Merge pull request #97 from sknetwork-team/develop

release 0.2.0

.gitignore

@@ -115,3 +115,5 @@ data/
 
 \.DS_Store
 
+
+*.ipynb

.pyup.yml

@@ -0,0 +1,33 @@
+#Taken from https://pyup.io/docs/bot/config/
+
+# configure updates globally
+# default: all
+# allowed: all, insecure, False
+update: all
+
+# configure dependency pinning globally
+# default: True
+# allowed: True, False
+pin: True
+
+# set the default branch
+# default: empty, the default branch on GitHub
+branch: develop
+
+# update schedule
+# default: empty
+# allowed: "every day", "every week", ..
+schedule: "every day"
+
+# search for requirement files
+# default: True
+# allowed: True, False
+search: True
+
+# configure the branch prefix the bot is using
+# default: pyup-
+branch_prefix: pyup/
+
+# allow to close stale PRs
+# default: True
+close_prs: True

AUTHORS.rst

@@ -9,8 +9,3 @@ Development Lead
 * Bertrand Charpentier <[email protected]>
 * Nathan De Lara <[email protected]>
 * Quentin Lutz <[email protected]>
-
-Contributors
-------------
-
-* Alexandre Hollocou <[email protected]>

README.rst

@@ -1,3 +1,8 @@
+.. figure:: ../logo_sknetwork.png
+    :align: right
+    :width: 100px
+    :alt: logo sknetwork
+
 ==============
 scikit-network
 ==============
@@ -25,11 +30,25 @@ Graph algorithms
 * Documentation: https://scikit-network.readthedocs.io.
 
 
-Features
---------
+How to use scikit-network?
+--------------------------
+
+Graphs have a unified format, namely ``scipy.sparse.csr_matrix``.
+
+
+About the documentation
+-----------------------
+
+We use the following notations in the documentation:
+
+* :math:`A` denotes the adjacency matrix for undirected and directed graphs.
+
+* :math:`B` denotes the biadjacency matrix for bipartite graphs (possibly non-square).
+
+* :math:`d = A1` or :math:`B1` is the out-degree vector and :math:`D = \text{diag}(d)` the associated diagonal matrix.
+
+* :math:`f = A^T1` or :math:`B^T1` is the in-degree vector and :math:`F = \text{diag}(f)` the associated diagonal matrix.
 
-* Embedding
-* Clustering
-* Hierarchy
+* :math:`w = 1^TA1` or :math:`1 ^TB1` is the total weight of the graph.
 
 

docs/conf.py

@@ -58,8 +58,8 @@
 
 # General information about the project.
 project = u'scikit-network'
-copyright = u"2018, Bertrand Charpentier"
-author = u"Bertrand Charpentier"
+copyright = u"2019, scikit-network"
+author = u"scikit-network team"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -94,7 +94,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-#html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -105,7 +105,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = []
 
 
 # -- Options for HTMLHelp output ---------------------------------------

docs/index.rst

@@ -1,3 +1,8 @@
+.. figure:: ../sknetwork/../logo_sknetwork.png
+    :align: right
+    :width: 200px
+    :alt: logo sknetwork
+
 Welcome to scikit-network's documentation!
 ==========================================
 
@@ -9,8 +14,6 @@ Welcome to scikit-network's documentation!
    installation
    usage
    reference/index
-   reference2
-   modules
    contributing
    authors
    history

docs/reference/clustering.rst

@@ -7,18 +7,38 @@ Clustering
 
 Louvain
 -------
-.. automodule:: sknetwork.clustering.louvain
-   :toctree: generated/
+.. automodule:: sknetwork.clustering
 
-.. autoclass:: Louvain
+.. autoclass:: sknetwork.clustering.Louvain
     :members:
 
-.. autoclass:: GreedyModularity
+.. autoclass:: sknetwork.clustering.GreedyModularity
     :members:
 
-.. autoclass:: GreedyModularityJiT
+.. autoclass:: sknetwork.clustering.GreedyModularityNumba
     :members:
 
