Forward-time population genetic simulation in Python
Project description
This is the main README for the fwdpy software.
This package is a testing ground for providing access to efficient forward-time population simulation machinery in Python.
This package is implemented in terms of:
Cython, which is a package allowing C++ and Python to work together
fwdpp, which is a C++11 template library for implementing efficient population genetic simulations
libsequence, which is a C++11 library for population genetic calculations.
gsl, which is a C-language library for numerical methods. This package uses the GSL random number generation system plus several other features.
Please note that this package is likely to be quite unstable/actively developed.
The package is usable now (in fact, we are currently using it for research), but the API, etc., could change without warning.
Citation
See the project home page for details (http://molpopgen.github.io/fwdpy).
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:
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:
You also need a C++11-compliant compiler. For linux users, GCC 4.8 or newer should suffice.
Notes for OS X users
OS X users are recommended to use Anaconda instead of brew. Further, use the Anaconda version of GCC instead of the system (Xcode) Clang if you compile fwdpy from source. This package requires OpenMP, which is not supported via the clang provided with Xcode.
See next section for some details.
Anaconda
Anaconda may be the easiest way to install this package for many users. The dependencies are available via the Bioconda “channel”.
Note that using Anaconda means over-riding some things that may be provided with your system. For example, if you install dependencies via Bioconda and then wish to install fwdpy from source, you will need GCC from Anaconda:
conda install gccThe GCC version in Anaconda is 4.8.5, which is a bit old but sufficient for the C++11 features needed for all dependencies and for this package.
In order to make sure that the Anaconda GCC is used, you will need to make sure that the bin directory of your Anaconda installation is prepended to your users’s PATH variable.
If we define CONDAROOT as the location of your Anaconda installation, then you should define the following environment variables for your user in the dotfile appropriate for your favorite shell. For example, for the bash shell:
export PATH=$CONDAROOT/bin:$PATH
export CPPFLAGS="-I$CONDAROOT/include $CPPFLAGS"
export CFLAGS="-I$CONDAROOT/include $CFLAGS"
export LDFLAGS=-L$CONDAROOT/lib $LDFLAGS"
export LD_LIBRARY_PATH="$CONDAROOT/lib:$LD_LIBRARY_PATH"What Python version?
I’m developing the package using Python 2.7.6 on an Ubuntu machine. However, I do occasionally run the tests using Python 3, and all appears to work! Reports of problems using python3 are appreciated!
Installation
The latest release of the package is available via PyPi, and can be installed with your favorite Python package manager:
$ pip install --upgrade fwdpyOS X users must first install a compiler that supports the -fopenmp option. I recommend GCC from Anaconda (see above).
Installation from GitHub
You may also use pip to install from GitHub. However, doing so requires that Cython be installed.
$ pip install git+git://github.com/molpopgen/fwdpy --install-option="--use-cython"The above command installs the latest version of the ‘master’ branch. Users wanting latest and buggiest may find this useful. OS X users should follow the instructions for using clang-omp shown above.
Do this at your own risk. While the version number of the master branch may be the same as the version on PyPi, there may be bugs, API changes, etc.
To install a specific branch:
$ pip install git+git://github.com/molpopgen/fwdpy@branchname –install-option=”–use-cython”
Installation from source
First, install the dependencies (see above).
The best way to install the package is to use ‘pip’. Once you have cloned the source repo and ‘cd’ into it:
pip install . --upgrade --intall-option=--use-cythonTo build the package in place and run the unit tests:
$ #build package locally:
$ python setup.py build_ext -i
$ #run the unit tests:
$ python -m unittest discover fwdpy/testsDependencies in non-standard locations
The instructions above assume that dependencies (fwdpp and GSL) are found in “standard” locations, which means in /usr/local on a typical system.
Many users, especially those on clusters, may not have the privileges needed to install to the standard system locations. Thus, it may be necessary to manually tell fwdpy where the dependencies are located.
For example, let us assume that fwdpp and GSL are installed into your home folder. On Unix-like systems, $HOME is a variable representing the location of your home folder. Thus, the header files for these libraries will be found in $HOME/include and any run-time libraries will be found in $HOME/lib.
To tell pip where to find these dependencies, you need to manually set CPPFLAGS and LDFLAGS:
$ CPPFLAGS="-I$HOME/include" LDFLAGS="-L$HOME/lib" pip install fwdpyTesting
Testing occurs via docstring tests and unit tests. Here is how to test using both methods:
$ #build the package
$ python setup.py build_ext -i
$ #build the manual--requires Sphinx
$ make -f Makefile.sphinx html
$ #run the tests
$ make -f Makefile.sphinx doctest
$ #run the unit tests
$ python -m unittest discover fwdpy/testsNote 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 CythonYou need Cython >= 0.24.0, so upgrade if you need to:
$ pip install --upgrade CythonIf 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-cythonNow, 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.
Compiling in an aggressive debug mode
To get rid of optimizations, and -DNDEBUG, you need to reset the OPT flag set by Python’s distutils:
$ OPT= python setup.py build_ext -iDoing this will mean that the fwdpp back-end will not be compiled with -DNDEBUG, which will enable aggressive run-time correctness testing. By “aggressive”, I mean that an error will trigger a failed assertion and the Python interpreter will be exited less-than-gracefully! Only to this when testing.
It is better to enable some optimizations, though, else things run too slowly:
$ OPT=-O2 python setup.py build_ext -iRough guide to installation on UCI HPC
Use the following module:
$ module load krthornt/thorntonlabThat command loads the proper dependencies for compiling much of the tools that we use.
Note: this module replaces/over-rules some modules already on HPC. The “thorntonlab” modules are all consistently compiled with a GCC version that we’ve deemed suitable.
Troubleshooting the installation
Incorrect fwdpp version
This package is compatible with fwdpp >= 0.5.4, which means that you should have a binary installed on your systems called fwdppConfig. You can check if you have it:
$ which fwdppConfigIf the above command returns nothing, then it is very likely that fwdpp is either too old, missing entirely from your system, or it is installed somewhere non-standard. For example, if you installed fwdpp locally for your user, and did not edit PATH to include ~/bin, then fwdppConfig cannot be called without referring to its complete path.
Dependencies in non-standard locations
Your system’s compiler has a default set of paths where it will look for header files, libraries, etc. Typically, these paths will include /usr and /usr/local. If you have installed the dependencies somewhere else (your home directory, for example), then the ./configure script may not be able to find them automatically.
NOTE: I sometimes get requests for installation help from users who have installed every dependency in a separate folder in their $HOME. In other words, they have some setup that looks like this:
$HOME/software/gsl
$HOME/software/fwdpp
If you insist on doing this, then you are on your own. You have to manually pass in all of the -I and -L flags to all of these locations. This setup is problematic because it violates the POSIX Filesystem Hierarchy Standard (http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard), and you cannot reasonably expect things to “just work” any more. It would be best to start over, and simply install all of the dependencies into the following prefix:
$ $HOME/softwareDoing so will allow $HOME/software/include, etc., to be populated as they were intended to be.
Better yet, use a system like Anaconda (see above).
Documentation
The manual is available online in html format at the project web page. The manual always corresponds to the version of fwdpy found on PyPi.
The API documentation may also be build using doxygen:
$ ./configure
$ doxygen fwdpy.doxygenThen, load html/index.html in your browser.
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