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graph-tool
Commit 41471e3c authored by Tiago Peixoto's avatar Tiago Peixoto
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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.
parent 4843cf1a
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    Showing with 16815 additions and 12982 deletions
    Makefile.am
    View file @ 41471e3c
    ......@@ -18,7 +18,7 @@ nobase_dist_graphtooldoc_DATA = \
    doc/draw.rst \
    doc/index.rst \
    doc/spectral.rst \
    doc/community.rst \
    doc/inference.rst \
    doc/flow.rst \
    doc/Makefile \
    doc/quickstart.rst \
    ......@@ -30,7 +30,6 @@ nobase_dist_graphtooldoc_DATA = \
    doc/topology.rst \
    doc/conf.py \
    doc/pyenv.py \
    doc/community.xml \
    doc/search_example.xml \
    doc/sphinxext/README.txt \
    doc/sphinxext/LICENSE.txt \
    ......
    configure.ac
    View file @ 41471e3c
    ......@@ -457,11 +457,12 @@ src/Makefile
    src/graph/Makefile
    src/graph/centrality/Makefile
    src/graph/clustering/Makefile
    src/graph/community/Makefile
    src/graph/community_old/Makefile
    src/graph/correlations/Makefile
    src/graph/draw/Makefile
    src/graph/flow/Makefile
    src/graph/generation/Makefile
    src/graph/inference/Makefile
    src/graph/layout/Makefile
    src/graph/search/Makefile
    src/graph/spectral/Makefile
    ......
    doc/community.rst deleted 100644 → 0
    View file @ 4843cf1a
    .. automodule:: graph_tool.community
    :no-members:
    :no-undoc-members:
    .. autofunction:: minimize_blockmodel_dl
    .. autoclass:: BlockState
    .. autoclass:: OverlapBlockState
    .. autoclass:: CovariateBlockState
    .. autofunction:: mcmc_sweep
    .. autofunction:: multilevel_minimize
    .. autofunction:: collect_edge_marginals
    .. autofunction:: collect_vertex_marginals
    .. autofunction:: mf_entropy
    .. autofunction:: bethe_entropy
    .. autofunction:: model_entropy
    .. autofunction:: get_max_B
    .. autofunction:: get_akc
    .. autofunction:: condensation_graph
    .. autofunction:: minimize_nested_blockmodel_dl
    .. autoclass:: NestedBlockState
    .. autofunction:: init_nested_state
    .. autofunction:: nested_mcmc_sweep
    .. autofunction:: nested_tree_sweep
    .. autofunction:: get_hierarchy_tree
    .. autofunction:: get_block_edge_gradient
    .. autofunction:: community_structure
    .. autofunction:: modularity
    doc/community.xml deleted 100644 → 0
    View file @ 4843cf1a
    This source diff could not be displayed because it is too large. You can view the blob instead.
    doc/graph_tool.rst
    View file @ 41471e3c
    ......@@ -207,11 +207,11 @@ Available subpackages
    centrality
    clustering
    collection
    community
    correlations
    draw
    flow
    generation
    inference
    search_module
    spectral
    stats
    ......
    doc/inference.rst 0 → 100644
    View file @ 41471e3c
    .. automodule:: graph_tool.inference
    :no-undoc-members:
    :show-inheritance:
    .. testcode:: inference_detailed
    :hide:
    import test_inference
    .. testoutput:: inference_detailed
    :hide:
    :options: -ELLIPSIS, +NORMALIZE_WHITESPACE
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