+Louvain for bipartite graphs
+----------------------------
+
+.. autoclass:: sknetwork.clustering.BiLouvain
+    :members:
+
+.. autoclass:: sknetwork.clustering.GreedyBipartite
+    :members:
+
+.. autoclass:: sknetwork.clustering.GreedyBipartiteNumba
+    :members:
+
+
 Metrics
 -------
+.. autofunction:: sknetwork.clustering.modularity
+
+.. autofunction:: sknetwork.clustering.bimodularity
+
+.. autofunction:: sknetwork.clustering.cocitation_modularity
+
+.. autofunction:: sknetwork.clustering.performance
 
+.. autofunction:: sknetwork.clustering.cocitation_performance

docs/reference/embedding.rst

@@ -6,17 +6,30 @@ Embedding
 .. currentmodule:: sknetwork
 
 
-Spectral embeddings
--------------------
-.. automodule:: sknetwork.embedding.forwardbackward_embedding
-   :toctree: generated/
+Spectral
+--------
+.. automodule:: sknetwork.embedding
 
-.. autoclass:: ForwardBackwardEmbedding
+.. autoclass:: sknetwork.embedding.SpectralEmbedding
     :members:
 
-.. automodule:: sknetwork.embedding.spectral_embedding
-   :toctree: generated/
+SVD
+---
 
-.. autoclass:: SpectralEmbedding
+.. autoclass:: sknetwork.embedding.GSVDEmbedding
     :members:
 
+Metrics
+-------
+.. autofunction:: sknetwork.embedding.dot_modularity
+
+.. autofunction:: sknetwork.embedding.hscore
+
+
+Randomized methods
+------------------
+.. autofunction:: sknetwork.embedding.randomized_range_finder
+
+.. autofunction:: sknetwork.embedding.randomized_svd
+
+.. autofunction:: sknetwork.embedding.randomized_eig

docs/reference/hierarchy.rst

@@ -0,0 +1,22 @@
+.. _hierarchical_clustering:
+
+Hierarchical clustering
+***********************
+
+.. currentmodule:: sknetwork
+
+Paris
+-----
+.. automodule:: sknetwork.hierarchy
+.. autosummary::
+   :toctree: generated/
+
+.. autoclass:: sknetwork.hierarchy.paris.Paris
+    :members:
+
+
+Metrics
+-------
+.. autofunction:: sknetwork.hierarchy.metrics.dasgupta_cost
+
+.. autofunction:: sknetwork.hierarchy.metrics.tree_sampling_divergence

docs/reference/index.rst

@@ -6,5 +6,7 @@ Reference
 .. toctree::
 
     embedding
-    flat_clustering
-    hierarchical_clustering
+    clustering
+    hierarchy
+    loader
+    toy_graphs

docs/reference/loader.rst

@@ -0,0 +1,9 @@
+.. _loader:
+
+Loader
+******
+
+.. currentmodule:: sknetwork
+
+.. autoclass:: sknetwork.loader.Parser
+    :members:

docs/reference/toy_graphs.rst

@@ -0,0 +1,12 @@
+.. _toy_graphs:
+
+Toy graphs
+**********
+
+.. currentmodule:: sknetwork
+
+.. autofunction:: sknetwork.toy_graphs.house_graph
+
+.. autofunction:: sknetwork.toy_graphs.karate_club_graph
+
+.. autofunction:: sknetwork.toy_graphs.star_wars_villains_graph

make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

sknetwork/__init__.py

@@ -1,7 +1,14 @@
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+"""Top-level package for scikit-network"""
 
-"""Top-level package for scikit-network."""
-
-__author__ = """Bertrand Charpentier"""
-__email__ = '[email protected]'
+__author__ = """scikit-network team"""
+__email__ = "[email protected]"
 __version__ = '0.2.0'
+
+from scipy.sparse.csgraph import *
+from sknetwork.toy_graphs import *
+from sknetwork.loader import *
+from sknetwork.clustering import *
+from sknetwork.hierarchy import *
+from sknetwork.embedding import *

sknetwork/clustering/__init__.py

@@ -0,0 +1,3 @@
+from sknetwork.clustering.louvain import *
+from sknetwork.clustering.bilouvain import *
+from sknetwork.clustering.metrics import *