Initial Github commit

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+docs/_build/

CONTRIBUTIONS.rst

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+
+**Copyright**
+    |copy| 2008-2015 Jonathan F. Donges and pyunicorn authors.
+
+**License**
+    BSD (3-clause)
+
+**URL**
+    http://www.pik-potsdam.de/members/donges/software
+
+**Mail**
+    Jonathan Donges, Potsdam Institute for Climate Impact Research,
+    P.O. Box 60 12 03, D-14412 Potsdam, Germany
+
+**Authors**
+    Written as part of a diploma/PhD thesis in physics by `Jonathan F. Donges
+    <[email protected]>`_ at Humboldt University Berlin and the Potsdam
+    Institute for Climate Impact Research (PIK) and completed at the University
+    of Potsdam, Germany. Substantially extended by `Jobst Heitzig
+    <[email protected]>`_.
+
+**Contributors**
+    - Jakob Runge (extended ``core`` and ``climate``)
+    - Alexander Radebach
+    - Hanna Schultz
+    - Marc Wiedermann (extended ``core`` and ``climate``)
+    - `Alraune Zech <[email protected]>`_
+      (extended ``timeseries`` during an internship at PIK)
+    - `Jan Feldhoff <[email protected]>`_ (extended ``timeseries``)
+    - Aljoscha Rheinwalt
+    - Hannes Kutza
+    - `Boyan Beronov <[email protected]>`_
+      (consolidated and updated codebase during an internship at PIK)
+    - `Paul Schultz <[email protected]>`_ and `Stefan Schinkel
+      <[email protected]>`_ supplied resistive networks and corresponding tests
+**Related publications**
+    See :doc:`publications` (``docs/source/publications.rst``).
+
+**Version**
+    0.4.1
+
+**Dependencies**
+    - Python 2.7
+    - `Numpy <http://numpy.scipy.org/>`_ 1.8+
+    - `Scipy <http://www.scipy.org/>`_ 0.14+
+    - `Weave <https://github.com/scipy/weave>`_ 0.15+
+    - `Matplotlib <http://matplotlib.sourceforge.net>`_ 1.3+
+    - `igraph, python-igraph <http://igraph.sourceforge.net/>`_ 0.7+
+
+**Included**
+    - `progressbar <http://pypi.python.org/pypi/progressbar/>`_ 2.3
+
+**To Do**
+  - A lot - See current product backlog.
+
+**Known Bugs**:
+  - ...

LICENSE.txt

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+
+Copyright (C) 2008-2015, Jonathan F. Donges (Potsdam-Institute for Climate
+Impact Research), pyunicorn authors
+
+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.
+
+    * Neither the name of pyunicorn authors and the Potsdam-Institute for
+      Climate Impact Research nor the names of its contributors may be used to
+      endorse or promote products derived from this software without specific
+      prior written permission.
+
+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.

README.rst

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+
+pyunicorn
+=========
+
+``pyunicorn`` (**Uni**\ fied **Co**\ mplex Network and **R**\ ecurre\ **N**\ ce
+analysis toolbox) is a fully object-oriented Python package for the advanced
+analysis and modeling of complex networks. Above the standard measures of
+complex network theory such as degree, betweenness and clustering coefficient
+it provides some **uncommon but interesting statistics** like Newman's random
+walk betweenness. ``pyunicorn`` features novel **node-weighted (node splitting
+invariant)** network statistics as well as measures designed for analyzing
+**networks of interacting/interdependent networks**.
+
+Moreover, ``pyunicorn`` allows to easily **construct networks from uni- and
+multivariate time series data** (functional (climate) networks and recurrence
+networks). This involves linear and nonlinear measures of time series analysis
+for constructing functional networks from multivariate data as well as modern
+techniques of nonlinear analysis of single time series like recurrence
+quantification analysis (RQA) and recurrence network analysis.
+
+Get more information
+--------------------
+This page only contains bare-bones instructions for installing ``pyunicorn``.
+For more information, jump right to the `pyunicorn homepage`_.
+
+.. _pyunicorn homepage: http://www.pik-potsdam.de/~donges/pyunicorn/
+
+Get the latest code
+-------------------
+Git repository not yet public.
+
+Dependencies
+------------
+``pyunicorn`` relies on the following additional open source or freely
+available packages that have to be installed on your machine.
+
+Required:
+  - `Numpy <http://numpy.scipy.org/>`_ 1.8+
+  - `Scipy <http://www.scipy.org/>`_ 0.14+
+  - `Weave <https://github.com/scipy/weave>`_ 0.15+
+  - `Matplotlib <http://matplotlib.sourceforge.net>`_ 1.3+
+  - `igraph, python-igraph <http://igraph.sourceforge.net/>`_ 0.7+
+
+Optional *(required for certain classes and methods)*:
+  - `PyNGL <http://www.pyngl.ucar.edu/Download/>`_ (for class
+    NetCDFDictionary)
+  - `netcdf4-python <http://code.google.com/p/netcdf4-python/>`_ (for classes
+    Data and NetCDFDictionary)
+  - `Matplotlib Basemap Toolkit <http://matplotlib.org/basemap/>`_ (for drawing
+    maps)
+  - `mpi4py <http://code.google.com/p/mpi4py/>`_ (for parallelizing costly
+    computations)
+  - `Sphinx <http://sphinx-doc.org/>`_ (for generating documentation in
+    formats other than HTML, e.g. PDF)
+
+Install pyunicorn
+-----------------
+Install ``pyunicorn`` using Python's ``distutils`` with the supplied
+``setup.py`` script::
+
+   $> python setup.py install
+
+Depending on your system, you may need root priviledges.  On UNIX-based
+operating systems (Linux, MacOSX etc.) this is achieved with ``sudo``.
+
+Documentation
+-------------
+Using ``Sphinx``, currently HTML and PDF can be generated::
+
+    $> cd docs; make clean html latexpdf
+
+Mailing list
+------------
+Not implemented yet.
+
+Test suite
+----------
+Before committing changes to the codebase, please make sure that all tests
+pass. The test suite is managed by `tox <https://testrun.org/tox/>`_ and
+configured to use system-wide packages when available. Thus to avoid frequent
+waiting, we recommend you to install the following packages::
+
+    $> pip install tox nose networkx Sphinx
+    $> pip install pytest pytest-xdist pytest-flakes pytest-pep8
+
+The test suite can be run from anywhere in the project tree by issuing::
+
+    $> tox
+
+To expose the defined test environments and target them independently::
+
+    $> tox -l
+    $> tox -e py27-doctest,py27-style
+
+To test single files::
+
+    $> tests/test_doctests.py core.interacting_networks      # doctests
+    $> nosetests tests/core/TestResitiveNetwork-circuits.py  # unit tests
+    $> py.test pyunicorn/core/network.py                     # style
+
+License
+-------
+``pyunicorn`` is **BSD-licensed** (3 clause), see ``LICENSE.txt``.