Python Tools for Computational Molecular Biology
Python Tools for Computational Molecular Biology
Biopython is currently released under the liberal “Biopython License Agreement”, but as part of a plan to switch to the more commonly used “3-Clause BSD License”, some of the code is explicitly dual licensed under your choice of these two options. For details, see our license file.
The Biopython source code is kept under a distributed version control system which allows multiple users from around the world to work on the same code base at the same time. We currently use git (developed by Linus Torvalds for Linux kernel development) hosted on GitHub.
Our core developers maintain a stable trunk from which we will roll releases as new functionality is integrated and bugs are fixed.
You can browse our latest source code on github.
You can track code development by RSS feed or the Biopython mailing list. See also our other mailing lists.
You can download the latest source code by clicking the Download link near the top of the Biopython GitHub page (this will offer you a tar ball or zip file).
Getting a copy of the repository (called “cloning” in git terminology) is very simple using the git command line tool, you don’t need an account or password:
git clone https://github.com/biopython/biopython.git
This command creates a local copy of the entire Biopython repository on your machine (your own personal copy of the official repository with its complete history). You can update this local copy at the command line (from within the Biopython repository directory) with:
git pull origin
You can even make local changes and commit them to this local copy, see GitUsage or the git documentation for further information.
Most changes are submitted as pull requests via GitHub.
In order to directly make changes to the official repository, you will need a GitHub account with collaborator status. Write access is available for Biopython developers (including all those who previously had CVS commit rights).
This is normally given on a case by case basis, and the best place to discuss getting write access is on the Biopython mailing list.
Once you have access, see the instructions on GitUsage
Most of the other Open Bioinformatics Foundation projects migrated from CVS to SVN (Subversion), and later to git hosted at GitHub.
While Biopython did considering moving from CVS to SVN, instead we migrated directly from CVS to git in September 2009.