Release 1.6

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BioPerl Release 1.6.0

The first stable release in the 1.6 series is now available for download.


General installation instructions for various platforms.


The release candidates can be downloaded here:

Signature file:


In process...

Anonymous Subversion

 svn co svn://

BioPerl Developer Subversion

Note: requires dev account

 svn co svn://

ActiveState PPM

In process...


  • ActiveState PPM4 is set up but is missing several key required PPMs, so does not install currently. We will try adding the PPMs when possible.

Installing Bioperl on Windows

Other BioPerl Distributions

We will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Links for those will be reported on the list and here when the time arrives.


Tests for the 1.6 release are on a separate page.

Release priorities for 1.6

Provisional proposals and bugs (no decision made yet) marked in red, accepted proposals/bugs marked in black, rejected proposals marked deleted, pushed back proposals/bugs marked in green.

Bio::Graphics and Splitting BioPerl

  • Split off Bio::Graphics
  • Subdistribution versioning schemes
  • Treat other bioperl distributions as independent subdistributions (independent release schedules)
  • Option to install subdistributions in the core build script
    • This will likely be a reconfiguration of Bundle::BioPerl for this purpose.

Bugs and Bugzilla

  • Outstanding bugs
    • Remaining bugs are to be addressed incrementally via point releases.
  • Outstanding issues added to bugzilla for tracking
    • Noting minor fixes and updates in bugzilla as TODOs.
  • Merging enhancement requests and the project priority list?

Test suite

  • Reorganization by splitting tests up by module
    • Tests reorganized based on categories and classes
  • How far do we want to take this? Should all modules be split up (or only parsers)?
  • Wrap BioPerl-specific test methods into core (Bio::Root::Test, Bio::Root::Build); add tests for BioPerl-specific test functions
    • Bio::Root::Test needs some way of dealing with situations when Test::Warn and Test::Exception are not installed
      • It already does --Senduran 01:01, 12 January 2009 (UTC)
  • Test coverage is already in place (thanks Mauricio, Nathan, Sendu, and everyone else involved)! What else needs to be done?

Developer vs. Stable releases

NOTE: These aren't really relevant to the 1.6 release per se but pertain to how we want to handle future releases

  • After 1.6, no more alternating of 'developer' and 'stable' releases.
  • Create bioperl-dev (this will be post-1.6)

Point releases vs minor releases

NOTE: These aren't really relevant to the 1.6 release per se but pertain to how we want to handle future releases

  • Release regular bug fixes (no API changes) as point releases.
  • Related: what will the module split version be (1.7? 2.0?)
  • Deprecation of modules is decided by the core devs.
    • Module is widely used, go through a routine deprecation cycle
    • Modules that no longer work can be immediately deprecated and removed in the next release.
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