This is a 4th year project developed as a part of Joint Honours Computer Science and Mathematics degree at University of Glasgow.
The naturalSelection framework is distributed in source form as a standard python module, and can be used and handled in the way any python module can.
In addition I'm including the project bash script, which has the purpose of running test cases to assure compliance with Cpython 2 and Cpython 3, as well as the execution of the particular experiment implemented using this framework.
To access framework's manual, make sure your working directory contains the naturalSelection directory and type pydoc
In order to run a simulation batch and create all the graph files, compute Tmrca and run Mann-Whitney statistics you can execute ./project --runExperiments s2 mrca2 proc2. The graphs will be generated and written in results directory. The step s2 does not have any dependencies required apart from Cpython 2.7, Cpython 3, pypi or jython. proc2 is dependent on the networkx package.
To carry out some symbolic derivation of mathematical formulae used in this project you can execute ./project --derive. This step has a dependency on the sage package, which can be installed, e.g. on modern Fedora by executing dnf install sagemath as root user. This dependency is optional and restricted to this particular command so as not to force any user to install sage as dependency in their system.
To unit test, execute ./project --test.
You can install all of dependencies described above using virtualenv in the following way: virtualenv venv source venv/bin/activate pip install -r requirements.txt This should install all required dependencies for python 2 (a.k.a. Cpython 2). Regarding python 3 pip is quite confused, I found necessary to install dependencies using my distribution's package manager.