/layout/graph_sfdp.hh
src/graph_tool/draw/__init__.py

commit 6749a383
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Implement topology.max_independent_vertex_set()

src/graph/topology/Makefile.am
src/graph/topology/graph_maximal_vertex_set.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 335cd9b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Implement topology.max_cardinality_matching()

src/graph/topology/Makefile.am
src/graph/topology/graph_random_matching.cc
src/graph/topology/graph_topology.cc
src/graph_tool/flow/__init__.py
src/graph_tool/topology/__init__.py

commit 76c86207
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Implement pseudo_diameter()

src/graph/topology/Makefile.am
src/graph/topology/graph_diameter.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 4ffe8be3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-15

    Fix bug in subgraph_isomorphism()
    
    This fixes a bug where some matches were skipped, due to a spurious,
    abrupt termination of the search.
    
    This also changes the default argument to 'random=False'.

src/graph/topology/graph_subgraph_isomorphism.hh
src/graph_tool/topology/__init__.py

commit cc140652
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-11

    Slight improvement of vertex property re-indexing
    
    This avoids copying property values when not necessary, if the index
    remains the same after purging

src/graph/graph_properties.cc

commit 9e612575
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-11

    Fix edge_difference() compilation in some GCC versions

src/graph/graph_properties.cc

commit 67a10cd3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Implement edge_difference()

src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit 46454b3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-11

    Implement reindexing of property maps after vertex purge
    
    After the removal of filtered vertices via Graph.purge_vertices(), the
    values of known property maps are now kept consistent with the
    unmodified graph.

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.cc
src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit 0595e4f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Implement infect_vertex_property()

src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph_tool/__init__.py

commit d7e364cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-10

    Fix bug with non-integer weights in modularity()

src/graph/community/graph_community.hh

commit e13b4d44
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-08

    Fix computation of modularity with edge weights
    
    This fixes ticket #92.

src/graph/community/graph_community.hh
src/graph/graph_util.hh

commit 0e8e05fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-08

    Fix bug in subgraph_isomorphism() with filtered graphs

src/graph/topology/graph_subgraph_isomorphism.hh

commit 7cfc2951
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-06

    Fix compilation problem with boost 1.49

src/boost-workaround/boost/graph/copy_alt.hpp
src/graph/Makefile.am
src/graph/clustering/graph_motifs.hh

commit 2e322f85
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-04-03

    Allow arbitrary non-scalar types for distance values in search functions
    
    This includes user-defined types, as well as vector types and strings.
    This affects dijkstra_search(), astar_search() and bellman_ford_search().

src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_dijkstra.cc
src/graph_tool/search/__init__.py

commit a1a6748f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-31

    Fix edge descriptor invalidation check
    
    This fixes the edge invalidation check, when either the source of the
    target vertex is removed.

src/graph/graph_python_interface.hh

commit 2e5abc00
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-21

    Fix bug in Graph.remove_edge()
    
    This fixes ticket #97.

src/graph_tool/__init__.py

commit 4026fb2a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-03-11

    Implement get_graph() method in Edge and Vertex classes
    
    This also makes all Edge classes inherit from the same base class of the
    same name.
    
    This fixes tickets #94 and #95

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph_tool/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/util/__init__.py

commit 70b50865
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-01-11

    Fix include file issue in gml.hh
    
    This fixes ticket #85.

src/graph/gml.hh

commit 2dbe0ce1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-01-11

    Disable some compilation warnings due to unused variables

src/graph/util/graph_search.hh

commit a2bb7ff8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-01-11

    Fix compatibility with boost 1.48
    
    This works around a regression introduced in boost 1.48, relating to the
    edge descriptors of reversed graphs.
    
    See: https://svn.boost.org/trac/boost/ticket/6391

src/boost-workaround/boost/graph/isomorphism.hpp
src/boost-workaround/boost/graph/reverse_graph_alt.hpp
src/graph/graph_filtering.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_util.hh
src/graph/topology/graph_subgraph_isomorphism.cc

commit 08ebe246
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-01-06

    Implement the Graph.own_property() method.

src/graph_tool/__init__.py

commit e710a285
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-01-06

    Fix bug with setting the PropertyMap.fa attribute
    
    This fixes a bug where the PropertyMap.fa attribute would not be set if
    filtering is disabled.

src/graph_tool/__init__.py

commit af7b47bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Implement more informative __repr__ function for vector types

src/graph_tool/__init__.py

commit 8f91834e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Slight improvements to DynamicMapWrap

src/graph/graph_properties.hh

commit 311fc510
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Whitespace fixup

src/boost-workaround/boost/graph/graphml.hpp
src/graph/layout/graph_arf.cc

commit a5bcb6b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-31

    Copyright header update

src/graph/topology/graph_distance.cc

commit 53788387
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2012-01-02

    Fix runtime error eigenvector() when no weights are used
    
    This fixes ticket #84

src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph_tool/centrality/__init__.py

commit 77ef683f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-29

    Remove cairomm test
    
    This also belongs to an upcoming commit.

configure.ac

commit c1ed1839
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-29

    Fall back to ctypes if the DLFCN or dl modules are not available

src/graph_tool/dl_import.py
src/graph_tool/run_action/inline.py

commit d874dec6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-29

    Fix configure.ac
    
    This modification belongs to an upcoming commit.

configure.ac

commit 90bace40
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-28

    Workaround for apple's gcc compilation error

src/graph/gml.hh

commit 8148224c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-12-21

    CGAL must be linked with gmp as well

configure.ac

commit 846dcdab
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-27

    ARF layout: position update must be inside a #pragma critical block

src/graph/layout/graph_arf.hh

commit e676dfc3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-27

    Fix typo bug in random_graph()

src/graph_tool/generation/__init__.py

commit b2e10d10
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-18

    graph generation/rewiring: slight improvements of blockmodel generation
    
    This changes stlightly the information passed to the auxiliary functions
    provided by the user, so that more arbitrary structures can be
    constructed more easily.

src/graph/generation/graph_rewiring.cc
src/graph_tool/generation/__init__.py

commit 22345394
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-15

    Fix typo bug in random_graph() when parallel_edges and self_loops equals True

src/graph_tool/generation/__init__.py

commit 231ec1a2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-05

    Include missing header in gml.hh

src/graph/gml.hh

commit bb5fb6d2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-05

    Trivial documentation style improvement

doc/conf.py
doc/gt_theme/static/gt_style.css

commit b15bbe0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-11-05

    Reflect directionality of the underlying graph for condensation_graph()

src/graph_tool/community/__init__.py

commit 494f9a64
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-10-12

    Fix documentation typo

doc/quickstart.rst

commit bcf54441
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-10-12

    Fix typo bug in random_graph()

src/graph_tool/generation/__init__.py

commit 7d08bc42
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-10-12

    Return community property in condensation_graph()
    
    The condensation_graph() function now returns a property map which
    contains the community values themselves for each vertex.

src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph_tool/community/__init__.py

commit 0945c5af
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-10-12

    Implement graph IO in gml format
    
    This includes a spirit parser for the gml syntax, and a graph writer.
    
    Additionaly, the general graph io code also been cleaned up.

doc/quickstart.rst
src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/graphml.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/graph/Makefile.am
src/graph/gml.hh
src/graph/graph_io.cc
src/graph/graphml.cpp
src/graph/read_graphviz_new.cpp
src/graph_tool/__init__.py

commit 15f1ba1b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-10-11

    graphml: load vertex and edge ids as string properties, if not canonical

src/boost-workaround/boost/graph/graphml.hpp
src/graph/graph_io.cc
src/graph/graphml.cpp

commit cf3440f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-26

    Implement parsing of HTML-like labels in graph_draw()

src/graph_tool/draw/__init__.py

commit 211f6788
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-22

    Include `value_type` parameter in PropertyMap.copy()

src/graph_tool/__init__.py

commit 505e795f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-22

    Use highest protocol when pickling internal property maps
    
    This fixes ticket:73

src/graph_tool/io.py

commit 510c25b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-14

    Implement PropertyMap.copy() method

src/graph_tool/__init__.py

commit 201bd5fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-14

    Fix compilation issue with older Ubuntu versions

src/graph/generation/graph_rewiring.hh

commit e88d4266
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-04

    doc Makefile fix: Do not modify pdf files in "build" directory

doc/Makefile

commit e3fe8159
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-04

    Fix small doc typo

src/graph_tool/topology/__init__.py

commit bc912f35
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-04

    Bump version to 2.2.16dev

configure.ac

commit b435362a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-31

    Bump version to 2.2.15

configure.ac

commit f231d035
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-02

    Generate pdf images in the documentation by default
    
    Images are now converted to png a posteriori for html output, but are
    used as pdf for latex.

doc/.templates/layout.html
doc/Makefile
doc/conf.py
doc/price.py
doc/quickstart.rst
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/search/__init__.py
src/graph_tool/topology/__init__.py

commit 44917c1c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-02

    Workaround for gcc + boost bug
    
    This fixes a compile error with gcc 4.4 and boost in debian squeeze.

src/graph/graph_properties_copy.cc

commit 990b4739
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-09-02

    Fix "correlated" rewiring mode
    
    This fixes a bug in the "correlated" mode in random_rewire().

src/graph/generation/graph_rewiring.hh
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit bad74126
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-25

    Generalize "probabilistic" random graph generation/rewiring to a blockmodel
    
    This implements a general "blockmodel" generation / rewiring algorithm,
    using Gibbs acceptence / rejection sampling (a.k.a Metropolis-Hastings).
    
    This also implements some optimizations in the rewiring code, which
    makes it more efficient on filtered graphs.

src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 8240714e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-21

    Several improvements to random_rewire() / random_graph()
    
    This introduces several simplifications and corrections to the graph
    rewire algorithm, to guarantee unbiased sampling.
    
    Now a move is outright rejected if it produces a
    self-loop/parallel-edge, instead of retried. This also adds a
    "non-sweep" mode, where edges are rewired randomly, possibly with
    repetition.
    
    The edge moves are now simplified to the target of the edges only,
    since swaping sources is redundant.
    
    The number of iterations can now be explicitly modified, so it is not
    necessary to call the function more than once, and it is emphasized in
    the documentation that only after sufficiently many iterations can the
    graph be guaranteed to be fully mixed.

src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/sampler.hh
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit aeaadabc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-24

    Implement the similarity() function

src/graph/topology/Makefile.am
src/graph/topology/graph_similarity.cc
src/graph/topology/graph_similarity.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 95470ff4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-24

    Implement eigenvector centrality

src/graph/centrality/Makefile.am
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigenvector.cc
src/graph/centrality/graph_eigenvector.hh
src/graph_tool/centrality/__init__.py

commit ef9ad955
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-15

    Trivial documentation fix

src/graph_tool/__init__.py

commit d5ab42b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-15

    Fix behaviour of new vertices or edges in filtered graphs
    
    Newly added vertices or edges in filtered graphs now automatically
    appear in them.

src/graph_tool/__init__.py

commit 49f2ec3b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-14

    Diverse documentation improvements
    
    This better organizes the documentation of the Graph class and provides
    other small fixes.

doc/conf.py
doc/graph_tool.rst
doc/gt_theme/static/gt_style.css
doc/quickstart.rst
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py

commit f96eec9e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-13

    Some improvements of graph_draw()
    
    This allows pinning of individual vertices via the `pin` paramenter, as
    well as string-valued color property maps, and some other minor
    improvements.

doc/conf.py
src/graph_tool/draw/__init__.py

commit 325878f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-12

    Cosmetic documentation changes

doc/gt_theme/static/flasky.css
doc/gt_theme/static/gt_style.css
doc/quickstart.rst

commit f075afdf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-12

    Small cleanups in graph_io.cc

src/graph/Makefile.am
src/graph/graph_io.cc
src/graph/str_repr.hh

commit 6c87b9b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-12

    Fix random_layout() for filtered graphs

src/graph_tool/draw/__init__.py

commit 0c002fae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-08-12

    Implement improved array access to property maps
    
    This implements access to filtered graphs either with boolean-indexed
    array or masked arrays, through the 'fa' and 'ma' attributes,
    respectively.

src/graph_tool/__init__.py

commit 36e6fe57
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-07-14

    Allow for community labels to be of arbitrary types in modularity()

src/graph/community/graph_community.cc
src/graph/community/graph_community.hh

commit 8123d30c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-07-14

    Trivial documentation fix

src/graph_tool/draw/__init__.py

commit ab2eff6b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-07-14

    Bump version to 2.2.15dev

configure.ac

commit 39b848dc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-07-09

    Bump version to 2.2.14

configure.ac

commit d6a70b7e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-07-09

    Remove non-existing fruchterman-reingold workaround from Makefile.am

src/graph/Makefile.am

commit 04a19cea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-30

    Fix bug in modularity

src/graph_tool/community/__init__.py

commit 0cacbb0a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-30

    Remove remaining useless C++ signature from html documentation

doc/gt_theme/static/gt_style.css

commit 1b4cd407
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-30

    Workaround for sphinx bug
    
    For some reason sphinx looks for a graph_tool module inside graph_tool.
    This commit defines such a thing.

src/graph_tool/__init__.py

commit 6be54cc4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-28

    Add personalization and edge weights to PageRank code

src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph_tool/centrality/__init__.py

commit 066411ac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-28

    Change community.xml example to an undirected graph

doc/community.xml

commit 19d972a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-28

    Use GraphView in community structure code to obtain undirected graphhs

src/graph/community/graph_community.cc
src/graph_tool/community/__init__.py

commit 35c18b6a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-21

    Fix label_largest_component() behavior with filtered graphs
    
    This fixes a bug where filtered vertices would be incorrectly marked, if
    the largest component index happend to be zero.

src/graph_tool/topology/__init__.py

commit 3a8a60e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-16

    Some trivial, almost cosmetical fixes

src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py

commit 4a61be54
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-14

    Provide fallback case in graph_draw() function when open_memstream is not available

src/graph_tool/draw/__init__.py

commit 26cce6a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-13

    Fix bug in GraphView with filtered vertices
    
    This fixes a bug where the filters where not correctly copied from the
    base graph.

src/graph/graph_copy.cc
src/graph_tool/__init__.py

commit 5ae329f1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-13

    Small doc and default argument modifications in draw module

src/graph_tool/draw/__init__.py

commit 582d400c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-13

    Implement Fruchterman-Reingold layout

src/boost-workaround/boost/graph/fruchterman_reingold.hpp
src/graph/graph_properties.hh
src/graph/layout/Makefile.am
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_fruchterman_reingold.cc
src/graph_tool/draw/__init__.py

commit aa38e9f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-11

    Ditch graphviz python module in favor of libgvc + ctypes
    
    By using directly the C bindings to graphviz, we are able to return the
    drawed graph as a string buffer in whatever format, which was not
    possible with the SWIGified python interface.
    
    Returning the drawed graph as a buffer is useful in doing animations,
    among other things.

src/graph_tool/draw/__init__.py

commit 7bedab86
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-05

    Fix correct overloading of <= operator in find_vertex/edge() functions

src/graph/util/graph_search.hh

commit 6aa4cfb9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-03

    Improve conversion of compatible types in search functions

src/graph_tool/__init__.py
src/graph_tool/util/__init__.py

commit 2a4f9320
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-02

    Fix lexicographic ordering of strings and sequences in search functions

src/graph/util/graph_search.hh
src/graph_tool/util/__init__.py

commit 825c22f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-01

    Fix some bugs in configure.ac relating to the enable/disable flags

configure.ac

commit 5a424b4c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-06-01

    Remove annoying GCC warnings when compiling without openmp

configure.ac

commit 51195c11
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-31

    Fix copy_property() to allow copying between non-identical graphs
    
    Now properties can be copied from vertices which are not identical
    (e.g. from unfiltered to filtered graphs, etc). This fixes a problem
    with graph copying and pruning, where the properties were not correclty
    copied.

src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_copy.cc
src/graph/graph_exceptions.hh
src/graph/graph_properties.hh
src/graph/graph_properties_copy.cc
src/graph/graph_python_interface.hh
src/graph_tool/__init__.py

commit 679bfe41
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-31

    Implement 'set' operation in 'a' properties of vector property values
    
    Now, statements like:
    
       prop[v].a = foo
    
    are perfectly valid (if prop[v] is a vector type).

src/graph_tool/__init__.py

commit df3471a1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-27

    Simple workaround for compilation under MacOS
    
    This works around a compilation bug in Apple GCC 4.2 + Macports.

src/graph/graph_bind.cc

commit 69b7afbd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-10

    Fix random_layout() bug
    
    This fixes an issue with group/ungroup_vector_property() and
    random_layout().

src/graph_tool/draw/__init__.py

commit 1564d81d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-10

    Fix some group/ungroup_vector_property() issues
    
    This also includes proper test strings.

src/graph_tool/__init__.py

commit c11b6af7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-05

    Improve price_network() seeding semantics
    
    Now, if 'm' is larger than the seed graph, it is set to the size of the
    seed graph, and is increased progressively until it matches the desired
    value. This removes the need to start with a random seed graph of the
    appropriate size.
    
