🆕 First Commit

.coveragerc

@@ -0,0 +1,5 @@
+[run]
+omit =
+ setup.py
+ scripts/NDQL_execute.py
+ scripts/NDQL_translate.py

.gitignore

@@ -1,3 +1,5 @@
+# Created by .ignore support plugin (hsz.mobi)
+### Python template
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -8,6 +10,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -23,7 +26,6 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -43,9 +45,8 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*.cover
+*,cover
 .hypothesis/
-.pytest_cache/
 
 # Translations
 *.mo
@@ -54,7 +55,6 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
 
 # Flask stuff:
 instance/
@@ -78,27 +78,22 @@ target/
 # celery beat schedule file
 celerybeat-schedule
 
-# SageMath parsed files
-*.sage.py
-
-# Environments
+# dotenv
 .env
+
+# virtualenv
 .venv
-env/
 venv/
 ENV/
-env.bak/
-venv.bak/
 
 # Spyder project settings
 .spyderproject
-.spyproject
 
 # Rope project settings
 .ropeproject
 
-# mkdocs documentation
-/site
+#docs
 
-# mypy
-.mypy_cache/
+docs/_build
+docs/_static
+docs/_templates

.travis.yml

@@ -0,0 +1,20 @@
+language: python
+python:
+  - "2.7"
+  - "3.4"
+  - "3.5"
+  - "3.6"
+
+before_install:
+  - pip install pytest pytest-cov
+  - pip install coveralls
+
+install:
+  - pip install .
+  - pip install -r requirements.txt
+
+script:
+  - py.test --cov=./ --cov-config=.coveragerc
+
+after_success:
+  - coveralls

LICENSE

@@ -0,0 +1,23 @@
+Copyright (c) 2016, Giulio Rossetti
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

_config.yml

@@ -0,0 +1 @@
+theme: jekyll-theme-minimal

nclib/models/map_equation.py

@@ -0,0 +1,28 @@
+import infomap as map
+import networkx as nx
+from collections import defaultdict
+from wurlitzer import pipes
+
+
+def infomap(g):
+
+    g1 = nx.convert_node_labels_to_integers(g, label_attribute="name")
+    name_map = nx.get_node_attributes(g1, 'name')
+    coms_to_node = defaultdict(list)
+
+    with pipes():
+        im = map.Infomap()
+        network = im.network()
+        for e in g1.edges():
+           network.addLink(e[0],e[1])
+        im.run()
+
+        for node in im.iterTree():
+           if node.isLeaf():
+               nid = node.physicalId
+               module = node.moduleIndex()
+               nm = name_map[nid]
+               coms_to_node[module].append(nm)
+
+    coms_infomap = [tuple(c) for c in coms_to_node.values()]
+    return coms_infomap

nclib/models/modularity.py

@@ -0,0 +1,28 @@
+import community as louvain_modularity
+import leidenalg
+import igraph as ig
+from collections import defaultdict
+
+
+def louvain(g, weight='weight', resolution=1., randomize=False):
+
+    coms = louvain_modularity.best_partition(g, weight=weight, resolution=resolution, randomize=randomize)
+
+    # Reshaping the results
+    coms_to_node = defaultdict(list)
+    for n, c in coms.items():
+        coms_to_node[c].append(n)
+
+    coms_louvain = [tuple(c) for c in coms_to_node.values()]
+    return coms_louvain
+
+
+def leiden(g):
+    gi = ig.Graph(directed=False)
+    gi.add_vertices(list(g.nodes()))
+    gi.add_edges(list(g.edges()))
+
+    part = leidenalg.find_partition(gi, leidenalg.ModularityVertexPartition)
+    coms = [gi.vs[x]['name'] for x in part]
+    return coms
+

nclib/models/node_centric.py

@@ -0,0 +1,33 @@
+import demon as d
+import angel as an
+import networkx as nx
+import os
+from nclib.utils import suppress_stdout
+
+
+def demon(g, epsilon, min_com_size=3):
+    """
+
+    :param g:
+    :param epsilon:
+    :param min_com_size:
+    :param filename:
+    :return:
+    """
+
+    with suppress_stdout():
+        dm = d.Demon(graph=g, epsilon=epsilon, min_community_size=min_com_size)
+        coms = dm.execute()
+
+    return coms
+
+
+def angel(g, threshold, min_community_size=3):
+
+    nx.write_edgelist(g, "temp.ncol")
+    with suppress_stdout():
+        a = an.Angel("temp.ncol", min_comsize=min_community_size, threshold=threshold, save=False)
+        coms = a.execute()
+    os.remove("temp.ncol")
+
+    return coms

