[Bioperl-l] 1.5.1 todo list

Ewan Birney birney at ebi.ac.uk
Thu Aug 25 04:59:23 EDT 2005

Jason Stajich wrote:
> 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  wilds.
> 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?

I've wrriten my interface class for TypedSeqFeature but not done
an implementation yet. I'll commit the interface and work on
an implementation.

>  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
> -- 
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
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