SourceCode

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Introduction

The source code from Biopython is freely available for your use and contribution under our liberal license.

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.

Viewing the source code

You can browse our latest source code on github.

Track changes

You can track changes via RSS.

Downloading the latest source

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).

An hourly updated copy of the code is also available at http://biopython.open-bio.org/SRC/biopython (just a snapshot - no history etc).

Anonymous Access

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 git://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.

Write Access

In order to 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 Development mailing list.

Once you have access, see the instructions on GitUsage

Migration from CVS

Most of the other Open Bioinformatics Foundation projects migrated from CVS to Subversion (SVN). Biopython had been considering moving from CVS to SVN for a while, but instead moved to git in September 2009. Note that BioRuby also uses github.

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