    This also includes modifications which make the code more robust
    against parameter choices which don't make much sense, e.g. lead to
    negative probabilites.

src/graph/generation/graph_price.hh
src/graph_tool/generation/__init__.py

commit 197fa68c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-03

    Properly norm pagerank() values
    
    This makes the calculation coherent with the definition given in the
    documentation.

src/graph/centrality/graph_pagerank.hh
src/graph_tool/centrality/__init__.py

commit 4dedb7f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-05-03

    Bump version to 2.2.14dev

configure.ac

commit b651ebad
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-27

    Bump version to 2.2.13

configure.ac

commit 649b6c9a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-27

    Remove some boost workaround files
    
    This removes reverse_graph.hpp, reverse_graph.hpp and copy.hpp, and
    introduces some modifications in graph_adaptor.hh. This modification
    fixes compilation problems across different boost versions.

src/boost-workaround/boost/graph/copy.hpp
src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/reverse_graph.hpp
src/graph/Makefile.am
src/graph/graph_adaptor.hh
src/graph/topology/graph_minimum_spanning_tree.cc

commit 4c5d479f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-27

    Fix bug in graph_draw() documentation

src/graph_tool/draw/__init__.py

commit fc1be898
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-21

    Bump version to 2.2.12

configure.ac

commit 631a574c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-21

    Fix example in graph_draw() docstring

src/graph_tool/draw/__init__.py

commit dc9d0a46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-21

    Add label_largest_component() to documentation summary

src/graph_tool/topology/__init__.py

commit 0e1083fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-20

    Fix dependence on DLFCN on buggy python installations
    
    I'm looking at you, macports.

src/graph_tool/run_action/inline.py

commit 42d0f5fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-19

    Avoid strict requirement on matplotlib
    
    This removes a strict requirement on matplotlib in the "draw" module.

src/graph_tool/draw/__init__.py

commit 12f0069b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-19

    Do not run ./configure automatically in autogen.sh

autogen.sh

commit 94f78344
Author: sebastian.weber@frias.uni-freiburg.de <sebastian.weber@frias.uni-freiburg.de>
Date:   2011-04-15

    fixed c_err reduction with openmp

src/graph/clustering/graph_clustering.hh

commit 6b0e1705
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-15

    Implement label_largest_component() and return label histogram in label_components()

src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph_tool/topology/__init__.py

commit 5cbf8593
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-14

    Improve documentation of Graph class
    
    This moves the documentation out of the constructor, and into the class
    definition.

src/graph_tool/__init__.py

commit ec544ea7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-14

    Fix bug in histogram with bin list of size 2
    
    This also changes the semantics of of bin list of size 2, and also
    simplifies the histogram code slightly.

src/graph/histogram.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph_tool/correlations/__init__.py
src/graph_tool/stats/__init__.py

commit b311b048
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-14

    Implement pruning of graph filters in graph instantiation
    
    This allows easy creation of unfiltered copies of filtered graphs.

src/graph/graph_copy.cc
src/graph_tool/__init__.py

commit e26e7516
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-11

    Work around strange python installations without DLFCN module

src/graph_tool/dl_import.py

commit 52508b9f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-11

    Fix parallel bug in get_global_clustering()

src/graph/clustering/graph_clustering.hh

commit 8af4ae36
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-04-11

    Workaround for bug in macports python/gcc

src/graph/graph_io.cc

commit 15b6e9c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-24

    Fix documentation typo

doc/quickstart.rst

commit 615ad7be
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-23

    Fix PropertyMap ownership problem with GraphView
    
    Now if a GraphView object is deleted, any property map created for it
    reverts its ownership to the base Graph object. This eliminates the
    problem of property maps created with transient GraphView objects.

src/graph_tool/__init__.py

commit b25014f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-23

    Fix compilation error with boost 1.46

src/boost-workaround/boost/graph/reverse_graph.hpp

commit 70edb974
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-19

    Change default vertex size in graph_draw()

src/graph_tool/draw/__init__.py

commit c4338767
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-19

    Fix autoconf detection of python
    
    This also fully honors the PYTHON_VERSION environment variable.

configure.ac
m4/ac_python_module.m4
m4/ax_python.m4

commit 19984ec5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-19

    Bump version to 2.2.12dev

configure.ac

commit 5d93cf96
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-07

    Bump version to 2.2.11.

configure.ac

commit c40c24bd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-07

    Improve quick start guide and include documentation for GraphView

doc/price.py
doc/quickstart.rst

commit d9f7b784
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-07

    Trivial documentation fixes

src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py

commit b73b71e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-07

    Remove some 'undirected' parameters
    
    This removes some 'undirected' parameters, in favour of graph views.

src/graph_tool/clustering/__init__.py

commit 086c6b21
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-07

    Change default draw color/shape
    
    The default vertex shape is now a circle (not an ellipse), and the
    default vertex/edge colors correspond to the Tango palette.

src/graph_tool/draw/__init__.py

commit b03e09f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-07

    Trivial indentation fix

src/graph/clustering/graph_extended_clustering.cc

commit 0b09a09b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-06

    Fix remove labelled edges
    
    This correctly maintains the edge index metadata.

src/graph/stats/graph_parallel.cc

commit ceabe654
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-06

    Fix graph copy
    
    This fixes a bug where the edge index metadata was not properly copied.

src/graph/graph_copy.cc

commit 641d0024
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-03-02

    Fix removal of 'core' submodule
    
    This fixes a leftover bug from the removal of the 'core' submodule.

src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 011d7b65
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-10

    Update copyright year

doc/conf.py
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph/shared_map.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/search/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit d69231e6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-10

    Change doc default font to Droid Serif

doc/gt_theme/static/flasky.css

commit c145b932
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-09

    Documentation typo correction

src/graph_tool/centrality/__init__.py

commit 70e68a19
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-04

    Trivial documentation fix

src/graph_tool/centrality/__init__.py

commit 31062410
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-04

    Change GraphView.get_parent() to GraphView.base
    
    Now GraphView.base points to the underlying, unfiltered, base graph,
    even if "g" is another GraphView instance.

src/graph_tool/__init__.py

commit 6e3cc364
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-02

    Documentation improvements

doc/conf.py
doc/graph_tool.rst
src/graph_tool/__init__.py

commit 59bdb757
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-02

    Merge core.py into __init__.py
    
    This makes sphinx's autodoc slightly happier.

src/graph_tool/Makefile.am
src/graph_tool/__init__.py
src/graph_tool/core.py

commit 5e975444
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-02

    Cosmetic documentation changes

doc/graph_tool.rst
doc/numpydoc.py
src/graph_tool/core.py

commit 72bd25b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-02

    Implement GraphView class
    
    This implements a GraphView class which allows for convenient,
    independent filtering graphs.

src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_util.hh
src/graph_tool/__init__.py
src/graph_tool/core.py

commit 15927c58
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-02-02

    Bump version to 2.2.11dev

configure.ac

commit b86665e5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-29

    Bump version to 2.2.10

configure.ac

commit 47aebb54
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-29

    Simple documentation fixes.

doc/quickstart.rst
src/graph_tool/topology/__init__.py

commit 931abc91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-25

    Improvements on the documentation layout
    
    Use Palatino as default font, and remove underline from links.

doc/gt_theme/static/flasky.css

commit 5e2a506e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-25

    Small documentation fix

src/graph_tool/centrality/__init__.py

commit 7b7ece48
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-25

    Fix simple compatilibity bug with older versions of numpy (~1.3)

src/graph_tool/core.py

commit 0982ad40
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-18

    Include workaround for push_relabel_max_flow(), wich disables some assert() calls

src/boost-workaround/boost/graph/push_relabel_max_flow.hpp
src/graph/Makefile.am

commit af0cad81
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-18

    Improve documentation for topology module

src/graph_tool/topology/__init__.py

commit db308330
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-18

    Improve documentation for flow module

src/graph_tool/flow/__init__.py

commit 72a6f2b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-18

    Fix graph augmentation for boykov_kolmogorov_max_flow()

src/graph/flow/graph_augment.hh
src/graph/flow/graph_kolmogorov.cc

commit 45ba6c96
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-16

    Assorted simple fixes in topology module

src/graph_tool/topology/__init__.py

commit 45b056f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-14

    Fix m4 scripts to properly detect python 2.7

m4/ax_python.m4

commit 2182538b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2011-01-14

    Add check for directed graphs in flow module, and rename kolmogorov_max_flow
    
    This adds a check for directed graphs in most functions of the flow
    module, and renames the kolmogorov_max_flow to
    koybov_kolmogorov_max_flow.
    
    This also optimizes the graph augmentation in
    koybov_kolmogorov_max_flow, where reversed edges are detected and used
    if they exist.

src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph_tool/flow/__init__.py

commit 8af15810
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-26

    Correct documentation typos

src/graph_tool/centrality/__init__.py
src/graph_tool/community/__init__.py

commit 42ff7e36
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-24

    Bump version to 2.2.10dev

configure.ac

commit 50effde9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-21

    Bump version to 2.2.9

configure.ac

commit fe000a33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-22

    Fix compilation problem with boost 1.44

src/graph/graph_io.cc

commit c16de313
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-21

    Remove spurious file from and add missing file to Makefile.am

src/graph/Makefile.am
src/graph/search/Makefile.am

commit b046908b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-21

    Add missing Makefile to configure.ac

configure.ac

commit cad9691d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-21

    Documentation improvements
    
    Added more DOI links to references, and other cosmetic changes.

doc/conf.py
doc/graph_tool.rst
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/topology/__init__.py

commit d2e8ce3a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-20

    Implement Graph.edge method

src/graph_tool/core.py

commit 9e353964
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-20

    Modify Graph.vertex() default semantics

src/graph_tool/core.py

commit 037cd9ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-15

    Fix compilation issues with boost 1.45
    
    This also keeps compatibility with earlier versions of boost.

src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/properties.hpp
src/graph/clustering/graph_motifs.hh
src/graph/graph_adaptor.hh
src/graph/graph_io.cc

commit 7bbef00e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-10

    Fix compilation error
    
    This fixes ticket 61:
    
    http://projects.skewed.de/graph-tool/ticket/61

src/graph/generation/graph_price.hh

commit 2e5803d2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-05

    Small doc changes.

doc/conf.py
doc/quickstart.rst
src/graph_tool/flow/__init__.py
src/graph_tool/topology/__init__.py

commit 00aa9c5d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Implement search module
    
    This module contains several search algorithms and a visitor interface.

doc/graph_tool.rst
doc/search_example.xml
doc/search_module.rst
src/graph/Makefile.am
src/graph/search/Makefile.am
src/graph/search/graph_astar.cc
src/graph/search/graph_astar.hh
src/graph/search/graph_astar_implicit.cc
src/graph/search/graph_bellman_ford.cc
src/graph/search/graph_bfs.cc
src/graph/search/graph_dfs.cc
src/graph/search/graph_dijkstra.cc
src/graph/search/graph_search_bind.cc
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/search/__init__.py

commit 38b991e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-04

    Add modification permissions to Graph class

src/graph_tool/core.py

commit 49bb2c8e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-04

    Fix @_wrap decorator

src/graph_tool/decorators.py

commit 2c35af58
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Add missing type aliases

doc/quickstart.rst
src/graph_tool/core.py

commit 5bfd6485
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Make network example downloadable.

src/graph_tool/community/__init__.py

commit 897f454f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Improve behaviour of property map type conversion
    
    Now an explicit conversion to a compatible python type is attempted if
    the value being set in a property map cannot be converted directly to a
    C++ type.
    
    This also fixes a bug with vector-valued property maps.

src/graph/graph_python_interface.hh
src/graph_tool/core.py

commit b3dd46c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Modify GraphWrap semantics
    
    Now, whenever GraphWrap is being used, the property maps are always
    in "checked" mode.

src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_wrap.hh

commit b50fc2fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Use extlinks for easy DOI references

doc/conf.py

commit 2831d443
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-12-03

    Documentation CSS improvements

doc/gt_theme/static/flasky.css

commit 7c3a1e99
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-23

    Implement PropertyArray to encapsulate property map data
    
    The arrays returned by PropertyMap.get_array() are now PropertyArray
    instances, which keep track of the PropertyMap data, and are able to
    detect when it changes, and raise a ValueError exception. As such, it
    becomes impossible to read or write to non-allocated memory if an array
    becomes invalid.

src/graph_tool/__init__.py
src/graph_tool/core.py

commit f8093386
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-21

    Fix innocuous compilation warning

src/graph/generation/graph_geometric.hh

commit 46956e09
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-18

    Fix detection of MacOS X in configure.ac

configure.ac

commit ddd2c98f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-18

    Small clarification in include order

src/graph/graph_bind.cc

commit d11c8dce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-18

    Small documentation fixes

doc/.templates/layout.html
doc/Makefile
doc/conf.py

commit 86ed2c2b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-18

    Small fixes to allow compilation in MacOS X

autogen.sh
configure.ac
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_price.hh

commit cee78307
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-18

    Fix typo in configure.ac

configure.ac

commit 56062a7a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-18

    Bump version to 2.2.9dev

configure.ac

commit 736d400b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-13

    Bump version to 2.2.8

configure.ac

commit c9e4bfe8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-13

    Fix compilation warnings

src/boost-workaround/boost/graph/isomorphism.hpp
src/graph/generation/graph_lattice.hh
src/graph/stats/graph_average.hh
src/graph/util/graph_search.hh

commit 6758e857
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-13

    Change domain to skewed.de

AUTHORS
ChangeLog
NEWS
README
TODO
configure.ac
doc/conf.py
src/boost-workaround/boost/graph/graphml.hpp
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/graphml.cpp
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/shared_map.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_distance.cc
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_support.hh
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 5dc74204
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-11-13

    Fix periodic boundary conditions in geometric_graph()

src/graph/generation/graph_geometric.hh

commit 7a0fef43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-10

    Small doc fixes

src/graph_tool/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/run_action/inline.py

commit b67503a8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-10

    Change default layout of graph_draw() to "sfdp" for large graphs

src/graph_tool/draw/__init__.py

commit 5697be4a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-10

    Add price and barabási-albert network generation

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_price.cc
src/graph/generation/graph_price.hh
src/graph_tool/generation/__init__.py

commit 912d9b24
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-10

    Fix compilation problem with older GCC versions

src/graph/generation/graph_geometric.hh

commit 6b3e6269
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-04

    Add lattice and geometric network generation

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_geometric.cc
src/graph/generation/graph_geometric.hh
src/graph/generation/graph_lattice.cc
src/graph/generation/graph_lattice.hh
src/graph_tool/generation/__init__.py

commit 0e1ad171
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-04

    Remove redundant parameter for group/ungroup_vector_property

src/graph_tool/centrality/__init__.py
src/graph_tool/core.py
src/graph_tool/draw/__init__.py

commit cab630fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-04

    Small documentation fixes

doc/quickstart.rst
src/graph/graph_python_interface.cc
src/graph_tool/__init__.py
src/graph_tool/core.py

commit 8f0b827d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-10-04

    Replace jsmath with MathJax and update sphinxext

doc/conf.py
doc/mathjax.py
doc/sphinxext/__init__.py
doc/sphinxext/autosummary.py
doc/sphinxext/autosummary_generate.py
doc/sphinxext/docscrape.py
doc/sphinxext/docscrape_sphinx.py
doc/sphinxext/numpydoc.py
doc/sphinxext/only_directives.py
doc/sphinxext/plot_directive.py
doc/sphinxext/tests/test_docscrape.py
doc/sphinxext/traitsdoc.py

commit 56152176
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-09-28

    Fix bug in shared histogram
    
    This fixes a bug where histograms constructed in parallel would
    sometimes fail to count some samples.

src/graph/histogram.hh

commit f60d6575
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-09-26

    Split correlation/histogram code in different files

src/graph/correlations/Makefile.am
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations.hh
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_corr_hist.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc

commit 6a810527
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-08-09

    Link libraries "as needed"

configure.ac

commit faa125d3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-08-09

    Bump version to 2.2.8dev

configure.ac

commit 2f017e36
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-08-09

    Specify std namespace for type_info
    
    This avoid a namespace clash when using run_action.inline().

src/graph/graph_filtering.hh
src/graph/graph_properties.hh

commit 60acdcfa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-30

    Include Graph.reindex_edges() and Graph.max_edge_index
    
    These functions/properties provide more information and control about
    edge indexing, which might be useful.

src/graph/graph_bind.cc
src/graph/graph_filtering.cc
src/graph_tool/core.py

commit 2baba488
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-28

    Fix bug in PropertyMap.get_array() for edge properties
    
    The reserved size for the array was set to g.num_edges(), but it should
    be set to the maximum edge index + 1, since some edges might have been
    deleted.

src/graph/graph_bind.cc
src/graph_tool/core.py

commit ad9dbc5e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-24

    Include support for older versions of GCC (>=4.2)
    
    This enables support for older versions of GCC (>=4.2), by falling back
    to the boost tr1 implementation when the GCC version is less than 4.4.

configure.ac
src/graph/centrality/graph_trust_transitivity.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.hh
src/graph/generation/graph_generation.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.hh
src/graph/generation/sampler.hh
src/graph/graph.hh
src/graph/graph_io.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/layout/graph_arf.hh
src/graph/shared_map.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_parallel.hh
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/util/graph_search.hh

commit b1b71405
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-14

    Dump dl module in favor of ctypes
    
    The module dl has been deprecated, and has been replaced by ctypes. This
    also fixes a problem where the dlopen() flags have different numbers in
    different architectures.

src/graph_tool/dl_import.py
src/graph_tool/run_action/inline.py

commit c68ed7e8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-08

    Bump version to 2.2.7

configure.ac

commit c59aa20b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-13

    Small documentations and comment fixes

src/graph_tool/centrality/__init__.py
src/graph_tool/core.py
src/graph_tool/dl_import.py
src/graph_tool/spectral/__init__.py

commit 31791c81
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-13

    Change histogram binning semantics
    
    Now the meaning of the bin edges given to the several histogram
    functions are the same as in numpy/scipy. This means that the last bin
    edge represents an upper bound on the last bin.

doc/conf.py
doc/price.py
src/graph/correlations/graph_correlations.hh
src/graph/histogram.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py

commit e75cf856
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-10

    Fix segfault bug in motifs()
    
    This fixes a bug in the motifs() code which generates a segfault for
    certain subgraph signatures. This also fixes a potential problem for
    multithreaded execution.

src/graph/clustering/graph_motifs.hh

commit 0d8112a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-08

    Fix a race condition in label_parallel_edges()
    
    This fixes a race condition when undirected graphs are used, and when
    OpenMP is enabled.

src/graph/stats/graph_parallel.hh

commit 736d6910
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-07-06

    Fix bug in shortest_distance() with filtered graphs.
    
    This fixes a bug where the distance map was not properly initialized
    when the graph is filtered, and the all pairs shortest paths are
    requested.

src/graph/topology/graph_all_distances.cc

commit d5ff8f90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-06-06

    Fix edge count bug in condensation_graph()

src/graph/community/graph_community_network.hh
src/graph_tool/community/__init__.py

commit e4e05a4d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-06-06

    Update README file.

README

commit 49d83026
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-06-04

    Include support for vertex and edge ordering in graph_draw()

src/graph_tool/draw/__init__.py

commit 3e5e39e5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-22

    Include vertex randomization in subgraph_isomorphism()
    
    This allows for sampling of random subgraph isomorphisms.

src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit a5d75e84
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-20

    Add numpy.array access to vector types of property maps
    
    Now vector types of property maps can be accessed as arrays with the
    get_array() and 'a' property, just like scalar property maps.

src/graph/graph_bind.cc
src/graph_tool/core.py

commit 7d0b68ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-20

    Fix bug in Graph.load() with file-like objects
    
    This fixes a small typo bug, which prevented loading from file-like
    objects.

src/graph_tool/core.py

commit 00238cfe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-20

    Fix standard deviation calculation in average correlation code

src/graph/correlations/graph_correlations.hh

commit 07f568f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-20

    Fix edge indexing bug in condensation_graph()
    
    Edges were not properly indexed after graph generation.

src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh

commit 9c5e0b16
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-20

    Small documentation fixes and updates

doc/.static/graph-icon.ico
doc/conf.py
doc/price.py
doc/quickstart.rst
src/graph_tool/__init__.py
src/graph_tool/generation/__init__.py

commit 8ecad8f5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-11

    Improve histogram performace
    
    This improves the binning performace, when suplied bins are of constant
    width.

src/graph/histogram.hh

commit 00a53d62
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-10

    Modify and rename absolute_trust()
    
    absolute_trust() is now called trust_transitivity(), and the whole
    trust matrix can now be efficiently calculated.

src/graph/centrality/Makefile.am
src/graph/centrality/graph_absolute_trust.hh
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_trust_transitivity.cc
src/graph/centrality/graph_trust_transitivity.hh
src/graph_tool/centrality/__init__.py

commit 82b11daf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-10

    New documentation theme

doc/gt_theme/static/flasky.css
doc/gt_theme/static/gt_style.css
doc/gt_theme/theme.conf

commit a3b9e782
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-10

    Bump version to 2.2.7dev

configure.ac

commit 5555e297
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-03

    Bump version to 2.2.6

configure.ac

commit c36685bf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-05-02

    Small documentation changes

doc/quickstart.rst
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 63c2cae1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-04-21

    Improve performace of random graph generation
    
    Vectors are used now instead of unordered_sets, which dramatically
    improves performace.

src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph_tool/generation/__init__.py

commit 42bffcd4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-04-01

    Fix bug in predecessor_tree()
    
    This fixes a bug where edges were left unindexed.

src/graph/generation/graph_predecessor.cc

commit 169265f7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-03-09

    Include maximum number of subgraphs in subgraph_isomorphism()

src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 6f43a01e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-03-07

    Remove spurious file from documentation

doc/numpydoc.pyc

commit 2051859d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-03-07

    Small pylint cleanups

src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/inline.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 13d4f7bc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-03-07

    Fix complilation bug with boost 1.42
    
    This also maintains compatibility with older boost versions.

src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/properties.hpp
src/graph/Makefile.am
src/graph/graph_adaptor.hh
src/graph/graph_wrap.hh

commit cea90112
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-26

    Small docstring fix

src/graph_tool/clustering/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/topology/__init__.py

commit b9bbc350
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-23

    Update encoding and copyright information in source files

configure.ac
src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/centrality/minmax.hh
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/fast_vector_property_map.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_line_graph.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph/generation/sampler.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/histogram.hh
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/mpl_nested_loop.hh
src/graph/numpy_bind.hh
src/graph/shared_map.hh
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_planar.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph_tool/__init__.py
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/decorators.py
src/graph_tool/dl_import.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/io.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit 2de3f607
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-21

    Bump version to 2.2.6dev

configure.ac

commit 44c6b515
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-21

    Bump version

configure.ac

commit 26921f2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-21

    Small doc typos and improvements

src/graph_tool/centrality/__init__.py
src/graph_tool/stats/__init__.py

commit aaf56142
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-14

    Small doc fixes

doc/quickstart.rst
src/graph_tool/topology/__init__.py

commit 33f7f0bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-20

    Fix doctests
    
    This fixes the expected values for several doctests, after
    random_graph() re-factoring.

src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 1f28345e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-14

    Refactor random_graph()
    
    Now the degree sequence is verified with Erdös-Gallai inequalities, and
    the edges are connected in a deterministic fashion. The edges then are
    rewired with the random_rewire() function.

