[Bioperl-l] Withdraw Bio::Graphics and Bio::DB::SeqFeature from bioperl distribution?

Chris Fields cjfields at illinois.edu
Mon Nov 10 16:46:03 EST 2008


I agree about the glacial pace.  It's also feeling more and more like  
only a couple of active developers are working on it (so the more that  
chip in the better).  Furthermore, the code base is so large now at  
this point it feels like steering an aircraft carrier with an oar and  
has become very hard to work on.

I don't have any objections personally if you want to withdraw  
Bio::Graphics/Bio::DB::SeqFeature, but how much work would that be  
(scott mentions a few issues I see)?

Personally, I think if Bio::Graphics remains in bioperl we have to do  
two things.  We should release the full bioperl-live as-is to CPAN as  
an official release (TODO any bugs) ASAP.  No RCs; we'll post point  
releases along the way for bug fixes (I like the 'release early/ 
release often' mantra).  I can work on this over the next couple of  
weeks, aiming for Thanksgiving for a 1.6, but I probably won't get  
rolling until this weekend (too much going on this week).  We can aim  
for more regular point releases then.

Following that, I think a more stable long-term solution is to split  
off some of the non-core-like modules so that we can speed up releases  
(this has been discussed in the past, http://www.bioperl.org/wiki/Proposed_1.6_core_modules) 
.  Basically, make a 'bare-bones' well-tested core containing the base  
classes and interfaces that remain stable long-term, such as  
Bio::Root, Bio::Seq/PrimarySeq, Bio::SeqFeature::*, with as few  
dependencies as possible.

Everything else requiring constant maintenance, not actively  
supported, or under development would go into a separate monolithic  
distribution listing the new core as a dependency; this could feasibly  
have it's own release schedule.  If we go this route, Bio::Graphics  
and related could also be in a second distribution (and thus also on a  
distinct release schedule).  This could be worked out in a separate  
subversion directory, so bioperl-live wouldn't be affected until we  
switch over.  Does that seem feasible?


On Nov 10, 2008, at 2:25 PM, Lincoln Stein wrote:

> Hi All,
> The glacial pace of official bioperl releases is interfering with my  
> ability
> to package GBrowse 2.00 into debian and rpm packages. Is there any  
> objection
> if I withdraw Bio::Graphics and Bio::DB::SeqFeature from the bioperl
> distribution and turn them into independent CPAN modules?
> Thanks,
> Lincoln
> -- 
> Lincoln D. Stein
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse at cshl.edu>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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