fwdpy 0.0.3

Citation

See the project home page for details (http://molpopgen.github.io/fwdpy).

Changelog (rough)

0.0.3

• Change from std::thread to std::async for concurrency.

• The asynchronous futures allow for the same “evolve” function to be used in different contexts.

• The different contexts include calculating things from the population every “k” generation or doing nothing.

• These things are implemented as classes with call operators and a minimal set of API requirements.

• Fixed a bug in “mutation views”

• Better parameter checking for various “evolve” functions

• Source code re-organized so that all header files are installed

Features:

So far, there is support for:

• Simulation of a recombining region with arbitrary variation in neutral mutation rate, recombination rate, and distribution of selective effects and their dominance along the region.

• Support for arbitrary changes in population size.

• The ability to sample from simulated populations.

• Calculate some standard summary statistics from samples taken from simulated populations.

• Selfing

• The ability to vary model parameters over time (recombination rates, genetic maps, selfing, selection, etc.)

• Sampling populations at various time points

• Parallel executiom of simulations. Multiple replicates may be run simultaenously via C++11’s threading mechanism. This is a “sneaky” end-run around Python’s Global Interpreter Lock, or GIL.

The following distributions of selection coefficients are supported:

• constant (i.e., s takes on a fixed value)

• uniform

• exponential

• gamma

• gaussian

The following distributions of dominance are supported:

• constant (i.e., h takes on a fixed value)

Google Group

For help with various issues, check out the fwdpy Google Group

Examples

Several examples exist in the form of output from “iPython”/Jupyter notebooks:

• Background selection

• Viewing simulated populations

• Sliding windows

• Tracking mutation frequencies

Availability

This package is distributed at the following github repository: https://github.com/molpopgen/fwdpy.

Dependencies

This section assumes that all packages are installed in fairly standard locations, such as /usr/local. See the troubleshooting section for more complex setups.

This package minimally depends on:

• GSL

• fwdpp

The configure script will enforce minimum version numbers of these dependencies, if necessary.

Note: fwdpy may require the ‘dev’ branch of fwdpp. The configure script checks for both the correct dependency version number and specific header files within each depdency. If the version number check passes, but a subsequent header check fails, then that is a sign that you need a development version of the relevant dependency. The reason for this situation is that the development of fwdpy has generated ideas for how to make fwdpp more accessible. This situation will remain until fwdpy stabilizes.

You also need a C++11-compliant compiler. For linux users, GCC 4.8 or newer should suffice. OS X users must use the clang-omp package from brew.

You may use one or the other of these libraries, but not both. See the Performance subsection of the Installation section below for how to use these libraries.

$ brew install clang-omp
$ brew install gsl
$ ##Risky:
$ brew install fwdpp
$ brew install google-perftools

What Python version?

I’m developing the package using Python 2.7.6 on an Ubuntu machine.

Currently, the package is not 100% compatible with Python 3. The goal is to make it work, though.

Installation

The latest release of the package is available via PyPi, and can be installed with your favorite Python package manager:

$ pip install --upgrade fwdpy

OS X users must first install clang-omp from brew and use the following command:

$ CC=clang-omp CXX=clang-omp++ pip install fwdpy

$ CC=clang-omp CXX=clang-omp++

$ sudo python setup.py install

$ python setup.py install --prefix=$HOME

$ #use 'sudo' here if it is installed system-wide...
$ pip uninstall fwdpy

$ #build package locally:
$ python setup.py build_ext -i
$ #run the unit tests:
$ python -m unittest discover fwdpy/tests

$ CPPFLAGS="-I$HOME/include" LDFLAGS="-L$HOME/lib" pip install fwdpy

Note for developers

Cython is a static compiler. Code written in Cython is compiled into C or, in the case of this package, C++. Finally, the system’s C/C++ compiler is used to compile the final Python module.

In order to modify the package, you will need Cython installed:

$ pip install Cython

You need Cython >= 0.22.2, so upgrade if you need to:

$ pip install --upgrade Cython

If you wish to modify the package, then you will want setup.py to “re-Cythonize” when you make changes to the package source code.

To do this, use the setup.py script as follows:

$ python setup.py build_ext -i --use-cython

Now, Cython will be a compilation depdendency, and any changes to .pyx/.pyd/.cc files in this package will trigger Cython to regenerate the .cpp files that make up the core of the package.

$ OPT= python setup.py build_ext -i

$ OPT=-O2 python setup.py build_ext -i

$ module load krthornt/thorntonlab

$ which fwdppConfig

$ $HOME/software

Documentation

The manual is available online in html format at the project web page.

The API documentation may also be build using doxygen:

$ ./configure
$ doxygen fwdpy.doxygen

Then, load html/index.html in your browser.