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EggLib documentation!
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:alt: EggLib Logo
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About
=====
EggLib is a Python library, largely implemented in C++, for evolutionary
genetics and genomics. Main features are sequence data management,
sequence polymorphism analysis, and coalescent simulations. EggLib is a
flexible Python module with a performant underlying C++ library and
allows fast and intuitive development of Python programs and scripts.
**EggLib home page:** `<https://www.egglib.org>`_
Installation
============
EggLib is available on pip. For more information on installing EggLib or
downloading source code please refer to the installation section of the
documentation: `<https://egglib.org/install.html>`_.
Cloning
=======
You can clone the whole package using::
git clone https://gitlab.com/demita/egglib.git
For example, this lets you access to the current version on development::
cd egglib
git checkout dev
Building local documentation
============================
To generate the documentation locally, you should clone the repository,
and run this (assuming the package has been installed)::
python setup.py build_sphinx
python setup.py build_pdf
The first command generates the html documentation (available in the
``doc/build/html`` directory) and the second generates three pdf
documents containing the main sections of the documentation (in the
``doc/build/latex`` directory).
To generate documentation, one needs:
* A LaTex processor, containing the following packages: anyfontsize,
amsmath, fncychap, capt-of, needspace, framed, upquote, wrapfig (and
possibly others).
* ``python3-sphinx``
* ``python3-svgwrite``
* ``latexmk``
Citation
========
De Mita S. and M. Siol. 2012. EggLib: processing, analysis and simulation tools for population genetics and genomics. *BMC Genet.* **13**:27.
`Open access <http://www.biomedcentral.com/1471-2156/13/27/abstract>`_
License
=======
EggLib is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your
option) any later version.
EggLib is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
`<https://www.egglib.org/licence.html>`_
.. |PythonVersions| image:: https://img.shields.io/badge/python-3.6+-blue.svg
:target: https://www.python.org/downloads
:alt: Python 3.6+
.. |PypiPackage| image:: https://badge.fury.io/py/EggLib.svg
:target: https://pypi.org/project/EggLib
:alt: PyPi package