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/generation/sampler.hh
src/graph_tool/generation/__init__.py

commit 64cb52b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-14

    Include probabilistic random_rewire() strategy
    
    This includes also some internal refactoring, and bug fixes.

src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/generation/sampler.hh
src/graph_tool/generation/__init__.py

commit b678e65a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-10

    Refactor random_rewire()
    
    This extensively modifies the random_rewire() algorithm, so that only
    either the source or the edge of each edge is rewired (not both, as
    previously), and no parallel edges are created during the algorithm (if
    desired).
    
    The new version is much faster, and never gets stuck. However, more than
    one run may be necessary in order to obtain a uniform shuffling.

src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit 0a9f69de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-08

    Fix implicit directionality bug in random_rewire()
    
    This fixes a implicit directionality bug in random_rewire() with
    undirected graphs.

src/graph/generation/graph_rewiring.hh

commit d158af8f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-08

    Fix rewiring bias bug for undirected graphs
    
    This fixes a problem, where the underlying edge directionality would
    cause correlations to arise when rewiring undirected graphs. Now each
    edge is correctly considered in both possible orientations, which are
    chosen randomly.

src/graph/generation/graph_rewiring.hh

commit 07e771c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-04

    Modify shortest_distances() and include shortest_path()
    
    This implements a shortest_path() function which returns the shortest
    path between two vertices.
    
    This also modifies shortest_distances, such that a predecessor map is
    optionally returned.

src/graph/topology/graph_distance.cc
src/graph_tool/topology/__init__.py

commit 4211214b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-02-04

    Fix bug in Graph.purge_vertices()
    
    This fixes a crash when purging filtered vertices.

src/graph/graph_filtering.cc

commit 4e60cbfe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-30

    Fix typos in subgraph_isomorphism() docstring

src/graph_tool/topology/__init__.py

commit 61ccc6f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-30

    Bump version to 2.2.5dev

configure.ac

commit e9b19ab4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-29

    Bump version to 2.2.4

configure.ac

commit 01cc0fe4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-28

    Disable deprecation warning, to silence some harmless BGL-related warnings

configure.ac

commit ed413845
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-28

    Implement subgraph_isomorphism()
    
    Support for edge/vertex labelling is 99% done, but it is currently
    impractical to compile with GCC. If GCC 4.5 doesn't do a better job,
    then a workaround would be necessary.

src/graph/topology/Makefile.am
src/graph/topology/graph_subgraph_isomorphism.cc
src/graph/topology/graph_subgraph_isomorphism.hh
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 9078afc3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-28

    Fix trivial bug in the example of triangulation()

src/graph_tool/generation/__init__.py

commit 90dce61e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-28

    Fix regression with Graph.purge_edges() and Graph.purge_vertices()

src/graph/graph_filtering.cc
src/graph_tool/core.py

commit 99b5126e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-28

    Fix bug in isomorphism() when using filtered graphs

src/boost-workaround/boost/graph/isomorphism.hpp

commit 045256ad
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-25

    Fix compilation issues in MacOS X
    
    This also cleans up some m4 boost macros, and includes other small
    corrections to configure.ac.

configure.ac
m4/ax_boost_iostreams.m4
m4/ax_boost_regex.m4
src/graph/numpy_bind.hh

commit 23a4cc30
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-25

    Bump version to 2.2.4dev

configure.ac

commit b67de147
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-12

    Bump version to 2.2.3

configure.ac

commit 0d9607cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2010-01-11

    Implement periodic delaunay triangulation

src/graph/generation/graph_generation.cc
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph_tool/generation/__init__.py

commit 1c0ebb8b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-30

    Bump version to 2.2.3dev

configure.ac

commit 2b9c2acc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-22

    Trivial documentation fix

src/graph_tool/generation/__init__.py

commit 51deb16b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-22

    Bump version to 2.2.2

configure.ac

commit 154ef865
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-22

    Relax boost version requirements
    
    This allows compilation with older versions of boost (>=1.38), which in
    some sistems are the only option. This commit also removes the linking
    of the boost_graph shared library, since none of its symbols are
    actually required.

configure.ac
src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/boost-workaround/boost/graph/copy.hpp
src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/graph/Makefile.am
src/graph/fast_vector_property_map.hh
src/graph/generation/graph_rewiring.hh
src/graph/graph_properties.hh
src/graph/read_graphviz_new.cpp

commit 5c3c3ae8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-22

    Improve triangulation() documentation

src/graph_tool/generation/__init__.py

commit 7ec1fbbc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-21

    Include "erdos" rewire strategy to random_rewire()
    
    This implements a simpler rewire strategy where the edges are randomly
    placed, without preserving the degrees of the vertices.

src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph_tool/generation/__init__.py

commit 9010eb48
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-21

    Trivial doc fix

src/graph_tool/generation/__init__.py

commit b230f226
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-21

    Bump version to 2.2.2dev

configure.ac

commit b5294135
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-14

    Bump version to 2.2.1

configure.ac

commit 703bd155
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-14

    Fix compilation of triangulation code with CGAL
    
    It is necessary to use -frounding-math to avoid run-time errors with
    certain versions of CGAL.

configure.ac
src/graph/generation/Makefile.am

commit d164b455
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-14

    Fix exception raising in run_action

src/graph_tool/run_action/inline.py

commit 9ebe6f70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-13

    Small docstring fixes.

src/graph_tool/clustering/__init__.py
src/graph_tool/draw/__init__.py

commit 0600864b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-13

    Bump version to 2.2.1dev

configure.ac

commit b1513c23
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Bump version to 2.2.0

configure.ac

commit b409528a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Remove empty space in the beginning of graph_topological_sort.cc

src/graph/topology/graph_topological_sort.cc

commit 1a65d24e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Remove useless any_cast in graph_rewiring.cc

src/graph/generation/graph_rewiring.cc

commit 360c2570
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Assorted documentation improvements in generation module.

src/graph_tool/generation/__init__.py

commit d1aa20b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Add support for triangulation() in generation module
    
    This also includes the library CGAL as a dependency.

configure.ac
src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_triangulation.cc
src/graph/generation/graph_triangulation.hh
src/graph_tool/generation/__init__.py

commit f5ba8ec6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Add numpy.ndarray wrapper as boost::multi_array_ref

src/graph/numpy_bind.hh

commit 6b10f14d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-06

    Include is_planar() in topology module
    
    This is a wrapper around BGL's boyer_myrvold_planarity_test.

src/graph/topology/Makefile.am
src/graph/topology/graph_planar.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 8028a3f8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-05

    Bump version to 2.1.2dev

configure.ac

commit 3b24419d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-02

    Bump version to 2.1.1

configure.ac

commit 9ca10d2f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-12-02

    Small documentation and test fixes

src/graph_tool/centrality/__init__.py
src/graph_tool/generation/__init__.py

commit cfc67930
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-20

    Simplify and re-implement absolute_trust()
    
    Now use _best weights_ to in-neighbours to determine trust, to avoid path
    multiplicity catastrophe.

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 8f787a13
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-16

    Limit the number of paths per vertex in absolute_trust()
    
    This also adds the epsilon parameter, which drops paths with weight
    below this value.

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit e0bd13c1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-15

    Revert and modify path weighting strategy in absolute_trust()

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 95b6a10a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-13

    Implement gamma parameter in absolute_trust()

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit c6897dcd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-28

    Improve behaviour of Graph.vertex() for filtered graphs.
    
    It is now possible to obtain the vertex with index i even for filtered graphs.

src/graph_tool/core.py

commit 03f0bc28
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-28

    Add return_bitmap parameter to graph_draw()

src/graph_tool/draw/__init__.py

commit 9b55b319
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-21

    Fix bug with locate and python detection in m4/ax_python.m4

m4/ax_python.m4

commit 0fcef394
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-21

    Fix segmentation fault in shortest_distance() with weights

src/graph/topology/graph_distance.cc

commit 9331a3d1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-09

    Do not forget "string" type in _check_prop_vector()

src/graph_tool/core.py

commit 3fea60ff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-09

    Fix problem with filtered graph in graph_draw()
    
    It is not useful to store vertices by index when the vertices are being
    filtered, since Graph.vertex() does not map to index in this case.

src/graph_tool/draw/__init__.py

commit 5c935bdd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-09

    Fix problem with filtered graph in absolute_trust()

src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 1a3d219f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-09

    Fix trivial bug in 'all' module

src/graph_tool/all.py

commit 6ed7bd2e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-06

    Small doc fixes.

README
src/graph_tool/centrality/__init__.py
src/graph_tool/flow/__init__.py

commit b4370e91
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-06

    Bump version to 2.1.1dev

configure.ac

commit 0d965324
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-05

    Bump version to 2.1.0

configure.ac

commit 23f6f40f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-05

    Fix bug with self-loops in Graph.clear_vertex()
    
    Since the same edge appears twice in Vertex.all_edges() if it is a
    self_loop, it would be deleted twice in Graph.clear_vertex(), raising an
    exception. Now, the edges are stored in a set first, avoiding this
    problem.

src/graph_tool/core.py

commit 4708d11d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-11-04

    Docstring examples fixes
    
    Small fixes of some examples in the docstrings.

doc/quickstart.rst
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/stats/__init__.py

commit f8d0e225
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-29

    Improve detection of invalid edge descriptors
    
    This fixes a crash when a "valid" copy of an invalid edge descriptor is
    removed from the graph. Now the invalidity of the descriptor is detected
    and exposed.

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh

commit 3b375c78
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-29

    Fix python path selection bug in autoconf
    
    This fixes the problem of generating invalid Makefiles when more than
    one python installation is found.

m4/ax_python.m4

commit 10dd7be8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-29

    Revert weight calculation in absolute_trust()
    
    Use the original, simpler, path weight calculation.

src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 6d1810e1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-24

    Sync with boost 1.40
    
    Fix compilation warnings with boost 1.40, remove unnecessary files, fix
    autoconf macros and link with "boost_graph".
    
    This also raises the minimum boost version to 1.40.

configure.ac
m4/ax_boost_graph.m4
m4/ax_boost_iostreams.m4
m4/ax_boost_regex.m4
src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/boost-workaround/boost/graph/copy.hpp
src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/detail/read_graphviz_spirit.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/graph/Makefile.am
src/graph/fast_vector_property_map.hh
src/graph/generation/graph_rewiring.hh
src/graph/generation/graph_union.hh
src/graph/graph.hh
src/graph/graph_properties.hh
src/graph/graph_selectors.hh
src/graph/read_graphviz_new.cpp
src/graph/read_graphviz_spirit.cpp

commit 3f400d2a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-23

    Include minimum distance algorithms
    
    This includes the shortest_distance() function in the topology module.

src/graph/topology/Makefile.am
src/graph/topology/graph_all_distances.cc
src/graph/topology/graph_distance.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 5d995ac9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-23

    Fix problem with dirty sys.path entries in inline()
    
    This is a workaround for strange entries in sys.path; either dirs that
    don't exist, or are in unicode.

src/graph_tool/run_action/inline.py

commit 512d70b8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-23

    Fix empty property problem in graphml
    
    Properties with empty values are now simply not printed in the output.

src/boost-workaround/boost/graph/graphml.hpp
src/graph/graph_io.cc

commit c9621bc6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-23

    Fix problem with property types
    
    Some property typles wrongly included the index map, when they
    shouldn't.

src/graph/graph_selectors.hh

commit 19b68a13
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-23

    Fix draw_graph() for filtered graphs

src/graph_tool/draw/__init__.py

commit 176e2630
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-23

    Clean up old dependency of line_graph.cc on graphml.hpp

src/graph/generation/graph_line_graph.cc

commit 4e89a1be
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-18

    Slightly improve xml escaping of strings

src/graph/graphml.cpp

commit b3212a66
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-17

    Allow empty strings as vector<string> values in graphml

src/graph/graph_util.hh

commit 083a4d64
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-12

    Fix path weights in absolute_trust()
    
    This fixes how paths are weighted in the absolute_trust algorithm.

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph/centrality/minmax.hh
src/graph_tool/centrality/__init__.py

commit e3c6b395
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-09

    Add missing read_graphviz_new.cpp file to repository

src/graph/read_graphviz_new.cpp

commit 49e60e9c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-05

    Bump version to 2.0.1dev

configure.ac

commit f30e6d52
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-04

    Bump version to 2.0.0

configure.ac

commit 079301cc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-04

    Modify README and Changelog

ChangeLog
README

commit 92402ecc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-04

    Synchronize graphviz support with boost 1.40

configure.ac
m4/ax_boost_regex.m4
src/boost-workaround/boost/graph/detail/read_graphviz_new.hpp
src/boost-workaround/boost/graph/detail/read_graphviz_spirit.hpp
src/boost-workaround/boost/graph/graphviz.hpp
src/boost-workaround/boost/graph/overloading.hpp
src/graph/Makefile.am
src/graph/read_graphviz_spirit.cpp

commit f0524b52
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-04

    Fix missing files in Makefile.am

Makefile.am
src/graph/Makefile.am
src/graph/centrality/Makefile.am
src/graph/clustering/Makefile.am
src/graph/community/Makefile.am

commit 2db745b1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-04

    Several documentation fixes and extensions
    
    This completes all the documentation up to this point.

doc/.templates/layout.html
doc/conf.py
doc/graph_tool.rst
doc/gt_theme/static/gt_style.css
doc/gt_theme/theme.conf
doc/index.rst
doc/price.py
doc/quickstart.rst
doc/sphinxext/autosummary.py
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/spectral/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py
src/graph_tool/util/__init__.py

commit bb499c3b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-10-04

    Rename dominator_tree()

src/graph/topology/Makefile.am
src/graph/topology/graph_dominator_tree.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 8aba5e72
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-18

    Fix 'penwidth' parameter in graph_draw()

src/graph_tool/draw/__init__.py

commit 1d47731d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-17

    Return None in PropertyMap.a if no array is available

src/graph_tool/core.py

commit f12d5416
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-17

    Modify absolute_centrality implementation
    
    This dumps the random-path approach, and implements a deterministic,
    priority queue algorithm.

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph/centrality/minmax.hh
src/graph_tool/centrality/__init__.py

commit c6c01d62
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-12

    Edge and vertex descriptors now carry a weakref to their Graphs
    
    This fixes an obvious problem, where the graph gets deleted, and the
    descriptors are still lying around. Usage of orphaned descriptors will
    now just raise a ValueError.
    
    The __repr__ function of Edge, Vertex, and PropertyMap now give
    something more informative about each object.

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph_tool/core.py
src/graph_tool/util/__init__.py

commit 06b2914a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-08

    Speed up motifs() and motif_significance()
    
    In both functions we can save some time by hashing the subgraphs found,
    according to their degree distribution signature (instead of number of
    edges). This avoids a large number of useless exactness or isomorphism
    comparisons.
    
    This also removes the "seed" parameter, which is redundant to
    the numpy.random.seed() function.

src/graph/clustering/graph_motifs.hh
src/graph_tool/clustering/__init__.py

commit 4d69fce0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-07

    Assorted docstring inclusions/modifications
    
    Mostly in the flow and spectral modules.

doc/graph_tool.rst
src/graph_tool/clustering/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/flow/__init__.py
src/graph_tool/spectral/__init__.py

commit effd22b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Fix Makefile.am in generation module
    
    The file graph_predecessor.hh was missing.

src/graph/generation/Makefile.am

commit 8b1d33e9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Fix bug in community_structure() documentation
    
    The value "random" should be "uncorrelated" instead.

src/graph_tool/community/__init__.py

commit 2d5dca6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Trivial fix for several compilation warnings

src/graph/centrality/graph_absolute_trust.hh
src/graph/clustering/graph_motifs.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph/generation/graph_generation.hh
src/graph/generation/graph_rewiring.hh
src/graph/graph_copy.cc
src/graph/graph_filtering.hh
src/graph/histogram.hh
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.hh
src/graph/topology/graph_denominator_tree.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_topology.cc
src/graph/util/graph_search.hh

commit c1c2aa9c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Fix openmp bug in community_structure()
    
    Call to random() must be protected by "omp critical".

src/graph/community/graph_community.hh

commit 0ac9b1f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Implement graph_union()
    
    This returns the union of two graphs, and optionally specified property
    maps.

