Initial Commit

.gitignore

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+*.pyc
+
+.installed.cfg
+bin
+develop-eggs
+
+*.egg-info
+
+tmp
+build
+dist

.hgignore

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+syntax: glob
+
+.installed.cfg
+bin
+develop-eggs
+
+*.egg-info
+
+tmp
+build
+dist

HACKING.txt

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+Development setup
+=================
+
+To create a buildout,
+
+  $ python bootstrap.py
+  $ bin/buildout
+
+Release HOWTO
+=============
+
+To make a release, 
+
+  1) Update release date/version in NEWS.txt and setup.py
+  2) Run 'python setup.py sdist'
+  3) Test the generated source distribution in dist/
+  4) Upload to PyPI: 'python setup.py sdist register upload'
+  5) Increase version in setup.py (for next release)
+

MANIFEST.in

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+include README.rst
+include NEWS.txt

NEWS.txt

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+.. This is your project NEWS file which will contain the release notes.
+.. Example: http://www.python.org/download/releases/2.6/NEWS.txt
+.. The content of this file, along with README.rst, will appear in your
+.. project's PyPI page.
+
+News
+====
+
+0.2a1
+-----
+
+*Release date: UNRELEASED*
+
+* Example news entry for the in-development version
+
+
+0.1
+---
+
+*Release date: 15-Mar-2010*
+
+* Example news entry for a released version
+

README.rst

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+This file requires editing
+==========================
+
+Note to the author: Please add something informative to this README *before*
+releasing your software, as `a little documentation goes a long way`_.  Both
+README.rst (this file) and NEWS.txt (release notes) will be included in your
+package metadata which gets displayed in the PyPI page for your project.
+
+You can take a look at the README.txt of other projects, such as repoze.bfg
+(http://bfg.repoze.org/trac/browser/trunk/README.txt) for some ideas.
+
+.. _`a little documentation goes a long way`: http://www.martinaspeli.net/articles/a-little-documentation-goes-a-long-way
+
+Credits
+-------
+
+- `Distribute`_
+- `Buildout`_
+- `modern-package-template`_
+
+.. _Buildout: http://www.buildout.org/
+.. _Distribute: http://pypi.python.org/pypi/distribute
+.. _`modern-package-template`: http://pypi.python.org/pypi/modern-package-template

bootstrap.py

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+##############################################################################
+#
+# Copyright (c) 2006 Zope Corporation and Contributors.
+# All Rights Reserved.
+#
+# This software is subject to the provisions of the Zope Public License,
+# Version 2.1 (ZPL).  A copy of the ZPL should accompany this distribution.
+# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
+# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
+# FOR A PARTICULAR PURPOSE.
+#
+##############################################################################
+"""Bootstrap a buildout-based project
+
+Simply run this script in a directory containing a buildout.cfg.
+The script accepts buildout command-line options, so you can
+use the -c option to specify an alternate configuration file.
+
+$Id: bootstrap.py 102545 2009-08-06 14:49:47Z chrisw $
+"""
+
+import os, shutil, sys, tempfile, urllib2
+from optparse import OptionParser
+
+tmpeggs = tempfile.mkdtemp()
+
+is_jython = sys.platform.startswith('java')
+
+# parsing arguments
+parser = OptionParser()
+parser.add_option("-v", "--version", dest="version",
+                          help="use a specific zc.buildout version")
+parser.add_option("-d", "--distribute",
+                   action="store_true", dest="distribute", default=True,
+                   help="Use Disribute rather than Setuptools.")
+
+options, args = parser.parse_args()
+
+if options.version is not None:
+    VERSION = '==%s' % options.version
+else:
+    VERSION = ''
+
+USE_DISTRIBUTE = options.distribute
+args = args + ['bootstrap']
+
+to_reload = False
+try:
+    import pkg_resources
+    if not hasattr(pkg_resources, '_distribute'):
+        to_reload = True
+        raise ImportError
+except ImportError:
+    ez = {}
+    if USE_DISTRIBUTE:
+        exec urllib2.urlopen('http://python-distribute.org/distribute_setup.py'
+                         ).read() in ez
+        ez['use_setuptools'](to_dir=tmpeggs, download_delay=0, no_fake=True)
+    else:
+        exec urllib2.urlopen('http://peak.telecommunity.com/dist/ez_setup.py'
+                             ).read() in ez
+        ez['use_setuptools'](to_dir=tmpeggs, download_delay=0)
+
+    if to_reload:
+        reload(pkg_resources)
+    else:
+        import pkg_resources
+
+if sys.platform == 'win32':
+    def quote(c):
+        if ' ' in c:
+            return '"%s"' % c # work around spawn lamosity on windows
+        else:
+            return c
+else:
+    def quote (c):
+        return c
+
+cmd = 'from setuptools.command.easy_install import main; main()'
+ws  = pkg_resources.working_set
+
+if USE_DISTRIBUTE:
+    requirement = 'distribute'
+else:
+    requirement = 'setuptools'
+
+if is_jython:
+    import subprocess
+
+    assert subprocess.Popen([sys.executable] + ['-c', quote(cmd), '-mqNxd',
+           quote(tmpeggs), 'zc.buildout' + VERSION],
+           env=dict(os.environ,
+               PYTHONPATH=
+               ws.find(pkg_resources.Requirement.parse(requirement)).location
+               ),
+           ).wait() == 0
+
+else:
+    assert os.spawnle(
+        os.P_WAIT, sys.executable, quote (sys.executable),
+        '-c', quote (cmd), '-mqNxd', quote (tmpeggs), 'zc.buildout' + VERSION,
+        dict(os.environ,
+            PYTHONPATH=
+            ws.find(pkg_resources.Requirement.parse(requirement)).location
+            ),
+        ) == 0
+
+ws.add_entry(tmpeggs)
+ws.require('zc.buildout' + VERSION)
+import zc.buildout.buildout
+zc.buildout.buildout.main(args)
+shutil.rmtree(tmpeggs)

