Metadata-Version: 1.1
Name: fwdpy11
Version: 0.1.4
Summary: Forward-time population genetic simulation in Python
Home-page: http://molpopgen.github.io/fwdpy11
Author: Kevin Thornton
Author-email: krthornt@uci.edu
License: GPL >= 3
Description: fwdpy11
        *************************
        
        This is the README for fwdpy11_, which is a Python package for forward-time population genetic simulation.  It uses
        fwdpp_ as its C++ back-end.
        
        Build status
        -----------------------
        
        Master:
        
        .. image:: https://travis-ci.org/molpopgen/fwdpy11.svg?branch=master
            :target: https://travis-ci.org/molpopgen/fwdpy11
        
        Development: 
        
        .. image:: https://travis-ci.org/molpopgen/fwdpy11.svg?branch=dev
            :target: https://travis-ci.org/molpopgen/fwdpy11
        
        Manual
        -----------------------
        
        Latest/master:
        
        .. image:: https://readthedocs.org/projects/fwdpy11/badge/?version=latest
        	:target: http://fwdpy11.readthedocs.io/en/latest/?badge=latest
        
        Development branch:
        
        .. image:: https://readthedocs.org/projects/fwdpy11/badge/?version=dev
        	:target: http://fwdpy11.readthedocs.io/en/dev/?badge=dev
        
        Features
        -----------------------
        
        * Picklable population objects
        * Parallel computation via multiprocessing_ or concurrent.futures_.
        * Custom temporal samplers to analyze populations *during* a simulation may be written in pure Python.
          
        Dependencies
        -----------------------
        
        The following must be present on your system:
        
        * GSL_. This is a C library.  It is available via `conda`.
        * pybind11_. This should be installed via `pip` or `conda` as appropriate for your system.
        
        fwdpy11_ also uses fwdpp_, which is included as a submodule.
        
        License
        -----------------------
        
        GPLv3 or later (See COPYING)
        
        Suppored Python version
        -----------------------
        
        fwdpy11 is written for Python 3.  We will not modify the package to be compatible with Python 2.7.
        
        .. code-block:: bash
        
            git submodule init
            git submodule update
            python setup.py build_ext -i
            python test.py
        
        .. note::
            The clang compiler is the assumed default on OS X.  However, life is simpler
            if you use gcc.  The setup.py takes a --gcc option that eliminates OS X-specific
            (really Xcode clang-specific) features so that an OS X/gcc build is possible.
        
        Installation
        ---------------------------------
        
        Using pip on OS X and Linux (or pip3 as appropriate for your system):
        
        .. code-block:: bash
        
            pip install --upgrade fwdpy11
        
        If you prefer a pip install on OS X using GCC instead of clang:
        
        .. code-block:: bash
        
            pip install --upgrade fwdpy11 --install-option=--gcc
        
        You may or may not need to prefix the above with
        
        .. code-block:: bash
        
            CC=gcc CXX=g++
        
        depending on whether or not your user's `$PATH` is set up to override Xcode's symlink of gcc to clang.
        
        Caution
        ==================================
        
        We use the GitHub "release_" mechanism to make stable versions available.  However, GitHub releases to not include the
        sub-modules, meaning that the releases themselves cannot be used for installation.  (A related irony is that the Zenodo
        DOI for the releases are somewhat meaningless.)
        
        To install a specific release:
        
        1. Use pip (see above).  This is the recommended approach if you do not use conda.
        2. Install from bioconda.  This is the recommended approach.
        3. Clone the repo, checkout the release, and update submodules:
        
        .. code-block:: bash
        
            git clone http://github.com/molpopgen/fwdpy11
            cd fwdpy11
            git submodule init
            git submodule update
        
        The latter method is probably the least appealing.
        
        We have a strict policy of putting releases on PyPi and bioconda_.  If there is a release on PyPi but not on bioconda_,
        then that is because we identified a bug and pushed a new release before the bioconda_ build happend.  It happens.
        That's life.
        
        
        Enabling debugging symbols in the C++ code
        ------------------------------------------------------------------
        
        .. code_block:: bash
        
            python setup.py build_ext -i --debug
        
        Enabling assertions in the C++ code
        ------------------------------------------------------------------
        
        The C++ code uses C's assert macros in several places.  These are disabled by default.  However, it can be useful to
        enable them when hacking the code.  To do so:
        
        .. code-block:: bash
        
            python setup.py build_ext -i --assert
        
        .. note::
            Never install the package compiled in assert mode!  First, things will run much more slowly.  
            Second, triggering an assertion will cause the Python interpreter to crash.  These assertions
            exist as a brute-force method to help developers quickly identify bugs.
        
        Bioconda
        =================================
        
        fwdpy11 is available through bioconda_ for Linux and for OS X:
        
        .. code-block:: bash
        
            conda install -c bioconda fwdpy11
        
        The OS X build is built using gcc.
        
        .. _fwdpy11: http://molpopgen.github.io/fwdpy11
        .. _fwdpp: http://molpopgen.github.io/fwdpp
        .. _GSL: http://gnu.org/software/gsl
        .. _pybind11: https://github.com/pybind/pybind11
        .. _multiprocessing: https://docs.python.org/3/library/multiprocessing.html
        .. _concurrent.futures: https://docs.python.org/3/library/concurrent.futures.html
        .. _bioconda: https://bioconda.github.io/
        .. _release: https://github.com/molpopgen/fwdpy11/releases
        
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: fwdpy11
Obsoletes: none