nclib/test/community_discovery_models.py

@@ -0,0 +1,39 @@
+import unittest
+from nclib.models.node_centric import demon, angel
+from nclib.models.modularity import louvain, leiden
+from nclib.models.map_equation import infomap
+import networkx as nx
+import os
+
+
+class NodeCentricTests(unittest.TestCase):
+
+    def test_demon(self):
+        g = nx.karate_club_graph()
+        coms = demon(g, epsilon=0.25)
+        self.assertEqual(len(coms), 2)
+
+    def test_angel(self):
+        g = nx.karate_club_graph()
+        coms = angel(g, threshold=0.25)
+        self.assertEqual(len(coms), 1)
+
+    def test_louvain(self):
+        g = nx.karate_club_graph()
+        coms = louvain(g)
+        self.assertEqual(len(coms), 4)
+
+    def test_leiden(self):
+        g = nx.karate_club_graph()
+        coms = leiden(g)
+        self.assertEqual(len(coms), 4)
+
+    def test_infomap(self):
+        g = nx.karate_club_graph()
+        coms = infomap(g)
+        self.assertEqual(len(coms), 3)
+        os.remove(".tree")
+
+
+if __name__ == '__main__':
+    unittest.main()

nclib/utils.py

@@ -0,0 +1,17 @@
+from contextlib import contextmanager
+import sys
+import os
+
+
+@contextmanager
+def suppress_stdout():
+    with open(os.devnull, "w") as devnull:
+        old_stdout = sys.stdout
+        old_stderr = sys.stderr
+        sys.stdout = devnull
+        sys.stderr = devnull
+        try:
+            yield
+        finally:
+            sys.stdout = old_stdout
+            sys.stderr = old_stderr

requirements.txt

@@ -0,0 +1,9 @@
+mock==2.0.0
+sphinx_rtd_theme==0.4.2
+numpy==1.15.2
+future==0.16.0
+networkx==2.2
+matplotlib==2.2.2
+python-igraph
+leidenalg
+wurlitzer

setup.cfg

@@ -0,0 +1,4 @@
+[bdist_wheel]
+# This flag says that the code is written to work on both Python 2 and Python
+# 3. If at all possible, it is good practice to do this. If you cannot, you
+# will need to generate wheels for each Python version that you support.

setup.py

@@ -0,0 +1,48 @@
+from setuptools import setup, find_packages
+from codecs import open
+from os import path
+
+__author__ = 'Giulio Rossetti'
+__license__ = "BSD-2-Clause"
+__email__ = "[email protected]"
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the README file
+with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
+
+
+setup(name='nclib',
+      version='0.0.1',
+      license='BSD-Clause-2',
+      description='Network Community Library',
+      url='https://github.com/GiulioRossetti/nclib',
+      author='Giulio Rossetti',
+      author_email='[email protected]',
+      use_2to3=True,
+      classifiers=[
+          # How mature is this project? Common values are
+          #   3 - Alpha
+          #   4 - Beta
+          #   5 - Production/Stable
+          'Development Status :: 3 - Alpha',
+
+          # Indicate who your project is intended for
+          'Intended Audience :: Developers',
+          'Topic :: Software Development :: Build Tools',
+
+          # Pick your license as you wish (should match "license" above)
+          'License :: OSI Approved :: BSD License',
+
+          "Operating System :: OS Independent",
+
+          # Specify the Python versions you support here. In particular, ensure
+          # that you indicate whether you support Python 2, Python 3 or both.
+          'Programming Language :: Python',
+          'Programming Language :: Python :: 3'
+      ],
+      keywords='epidemics opinion-dynamics simulator complex-networks',
+      install_requires=['numpy', 'networkx', 'scipy', 'future', ''],
+      packages=find_packages(exclude=["*.test", "*.test.*", "test.*", "test", "nclib.test", "nclib.test.*"]),
+      )