Biopython 1.63 released

 Posted on December 6, 2013  |  tiago

Source distributions and Windows installers for Biopython 1.63 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI). The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5). This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3. The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. [Read More]

Biopython 1.63 beta released

 Posted on November 12, 2013  |  tiago

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website. This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5). This release of Biopython supports Python 2. [Read More]

BioPerl v.1.6.910 released

 Posted on September 8, 2013  |  cjfields

UPDATE: As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio to CPAN this past March. Unfortunately that release (v1.7) appears to have version collisions with this one (v.1.6.910); therefore I’m packaging a new point release ( v1.6.920) that removes Bio::Biblio to prevent this. That has now been uploaded to CPAN and should be available shortly. [Read More]

Biopython 1.62 released

 Posted on August 28, 2013  |  peterc

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI). Python support This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported. We still fully support Python 2. [Read More]

BioRuby 1.4.3.0001 Released

 Posted on May 27, 2013  |  NaohisaGoto

We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs.

  • “gem install bio” failed with Ruby 2.0 or later versions.
  • lib/bio/db/gff.rb script encoding issue
  • Bio::Blast::Default::Report parse error when subject sequence contains spaces.

For more information, see RELEASE_NOTES.rdoc and ChangeLog.

[Read More]

Biopython 1.61 released

 Posted on February 5, 2013  |  peterc

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online ( PDF). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). [Read More]

BioRuby 1.4.3 released

 Posted on August 21, 2012  |  NaohisaGoto

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius. Here is a brief summary of changes. Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element. Many failures and errors running on JRuby and Rubinius are resolved. Strange behavior related with “circular require” is fixed. Fixed: Genomenet remote BLAST does not work. Fixed: Bio::NucleicAcid. [Read More]

Travis-CI for Testing

 Posted on July 30, 2012  |  peterc

Earlier this year BioRuby and then Biopython and BioPerl started using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated: BioRuby Biopython BioPerl The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems. Travis-CI gives us continuous testing, but for the moment only covers one operating system (currently 32 bit Ubuntu Linux using Virtual Machines). [Read More]

Biopython 1.60 released

 Posted on June 25, 2012  |  peterc

Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 and PyPy 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported. Most functionality is also working under Python 3. [Read More]