buildout.cfg

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+[buildout]
+parts = python scripts
+develop = .
+eggs = MapEquation
+
+[python]
+recipe = zc.recipe.egg
+interpreter = python
+eggs = ${buildout:eggs}
+
+[scripts]
+recipe = zc.recipe.egg:scripts
+eggs = ${buildout:eggs}

requirement.txt

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+numpy
+networkx

setup.py

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+from setuptools import setup, find_packages
+import sys, os
+
+here = os.path.abspath(os.path.dirname(__file__))
+README = open(os.path.join(here, 'README.rst')).read()
+NEWS = open(os.path.join(here, 'NEWS.txt')).read()
+
+
+version = '0.1'
+
+install_requires = [
+    numpy,
+    networkx,
+    # List your project dependencies here.
+    # For more details, see:
+    # http://packages.python.org/distribute/setuptools.html#declaring-dependencies
+]
+
+
+setup(name='MapEquation',
+    version=version,
+    description="Implementation of the MapEquation algorithm with networkx",
+    long_description=README + '\n\n' + NEWS,
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Developers',
+        'Intended Audience :: End Users/Desktop',
+        'Intended Audience :: System Administrators',
+        'Natural Language :: English',
+        'Operating System :: POSIX',
+        'Operating System :: Unix',
+        'Operating System :: MacOS :: MacOS X',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+        'Topic :: Graph',
+        'License :: OSI Approved :: MIT License',
+        'Environment :: Console',
+    ],
+    keywords='graph, community detection',
+    author='Vincent Gauthier',
+    author_email='[email protected]',
+    url='http://complex.luxbulb.org',
+    license='MIT',
+    packages=find_packages('src'),
+    package_dir = {'': 'src'},include_package_data=True,
+    zip_safe=True,
+    install_requires=install_requires,
+    test_suite='nose.collector',
+    entry_points={
+        'console_scripts':
+            ['MapEquation=mapequation:main']
+    }
+)

src/mapequation/Bootstrap.py

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+# -------------------------------------------------------------------------------
+# Copyright (c) 2013 Vincent Gauthier Telecom SudParis.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+# -------------------------------------------------------------------------------
+
+__author__ = """\n""".join(['Vincent Gauthier <[email protected]>'])
+
+import numpy as np
+
+class Bootstrap:
+  def __init__(self, Graph, n=10, weight='weight'):
+    self._Graph = Graph
+    self._n = n
+    self._weight_attribut = weight
+    self._current = 0
+    # Test if each edge of the graph has an attribut 'weight'
+    for u,v,edata in self._Graph.edges(data=True):
+      if self._weight_attribut not in self._Graph[u][v]:
+        raise AttributeError('The Graph has a missing weight attribut on his edges {} {}'.format(u,v))
+
+  def __iter__(self):
+    return self
+
+  def next(self):
+    if self._current > self._n:
+      raise StopIteration
+    else:
+      self._current += 1
+      return self.generate()
+
+  def generate(self):
+    '''
+    Generate a random boostrap of the Graph (G)
+    '''
+
+    H = self._Graph.copy()
+    for u,v,edata in H.edges(data=True):
+      lam = int(edata[self._weight_attribut])
+      H[u][v]['weight'] = np.random.poisson(lam, 1).item(0  )
+
+    return H