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_union.cc
src/graph/generation/graph_union.hh
src/graph/generation/graph_union_eprop.cc
src/graph/generation/graph_union_vprop.cc
src/graph_tool/generation/__init__.py

commit 389812f4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Enable value type selection in Graph.copy_property()

src/graph_tool/core.py

commit a64da5dc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-06

    Enable -Wall in compilation

configure.ac

commit 494a203c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-05

    Allow for simple scaling in vertex and edge sizes in graph_draw()

src/graph_tool/draw/__init__.py

commit 5540d1eb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-05

    Include PropertyMap.a property
    
    This provides convienent access to the underlying array values, such as:
    
       p.a = random(len(p.a))
    
    instead of:
    
       p.get_array()[:] = random(len(p.get_array()))
    
    (the latter is still supported)

src/graph_tool/core.py

commit 41a677ae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-05

    Change default number of shuffles to 100 in motif_significance()

src/graph_tool/clustering/__init__.py

commit 88fe8214
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-05

    Implement 'spectral' module
    
    This includes generations of releated matrices for spectral analysis,
    such as the adjacency matrix, laplacian matrix and incidence matrix.

doc/spectral.rst
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/spectral/__init__.py

commit a9b5ee3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-03

    Fix typo bug in isomorphism()

src/graph_tool/topology/__init__.py

commit f2f45f0a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-03

    Small fixes in docstrings to reflect changes in graph_draw()

src/graph_tool/community/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/generation/__init__.py

commit 62dc2518
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-03

    Include option to produce no output in graph_draw()
    
    If output==None, no output is produced, and only the layout positions
    are returned.

src/graph_tool/draw/__init__.py

commit 8848d6c7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-09-03

    Fix bug in absolute_trust()
    
    Random salt should be protected with "omp critical", and edge sampler
    should check for the case when all edges have zero probability, and
    sample uniformly.

src/graph/centrality/graph_absolute_trust.hh

commit cdfc8b05
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-31

    Fix import bug in clustering module
    
    Load 'topology' instead of 'misc'.

src/graph_tool/clustering/__init__.py

commit 73fe12a8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-31

    Implement layout module ('draw' from python) and arf layout
    
    This implements a layout module (called 'draw' from python) with an
    implementation of the arf spring-block layout.

configure.ac
src/graph/Makefile.am
src/graph/layout/Makefile.am
src/graph/layout/graph_arf.cc
src/graph/layout/graph_arf.hh
src/graph/layout/graph_bind_layout.cc
src/graph/layout/graph_layout.cc
src/graph_tool/draw/__init__.py

commit 0db15a14
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-31

    Implement group_vector_property() and ungroup_vector_property()
    
    These functions group several scalar properties into one vector
    properties, and ungroup a vector property into several scalar
    properties.

src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph/graph_properties_group.cc
src/graph/graph_properties_group.hh
src/graph/graph_properties_ungroup.cc
src/graph_tool/__init__.py
src/graph_tool/core.py

commit 8dd99577
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-31

    Fix unecessary pass in correlation histogram
    
    It is not necessary to gather the data range if the bin size is
    constant. This also changes the histogram code, to better handle the
    constant-size bin situation.

src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_correlations.hh
src/graph/histogram.hh

commit 29f83ea6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-31

    Resuscitate distance_histogram() and sampled_distance_histogram()

src/graph/histogram.hh
src/graph/stats/Makefile.am
src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_stats_bind.cc
src/graph_tool/stats/__init__.py

commit b4249772
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-28

    Resuscitate the line_graph() code

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_line_graph.cc
src/graph/topology/graph_line_graph.cc
src/graph_tool/generation/__init__.py

commit 1d16a08d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-22

    Include max_cardinality_matching() in flow module

src/graph/flow/Makefile.am
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_maximum_cardinality_matching.cc
src/graph_tool/flow/__init__.py

commit a35d46b9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-22

    Include (empty) flow module documentation

doc/centrality.rst
doc/flow.rst
doc/graph_tool.rst

commit 7fb5d71d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-21

    Dump lambda::bind in favor of boost::bind
    
    This is a large commit which replaces lambda::bind with boost::bind in
    most parts of the code. This improves compilation time, and slightly
    decreases compilation memory usage in some cases.

src/boost-workaround/boost/graph/graphml.hpp
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_pagerank.cc
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/generation/graph_generation.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_rewiring.cc
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_selectors.cc
src/graph/graph_util.hh
src/graph/topology/graph_denominator_tree.cc
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_line_graph.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_topological_sort.cc
src/graph/util/graph_search.cc
src/graph_tool/run_action/run_action_support.hh

commit a89e069c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-21

    Implement flow algorithms
    
    This includes the edmonds karp, push relabel and kolmogorov maximum flow
    algorithms from the BGL.

configure.ac
src/graph/Makefile.am
src/graph/flow/Makefile.am
src/graph/flow/graph_augment.hh
src/graph/flow/graph_edmonds_karp.cc
src/graph/flow/graph_flow_bind.cc
src/graph/flow/graph_kolmogorov.cc
src/graph/flow/graph_push_relabel.cc
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/flow/__init__.py

commit 4a1b3817
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-21

    Small fixes in GraphWrap
    
    Use correct types and always pass GraphWrap objects by value.

src/graph/graph_util.hh
src/graph/graph_wrap.hh

commit dd981325
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-17

    Implement silent compilation mode by default with automake 1.11

configure.ac

commit d05fffac
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-17

    Properly raise IOError when a parse error occurs in graph_io.cc

src/graph/graph_io.cc

commit 55bee9c1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-17

    Rename community_network() to condensation_graph()

src/graph_tool/community/__init__.py

commit db7589d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-17

    Move graph component code from 'stats' to 'topology' module

src/graph/stats/Makefile.am
src/graph/stats/graph_stats_bind.cc
src/graph/topology/Makefile.am
src/graph/topology/graph_components.cc
src/graph/topology/graph_components.hh
src/graph/topology/graph_topology.cc
src/graph_tool/stats/__init__.py
src/graph_tool/topology/__init__.py

commit 6d1a9eff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Implement label_biconnected_components()

src/graph/stats/graph_components.cc
src/graph/stats/graph_components.hh
src/graph_tool/stats/__init__.py

commit 217b9d7a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Implement predecessor_tree()

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_predecessor.cc
src/graph/generation/graph_predecessor.hh
src/graph_tool/generation/__init__.py

commit c21a36c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Implement denominator_tree(), min_spanning_tree() and transitive_closure()

src/graph/topology/Makefile.am
src/graph/topology/graph_denominator_tree.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_topological_sort.cc
src/graph/topology/graph_topology.cc
src/graph/topology/graph_transitive_closure.cc
src/graph_tool/topology/__init__.py

commit c0b0a6b7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Add is_writable() method to PropertyMap
    
    This also includes convenience property map checks.

src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph_tool/core.py

commit 5292b8ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Fix bug in remove_edge() in graph_wrap

src/graph/graph_wrap.hh

commit ebccfe1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Add min_spanning_tree() function

src/graph/topology/Makefile.am
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_topology.cc
src/graph_tool/topology/__init__.py

commit 48e384e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Move old distance code to stats module

src/graph/stats/graph_distance.cc
src/graph/stats/graph_distance.hh
src/graph/stats/graph_distance_sampled.cc
src/graph/stats/graph_distance_sampled.hh

commit 5faf4043
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Fix example in community_structure()
    
    load() function no longer supported in scipy.

src/graph_tool/community/__init__.py

commit d34568d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-16

    Rename "misc" module as "topology"

configure.ac
doc/graph_tool.rst
doc/misc.rst
doc/topology.rst
src/graph/Makefile.am
src/graph/misc/Makefile.am
src/graph/topology/Makefile.am
src/graph/topology/graph_isomorphism.cc
src/graph/topology/graph_line_graph.cc
src/graph/topology/graph_minimum_spanning_tree.cc
src/graph/topology/graph_reciprocity.cc
src/graph/topology/graph_topology.cc
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/topology/__init__.py

commit 2f7a47ca
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-13

    Fix edge/vertex normalization option in graph_draw()

src/graph_tool/draw/__init__.py

commit f257d426
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-13

    Reorganize exceptions thrown
    
    No longer only thrown GraphError upon any error, but instead throw
    specific exceptions which are more meaninful and are mapped to standard
    python exceptions, such as IOError, ValueError and RuntimeError.

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_pagerank.cc
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_io.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_selectors.cc
src/graph_tool/__init__.py
src/graph_tool/core.py
src/graph_tool/decorators.py

commit 54f5c469
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-09

    Modify absolute_trust() algorithm
    
    Path sampling is done using different bias, and the edge sampling is now
    done correctly. There is now only one parameter 'n_iter' which replaces
    'min/max_iter' and 'epslon'.

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit e05fa740
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-07

    Include docstring for random_rewire()

src/graph_tool/generation/__init__.py

commit c72e48d5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-07

    Fix bug in random_rewire() with undirected graphs
    
    When using undirected graphs, the implicit direction of each edge was
    not properly handled, and the correlated case would not work. Now, in
    this case, the direction is always checked, and the edge is inverted if
    necessary.

src/graph/generation/graph_rewiring.hh

commit b4876dba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-07

    Fix stash/pop_filter() bug
    
    This would cause the graph to become directed (when previously
    undirected) in some circumstances.

src/graph_tool/core.py

commit b18d327a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-07

    Fix returned position scale in graph_draw()
    
    This is a workaround for a behaviour of graphviz which is not well
    understood.

src/graph_tool/draw/__init__.py

commit 25e31f3d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-04

    Include version string automatically in documentation

doc/conf.py

commit 0f1ea319
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-04

    Fix bug in usage of tr1::variate_generator
    
    The RNG object must be passed by _reference_ not by value, as is the
    default! Otherwise the RNG state does not change...

src/graph/centrality/graph_absolute_trust.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/correlations/__init__.py

commit 54880035
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-04

    Fix bias bug in random_graph() in correlated mode
    
    Target degrees were not being sampled correctly from their probability.

src/graph/generation/graph_generation.hh
src/graph_tool/generation/__init__.py

commit b0c2a3c3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-04

    Move random_rewire() to 'generation' module

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_rewiring.cc
src/graph/generation/graph_rewiring.hh
src/graph/misc/Makefile.am
src/graph/misc/graph_misc.cc
src/graph_tool/generation/__init__.py
src/graph_tool/misc/__init__.py

commit 400a8d1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-03

    Simple workaround for GCC 4.4.1

src/graph/graph_selectors.cc

commit 8ab0947a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-03

    Fix memory leak in numpy integration
    
    Reference counts of newly created arrays must always be incremented, and
    not borrowed().

src/graph/numpy_bind.hh

commit 014d0529
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-02

    Small modifications in the quick start guide

doc/price.py
doc/quickstart.rst

commit 7e6968aa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-08-02

    Implement show_config()
    
    This prints useful library information.

configure.ac
src/graph/graph_bind.cc
src/graph_tool/__init__.py
src/graph_tool/core.py

commit 36b30534
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-30

    Remove obsolete test units
    
    We will rely on sphinx + docstrings instead.

src/graph_tool/Makefile.am
src/graph_tool/test/__init__.py
src/graph_tool/test/basic.py
src/graph_tool/test/io.py
src/graph_tool/test/properties.py

commit 11e04983
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-30

    Force loading of numpy and scipy during import
    
    Import numpy and scipy before everything to avoid weird segmentation
    faults depending on the order things are imported.

src/graph_tool/__init__.py

commit 30ac60fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-30

    Add random_graph() docstring

src/graph_tool/generation/__init__.py

commit 3b958a22
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-30

    Trivial doc configuration modifications

doc/Makefile
doc/conf.py

commit d9ea11a0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-30

    Small fix in draw module docstrings

src/graph_tool/draw/__init__.py

commit 59237426
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-30

    Fix typo in avg_neighbour_corr()

src/graph_tool/correlations/__init__.py

commit 47394f90
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-17

    Add google analytics script to documentation html

doc/.templates/layout.html

commit 87b69927
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-17

    Sync graphviz_spirit with boost 1.39

src/graph/read_graphviz_spirit.cpp

commit 602541aa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-12

    Include docstrings in graph_draw()

src/graph_tool/draw/__init__.py

commit 58fe4de2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-07-12

    Include min_inter parameter in absolute_trust()

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 40fb818c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-30

    Improve community detection code and write documentation

doc/community.xml
doc/conf.py
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph_tool/community/__init__.py

commit 7936e130
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-22

    Fix OpenMP bug with find_vertex()
    
    Python types cannot be checked in parallel. This commit forces the
    number of threads to be 1 in such case.

src/graph/util/graph_search.hh

commit 300dc115
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-18

    Fix find_vertex()
    
    This changes degree_selector(). Now all properties should be tested, not
    only scalar properties. Later it can be decided which properties are
    valid.

src/graph/graph_selectors.cc

commit e1dd1665
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-16

    Improve correlated graph generation
    
    random_graph() now uses a modified algorithm for generation of
    correlated graphs, which is more efficient. Instead of giving a function
    which returns a sample of the correlated target degree, the user must
    give a function which will just compute its probability. This
    probability will then be used to choose the edges.

src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph_tool/generation/__init__.py

commit 6c77669e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-14

    Fix variance of scalar_assortativity()
    
    This also simplifies the calculation of the coefficient.

src/graph/correlations/graph_assortativity.hh

commit 7da1f0a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-15

    Ongoing documentation improvement
    
    This modified several docstrings and introduces a quick-start guide.

doc/.static/graph-icon.ico
doc/.templates/layout.html
doc/Makefile
doc/centrality.rst
doc/clustering.rst
doc/community.rst
doc/conf.py
doc/correlations.rst
doc/draw.rst
doc/generation.rst
doc/graph_tool.rst
doc/misc.rst
doc/price.py
doc/quickstart.rst
doc/run_action.rst
doc/stats.rst
doc/util.rst
src/graph_tool/__init__.py
src/graph_tool/centrality/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/community/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/draw/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/misc/__init__.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/stats/__init__.py
src/graph_tool/util/__init__.py

commit 9d542a89
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-11

    Make tgt parameter of Graph.copy_property() optional

src/graph_tool/core.py

commit c2d45e12
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2009-06-02

    graph_rewiring: some improvements to random_permutation_iterator

src/graph/misc/graph_rewiring.hh

commit 90071a37
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-06-01

    graph_rewiring: completely purge boost::random

src/graph/misc/graph_rewiring.hh

commit a8f2c8fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-23

    Fix missing symbol bug in weighted avg_neighbour_corr()

src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.hh

commit 7505190f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-23

    Switch from boost::random to tr1::random
    
    The generators from boost::random seem to have a bug which causes them
    to be biased. The generators from tr1::random seem to be in better
    shape.
    
    See: http://thread.gmane.org/gmane.comp.lib.boost.user/48006

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh
src/graph/misc/graph_rewiring.cc
src/graph/misc/graph_rewiring.hh

commit b334e1cd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-21

    Fix zero-trust computation in absolute_trust()

src/graph/centrality/graph_absolute_trust.hh

commit 9c825c08
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-18

    Fix absolute trust weighting and add reverse trust

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit b93b5010
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-18

    Change Graph.stash_filter() semantics
    
    Now the parameter "all" is ignored, if any of the other parameters is
    True.

src/graph_tool/core.py

commit f5d54203
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-15

    Allow for direct creation of undirected graphs
    
    The following is now possible:
    
        g = Graph(directed=False)
    
    Instead of the only way previously:
    
       g = Graph()
       g.set_directed(False)

src/graph_tool/core.py

commit 2867d7b0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-15

    Add conversion from Vertex and Edge to int and tuple
    
    The following conversions are now possible: int(v) and tuple(e), where v
    and e are Vertex and Edge instances, respectively.

src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph_tool/core.py

commit ca4c120f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-12

    Modify absolute trust
    
    Now paths are weighted according to their trust value until the last
    hop, and paths are not counted twice.

src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 95484cb5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-11

    Some improvements in graph_draw()
    
    Vertex/edge colors are properly plotted even when value range is zero
    lenght. The behaviour of the 'fork' option was slightly modified.

src/graph_tool/draw/__init__.py

commit 18445c39
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-11

    Allow choosing of different shuffling strategies in motif profile code

src/graph_tool/clustering/__init__.py

commit a5eabf2b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-11

    Better documentation for graph filtering

src/graph_tool/core.py

commit 22869590
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-11

    Fix property type parsing in new_*_property()

src/graph_tool/core.py

commit 8a6edecb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-11

    Fix includes in graph_wrap.hh

src/graph/graph_wrap.hh

commit ede94aaf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-08

    Still import draw module, even when gv not present
    
    graph_draw() won't work if gv is not available, and just a warning is
    printed... This makes graph_tool.all work when gv is not available.

src/graph_tool/draw/__init__.py

commit a79f5dbb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-08

    Fix weighted betweeness centrality
    
    Fix bad_any_cast bug when passing a weight property.

src/graph/centrality/graph_betweenness.cc
src/graph/graph.hh

commit b7188ade
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-05-08

    Add support for a single source in absolute trust code

src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph_tool/centrality/__init__.py

commit 0f15b1fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-26

    Small docstring fix.

src/graph_tool/core.py

commit 07a2d099
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-26

    Docstrings and small fixes in centrality algorithms
    
    This fully documents the centrality module.

src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_pagerank.cc
src/graph_tool/centrality/__init__.py

commit 95405617
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-25

    Fix small bug in local/extendend_clustering
    
    The function directed() no longer exists, is_directed() should be used
    instead.

src/graph_tool/clustering/__init__.py

commit 08d96f56
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-25

    Adds support for removal of labeled edges, self-loops and parallel-edges

src/graph/graph_filtering.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph_tool/stats/__init__.py

commit 58e45bfd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-25

    Fix important bug in graph i/o
    
    The _max_edge_index variable was not set when reading a graph, which
    caused memory corruption when deleting and adding edges.

src/graph/graph_io.cc

commit 44d4dbee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-25

    Change default parameters of stash_filter() and pop_filter()
    
    Now all filters are stashed by default. In order to override this, the
    parameter all=False needs to be passed, and the individual filters need
    to be specified.

src/graph_tool/core.py

commit 7732bedf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-24

    Enable openmp loop in get_all_motifs()
    
    This also doesn't build a parallel vertex list if motifs aren't being
    sampled.

src/graph/clustering/graph_motifs.hh

commit 1615ec5a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-24

    Include support for motif significance profile
    
    This includes the function motif_significance() into the clustering
    module.

src/graph_tool/clustering/__init__.py

commit f3c37d4c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-24

    Fix vertex_range to consider all types of properties
    
    This changes the meaning of the all_selectors type, which includes all
    property types, and creates a scalar_selectors type, which includes only
    the scalar types.

src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/graph_selectors.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_histograms.cc
src/graph/util/graph_search.cc

commit de3f34f5
Merge: 5b0f9286 8358ecb9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-21

    Merge branch 'no-conversions'
    
    Conflicts:
            acinclude.m4
            configure.in
            src/graph-tool
            src/graph/Makefile.am
            src/graph/correlations/graph_assortativity.hh
            src/graph/graph.cc
            src/graph/graph_betweenness.cc
            src/graph_tool/__init__.py

commit 8358ecb9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-16

    Fix i/o of floating point vector types
    
    This ensures that vector types also don't suffer from data loss due to
    representation change.

src/graph/graph_io.cc
src/graph/graph_util.hh

commit 1270f0fb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-14

    Selective stash/pop of graph filter state
    
    Individual filters can be stashed and popped by passing keyword
    arguments to the respective functions. Additionally the filter state can
    be obtained and set directly, with the get_filter_state() and
    set_filter_state() functions.

src/graph_tool/core.py

commit 6f223eaa
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-14

    Small docstring typo

src/graph_tool/core.py

commit 7a26fd5a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-04-14

    Add type alias in property creation for convenience

src/graph_tool/core.py

commit 6defdb43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-10

    Fix graph_rewire "can't rewire" bug
    
    This finally fixes in the bug addressed by commit 309ddbbddb, where
    parallel edges could be erroneously created. In fact, the bug was more
    serious: The source and target edge lists always pointed to the same
    list (in the uncorrelated case, but could occasionally happen for the
    correlated case also) which got shuffled during iteration. Since the
    shuffling of one list interfered with the shuffling of the other, some
    combinations of source and target edges could simply never be
    considered... This commit forces both lists to always be independent.

src/graph/misc/graph_rewiring.hh

commit 684efca7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-10

    Implement optional wrapping of graphs to deal with edge index housekeeping
    
    Thins changes the graph filtering code slightly to wrap graph types with
    GraphWrap, which automatically updates the edge index list when edges
    are removed and added to the graph.
    
