Metadata-Version: 1.1
Name: fwdpy11
Version: 0.4.3
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
        
        .. image:: https://circleci.com/gh/molpopgen/fwdpy11/tree/master.svg?style=svg
            :target: https://circleci.com/gh/molpopgen/fwdpy11/tree/master
        
        Development: 
        
        .. image:: https://travis-ci.org/molpopgen/fwdpy11.svg?branch=dev
            :target: https://travis-ci.org/molpopgen/fwdpy11
        
        .. image:: https://circleci.com/gh/molpopgen/fwdpy11/tree/dev.svg?style=svg
            :target: https://circleci.com/gh/molpopgen/fwdpy11/tree/dev
        
        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`.  fwdpy11 requires version 2.3 or greater.
        * pybind11_. This should be installed `conda` as appropriate for your system, or via your system's package manager or
          manually.  See note below.
        * cmake_. This should be installed by `conda` or your favorite package manager.
        
        fwdpy11_ also uses fwdpp_, which is included as a submodule.
        
        .. note::
        
            The C++ modules are built using cmake_, which requires that pybind11_'s cmake macros are visible.
            Installing pybind11_ via `pip` does **not** install the macros.  However, installs using `conda`, 
            apt-get, or manual installation from source will install both the Python module and the cmake macros.
        
        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.
        
        
        Installation
        ---------------------------------
        
        Building from the git repository:
        
        .. code-block:: bash
        
            git submodule init
            git submodule update
            python setup.py build_ext -i
            python -m unittest discover tests
        
        Using pip on OS X and Linux (or pip3 as appropriate for your system):
        
        .. code-block:: bash
        
            pip install --upgrade fwdpy11
        
        It is possible that the cmake macros to detect the GSL can fail to detect the correct version.  Issues like this are a
        basic weakness of cmake.  I've seen this in conda environments, where the macro prefers the system version over the
        newer version in the environment.  To "fix" this, give it a hint:
        
        .. code-block:: bash
        
            GSL_ROOT_DIR=/path/to/gsl python3 setup.py build_ext -i
        
        OS X
        ==================================
        
        On Apple's OS X, we strongly encourage that you use conda with the clang-4.0 compiler packages:
        
        .. code-block:: bash
        
            conda install clang_osx_64 clangxx_osx-64
        
        Installing these packages will mean that you can get away from the relatively old versions of these compilers that ship
        with Xcode.   However, you do need to add the following flag when building the package:
        
        .. code-block:: bash
        
            CONDA_BUILD_SYSROOT=/ python3 setup.py build_ext -i
        
        Do the same for a `pip install` from the source directory.
        
        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
        
        Debug mode disables all compiler optimizations, allows C-like assertions, and generated debug symbols.
        
        .. note::
            Never install the package compiled in debug 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.
        
        Enabling assertions in the C++ code
        ------------------------------------------------------------------
        
        The fwdpp library 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, you must manually set your compiler flags with cmake:
        
        .. code-block:: bash
            
            cmake . -DCMAKE_CXX_FLAGS="-UNDEBUG -O2 -g"
        
        When compiling this way, fwdpy11 makes some extra checks that will throw `RuntimeError` if they fail.  The fwdpp_ back
        end also makes extra checks.  If those fail, `abort` will be called, which will crash the Python interpreter.  Thus,
        compiling with this option is a "serious debugging mode only" option.
        
        
        Bioconda
        =================================
        
        fwdpy11 is available through bioconda_ for Linux and for OS X:
        
        .. code-block:: bash
        
            conda install -c bioconda fwdpy11
        
        .. _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
        .. _cmake: https://cmake.org
        
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
Requires: tskit
Provides: fwdpy11
Obsoletes: none
