Git

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About git

The Biopython source code is kept under a 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). Prior to September 2009, we used to use CVS.

An hourly updated CVS checkout of Biopython was available at http://biopython.open-bio.org/SRC/biopython and we intend to have this updated from git shortly.

You can also track changes via RSS.

Viewing git sources

Our current development git sources are available for viewing via GitHub:

Biopython GitHub Home

This is the main repository. You can download these sources by clicking the Download link near the top of the page.

Anonymous Access

Getting a copy of the repository (called "cloning" in Git terminology) without a GitHub account is very simple using the git command line tool:

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. BioRuby also uses github.

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