    This also changes how graphs are passed to algorithms, which is now by
    reference instead of pointer. (hence this touches lots of code, but
    changes are trivial)

src/graph/centrality/graph_absolute_trust.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_pagerank.hh
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.hh
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/generation/graph_generation.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_util.hh
src/graph/graph_wrap.hh
src/graph/misc/graph_isomorphism.cc
src/graph/misc/graph_rewiring.hh
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_components.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.hh
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh

commit e03b1758
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-09

    Fix all_edges selector

src/graph/graph_selectors.hh

commit e4c09389
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-02

    Fix pickle support
    
    This was not working due to filtering semantics modifications.

src/graph_tool/core.py

commit aa027588
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-02

    Fix save() and load() when 'filename' is a file object

src/graph_tool/core.py

commit 5cca53ce
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-01

    Add motifs() function to clustering module
    
    This implements an efficient motif counting algorithm.

src/boost-workaround/boost/graph/copy.hpp
src/graph/clustering/Makefile.am
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_motifs.cc
src/graph/clustering/graph_motifs.hh
src/graph_tool/clustering/__init__.py

commit c3db0a4a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-01

    Fix GraphInterface copying
    
    Edge index housekeeping was not preserved during copy.

src/graph/graph_copy.cc

commit b1582025
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-01

    Include isomorphism() function in misc module

src/boost-workaround/boost/graph/isomorphism.hpp
src/graph/misc/Makefile.am
src/graph/misc/graph_isomorphism.cc
src/graph/misc/graph_misc.cc
src/graph_tool/misc/__init__.py

commit d836b5d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-03-01

    Uses boost_workaround files
    
    This fixes bug where boost overlay files were not being used, when not
    compiling from source dir.

configure.ac
src/boost-workaround/boost/graph/betweenness_centrality.hpp

commit 26788729
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-22

    Hash all include files in run_action to force recompilation if any header changes

src/graph_tool/run_action/inline.py

commit a962d139
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-22

    Properly remove in- and out-edges when vertex is removed
    
    The edge index housekeeping was not performed on edges which were
    deleted due to vertex removal.

src/graph/graph_wrap.hh
src/graph_tool/core.py

commit ff5db995
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-22

    Add member functions remove_vertex_if and remove_edge_if to Graph
    
    This provides a more convenient way of deleting vertices or edges
    according to a simple criterion.

src/graph_tool/core.py

commit 0896d088
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-21

    Properly fix problem with libtool and libstdc++ linkage
    
    Make sure libtool is properly modified, by doing it last in
    configure.ac.

configure.ac

commit 9b12a427
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-21

    Fix trivial error in node/edge search functions

src/graph_tool/util/__init__.py

commit 52eaa36f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-17

    Add convenient neighbour traversal functions
    
    Add support for v.{out|in}_neighbours(), for direct iteration over the
    neighbours, as well as v.all_edges() and v.all_neighbours(). This also
    properly exports the Vertex and Edge classes, with docstrings.

src/graph/graph_python_interface.cc
src/graph_tool/__init__.py
src/graph_tool/core.py

commit 96b9c5e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-14

    Add centrality module
    
    This adds the centrality module, which supports betweenness, eigentrust,
    pagerank and absolute trust.

configure.ac
src/graph/Makefile.am
src/graph/centrality/Makefile.am
src/graph/centrality/graph_absolute_trust.cc
src/graph/centrality/graph_absolute_trust.hh
src/graph/centrality/graph_betweenness.cc
src/graph/centrality/graph_centrality_bind.cc
src/graph/centrality/graph_eigentrust.cc
src/graph/centrality/graph_eigentrust.hh
src/graph/centrality/graph_pagerank.cc
src/graph/centrality/graph_pagerank.hh
src/graph/misc/graph_betweenness.cc
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/centrality/__init__.py

commit d0a73fff
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-14

    Rename fast_vector_property_map to checked_vector_property_map
    
    This makes the naming more sensible.

src/graph/fast_vector_property_map.hh
src/graph/graph.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.hh

commit bd6ebfb7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-10

    Fix semantics of detail::never_reversed
    
    It now does not implies automatically "always_directed".

src/graph/graph_filtering.hh

commit 50eec674
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-10

    Fix spurious parallel edge creation in random_rewire()
    
    In some circumstances, the test for parallel edges would fail to detect
    one, if it involved another "new" edge and one of the current ones being
    rewired.
    
    This commit also removes the requirement that edge indexes be continuous
    in the range [0, num_edges(g)), which is not in general the case.

src/graph/misc/graph_rewiring.hh

commit 47dba275
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-10

    Fix (yet again) edge index housekeeping

src/graph/graph_python_interface.cc
src/graph/graph_wrap.hh

commit 7f10e926
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-06

    Fix seeding in random_graph()
    
    The seed option is now correctly interpreted.

src/graph_tool/generation/__init__.py

commit be9b2596
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-06

    Fix graph_draw() seeding
    
    The seed option is now properly passed to graphviz.

src/graph_tool/draw/__init__.py

commit 548d61bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-06

    Fix get_array() for property maps
    
    This includes the missing function declarations for edge and graph
    properties.
    
    Property maps of value type "string" do not return an array, since the
    numpy string and std::string are different things.

src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/numpy_bind.hh

commit 2586bae6
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2009-02-05

    Improves small fix for 64bit architectures.
    
    graph_rewiring.cc: use static_cast<rng_t::result_type> instead of
    uint32_t to convert the seed value for the rng_t constructor, so
    the code becomes compatible with any rng_t.

src/graph/misc/graph_rewiring.cc

commit 0c87c492
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-03

    Improve run_action module
    
    Now inline() automatically converts known variables (such as property
    maps) and defaults to boost::python objects, instead of scxx objects.
    
    The code now is only generated for the current filtered, reversed and/or
    directed status of the graph, reducing compile time and binary size.
    
    Edge modification (remove and add) is now protected by a GraphWrap
    class, which takes care of the edge index housekeeping, which does not
    need to be done by hand anymore.
    
    The function is also no longer bound to one graph, and can take an
    arbitrary number of variables of known or unknown types, including
    graphs.

src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_wrap.hh
src/graph_tool/Makefile.am
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_support.hh
src/graph_tool/run_action/run_action_template.hh

commit ba56ebd9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-02-01

    Fix edge index housekeeping

src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_filtering.cc
src/graph/graph_python_interface.cc

commit d6422b73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-31

    Fix symbol visibility
    
    Now all symbols are exported by default, except those strictly marked
    as hidden.

configure.ac
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/mpl_nested_loop.hh

commit b5da5356
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-31

    Autoconf clean-up and new m4 macros

acinclude.m4
autogen.sh
configure.ac
m4/ac_python_devel.m4
m4/ac_python_module.m4
m4/ax_boost_base.m4
m4/ax_boost_iostreams.m4
m4/ax_boost_python.m4
m4/ax_python.m4
src/graph/Makefile.am

commit 4a9bf9f6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-30

    Fix compilation in 64 bit architecture

src/graph/misc/graph_rewiring.cc
src/graph/numpy_bind.hh

commit 7ea1d8c4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-23

    Fix small warning in community code

src/graph/community/graph_community.hh

commit 0ababf9c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-23

    Disable internal bounds checking in property maps
    
    This includes a new vector property map type (fast_vector_property_map)
    which has optional disabling of bounds checking, through its associate
    map type (unchecked_fast_vector_property_map). This should improve
    performance on algorithms which depend on tight loops which access
    property maps.
    
    Bounds checking is only disabled locally just before the algorithms run,
    and proper care is taken for bounds checking _beforehand_. The property
    maps exposed to python still have internal bounds checking.

src/boost-workaround/boost/vector_property_map.hpp
src/graph/Makefile.am
src/graph/clustering/graph_extended_clustering.cc
src/graph/community/graph_community_network.cc
src/graph/fast_vector_property_map.hh
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/misc/graph_rewiring.hh

commit 64018e6f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-18

    Expand user dir (~) in file IO
    
    e.g., g.save("~/foo.xml")

src/graph_tool/core.py

commit 8ae75c9f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-18

    Add direct support for degree propery map creation
    
    i.e. g.degree_property_map("in") will create and return a vertex property map
    which corresponds to the in-degrees of the vertices. This is useful for
    temporarily modifying or getting an array of degrees.

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_python_interface.cc
src/graph_tool/core.py

commit e84aaf3c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-18

    Add support for array access to property maps
    
    A property map object has now a get_array() member which returns an internally
    owned array pointing to the property values.

src/boost-workaround/boost/vector_property_map.hpp
src/graph/graph_bind.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph_tool/core.py

commit e4d79af6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-18

    Several improvements to graph_draw()
    
    Allow direct specification of vertex size, which accepts property maps,
    and a couple of bug fixes.

src/graph_tool/draw/__init__.py

commit b965528d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-18

    Implement missing ClearEdges()

src/graph/graph.cc

commit dd98225a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-11

    Initial doc framework and several docstrings

doc/clustering.rst
doc/conf.py
doc/graph_tool.rst
doc/index.rst
doc/modules.rst
doc/numpydoc.py
doc/numpydoc.pyc
doc/quickstart.rst
doc/sphinxext/LICENSE.txt
doc/sphinxext/__init__.py
doc/sphinxext/autosummary.py
doc/sphinxext/autosummary_generate.py
doc/sphinxext/comment_eater.py
doc/sphinxext/compiler_unparse.py
doc/sphinxext/docscrape.py
doc/sphinxext/docscrape_sphinx.py
doc/sphinxext/numpydoc.py
doc/sphinxext/only_directives.py
doc/sphinxext/phantom_import.py
doc/sphinxext/plot_directive.py
doc/sphinxext/tests/test_docscrape.py
doc/sphinxext/traitsdoc.py
src/graph_tool/__init__.py
src/graph_tool/clustering/__init__.py
src/graph_tool/core.py

commit 60d0ec8e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-11

    Fix seeding problem with random graph generation

src/graph_tool/generation/__init__.py

commit 9e8fd596
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-11

    Fix drawing of undirected graph

src/graph_tool/draw/__init__.py

commit 7e99bed0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-11

    Add docstrings to clustering module

src/graph_tool/clustering/__init__.py

commit 300589cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2009-01-11

    Add vertex and edge average calculation
    
    This adds vertex_average() and edge_average() to the stats module.

src/graph/stats/Makefile.am
src/graph/stats/graph_average.cc
src/graph/stats/graph_average.hh
src/graph/stats/graph_stats_bind.cc
src/graph_tool/stats/__init__.py

commit 8cd70848
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-12-07

    Fix compilation with boost 1.37

configure.ac
src/graph/graph.hh

commit 3a5c196e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-12-02

    Re-implement community graph calculation

src/graph/community/Makefile.am
src/graph/community/graph_community.cc
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph_tool/community/__init__.py

commit 7cdf9658
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-12-02

    Expose internal graph and index maps in GraphInterface
    
    This makes operations on graphs more flexible in some circumstances.

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh

commit c153e0c0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-12-01

    Re-activate community detection code
    
    This includes the community sub-module.

configure.ac
src/graph/Makefile.am
src/graph/community/Makefile.am
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/community/__init__.py

commit 5b0f9286
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-11-18

    Fix bug in option parsing

src/graph-tool

commit 274511e6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-11-17

    Fix command line parsing of scalar assortativity coefficient

src/graph_tool/__init__.py

commit 6ba338ef
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-11-07

    Graph drawing: fix edge properties and other things

src/graph_tool/draw/__init__.py

commit 869ac654
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-26

    Clean-up module loading
    
    Reduce duplication of code for loading C++ modules.

src/graph_tool/Makefile.am
src/graph_tool/clustering/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/dl_import.py
src/graph_tool/generation/__init__.py
src/graph_tool/misc/__init__.py
src/graph_tool/stats/__init__.py
src/graph_tool/util/__init__.py

commit 86436d9d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-26

    Clean up Makefile.am files
    
    Add global variables to configure.ac, to avoid unnecessary multiple
    definitions.

configure.ac
src/graph/clustering/Makefile.am
src/graph/correlations/Makefile.am
src/graph/generation/Makefile.am
src/graph/misc/Makefile.am
src/graph/util/Makefile.am
src/graph_tool/Makefile.am

commit 93db6fa9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-23

    Get rid of virtual functions in graph rewiring code
    
    Unnecessary dynamic polymorphism is replaced by static polymorphism, in
    the definitions of the rewiring strategies.

src/graph/misc/graph_rewiring.hh

commit 5fa50e88
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-21

    Re-include graph rewiring code in the new scheme
    
    This also creates the misc sub-module. This may be re-organized in the
    future.

configure.ac
src/graph/Makefile.am
src/graph/misc/Makefile.am
src/graph/misc/graph_misc.cc
src/graph/misc/graph_rewiring.cc
src/graph/misc/graph_rewiring.hh
src/graph_tool/Makefile.am
src/graph_tool/all.py
src/graph_tool/misc/__init__.py

commit b1e1bc5e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-05

    Rewiring: bugfix, improvements and restructuring resulting in cleaner and faster code
    
    Restructure the rewiring code, introducing further abstraction through
    class inheritance.
    
    Both uncorrelated and correlated cases draw edges directly.
    This has actually proven faster than drawing vertices for the correlated
    case, since realizing that indexes could be stored instead of edges.
    Doing so avoids changes in the pool of candidate edges, which in turn
    removes the need to rebuild it for each edge to rewire.
    Consequently, it also makes the uncorrelated case a lot quicker.
    
    In the uncorrelated undirected case, the new code also fixes a serious
    bug: when building the edge pool, only one end of each edge was looked
    at, because the "edges" vector is not equivalent to drawing all
    out_edges from all vertices, as is done now.

src/graph/misc/graph_rewiring.hh

commit e4aaa63b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-21

    Add graph_tool.clustering to graph_tool.all

src/graph_tool/all.py

commit a204d6f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-20

    Fix compilation with openmp in graph_search code

src/graph/util/graph_search.hh

commit 4cfd772d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-13

    Added util sub-module
    
    This contains at the moment functions to perform basic vertex and edge
    searches.

configure.ac
src/graph/Makefile.am
src/graph/util/Makefile.am
src/graph/util/graph_search.cc
src/graph/util/graph_search.hh
src/graph/util/graph_util_bind.cc
src/graph_tool/Makefile.am
src/graph_tool/util/__init__.py

commit 7538d895
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-13

    Add --with-numpy and --with-scipy options to configure
    
    This allows specifying where numpy and scipy are installed, which can be
    useful when installing graph_tool in a different location.

configure.ac

commit d6b03c17
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-10

    Fix compilation error on 64 bit architectures
    
    This adds missing uint64_t type to the list o supported numpy types.

src/graph/numpy_bind.hh

commit 1dad209a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-10

    Fix compilation error with OpenMP

src/graph/correlations/graph_correlations.hh

commit 16d85651
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-07

    Add convenience module graph_tool.all
    
    This allows to import all submodules from graph_tool with one command,
    e.g.,
    
       from graph_tool.all import *

src/graph_tool/all.py

commit 1c84328d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-10-07

    Makefiles: AM_CPPFLAGS use srcdir
    
    Add $(srcdir) to include paths in AM_CPPFLAGS so that we can
    compile the program writing all targets into a directory separate
    from the sources.
    This is done simply by creatig a subdirectory of the project root
    and running "../configure" and "make" inside it.

src/graph/Makefile.am
src/graph/clustering/Makefile.am
src/graph/correlations/Makefile.am
src/graph/generation/Makefile.am
src/graph/stats/Makefile.am

commit 48aec77d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-26

    Add dedicated average correlation calculation
    
    This is a re-implementation based on new histogram code, which does not
    build a 2D histogram, and is thus more exact and uses less memory.

src/graph/correlations/Makefile.am
src/graph/correlations/graph_avg_correlations.cc
src/graph/correlations/graph_avg_correlations_combined.cc
src/graph/correlations/graph_avg_correlations_imp1.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/histogram.hh
src/graph_tool/correlations/__init__.py

commit dc184b46
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-24

    Fix edge indexing problem when modifying graph
    
    This fixes a rather central bug, which causes duplicated indexes if
    edges are removed and then new ones are added. Edge indexes are now
    recycled as they are removed and then new ones are added. This still
    guarantees O(1) complexity when adding or removing edges.

src/graph/graph.hh
src/graph/graph_python_interface.cc
src/graph_tool/core.py

commit 562d8aa5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-24

    Fix autogen.sh
    
    Simplify autogen.sh and remove ltmain.sh from repository, which should
    be included as necessary from libtoolize.

autogen.sh
ltmain.sh

commit c804ff8e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-22

    Add load_graph utility function
    
    Avoids having to do
    
        g = Graph()
        g.load("foo")
    
    each time. Now one can do simply,
    
        g = load_graph("foo")
    
    Fantastic.

src/graph_tool/__init__.py
src/graph_tool/core.py

commit ecabb934
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-19

    Avoid unnecessary string assembly inside inline()

src/graph_tool/run_action/inline.py

commit a4bff0c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-10

    Fix proper handling of properties in graph_draw

src/graph_tool/draw/__init__.py

commit 1d474dee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-10

    Fix problem with ugly type names in run_action

src/graph_tool/run_action/inline.py

commit 98ee958f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-09-10

    Convert histograms counts to float64 by default

src/graph_tool/stats/__init__.py

commit ccebfe00
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-08-15

    Fix possible circular reference with property maps
    
    Use weakrefs to keep track of known property maps in graphs, and owner
    graphs in property maps to avoid circular references, which may lead to
    memory leaks.
    
