Development

This is a reminder that the forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4.

Looking back, we supported Python 2.3 for about six years - it was released July 2003, and Biopython 1.50 released in April 2009 was the last to support it. Similarly, Python 2.4 was released six years ago (November 2004).

Dropping Python 2.4 support will allow use to assume standard library modules like the ElementTree XML parser and SQLite 3 support will be available. There are also several new language features in Python 2.5+ which will be useful, and it should make supporting Python 3 a little easier as well.

This is a reminder from the BOSC 2009 Organizing committee that abstracts for BOSC are due on Monday, April 13.

Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of Biopython on GitHub, which is automatically updated from the OBF hosted Biopython CVS repository. See our git migration wiki page for details. If this is favorably received, then moving Biopython from CVS to git seems likely at some point this year.

Originally, all the OBF hosted projects used CVS for their source code repositories. At the start of 2008, BioPerl and BioJava moved over to Subversion (SVN), followed by BioSQL. Biopython was originally going to do the same, but this didn’t actually happen. Having all the Bio* projects using the same version control system would have simplified server administration for the OBF, but using SVN wouldn’t really have made that much difference to Biopython development. Discussion on the Biopython development mailing list has since shifted towards next-generation distributed version control systems like git or Bazaar.

RC4 is up, we are days away from final release…

BioPerl has branched for 1.6 and the RC1 is up for testing as Chris announced.

BioPerl is preparing for version 1.6 release in the coming months. As part of this some restructuring and simplification of the packaging is occurring.

• Bio-Graphics has been split off into its own package back on Sourceforge to allow for a separate release schedule. It will be uploaded to CPAN as a separate package. In the future other small groups of modules will also be split off from the Core.  Eventually the Core will constitute components that will be the main parsers and data objects while less-common use cases or tightly related modules (like bioperl-network) will be released to CPAN on their own.
• Tests have been split off into smaller chunks.
• Anyone who has contributed to the code and feels their name should be included in the authors’ list needs to either add it or email the mailing list or Chris Fields.
• S endu has moved ModuleBuildBioperl and BioperlTest into Bio::Root
• Bugs are being triaged at bugzilla so if you have any opinions you can vote on the bugs in the queue.