[Bioperl-l] Splits again

Hilmar Lapp hlapp at gmx.net
Thu Jun 28 06:31:29 EDT 2007

On Jun 28, 2007, at 12:51 AM, Jason Stajich wrote:

> [...] Also - the main point I wanted to make - Can I suggest we  
> spend a
> little time discussing what it will take to get a stable release for
> the current code as it stands (bioperl-live and bioperl-run)?  It
> seems like we really need to do this first so that we have a stable
> release that can be followed by CVS -> SVN migration, then consider
> major changes to the repository structure and release packaging, and
> potential deprecation and incorporation of other modules.

I agree we need to discuss a path towards 1.6, but I think that  
should be kept separate from the cvs->svn migration. Otherwise one  
stalls the other (by stopping people who seem to have the energy and  
motivation right now to do one but not the other) for no really good  

> I assume there is no chance that we'd have a 1.6 candidate by BOSC
> next month?

I'm not sure that's feasible to be happening but if someone steps up  
it maybe it is.

> Will it be productive to schedule a fair amount of time at BOSC
> discussing how to partition out the packages into separate sub-
> packages after we've done a successful release rather than trying to
> change things right now?

I agree. I also don't think that people are partitioning right now  
(other than the existing partitioning), though maybe I'm mistaken.

> [...]
> It would  probably mean moving Bio::Graphics, Bio::DB::GFF and
> Bio::DB::SeqFeature and gff tools for Gbrowse into separate packages
> so they could be released more regularly on par with Gbrowse
> schedules.

Possibly. I'm not fully sure why those modules couldn't also be  
released more often out of the "main trunk" of modules. In Java/ant,  
it'd be relatively easy to write build script filters that select the  
appropriate modules and package them on the fly. I'm not sure whether  
the build tools for Perl can do that too, though.

>   Also I think someone needs to figure out Bio::Tools::GFF
> vs Bio::FeatureIO -- what do we want to do?

I believe FeatureIO has the ontology download tied into it?

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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