    This also fixes a vertex removal bug.

src/graph_tool/core.py

commit 403f2605
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-08-10

    Add graph_tool.draw module
    
    This adds a graph_draw() functions which draws graphs in variety of
    layouts and formats, and also to the screen, using the python graphviz
    bindings.

src/graph_tool/Makefile.am
src/graph_tool/draw/__init__.py

commit c029a582
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-28

    Fix deadlock in random graph generation
    
    Fix possible deadlock condition in random graph generation with
    no_parallel and/or no_self_loops.

src/graph/generation/graph_generation.hh

commit ace9d758
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-22

    Fix OpenMP reduction problem

src/graph/clustering/graph_clustering.hh

commit 3ba46e75
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-22

    Fix graph copying and filtered graph copying semantics
    
    Graphs are now exactly copied, including filter state and filter
    property maps.

src/graph/graph_copy.cc
src/graph_tool/core.py

commit 919ade0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-21

    Improve run_action module
    
    Use tr1::tuple instead of boost::tuple to get around maximum tuple size
    limit (this requires GCC 4.3). Introduce get_prop<> template function to
    facilitate access of property maps from inline C++ code.

src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_template.hh

commit 149c5c94
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-21

    Install missing decorators.py

src/graph_tool/Makefile.am

commit 872d1c5d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-21

    Fix bug when copying graph with filtering disabled
    
    Also, get rid of g.underlying_graph(), and rely on "private" variable
    g._Graph__graph instead.

src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph_tool/clustering/__init__.py
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/stats/__init__.py

commit 36982c7a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-20

    Correctly normalize betweenness centrality
    
    Betweenness centrality should be differently normalized for undirected
    and directed graphs, i.e., (n-2)*(n-1)/2 vs. (n-2)*(n-1),
    respectively. Also, edge centrality should be respectively normalized
    with n*(n-1)/2 and n*(n-1).

src/graph/misc/graph_betweenness.cc

commit 2cb064cf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-20

    Correctly normalize betweenness centrality
    
    Betweenness centrality should be differently normalized for undirected
    and directed graphs, i.e., (n-2)*(n-1)/2 vs. (n-2)*(n-1),
    respectively. Also, edge centrality should be respectively normalized
    with n*(n-1)/2 and n*(n-1).

src/graph/graph_betweenness.cc

commit 3e874f0c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-15

    Fix automake files

configure.ac
src/Makefile.am
src/graph_tool/Makefile.am

commit 115b480f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-15

    Remove internal properties from run_action code

src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_template.hh

commit 025fe7d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-15

    Delete graph-tool script
    
    No longer functional or relevant.

src/graph-tool

commit 003bd47f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-15

    Port clustering algorithms to new interface
    
    A new 'clustering' sub-module was created.

configure.ac
src/graph/Makefile.am
src/graph/clustering/Makefile.am
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph_tool/clustering/__init__.py

commit 242bfff7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-07-15

    Propagate external property map usage to all algorithms

src/graph/graph_bind.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/stats/graph_histograms.cc
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/stats/__init__.py

commit e984bf8e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-06-17

    Externalize property maps by default
    
    This commit removes the internal property maps from the GraphInterface
    class, and makes all property maps external by default. The internal
    property maps were moved to the python layer.

src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/stats/graph_components.cc
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_parallel.cc
src/graph_tool/core.py
src/graph_tool/decorators.py

commit 07dbd3b0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-06-17

    Always convert histogram counts to float64
    
    This is to avoid a common error of not being able to correctly normalize
    a histogram because of truncated integer division.

src/graph_tool/stats/__init__.py

commit e5a0b5e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-06-01

    Fix edge re-indexing, when only one edge is deleted

src/graph/graph_filtering.cc

commit 818bf153
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-30

    Fix graphviz I/O

src/graph/graph_io.cc

commit e1879d1c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-19

    Add support for masking return values in run_action

src/graph_tool/run_action/inline.py

commit 9329cd53
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-13

    Fix installation of stats module

src/graph_tool/Makefile.am

commit 6a70e32f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-09

    Fix handling of edge index property maps

src/graph/graph_properties.hh
src/graph/graph_python_interface_export.cc

commit 7d8195d4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-06

    Improve compatibility between weave's cxx and boost::python
    
    Other objects are now automatically converted (tuple, lists, dicts,
    str).

src/graph/graph_bind.cc

commit 811cc97b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-06

    Fix index property python interface
    
    This fixes the representation of property maps which don't have a
    value type included in the value_types list, such as index properties.

src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc

commit 172e1326
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-06

    Improve edge re-indexing complexity
    
    It was needlessly O(E^2), and now is O(E).

src/graph/graph_filtering.cc

commit 7c957a60
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-06

    Fix graph copying
    
    Edge indexes weren't properly copied.

src/graph/graph_copy.cc

commit dab78eee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-02

    Fix usage of bool property maps in run_action

src/graph_tool/run_action/run_action_template.hh

commit 5e8d708e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-02

    Fix edge re-indexing

src/graph/graph_filtering.cc

commit 713c9854
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-01

    Fix assortativity for undirected graphs (ticket #52)

src/graph/correlations/graph_assortativity.hh
src/graph/graph_bind.cc
src/graph/graph_util.hh

commit b74c2919
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-05-01

    Fix assortativity for undirected graphs (ticket #52)

src/graph/graph_assortativity.cc

commit b96e8035
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-23

    Finish up stats module

src/graph/stats/graph_histograms.hh
src/graph_tool/stats/__init__.py

commit cfb62351
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-15

    Fix boost and boost::python ambiguity and numpy problems in run_action

configure.ac
src/graph/graph_bind.cc
src/graph_tool/run_action/inline.py

commit 780a8055
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-14

    Port graph histograms and misc statistics to new filtering engine
    
    Python binding will follow

src/graph/stats/Makefile.am
src/graph/stats/graph_components.cc
src/graph/stats/graph_components.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph/stats/graph_parallel.cc
src/graph/stats/graph_parallel.hh
src/graph/stats/graph_stats_bind.cc

commit 0097e2ba
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-14

    Fix GCC 4.3 compilation error
    
    GCC 4.3 complains when a typedef overrides the meaning of another type.

src/graph/graph_filtering.hh

commit 5e32b3b6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-14

    Improve memory usage during compilation
    
    Avoiding use of lambda::bind when not necessary (or very convenient).

src/graph/correlations/graph_correlations_combined.cc

commit ee25eabe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-14

    Fix run_action
    
    A couple of bugs fixed. Local frame dict is read-only in python, so the
    updated arguments are returned in a dict instead.

src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_properties.hh
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_template.hh

commit 3799da5b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-14

    Cleanup and update autoconf and automake files

autogen.sh
configure.ac
src/graph/Makefile.am
src/graph/correlations/Makefile.am
src/graph/generation/Makefile.am

commit 360a3395
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-10

    Correlations algorithms refactoring
    
    The whole histogram code has been redone, and the code has been
    simplified. The three-point vertex-edge-vertex correlation has been
    scrapped, since it's not frequently used, and would make compilation
    even more expensive.
    
    This also adds some missing files to the generation routine.

configure.in
src/graph/Makefile.am
src/graph/correlations/Makefile.am
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_bind.cc
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_combined.hh
src/graph/correlations/graph_correlations_combined_corr.cc
src/graph/correlations/graph_correlations_combined_imp1.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/correlations/graph_correlations_imp2.cc
src/graph/correlations/graph_correlations_imp3.cc
src/graph/correlations/graph_correlations_neighbours.cc
src/graph/correlations/graph_correlations_neighbours.hh
src/graph/correlations/graph_correlations_neighbours_imp1.cc
src/graph/correlations/graph_correlations_neighbours_imp2.cc
src/graph/correlations/graph_correlations_neighbours_imp3.cc
src/graph/correlations/graph_correlations_neighbours_imp4.cc
src/graph/correlations/graph_correlations_neighbours_imp5.cc
src/graph/correlations/graph_correlations_neighbours_imp6.cc
src/graph/correlations/graph_edge_correlations.cc
src/graph/correlations/graph_edge_correlations.hh
src/graph/correlations/graph_edge_correlations_imp1.cc
src/graph/correlations/graph_edge_correlations_imp2.cc
src/graph/correlations/graph_edge_correlations_imp3.cc
src/graph/correlations/graph_edge_correlations_imp4.cc
src/graph/correlations/graph_edge_correlations_imp5.cc
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/histogram.hh
src/graph/numpy_bind.hh
src/graph_tool/Makefile.am
src/graph_tool/core.py
src/graph_tool/correlations/__init__.py
src/graph_tool/generation/__init__.py

commit 6063ece0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-06

    Rewritten graph generation routine.
    
    It is now much simpler, and works better.

src/graph/generation/Makefile.am
src/graph/generation/graph_generation.cc
src/graph/generation/graph_generation.hh

commit 90462548
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-04-04

    Fix graph copying

src/graph/graph_copy.cc

commit b7237044
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-03-27

    Add test suites
    
    This adds the graph_tool.test module, which can be run with
    graph_tool.test.run()

src/graph_tool/graph.pyc
src/graph_tool/test/__init__.py
src/graph_tool/test/basic.py
src/graph_tool/test/io.py
src/graph_tool/test/properties.py

commit 275b4c3e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-03-27

    Port run_action to the new filtering engine
    
    Put the run_action function in a separate submodule, and make it work
    properly with the new code.

src/graph_tool/run_action.py
src/graph_tool/run_action/__init__.py
src/graph_tool/run_action/inline.py
src/graph_tool/run_action/run_action_template.hh

commit 99bf21c8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-03-27

    Port graph I/O to new filtering engine, enable graph pickling, and fix several issues
    
    Now graphml files properly contain all the supported value types, which
    are all perfectly preserved when read (floating point data is now saved
    in hexadecimal format). Several other improvements were made, such as
    the ability to read and write to python file-like objects.
    
    It is also now possible to have arbitrary python object properties, and
    store them persistently (which is done internally with the pickling
    interface).
    
    vector<bool> was totally abolished, since its implementation is quite
    broken. See: http://www.gotw.ca/publications/N1211.pdf and
    http://www.gotw.ca/publications/N1185.pdf Now a uint8_t (aka. char) is
    used in graph properties instead of a bool.
    
    Graph types can now be fully pickled (this may not be feasible
    memory-wise if the graph is too large, since the whole XML
    representation is dumped to a string before it is saved on disc).

src/boost-workaround/boost/graph/graphml.hpp
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graphml.cpp
src/graph/histogram.hh
src/graph/numpy_bind.hh
src/graph_tool/Makefile.am
src/graph_tool/__init__.py
src/graph_tool/__init__.pyc
src/graph_tool/core.py
src/graph_tool/core.pyc
src/graph_tool/io.py

commit 3cfff0cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-02-17

    Split libgraph_tool into sub-modules and add test cases
    
    This commit splits libraph_tool into different libraries:
    
       - libgraph_tool_core
       - libgraph_tool_clustering (*)
       - libgraph_tool_community (*)
       - libgraph_tool_correlations (*)
       - libgraph_tool_distance (*)
       - libgraph_tool_generation (*)
       - libgraph_tool_layout (*)
       - libgraph_tool_misc (*)
       - libgraph_tool_stats (*)
    
    It also adds the python sub-module 'test', which provides extensive unit
    testing of the core functionality. The core library is fully functional
    and all test pass successfully.
    
    (*) -> module needs to be ported to new refactoring, and does not yet build

Makefile.am
configure.in
src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/fruchterman_reingold.hpp
src/boost-workaround/boost/graph/graphml.hpp
src/boost-workaround/boost/graph/kamada_kawai_spring_layout.hpp
src/graph/Makefile.am
src/graph/clustering/graph_clustering.cc
src/graph/clustering/graph_clustering.hh
src/graph/clustering/graph_extended_clustering.cc
src/graph/clustering/graph_extended_clustering.hh
src/graph/community/graph_community.cc
src/graph/community/graph_community.hh
src/graph/community/graph_community_network.cc
src/graph/community/graph_community_network.hh
src/graph/correlations/Makefile.am
src/graph/correlations/graph_assortativity.cc
src/graph/correlations/graph_assortativity.hh
src/graph/correlations/graph_correlations.cc
src/graph/correlations/graph_correlations.hh
src/graph/correlations/graph_correlations_combined.cc
src/graph/correlations/graph_correlations_combined.hh
src/graph/correlations/graph_correlations_combined_corr.cc
src/graph/correlations/graph_correlations_combined_corr_imp1.cc
src/graph/correlations/graph_correlations_combined_imp1.cc
src/graph/correlations/graph_correlations_imp1.cc
src/graph/correlations/graph_correlations_imp2.cc
src/graph/correlations/graph_correlations_imp3.cc
src/graph/correlations/graph_correlations_neighbours.cc
src/graph/correlations/graph_correlations_neighbours.hh
src/graph/correlations/graph_correlations_neighbours_imp1.cc
src/graph/correlations/graph_correlations_neighbours_imp2.cc
src/graph/correlations/graph_correlations_neighbours_imp3.cc
src/graph/correlations/graph_correlations_neighbours_imp4.cc
src/graph/correlations/graph_correlations_neighbours_imp5.cc
src/graph/correlations/graph_correlations_neighbours_imp6.cc
src/graph/correlations/graph_edge_correlations.cc
src/graph/correlations/graph_edge_correlations.hh
src/graph/correlations/graph_edge_correlations_imp1.cc
src/graph/correlations/graph_edge_correlations_imp2.cc
src/graph/correlations/graph_edge_correlations_imp3.cc
src/graph/correlations/graph_edge_correlations_imp4.cc
src/graph/correlations/graph_edge_correlations_imp5.cc
src/graph/distance/graph_distance.cc
src/graph/distance/graph_distance.hh
src/graph/distance/graph_distance_sampled.cc
src/graph/distance/graph_distance_sampled.hh
src/graph/generation/graph_generation.cc
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_copy.cc
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/graphml.cpp
src/graph/histogram.hh
src/graph/layout/graph_layout.cc
src/graph/misc/graph_betweenness.cc
src/graph/misc/graph_line_graph.cc
src/graph/misc/graph_minimum_spanning_tree.cc
src/graph/misc/graph_reciprocity.cc
src/graph/misc/graph_rewiring.cc
src/graph/misc/graph_rewiring.hh
src/graph/mpl_nested_loop.hh
src/graph/read_graphviz_spirit.cpp
src/graph/shared_map.hh
src/graph/stats/graph_histograms.cc
src/graph/stats/graph_histograms.hh
src/graph_tool/Makefile.am
src/graph_tool/__init__.py
src/graph_tool/__init__.pyc
src/graph_tool/core.py
src/graph_tool/core.pyc
src/graph_tool/graph.pyc
src/graph_tool/run_action.py

commit 0b66e272
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-02-08

    Refactor metaprogramming engine
    
    This is a huge commit which completely refactors the metaprogramming
    engine which generates and selects (at run time) the graph view type and
    the desired algorithm implementation (template instantiation) that runs
    on it.
    
    Things are laid out now as following. There exists a main underlying
    graph type (GraphInterface::multigraph_t) and several other template
    classes that mask it some way or another, in a hierarchic fashion:
    
         multigraph_t -> filtered_graph (edges only, vertices only, both)
             |                               |           |           |
             |                               |           |           |
             |-------(reversed_graph)--------|-----------|-----------|
             |                               |           |           |
             \------(UndirectedAdaptor)------------------------------/
    
    The filtered_graph filters out edges and/or vertices from the graph
    based on some scalar boolean property. The reversed_graph reversed the
    direction of the edges and, finally, the UndirectedAdaptor treats the
    original directed graphs as undirected, transversing the in- and
    out-edges of each vertex indifferently. Thus, the total number of graph
    view types is 12. (The option --disable-graph-filtering can be passed to
    the configure script, which will disable graph filtering altogether and
    bring the total number down to 3, to reduce compile time and memory
    usage)
    
    In general, some specific algorithm, implemented as a template function
    object, needs to be instantiated for each of those types. Furthermore,
    the algorithm may also depend on other types, such as specific
    property_maps. Thus, the following scheme is used:
    
        struct my_algorithm // algorithm to be implemented
        {
            template <class Graph, class PropertyMap>
            void operator()(Graph *g, PropertyMap p, double& result) const
            {
                // ...
            }
        };
    
        // in order for the above code to be instantiated at compile time
        // and selected at run time, the run_action template function object
        // is used from a member function of the GraphInterface class:
    
        double GraphInterface::MyAlgorithm(string prop_name)
        {
            double result;
            boost::any vprop = prop(property, _vertex_index, _properties);
            run_action<>()(*this, bind<void>(my_algorithm(), _1, _2,
                                             var(result)),
                           vertex_scalar_properties())(vprop);
            return result;
        }
    
    The whole code was changed to reflect this scheme, but now things are
    more centralized and less ad-hoc code needed to be
    written. Unfortunately, due to GCC's high memory usage during template
    instantiations, some of the code (namely all the degree correlation
    things) had to be split in multiple compilation units... Maybe this will
    change in the future if GCC gets optimized.
    
    This commit also touches other parts of code. More specifically, the way
    filtering gets done is very different. Now we only filter on boolean
    properties, and with the above scheme, the desired implementation runs
    with the correct chosen type, and no implicit type conversions should
    ever happen, which would have a bad impact on performance.

configure.in
ltmain.sh
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_assortativity.cc
src/graph/graph_assortativity.hh
src/graph/graph_betweenness.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_clustering.hh
src/graph/graph_community.cc
src/graph/graph_community.hh
src/graph/graph_community_network.cc
src/graph/graph_community_network.hh
src/graph/graph_correlations.cc
src/graph/graph_correlations.hh
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_combined.hh
src/graph/graph_correlations_combined_corr.cc
src/graph/graph_correlations_imp1.cc
src/graph/graph_correlations_imp2.cc
src/graph/graph_correlations_imp3.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_correlations_neighbours.hh
src/graph/graph_correlations_neighbours_imp1.cc
src/graph/graph_correlations_neighbours_imp2.cc
src/graph/graph_correlations_neighbours_imp3.cc
src/graph/graph_correlations_neighbours_imp4.cc
src/graph/graph_correlations_neighbours_imp5.cc
src/graph/graph_correlations_neighbours_imp6.cc
src/graph/graph_distance.cc
src/graph/graph_distance.hh
src/graph/graph_distance_sampled.cc
src/graph/graph_distance_sampled.hh
src/graph/graph_edge_correlations.cc
src/graph/graph_edge_correlations.hh
src/graph/graph_edge_correlations_imp1.cc
src/graph/graph_edge_correlations_imp2.cc
src/graph/graph_edge_correlations_imp3.cc
src/graph/graph_edge_correlations_imp4.cc
src/graph/graph_edge_correlations_imp5.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_extended_clustering.hh
src/graph/graph_filtering.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_io.cc
src/graph/graph_layout.cc
src/graph/graph_line_graph.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_python_interface_export.cc
src/graph/graph_reciprocity.cc
src/graph/graph_rewiring.cc
src/graph/graph_rewiring.hh
src/graph/graph_selectors.cc
src/graph/graph_selectors.hh
src/graph/graph_util.hh
src/graph/mpl_nested_loop.hh

commit 20574c73
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-01-24

    Fix problem with linkers that don't support the '-E' flag
    
    The '-E' flag is necessary with GNU ld so that all dynamic symbols are
    properly exported, and things like typeid() work across DSO
    boundaries. However there are other linkers out there which don't accept
    this option. This commit checks for this and drops the option in that
    case. Let us hope those linkers do the right thing, or wait until
    someone complains...

acinclude.m4
configure.in
src/graph/Makefile.am

commit 6ce01477
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2008-01-22

    Check if SIGPWR is defined, for systems that don't support it (ie. MacOSX).

src/graph/graph.cc

commit 1e9d11d1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-21

    Add vprop_long_t and eprop_long_t to run_action() generated code

src/graph_tool/__init__.py

commit 4a7da8a9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-21

    Directory restructuring of graph_tool Python module (now a package)
    
    Everything was moved into the graph_tool directory, which should have,
    after installation, the following structure:
    
    graph_tool/                          Top-level package
          __init__.py                    Initialize the graph_tool package
          libgraph_tool.so               libgraph_tool submodule
          libgraph_tool.la               libtool file for libgraph_tool
          include/                       C++ include files for dynamically
                                         compiled code

configure.in
src/Makefile.am
src/graph/Makefile.am
src/graph/graph_bind.cc
src/graph_tool/Makefile.am
src/graph_tool/__init__.py

commit 0c1f0df2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-14

    Fix visibility/RTTI problem with run_action()
    
    Some visibility voodoo is necessary to ensure that RTTI work properly
    across DSO boundaries, which is necessary to properly handle dynamic
    property maps and such. Additionally, the action template must have a
    different name each time the action code changes, to avoid additional
    weirdness.
    
