Forward-time population genetic simulation in Python
Project description
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:
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.
git submodule init
git submodule update
python setup.py build_ext -i
python test.pyInstallation
Using pip on OS X and Linux (or pip3 as appropriate for your system):
pip install --upgrade fwdpy11If you prefer a pip install on OS X using GCC instead of clang:
pip install --upgrade fwdpy11 --install-option=--gccYou may or may not need to prefix the above with
CC=gcc CXX=g++depending on wheter or not your user’s $PATH is set up to override Xcode’s symlink of gcc to clang.
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:
python setup.py build_ext -i --debugBioconda
fwdpy11 is available through bioconda for Linux and for OS X:
conda install -c bioconda fwdpy11The OS X build is built using gcc.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
