fwdpy11 0.2.0a0

Forward-time population genetic simulation in Python

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`. fwdpy11 requires version 2.2 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.

.. code-block:: bash

git submodule init
git submodule update
python setup.py build_ext -i
python -m unittest discover tests

.. 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

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

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
.. _cmake: https://cmake.org