    This also adds some other utility functions/typedefs to make writing
    "inline" c++ code easier.

src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_properties.hh
src/graph_tool.py

commit 5b45d806
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-14

    Fix add_edge_property()
    
    add_edge_property() should return a edge property not a vertex_property

src/graph_tool.py

commit 866bb994
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-14

    Add support for running arbitrary C++ code from python
    
    It is now possible to run arbitrary "inline" C++ code from python, using
    scipy.weave, as such:
    
            g = graph_tool.Graph()
            g.load("foo.xml")
            value = 2.0
            g.run_action('cout << num_vertices(g) << " " << value << endl;',
                         ["value"]);
    
    The code gets compiled the first time, and is reused after that. Python
    local and global variables can be passed to C++, as shown above, by
    specifying a list of passed variables as the second argument.

src/graph/Makefile.am
src/graph/graph.hh
src/graph_tool.py

commit cb15708b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-13

    Some reorganization and change check_filter() to run_action()

src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_assortativity.cc
src/graph/graph_betweenness.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_community_network.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_edge_correlations.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_io.cc
src/graph/graph_layout.cc
src/graph/graph_line_graph.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/graph_reciprocity.cc
src/graph/graph_rewiring.cc
src/graph/histogram.hh

commit db440664
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-06

    Fix edit_{vertex|edge|graph}_property()
    
    The graph object passed to the edit function is now a instance of the
    Graph class which wraps GraphInterface, not a GraphInterface instance.

src/graph/graph.hh
src/graph/graph_properties.cc
src/graph_tool.py

commit de0a0a8e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-06

    Implement lazy loading of graphs
    
    Graphs can now be loaded "lazily" with the lazy_load() function, which
    works just like load(), but doesn't actually load the graph, which is
    delayed until the graph is accessed for the first time, e.g.
    
        import graph_tool
    
        g = graph_tool.Graph()
        g.lazy_load("example.xml")
    
        g.number_of_vertices()  # <- the graph is only loaded here

src/graph_tool.py

commit 5c37ba28
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-03

    Move remaining parallelism check out of the outer/inner loops and into the parallel_check() function.

src/graph/graph_rewiring.cc

commit fb8200fe
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-12-03

    Fixes bugs introduced in code restructuring.
    
    3) missing parallel edge check in uncorrelated strategy
    2) "_in()" for target and source of "target swap edge"
    1) order of arguments of swap_edge_triad::parallel_check
    
    melodrama time...
    "premature optimization is the root of all evil"
    "careless abstraction are the fruits of its tree"

src/graph/graph_rewiring.cc

commit a1be5db4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-03

    Trivial indentation fix

src/graph/graph_adaptor.hh

commit c65210b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-03

    Properly parse some degree arguments, which can also be properies

src/graph_tool.py

commit d5356666
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-03

    Properly parse command line options with empty arguments, eg. "foo||bar"

src/graph-tool

commit 4a3e0468
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-12-03

    Some reorganization and more code comments of graph_rewiring.cc
    
    The check for parallel edges was cleaned up and abstracted into a
    function, and other minor things were changed. Code comments were added
    to places where it might have been hard to understand.

src/graph/graph_python_interface.hh
src/graph/graph_rewiring.cc
src/graph/graph_selectors.hh

commit d0cf197c
Merge: 1a0e9b5f 981d3b76
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-30

    Merge branch 'rewiring'
    
    Improve formatting of src/graph/graph_rewiring.cc (line breaks at column
    80, typedefs, trailing whitespace removal, etc)
    
    Conflicts:
    
            src/graph-tool
            src/graph/graph_bind.cc

commit 1a0e9b5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-30

    Further improvements of the python interface
    
    Property maps can now be obtained as such:
    
             weight = g.edge_properties['weight']
             print weight[v] # v is a Vertex object
             weight[v] = 2.0
             # and so on...
    
    The list of properties is obtained from g.vertex_properties,
    g.edge_properties and g.graph_properties, which can be read as
    dictionaries. The last can be set also, as such:
    
             g.graph_properties = {foo:"bar", baz:42}
    
    Functions to add and remove vertices or adges were also added
    (add_{vertex|edge}, remove_{vertex|edgge}).
    
    Vertex and Edge types can also now be printed for convenience, as such:
    
           for v in g.vertices():
               print v
           for e in g.edges():
               print e
    
    which results, for example, in:
    0
    1
    2
    3
    4
    5
    6
    (0,1)
    (1,2)
    (2,6)
    (3,4)
    (4,5)
    (4,2)
    (5,6)
    (6,1)
    
    (this also adds the forgotten graph_tool.py file, which was previously
    on .gitignore)

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph_tool.py

commit 981d3b76
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-11-27

    Working and fast rewiring code for correlated and uncorrelated.
    
    Major changes to both correlated and uncorrelated rewiring code.
    Both cases are now functional and use iterative shuffling.
    Uncorrelated picks edges to rewire directly, correlated picks
    vertices in order to choose edges.

src/graph/graph_rewiring.cc

commit e1375c3c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-26

    Line breaks at column 80 and remove trailing whitespace

src/graph/graph_extended_clustering.cc

commit 069e3599
Merge: 06358b7c e87d0713
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-26

    Merge git://milgram.sociology.columbia.edu/graph-tool into abdo-clustering

commit 06358b7c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-26

    Further improvement of python interface
    
    Vertices and edges can be accessed from the graph class, as such:
    
        import graph_tool
        g = graph_tool.Graph()
        for v in g.vertices():
            for e in v.out_edges():
               # do something...
    
    Additionally, the --edit-{vertex|edge|graph}-property was ported to the
    new interface, and is working again, as it used to.
    
    The Vertex and Edge class no longer have the 'get_property' and
    'set_property' method. They'll be replaced by a new method of accessing
    property maps.

src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_properties.cc
src/graph/graph_python_interface.cc
src/graph/graph_python_interface.hh
src/graph/graph_selectors.hh

commit 8b32d7fc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-20

    Complete re-factoring of python module and command line tool
    
    The program was split in two parts:
    
        1. A python module, graph_tool.py, which encapsulates the graph
           manipulation under a Graph class. Now the following can be done:
    
                  import graph_tool
                  g1 = graph_tool.Graph()
                  g2 = graph_tool.Graph()
                  g1.load("foo.xml")
                  g2.load("bar.xml")
                  print g1.number_of_vertices(), g2.number_of_vertices()
    
        2. A standalone command line tool, graph-tool, which imports
           graph_tool.py, and exposes the Graph methods as command line
           options.
    
    The whole command line engine was thus (once again) entirely
    rewritten. It is now Crack-Free™, and simply mirrors the methods of the
    Graph class as command line options, using, for this, the beauty of
    function decorators. It classifies now, I believe, as Pythonic™.

src/Makefile.am
src/graph-tool

commit f005e928
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-11

    Removed unnecessary semicolon

src/graph/graph_assortativity.cc

commit 4e2522a4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-10

    Sync properties 'value_types' to that of graph_properties.hh in python interface
    
    This fixes a bug where properties with 'long long' types were not handled
    properly through the python interface.

src/graph/graph_python_interface.hh

commit 9aea846e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-10

    Remove useless unsigned comparison

src/graph/graph.cc

commit 0b15235f
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-11-04

    Correlated random rewiring functional
    
    Several changes in the random rewiring code, making it fully
    functional for the correlated case.
    The reshuffling operations lag in efficiency, even though already
    the algorithm runs in little time.

src/graph/graph_rewiring.cc

commit e87d0713
Merge: 5ffa57c4 07be3fdc
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-11-04

    Merge branch 'master' of git://git.forked.de/graph-tool into directed_extended_clustering
    
    Conflicts:
    
            src/graph/graph_extended_clustering.cc

commit 3fedbb09
Merge: a76a512a 07be3fdc
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-11-04

    Merge branch 'master' of git://finn.forked.de/~count0/stuff/workspace/graph-tool into rewiring-merge

commit 07be3fdc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-04

    Code cleanups, and cosmetic changes
    
    Line breaks at column 80 were added, and all trailing whitespace was deleted. Code
    comments were modified and some more were added.

src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_assortativity.cc
src/graph/graph_betweenness.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_community_network.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_edge_correlations.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_io.cc
src/graph/graph_layout.cc
src/graph/graph_line_graph.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_interface.hh
src/graph/graph_reciprocity.cc
src/graph/graph_selectors.hh
src/graph/graphml.cpp
src/graph/histogram.hh
src/graph/shared_map.hh

commit a510c363
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-11-04

    Fix label-parallel-edges property type
    
    It should be 'size_t' instead of 'long'.

src/graph/graph.cc

commit a76a512a
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-26

    fixes option definition for random-rewire
    
    bool entries in option random-rewire were stated as string,
    causing graph-tool to crash before loading.

src/graph-tool

commit f0e41bb2
Merge: 42a8d6c3 8ed48c65
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-24

    updates from master

commit 8ed48c65
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-24

    Fix Set{Vertex|Edge}FilterRange() when boundaries are -inf
    
    This fixes the same problem as commit 6663be7135, but which arises
    when a filter range boundary is -inf (such as "<=100").

src/graph/graph.cc

commit 5ffa57c4
Merge: 74f1cdae 300d6f4a
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-23

    updates from master

commit 42a8d6c3
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-23

    Fix little bug in commit a6a8068
    
    A comma (,) was missing before the rewiring option in src/graph-tool

src/graph-tool

commit 307deccb
Merge: e1e2f3c2 300d6f4a
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-23

    updates from master

commit 300d6f4a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-24

    Fix vertex and edge filtering, when only one is active
    
    When only one of vertex or edge filtering was disabled, the allowed
    range of the disabled filter was set to
    ]numeric_limits<double>::min(), numeric_limits<double>::max()[, and
    the selected filtering property was the respective index. But
    according to the STL documentation from GCC,
    numeric_limits<>::min() returns:
    
       "The minimum finite value, or for floating types with
        denormalization, the minimum positive normalized value."
    
    which is always positive for double (!), thus introducing a weird
    regression, where the first vertex (index 0) is always filtered out if
    only the edge filter is active, and vice-versa.

src/graph/graph.cc

commit d28e2f34
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-24

    Fix --insert-edge-index

src/graph-tool

commit e1e2f3c2
Merge: ae2fe620 f51a6bd2
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-23

    merging changes from old rewiring branch
    
    and now we have a good consistent branch where the removal of rewiring
    has been properly reverted before new work is added, so it can be
    easily merged with the master branch in the future.
    
    Conflicts:
    
            src/graph-tool

commit ae2fe620
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-23

    Revert "Remove graph rewiring"
    
    It's still buggy (of course), but now we'll try to fix it in it's own
     branch.
    
    This reverts commit 1cdbdeef312ea80d5744ef3fe7542f8b44d0bb03.

src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_rewiring.cc

commit 32ae550d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-23

    Fix GetEdgeHistogram() for undirected graphs
    
    The Histogram type 'hist_t' should have a 'double' value, so that
    counts of 1/2 can be added when it's known things are going to be
    counted twice.
    
    (and I don't know what that 'double_t' thing was doing there)

src/graph/graph.hh

commit 74f1cdae
Merge: 622cc24e 23e319bf
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-23

    Merge branch 'master' of git://git.forked.de/graph-tool into directed_extended_clustering

commit efff0017
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-15

    Fix evaluation of 'string' sub-options, and further Python 2.4 compatibility

src/graph-tool

commit 622cc24e
Author: Alexandre Hannud Abdo <abdo@member.fsf.org>
Date:   2007-10-12

    Implements extended_clustering for directed graphs, based on the fraction of possible directed cycles (out-in edges combination).
    The old behavior is still present since it was equivalent to treating the directed graph as undirected (use --undirected option).

src/graph/graph_extended_clustering.cc

commit 23e319bf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-12

    Added --purge-edges and --purge-vertices option
    
    Filtered vertices and edges can be permanently removed from the graph
    with --purge-vertices and --purge-edges, respectively. The edge or
    vertex filter is automatically removed, afterwards. This is useful if
    maximum speed is necessary, and saving and reloading the graph without
    filtering is not desired.
    
    (this commit also removes some trailing whitespaces)

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc

commit 777742e7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-11

    Sort properties in --list-properties in the order 'graph', 'vertex' and 'edge'

src/graph/graph_properties.cc

commit 3cc343fe
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-10

    Properly wrap edit expression for --edit-edge-property/--edit-graph-property

src/graph-tool

commit 8cdbd13c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-10

    Fix handling of options that take no arguments, when graph-tool is loaded as a module

src/graph-tool

commit e7e90c35
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-10

    Recover missing SetVertexFilterRange() python binding

src/graph/graph_bind.cc

commit c0bc49d7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-10

    Cosmetic improvements in error reporting in the graphml reader

src/boost-workaround/boost/graph/graphml.hpp

commit dd41507e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-10

    Internally use C++ type 'long long', instead of 'long', for properties of (graphml) type 'long'
    
    This will increase memory usage, but guarantees, across different
    platforms, that 'long' will always hold larger values than 'int'.

src/boost-workaround/boost/graph/graphml.hpp
src/graph/graph_properties.hh

commit e26b5522
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-08

    More compatibility fixes for python 2.4 and more home dir (~) expansion for supplied file names

src/graph-tool

commit da71afbf
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-08

    Small compatibility fix for Python 2.4

src/graph-tool

commit dc609852
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-07

    Fix installation of graph_tool.py (in case it's already installed)

src/Makefile.am

commit f618944c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-07

    Remove graph rewiring
    
    Remove graph rewiring for now, since it's quite buggy. It will be
    re-commited when ready.

src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_rewiring.cc

commit f51a6bd2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-07

    Added --random-rewire option

src/graph-tool

commit a2ca129e
Merge: 85929aee cb61cc74
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-07

    Merge branch 'master' into rewiring
    
    Conflicts:
    
            src/graph/graph.hh

commit cb61cc74
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-07

    Complete overhaul of command line parsing, and support for loading graph-tool as whole as a python module
    
    The command line parsing was completely rewritten. It now supports
    better parsing of sub-options, with type checking and grouping
    support. Error reporting was also significantly improved, and it now
    warns of invalid options and option values, before the option is
    executed. Some syntax has changed, such as range filtering:
    --[vertex|edge]-range-filter was replaced by
    --exclude-[vertex|edge]-range and --keep-[vertex|edge]-range, which
    should have a clearer meaning. Ranges can also be specified now by
    comparison operators (>,<,>=,<=,=), such as ">=10", to indicate a
    range of (10, inf). In addition, ranges can now be easily open or
    closed at either end, by suffixing the specific end with '*', to
    indicate it is closed, ex: "10 700*" means (10,700].
    
    The graph-tool script can now be loaded as a python module (it must be
    renamed first to 'something.py'). All the command line options (except
    'for' and 'history' which become irrelevant) are available as
    functions, with full description and optional parameter support. In
    addition, pure function objects can be given as parameters where
    expressions are asked, instead of strings and files, which enables
    convenient extension of graph-tool.

configure.in
src/Makefile.am
src/graph-tool
src/graph/graph.cc
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_layout.cc

commit 55028b02
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-07

    fix edge vs. vertex betweenness mixup, and GetCentralPointDominance
    for undirected graphs

src/graph/graph_betweenness.cc

commit 8e962092
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-10-03

    Simplify range filtering, and definitely remove python filtering
    
    Simplify range filtering of vertices and edges, by always filtering
    both at once, even if all vertices or edges are being considered. This
    severely reduces compilation time and memory, at a small potential
    cost in run-time speed, which will probably be overshadowed by other
    things, such as dynamic_map look-ups ("premature optimization is the
    root of all evil"). Also, remove python-filtering, since, in the end,
    it is just code bloat, since it is quite slow for most uses and can be
    replaced, generally, by python property editing + range filtering.

configure.in
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.cc
src/graph/graph_python_interface.hh

commit fbf7f175
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-09-28

    Add dummy ChangeLog file, so that automake is happy.

ChangeLog

commit f05f9a9c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-09-13

    remove ChangeLog file, since it makes a lot more sense just to use git

ChangeLog
Makefile.am

commit d4f313b3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-09-12

    better handling of out-of-memory error

src/graph-tool

commit 85929aee
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-09-12

    experimental graph rewiring code

src/graph/graph.hh
src/graph/graph_rewiring.cc

commit c3c04cbc
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-09-12

    added git commit information to program version

configure.in
src/graph/graph_bind.cc

commit c3a6567d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-08-09

            * src/graph-tool: change layout and community graph options.
    
            * src/boost-workaround/boost/graph/kamada_kawai_spring_layout.hpp: annotated code with openmp constructs.
    
            * src/graph/graph_adaptor.hh: graph_type should be a typedef to the original graph.
    
            * src/graph/graph_properties.hh, src/graph/graph_properties.cc: added pos_t type.
    
            * src/boost-workaround/boost/graph/fruchterman_reingold.hpp: annotated code with openmp constructs.
    
            * src/graph/graph_layout.cc: new file with graph layout routines.
    
            * src/graph/graph.cc: removed graph layout routines.
    
            * src/graph/graph_community_network.cc (struct get_community_network): fixed inversion of directedness test.
    
            * src/graph/graph.cc (GraphInterface::LabelComponents): use vector_property_map instead of HashedDescriptor. Don't use a static map!
    
            * src/graph/graph_adaptor.hh: fixed edge descriptor equality comparison, which must rely on underlying edge, regardless of whether it's inverted or not.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@121 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/boost-workaround/boost/graph/fruchterman_reingold.hpp
src/boost-workaround/boost/graph/kamada_kawai_spring_layout.hpp
src/graph-tool
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_community_network.cc
src/graph/graph_layout.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh

commit d997442a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-08-01

    * src/graph/graph.cc (GraphInterface::LabelParallelEdges): use long instead of size_t for parallel edges property.
    
    * src/graph/graph_properties.cc: call size_t by "size_t" not "long", since those are not the same type. This removes a bug where it is impossible to create/edit properties with type long.
    
    * src/graph/graph.cc (GraphInterface::LabelParallelEdges): use vector_property_map instead of HashedDescriptorMap.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@120 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/graph/graph.cc
src/graph/graph_properties.cc

commit 81c63f0f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-08-01

            * src/graph/graph.cc (GraphInterface::LabelParallelEdges): use vector_property_map instead of HashedDescriptorMap.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@119 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/graph/graph.cc

commit 85ea7b33
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-31

            * configure.in: clearer configure help
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@118 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
configure.in

commit a54d9ad6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-31

            * src/graph-tool: added better error handling (output to stderr, cleaner information, return error status)
    
            * src/graph/graph_bind.cc: added license info
    
            * src/graph-tool: added python metadata
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@117 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/graph-tool
src/graph/graph_bind.cc

commit f063fbed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-30

    * src/graph/Makefile.am: added 'boost_workaround' files
    
    * src/Makefile.am: removed 'boost_workaround' dist files
    
    * src/graph/graph_rewiring.cc: deleted blank lines.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@116 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/Makefile.am
src/graph/Makefile.am
src/graph/graph_rewiring.cc

commit e5d146c6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-11

    * src/graph/graph_extended_clustering.cc (GraphInterface::SetExtendedClusteringToProperty): init vector_property_map size, so that access becomes thread safe.
    
