[Bioperl-l] 1.5.1 todo list

Jason Stajich jason.stajich at duke.edu
Wed Aug 24 13:11:29 EDT 2005

So after those exchanges on what version of Bioperl needs to be run,  
and the various floating bugs in the release soup....

If we had to make a list of showstoppers for 1.5.1 release what would  
they be?

To explicitly state, I think the purpose of 1.5.1 release should
a) clean up know showstopper bugs in 1.5.0
b) allow new modules/functionality to be introduced since 1.4 and 1.5.0
c) be preparing the way for 1.6 release by putting code out in the  

I am fairly adamant API changes that are not backwards compatible  
need to be CAREFULLY thought out before being allowed in.  Since the  
code base is so big at this point, there need to be good tests in  
place to confirm this, and a responsibility from the developers to  
make sure this is the case.

My hope is that Gbrowse (live) could be successfully run on a 1.5.1  
as I feel that is largest 'external' consumer of Bioperl, with BioSQL  
and of course everyone's scripts which use a handful of modules.

What is the status of bioperl code for:
  Ontology work
  BioSQL support (from the Core code at least, how much in sync would  
1.5.1 be with biosql-perl release?)
  Bio::FeatureIO stuff + Bio::SeqFeature changes?
  Bio::DB::GFF work?  the GFF3 schema would be way past 1.5.1, but is  
that something we'd want to shoot for in 1.6?
  Other things?

Please report in.  Times like this sort of make me want a Wiki so we  
can keep track but I'll at least volunteer to collate the results  
into a summary email.


Jason Stajich
jason.stajich at duke.edu

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