fwdpy11 0.1.post1

Forward-time population genetic simulation in Python

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:

Development:

Manual

Latest/master:

Development branch:

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. Given time/energy, we may look into supporting Python 2.7. However, it is impossible to support all fwdpy11 features in Python 2.7. Specifically, it is not possible to provide full pickling support.

git submodule init
git submodule update
python setup.py build_ext -i
python test.py

Installation

Using pip on Linux (or pip3 as appropriate for your system):

pip install --upgrade fwdpy11

On OS X, you must use GCC. It is highly recommended that you use a GCC installed from Anaconda. We do all of our OS X testing using the GCC 4.8.5 from Anaconda:

CC=gcc CXX=g++ pip install --upgrade fwdpy11