    * src/graph/graph_clustering.cc (GraphInterface::SetLocalClusteringToProperty): init vector_property_map size, so that access becomes thread safe.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@115 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/graph/graph_clustering.cc
src/graph/graph_extended_clustering.cc

commit 32990eb6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-11

            * ChangeLog: updated ChangeLog file with svn history
    
            * src/graph/graph_filtering.hh: added add_edge() and remove_edge() functions for filtered graphs
    
            * src/graph/shared_map.hh: included SharedContainer
    
            * src/graph/graph_rewiring.cc: initial support for random graph rewiring
    
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@114 d4600afd-f417-0410-95de-beed9576f240

ChangeLog
src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_rewiring.cc
src/graph/shared_map.hh

commit 73195ddd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-07

    * fixed bug in scalarS where undirected edge properties were not properly handled
    * removed exeption throwing in scalarS to improve performance
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@113 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph.cc
src/graph/graph_assortativity.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_edge_correlations.cc
src/graph/graph_selectors.hh

commit cf706874
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-06

    * fix edge vs. vertex centrality swap
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@112 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit bcf9f944
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-05

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@109 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 921a5076
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-05

    * add option to disable hidden visibility for 64-bit systems
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@107 d4600afd-f417-0410-95de-beed9576f240

configure.in
ltmain.sh

commit 4572bb69
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-02

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@106 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 393242e9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-02

    bump version
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@104 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 0075ec76
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-07-02

    * normalize betweenness centrality
    * include central point dominance
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@103 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_betweenness.cc
src/graph/graph_bind.cc

commit ba2aee8a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-06-30

    * add support for betweenness centrality
    * change from HashedDescriptorMap to vector_property_map in several
      algorithms to save memory and increase speed in the most common
      case, where the graph is unfiltered.
    
    
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@102 d4600afd-f417-0410-95de-beed9576f240

src/boost-workaround/boost/graph/betweenness_centrality.hpp
src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_betweenness.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh

commit d199d4bb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-06-30

    graph-tool is now GPL v3
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@101 d4600afd-f417-0410-95de-beed9576f240

COPYING
src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_assortativity.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_community_network.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_edge_correlations.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_io.cc
src/graph/graph_line_graph.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_filtering.hh
src/graph/graph_reciprocity.cc
src/graph/graph_selectors.hh
src/graph/histogram.hh
src/graph/shared_map.hh

commit 97e40199
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-06-15

    fixed small reciprocity compile bug with openmp
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@100 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_reciprocity.cc

commit 0c98262b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-06-15

    * fixed bug in graph_assortativity.cc
    * further code parellelization with openmp (vertex and edge histograms, correlations, and reciprocity)
    
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@99 d4600afd-f417-0410-95de-beed9576f240

configure.in
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph_assortativity.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_edge_correlations.cc
src/graph/graph_reciprocity.cc
src/graph/shared_map.hh

commit 0d0f4966
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-18

    * graph_community.cc: code parallelization and speed improvements
    * graph/graph_distance.cc: trivial "one-liner" speed improvement
    
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@98 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_community.cc
src/graph/graph_distance.cc

commit 54b33836
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-18

    * Initial support for parallel code with openmp from GCC 4.2.0. The following code is now parallel:
      * src/graph/graph_clustering.cc
      * src/graph/graph_distance.cc
      * src/graph/graph_extended_clustering.cc
      * src/graph/graph_distance_sampled.cc
    * fixed "jacknife" variance bug in src/graph/graph_clustering.cc
    
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@97 d4600afd-f417-0410-95de-beed9576f240

configure.in
src/boost-workaround/boost/graph/graphml.hpp
src/graph/Makefile.am
src/graph/graph_clustering.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.cc

commit df8d400a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-17

    configure cleanup
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@96 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 8b283d7c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-16

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@95 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit a74769d3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-16

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@93 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit a4eb8027
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-15

    * fixed issue with != operator for PythonEdge and PythonVertex
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@92 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_python_filtering.hh

commit f29a6aa1
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-15

    * fix more issues with --edit-edge-properties and undirected graphs
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@91 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_properties.cc
src/graph/graph_python_filtering.hh

commit 4f7c6cd8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-15

    * fixed issue with --edit-edge-property and undirected graphs
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@90 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_properties.cc

commit 3ee3d1d2
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-06

    * update copyright and contact info
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@89 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 8438b839
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-05

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@88 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 9759c9e4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-05

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@86 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 4bbb71da
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-05

    * integrate svn revision number in source code
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@85 d4600afd-f417-0410-95de-beed9576f240

configure.in
src/graph/graph_bind.cc

commit f7617df4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-05

    * fix property handling for line graph creation
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@84 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_line_graph.cc

commit f55fcbf5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-01

    * expand '~' to home dir in "file:" constructs
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@83 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit c0534fa8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-05-01

    * edit graph property support
    * 'Graph' type now available to python editing, with iterators to access all vertices and edges
    * out_edges and in_edges return iterators instead of lists for python editing
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@82 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_properties.cc
src/graph/graph_python_filtering.hh

commit 0cf8f07e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-04-30

    * added "--list-properties" option
    * added support for specifying property type when creating/editing properties
    * added initial support for graph properties (are loaded, listed, and saved)
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@81 d4600afd-f417-0410-95de-beed9576f240

src/boost-workaround/boost/graph/graphml.hpp
src/graph-tool
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh

commit 74030f01
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-04-17

     graph/graph_adaptor.hh: remove function in_edges
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@80 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_adaptor.hh

commit 133ce532
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-04-15

    * clean up undirected adaptor (see ticket #13)
    * fix python filtering in-edges bug
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@79 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_adaptor.hh
src/graph/graph_python_filtering.hh

commit 89004f4b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-04-12

    sync graphml reader with boost library
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@78 d4600afd-f417-0410-95de-beed9576f240

ltmain.sh
src/Makefile.am
src/boost-workaround/boost/graph/graphml.hpp
src/graph/Makefile.am
src/graph/graph_community_network.cc
src/graph/graph_io.cc
src/graph/graph_line_graph.cc
src/graph/graphml.cpp

commit 3dd3d3d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-04-11

    fix ticket #12
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@77 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit f2e6fc68
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-03-25

    * fix expat error reporting, and reorder element start check for better average performace.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@76 d4600afd-f417-0410-95de-beed9576f240

src/graph/graphml.cpp
src/graph/graphml.hpp

commit dd8d12ea
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-03-01

    added __eq__ and __hash__ member functions to Vertex and Edge python classes, so they can be compared.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@75 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_python_filtering.hh

commit c7fe00fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-30

    * src/graph/graph.cc: fix reset filter when it's not enabled
    * src/graph-tool allow for parameter setting before loading property editing script
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@74 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc

commit a5935300
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-30

    fix option parsing
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@73 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit 08806f70
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-30

    * complete modification of how python filtering works. Now it's much more general.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@72 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_filtering.hh
src/graph/graph_properties.cc
src/graph/graph_python_filtering.hh

commit 51632e6c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-29

    * make range and python filtering independently optional
    * accept external files for property editing routines
    * include in_PROP() andd out_PROP() functions to be used in python filtering/property editing routines.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@71 d4600afd-f417-0410-95de-beed9576f240

configure.in
src/graph-tool
src/graph/graph.cc
src/graph/graph_filtering.hh
src/graph/graph_python_filtering.hh

commit 28411b14
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-27

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@70 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 2f3a8545
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-27

    version bump
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@68 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit acac6789
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-27

    src/graph/graph_community.cc: label spins continuously starting from zero
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@67 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_community.cc

commit 1ffb38cb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-27

    fixed line graph
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@66 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_line_graph.cc

commit a9e10b6b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-25

    add support for bash-completion through optcomplete (http://furius.ca/optcomplete)
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@65 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit 00d1e489
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-25

    included option to disable python and range filtering during compilation, thus reducing compile-time memory requirements
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@64 d4600afd-f417-0410-95de-beed9576f240

configure.in
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_filtering.hh

commit aca4479d
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2007-01-12

    add support for weights in degree correlations
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@63 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_correlations.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_edge_correlations.cc

commit 9795ffe9
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-12-21

    graphml.cpp: fixed handling of node ids, which are now optional (ignored, actually) and added support for xml namespaces
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@62 d4600afd-f417-0410-95de-beed9576f240

src/graph/graphml.cpp

commit 5320d59f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-20

    fix prefix handling in for/history option
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@61 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit 7e06567e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-19

    changed sampled distance semantics
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@60 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph_distance_sampled.cc

commit 531da979
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-15

    _really_ change all tabs to spaces (sed, why have you forsaken me?)
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@59 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_assortativity.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_community_network.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_io.cc
src/graph/graph_line_graph.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_python_filtering.hh
src/graph/graph_reciprocity.cc
src/graph/graph_selectors.hh
src/graph/graphml.cpp
src/graph/graphml.hpp
src/graph/histogram.hh

commit 6b764b67
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-14

    converted tabs to spaces (emacs, why have you forsaken me?)
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@58 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_assortativity.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_community_network.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_io.cc
src/graph/graph_line_graph.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_python_filtering.hh
src/graph/graph_reciprocity.cc
src/graph/graph_selectors.hh
src/graph/graphml.cpp
src/graph/graphml.hpp
src/graph/histogram.hh

commit dbb7bb2c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-13

    Added LabelParallelEdges()
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@57 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc

commit 05414a53
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-12

    * Added community network generation
    * Added line graph generation
    * src/graph-tool: some code de-uglification
    * src/graph-tool: terminal output format changes
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@56 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_community_network.cc
src/graph/graph_line_graph.cc

commit 7287af55
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-05

    graphml: added support for graph properties
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@55 d4600afd-f417-0410-95de-beed9576f240

src/graph/graphml.cpp
src/graph/graphml.hpp

commit 3243afae
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-11-01

    * graph_community.cc:
       - added support for saving annealing history to file
       - added support for continuing from an existing community partition
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@54 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_community.cc

commit fd7e85eb
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-10-31

    * ComponentSizeHistogram() becomes LabelComponents()
    * fixed saving of undirected filtered graphs in graph_io.cc
    * fixed correlated community detection in graph_community.cc
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@53 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_community.cc
src/graph/graph_io.cc

commit adb1700e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-10-14

    * src/graph/graph_community.cc: Extensively re-written. Now it's a bit slower, but hopefully correct.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@52 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_community.cc

commit b6694f7f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-10-10

    fixed buglet in graph/graphml.hpp
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@51 d4600afd-f417-0410-95de-beed9576f240

src/graph/graphml.hpp

commit 19068a5f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-10-09

    * corrected and improved graph community code, thereby fixing ticket:6
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@50 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_community.cc

commit c27d124c
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-10-05

    * fix bug with mersenne twister rng seeding on amd64
    * fix command line help
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@49 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph_community.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_generation.cc

commit 236dafb8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-09-26

    * fix bug with --save
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@48 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_io.cc

commit 999db6d6
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-09-24

    * correct graphml headers
    * fix ticket [9]
    * fix --for bug with multiple options with different parameters
    * Add initial support for community detection (ticket [6])
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@47 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_community.cc
src/graph/graph_io.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graphml.hpp

commit c759f2f3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-09-04

    * Added minimum spanning tree support
    * Range filters now support all kinds of scalar properties without falling back to python code
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@46 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graph_minimum_spanning_tree.cc
src/graph/graph_properties.hh

commit 3266b079
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-09-03

    * added support for reciprocity
    * python_filtering: added n_parallel() function
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@45 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_python_filtering.hh
src/graph/graph_reciprocity.cc

commit feb7071b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-09-03

    changed extended clustering start index from 0 to 1
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@44 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph_extended_clustering.cc

commit 05fa231a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-09-03

    introduce a "for" option, which is just like "history" but files are always overwritten.
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@43 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit 2a9b92a7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-23

    * src/graph/graph.cc: fixed range filter fallback
    * src/graph/graph_python_filtering.hh: changed is_loop to is_self
    * src/graph-tool: fixed memory leak related to exec statements and filtering
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@42 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph_python_filtering.hh

commit be38bf3b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-22

    graph/graph_extended_clustering.cc: check for self-edges
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@41 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_extended_clustering.cc

commit 20fc25d0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-18

    * fix bug in graph/graph_extended_clustering.cc (error in BFS target management)
    * fix bug in graph/graph_correlations_combined.cc (precision error when error is very small)
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@40 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_correlations_combined.cc
src/graph/graph_extended_clustering.cc

commit 224bd568
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-17

    * add EditVertexProperty() and EditEdgeProperty()
    * cleanup src/graph/graph_python_filtering.hh
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@39 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.cc
src/graph/graph_python_filtering.hh

commit 1152b5ed
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-16

    * add GetDistanceHistogram, instead of GetAverageDistance
    * add GetSampledDistanceHistogram (in src/graph/graph_distance_sampled.cc)
    * fix BFS initialization bug in src/graph/graph_extended_clustering.cc
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@38 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_distance.cc
src/graph/graph_distance_sampled.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_properties.hh

commit ec124ab3
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-15

    fix extended clustering when graph has parallel edges
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@37 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_extended_clustering.cc

commit 8f495045
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-15

    * added extended clustering code
    * separated graphml code into graphml.hpp and graphml.cpp, and added support for default property values
    * added HashedDescriptorMap with automatic memory management
    
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@36 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_extended_clustering.cc
src/graph/graph_filtering.hh
src/graph/graph_io.cc
src/graph/graphml.cpp
src/graph/graphml.hpp

commit d108f600
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-14

    get rid of some exception throwing
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@35 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_python_filtering.hh

commit c8506c63
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-13

    * new python filtering code with different syntax. Now faster...
    * definition of HashedDescriptorMap
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@34 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph_clustering.cc
src/graph/graph_distance.cc
src/graph/graph_filtering.hh
src/graph/graph_python_filtering.hh

commit 0ef1419f
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-11

    * changed python filtering semantics: edges are filtered before vertices, not simultaneously. Original (unfiltered) vertices degrees are available to the vertex filter prefixed with "orig_".
    * added missing boost licence file to src/boost-workaround/LICENSE_1_0.txt
    * updated FSF address in src/graph-tool
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@33 d4600afd-f417-0410-95de-beed9576f240

src/boost-workaround/LICENSE_1_0.txt
src/graph-tool
src/graph/graph_filtering.hh

commit 682d867b
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-10

    average neighbour correlation must actually count neighbours twice, if double edges exist
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@32 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_correlations_neighbours.cc

commit 53f38d38
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-10

    if not running inside a terminal, it's not possible to get the terminal geometry
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@31 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit 1bc70be5
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-09

    version bump
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@30 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit 3445d826
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-09

    * added GetAverageCombinedVertexCorrelation()
    * put combined degree correlation stuff in src/graph/graph_correlations_combined.cc
    * some code cleanups in src/graph-tool
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@29 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_combined.cc

commit 4eb835ec
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-04

    fix another trivial automake bug
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@26 d4600afd-f417-0410-95de-beed9576f240

src/Makefile.am

commit 22bdba10
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-03

    fix trivial automake bug
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@22 d4600afd-f417-0410-95de-beed9576f240

configure.in
src/Makefile.am

commit cadf2406
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-03

    bump version
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@21 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit b8788979
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-03

    bump version
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@19 d4600afd-f417-0410-95de-beed9576f240

configure.in

commit aaaa4bb7
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-03

    * generalized GetCombinedDegreeHistogram() into GetCombinedVertexHistogram()
    * removed GetVectorScalarCorrelation(), since it is substituted by the above
    * changed range filter policy: if property is non-double, use generic python filtering instead
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@18 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_correlations.cc
src/graph/graph_properties.hh

commit 53c936d8
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-08-01

    * move distance stuff to src/graph/graph_distance.cc
    * average distances now accept weights
    * added DynamicPropertyMapWrap
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@17 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/Makefile.am
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_distance.cc
src/graph/graph_properties.hh

commit 9a7b7361
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-31

    psyco and scipy should be optional
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@16 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit a4c0927a
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-31

    default to uncorrelated case also when doing rejection sampling
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@15 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit ed814636
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-30

    * much improved directed correlation generation
    * fixed bug related to negative sampled degrees
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@14 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_bind.cc
src/graph/graph_generation.cc

commit 017675f0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-24

    * added possibility to load expression from file
    * fixed rounding error
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@13 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit b11d52fd
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-24

    improved correlated vertex sampling
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@12 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_generation.cc

commit 6855de1e
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-22

    * fix assortativity coefficient
    * add jackknife variance
    * add scalar assortativity coefficient
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@11 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_assortativity.cc
src/graph/graph_bind.cc
src/graph/histogram.hh

commit 479e4da0
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-21

    * fix clustering and add jackknife variance
    * fix history temp file handling buglet
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@10 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_clustering.cc

commit 3412e2df
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-18

    * removed neighbour selectors (not really needed at all). Improves compilation speed, memory usage and binary size!
    * removed clustering specific code in favour of more generic property code
    * added GetEdgeHistogram()
    * renamed some functions/options ("degree"->"vertex")
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@9 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_selectors.hh

commit 8f3424de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-15

    set mime/type to text/x-python in src/graph-tool
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@8 d4600afd-f417-0410-95de-beed9576f240

commit 55cdce65
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-13

    removing edge selectors, since the same behaviour can be obtained by using the --undirected and --reverse filters, as long as the in-degree is also seen when the undirected filter is turned on
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@7 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool
src/graph/graph.hh
src/graph/graph_assortativity.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_selectors.hh

commit de3bae43
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-11

    correct (invert) edge/vertex filtering semantics
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@6 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

commit c28d25de
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-10

    ancient code... shouldn't be here
    
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@5 d4600afd-f417-0410-95de-beed9576f240

src/graph/graph_history.hh

commit 3a45d7be
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-10

    unneeded stuff
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@2 d4600afd-f417-0410-95de-beed9576f240

src/graph/.dirstamp
src/graph/adaptor-test/adaptor_test.cc
src/graph/adaptor-test/component_test.cc
src/graph/adaptor-test/filter_test.cc
src/graph/adaptor-test/graph.cpp
src/graph/adaptor-test/graph_type.hpp

commit a9aff6b4
Author: Tiago de Paula Peixoto <tiago@skewed.de>
Date:   2006-07-10

    Initial import
    
    git-svn-id: https://svn.forked.de/graph-tool/trunk@1 d4600afd-f417-0410-95de-beed9576f240

AUTHORS
COPYING
ChangeLog
INSTALL
Makefile.am
NEWS
README
TODO
acinclude.m4
autogen.sh
configure.in
ltmain.sh
src/Makefile.am
src/boost-workaround/boost/graph/filtered_graph.hpp
src/boost-workaround/boost/graph/fruchterman_reingold.hpp
src/graph-tool
src/graph/.dirstamp
src/graph/Makefile.am
src/graph/adaptor-test/adaptor_test.cc
src/graph/adaptor-test/component_test.cc
src/graph/adaptor-test/filter_test.cc
src/graph/adaptor-test/graph.cpp
src/graph/adaptor-test/graph_type.hpp
src/graph/graph.cc
src/graph/graph.hh
src/graph/graph_adaptor.hh
src/graph/graph_assortativity.cc
src/graph/graph_bind.cc
src/graph/graph_clustering.cc
src/graph/graph_correlations.cc
src/graph/graph_correlations_neighbours.cc
src/graph/graph_filtering.hh
src/graph/graph_generation.cc
src/graph/graph_history.hh
src/graph/graph_io.cc
src/graph/graph_properties.cc
src/graph/graph_properties.hh
src/graph/graph_selectors.hh
src/graph/graphml_io.hh
src/graph/histogram.hh
src/graph/read_graphviz_spirit.cpp
