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        "author": "Kevin Thornton",
        "author_email": "krthornt@uci.edu",
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        "classifiers": [
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            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "pylibseq: Python bindings for libsequence\n***************************************************************\n\nThis package provides Python_ bindings for the C++11 library libsequence_.\n\nThe bindings are implemented using pybind11_.\n\nThis package serves two roles:\n\n* It provides a means of using some of the more widely-used bits of libsequence_ within the Python language\n* The unit tests of this package also serve as unit tests for libsequence_.\n\nWhat this package does **not** (currently) do:\n\n* provide an interface for I/O operations.  Python I/O and C++ I/O are fundamentally very different.  Bridging the gap requires either adding features to pybind11 and/or adding modules to this package that depend on the boost_ Python interface, which would add an additional C++ dependency to this package.\n\nBuild status\n==========================================\n\nMaster branch:\n\n.. image:: https://travis-ci.org/molpopgen/pylibseq.svg?branch=master\n   :target: https://travis-ci.org/molpopgen/pylibseq\n   :alt: Travis CI Build Status (master branch)\n\n.. image:: https://circleci.com/gh/molpopgen/pylibseq/tree/master.svg?style=svg\n    :target: https://circleci.com/gh/molpopgen/pylibseq/tree/master\n\nDevelopment branch:\n\n.. image:: https://travis-ci.org/molpopgen/pylibseq.svg?branch=dev\n   :target: https://travis-ci.org/molpopgen/pylibseq\n   :alt: Travis CI Build Status (dev branch)\n\n.. image:: https://circleci.com/gh/molpopgen/pylibseq/tree/dev.svg?style=svg\n    :target: https://circleci.com/gh/molpopgen/pylibseq/tree/dev\n\nCitation\n====================================================\n\nIf you use this software for your research, please cite:\n\n::\n\n    @ARTICLE{Thornton2003-wj,\n      title    = \"Libsequence: a C++ class library for evolutionary genetic\n                  analysis\",\n      author   = \"Thornton, Kevin\",\n      abstract = \"UNLABELLED: A C++ class library is available to facilitate the\n                  implementation of software for genomics and sequence polymorphism\n                  analysis. The library implements methods for data manipulation\n                  and the calculation of several statistics commonly used to\n                  analyze SNP data. The object-oriented design of the library is\n                  intended to be extensible, allowing users to design custom\n                  classes for their own needs. In addition, routines are provided\n                  to process samples generated by a widely used coalescent\n                  simulation. AVAILABILITY: The source code (in C++) is available\n                  from http://www.molpopgen.org\",\n      journal  = \"Bioinformatics\",\n      volume   =  19,\n      number   =  17,\n      pages    = \"2325--2327\",\n      month    =  nov,\n      year     =  2003,\n      url      = \"https://www.ncbi.nlm.nih.gov/pubmed/14630667\",\n      language = \"en\",\n      issn     = \"1367-4803\",\n      pmid     = \"14630667\",\n      doi      = \"10.1093/bioinformatics/btg316\"\n    }\n\n\nRequirements:\n===================================\n\n* Python 3\n* cmake\n* An up-to-date C++ compiler that is C++11 compatible via the flag -std=c++11.  Roughly, this means GCC >= 4.8 and clang >= 3.5.\n\n.. note:: \n\n   As of version 0.2.2, libsequence is included as a git submodule compiled\n   directly into the Python package.\n\n   If you installing from GitHub, then pybind11_ is a dependency.  Further, \n   pybind11 must not be installed from a source like PyPi. Rather, it must be\n   installed either from source or via your favorite package manager.  The\n   reason is that we use their cmake macros during the build process.\n\nChangelog (rough)\n==============================\n\n* 0.2.0: The package has been completely refactored.  We now use pybind11_ to integrate C++ and Python.  Previous\n  versions of this project used Cython_.  The API now corrresponds to libsequence_ 1.9.2.  Python_ >= 3.4 is required.\n* 0.1.9: Made memory management more robust: more unique_ptr instead of raw pointers.  Cleanup __dealloc__ functions in extension types.  Package now sets __version__.  Class names are now \"Pythonic\" (and identical to the corresponding type names from libsequence) due to aliasing the C++ names from libsequence. Change from distutils to setuptools.  Documentation fixes.  Expose haplotype diversity and number of haplotype statistics.  First (very alpha) release of pymsstats.\n* 0.1.8: made sure C++ objects/fxns are declared \"nogil\".  Raw pointers replaced with C++'s unique_ptr.\n* 0.1.7: improvements to build system.  Add option to build from GitHub.\n* 0.1.6: update to libsequence 1.8.9.  Add --use-cython option to setup.py\n\nInstallation:\n=======================\n\nFor many users, the best way to install the latest release will be via bioconda_,\n\n.. code-block:: bash\n\n    conda -c bioconda install pylibseq\n\nThe latest release of the package is available via PyPi_, and can be installed with your favorite Python package manager:\n\n.. code-block:: bash\n\n   $ pip install --upgrade pylibseq\n\nOr, you may install from GitHub:\n\n.. note:: The GitHub version does not contain the .cpp files generated by pybind11.  You need to generate those!\n\n.. code-block:: bash\n\n   $ git clone http://github.com/molpopgen/pylibseq\n   $ cd pylibseq\n   $ git submodule init\n   $ git submodule update\n\n.. code-block:: bash\n\n   $ ./configure\n   $ sudo pip install . \n\n\nYou may also install from GitHub using pip:\n\n.. code-block:: bash\n\n   $ pip install git+git://github.com/molpopgen/pylibseq \n\n\nUnit testing:\n=======================\n\n.. code-block:: bash\n\n   $ ./configure\n   $ python setup.py build_ext -i \n   $ python -m unittest discover tests\n\nDocumentation:\n======================\n\n* Project homepage_\n* Manual_\n\n.. _libsequence: http://molpopgen.github.io/libsequence/\n.. _boost: http://www.boost.org/\n.. _pybind11: http://pybind11.readthedocs.io/\n.. _Cython: http://www.cython.org\n.. _Python: http://www.python.org/\n.. _Manual: http://molpopgen.github.io/pylibseq/docs/_build/html/index.html\n.. _homepage: http://molpopgen.github.io/pylibseq/\n.. _PyPi: https://pypi.python.org\n.. _bioconda: https://bioconda.github.io",
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