[Bioperl-l] Priorities for a bioperl-1.6 release

Chris Fields cjfields at uiuc.edu
Tue Feb 12 12:02:13 EST 2008


Now that SVN migration is complete and a BioSQL 1.0 release is  
imminent (congrats Hilmar and Heikki), I would like to get a new  
bioperl core release out the door soon, preferably by the next BOSC  
meeting, end of summer by the latest.  One major issue that all the  
core devs have right now is time, or a serious lack thereof.  I, for  
instance, will be moving into a new research position in the next few  
months or so.  I'm assuming Jason, Hilmar, Heikki, Sendu, and the  
other core developers are facing similar time constraints.

In that light, we need to decide whether we are planning a new 1.5  
release, or if we want to start a new stable (1.6) release.  With the  
latter, we need to define very specifically what needs to be  
accomplished for that release, and it needs to be realistic with the  
timeframe above in mind.  I would also like to extend the invitation  
for anyone who wishes to help to join in.

For my vote, I would like to release a new stable 1.6; 1.5.x has been  
around for too long and the end goals were never really defined  
clearly (something we need to keep in mind for the next dev release).   
I also vote for separating out experimental/untested/undocumented/ 
unmaintained modules into a separate 'bioperl-dev' release (the 'here  
be dragons' of bioperl).  I believe it would help the core release  
cycle tremendously.

Issues raised in the past just off the top of my head (add more as  
needed):

* perl 5.10 compliance (appears to mostly work now)
* outstanding bugs (core only)
* GFF/GFF3 compliance
* BioSQL 1.0 compliance (impending)
* POD and test coverage
* smoke tests for bioperl-live/db/etc.
* smaller, more focused core (less dependencies)
* separating out experimental or poorly maintained modules into a  
separate 'bioperl-dev' distribution
* bioperl-db issues with Bio::Species changes
* module maintenance
* sequence format roundtripping (i.e. genbank, embl, swissetc)
* additional sequence parsers (insdcxml, etc)
* enhancement requests in bugzilla (Albert?)

chris


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