fwdpy11

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

Main:

.. image:: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main :target: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main

.. image:: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main :target: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main

Development:

.. image:: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev :target: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev

.. image:: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev :target: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev

Conda status

.. image:: https://anaconda.org/bioconda/fwdpy11/badges/version.svg
:target: https://anaconda.org/bioconda/fwdpy11

.. image:: https://anaconda.org/bioconda/fwdpy11/badges/platforms.svg
:target: https://anaconda.org/bioconda/fwdpy11

Miscellaneous

Python code style:

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black

Features

• Pickle-able population objects
• Parallel computation via multiprocessing_ or concurrent.futures_.
• Custom temporal samplers to analyze populations during a simulation may be written in pure Python.
• Flexible interface for simulating models with multiple populations.

Documentation

The manual can be found here <https://molpopgen.github.io/fwdpy11>_.

License

GPLv3 or later (See COPYING)

Supported Python version

fwdpy11 is written for Python 3. We will not modify the package to be compatible with Python 2.7.

Dependencies and installation

These topics are covered in the user manual:

• People wishing to run fwpdy11 should see this section <https://molpopgen.github.io/fwdpy11/pages/userenv.html>_.
• Those who need to build the package from source should look the developer's guide <https://molpopgen.github.io/fwdpy11/misc/developersguide.html>_.

Citation

If you use this software for research, please cite the following publications:

• Kevin R Thornton. Polygenic adaptation to an environmental shift: temporal dynamics of variation under gaussian stabilizing selection and additive effects on a single trait. Genetics, 213(4):1513–1530, December 2019.

• Kevin R Thornton. A c++ template library for efficient forward-time population genetic simulation of large populations. Genetics, 198(1):157–166, September 2014.

This software was developed for the first paper. The second paper describes a key part of this software's back end.

.. _fwdpy11: https://github.com/molpopgen/fwdpy11 .. _fwdpp: https://github.com/molpopgen/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