Metadata-Version: 1.1
Name: pylibseq
Version: 0.2.2
Summary: Python interface to libsequence.
Home-page: http://molpopgen.github.io/pylibseq
Author: Kevin Thornton
Author-email: krthornt@uci.edu
License: GPL >= 3
Description: pylibseq: Python bindings for libsequence
        ***************************************************************
        
        This package provides Python_ bindings for the C++11 library libsequence_.
        
        The bindings are implemented using pybind11_.
        
        This package serves two roles:
        
        * It provides a means of using some of the more widely-used bits of libsequence_ within the Python language
        * The unit tests of this package also serve as unit tests for libsequence_.
        
        What this package does **not** (currently) do:
        
        * 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.
        
        Build status
        ==========================================
        
        Master branch:
        
        .. image:: https://travis-ci.org/molpopgen/pylibseq.svg?branch=master
           :target: https://travis-ci.org/molpopgen/pylibseq
           :alt: Travis CI Build Status (master branch)
        
        .. image:: https://circleci.com/gh/molpopgen/pylibseq/tree/master.svg?style=svg
            :target: https://circleci.com/gh/molpopgen/pylibseq/tree/master
        
        Development branch:
        
        .. image:: https://travis-ci.org/molpopgen/pylibseq.svg?branch=dev
           :target: https://travis-ci.org/molpopgen/pylibseq
           :alt: Travis CI Build Status (dev branch)
        
        .. image:: https://circleci.com/gh/molpopgen/pylibseq/tree/dev.svg?style=svg
            :target: https://circleci.com/gh/molpopgen/pylibseq/tree/dev
        
        Citation
        ====================================================
        
        If you use this software for your research, please cite:
        
        ::
        
            @ARTICLE{Thornton2003-wj,
              title    = "Libsequence: a C++ class library for evolutionary genetic
                          analysis",
              author   = "Thornton, Kevin",
              abstract = "UNLABELLED: A C++ class library is available to facilitate the
                          implementation of software for genomics and sequence polymorphism
                          analysis. The library implements methods for data manipulation
                          and the calculation of several statistics commonly used to
                          analyze SNP data. The object-oriented design of the library is
                          intended to be extensible, allowing users to design custom
                          classes for their own needs. In addition, routines are provided
                          to process samples generated by a widely used coalescent
                          simulation. AVAILABILITY: The source code (in C++) is available
                          from http://www.molpopgen.org",
              journal  = "Bioinformatics",
              volume   =  19,
              number   =  17,
              pages    = "2325--2327",
              month    =  nov,
              year     =  2003,
              url      = "https://www.ncbi.nlm.nih.gov/pubmed/14630667",
              language = "en",
              issn     = "1367-4803",
              pmid     = "14630667",
              doi      = "10.1093/bioinformatics/btg316"
            }
        
        
        Requirements:
        ===================================
        
        * Python 3
        * cmake
        * 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.
        
        .. note:: 
        
           As of version 0.2.2, libsequence is included as a git submodule compiled
           directly into the Python package.
        
           If you installing from GitHub, then pybind11_ is a dependency.  Further, 
           pybind11 must not be installed from a source like PyPi. Rather, it must be
           installed either from source or via your favorite package manager.  The
           reason is that we use their cmake macros during the build process.
        
        Changelog (rough)
        ==============================
        
        * 0.2.0: The package has been completely refactored.  We now use pybind11_ to integrate C++ and Python.  Previous
          versions of this project used Cython_.  The API now corrresponds to libsequence_ 1.9.2.  Python_ >= 3.4 is required.
        * 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.
        * 0.1.8: made sure C++ objects/fxns are declared "nogil".  Raw pointers replaced with C++'s unique_ptr.
        * 0.1.7: improvements to build system.  Add option to build from GitHub.
        * 0.1.6: update to libsequence 1.8.9.  Add --use-cython option to setup.py
        
        Installation:
        =======================
        
        For many users, the best way to install the latest release will be via bioconda_,
        
        .. code-block:: bash
        
            conda -c bioconda install pylibseq
        
        The latest release of the package is available via PyPi_, and can be installed with your favorite Python package manager:
        
        .. code-block:: bash
        
           $ pip install --upgrade pylibseq
        
        Or, you may install from GitHub:
        
        .. note:: The GitHub version does not contain the .cpp files generated by pybind11.  You need to generate those!
        
        .. code-block:: bash
        
           $ git clone http://github.com/molpopgen/pylibseq
           $ cd pylibseq
           $ git submodule init
           $ git submodule update
        
        .. code-block:: bash
        
           $ ./configure
           $ sudo pip install . 
        
        
        You may also install from GitHub using pip:
        
        .. code-block:: bash
        
           $ pip install git+git://github.com/molpopgen/pylibseq 
        
        
        Unit testing:
        =======================
        
        .. code-block:: bash
        
           $ ./configure
           $ python setup.py build_ext -i 
           $ python -m unittest discover tests
        
        Documentation:
        ======================
        
        * Project homepage_
        * Manual_
        
        .. _libsequence: http://molpopgen.github.io/libsequence/
        .. _boost: http://www.boost.org/
        .. _pybind11: http://pybind11.readthedocs.io/
        .. _Cython: http://www.cython.org
        .. _Python: http://www.python.org/
        .. _Manual: http://molpopgen.github.io/pylibseq/_build/html/index.html
        .. _homepage: http://molpopgen.github.io/pylibseq/
        .. _PyPi: https://pypi.python.org
        .. _bioconda: https://bioconda.github.io
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Requires: pybind11
Requires: numpy
Provides: pylibseq
Obsoletes: none
