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

Lincoln Stein lincoln.stein at gmail.com
Mon Nov 10 17:57:49 EST 2008


Hi Folks,

Sorry, I sent my letter out while multitasking, which was inappropriate for
such a nuanced subject.

Here's my feeling about the issue, which is very similar to Chris's
approach: Bioperl should be split up into a core API containing Bio::Root,
the interface modules, and some of the really basic modules such as
Bio::SeqIO. There are then a series of separately maintained and released
modules that build on top of BioPerl and using it as a dependency. I am not
in favor of having a "separate monolithic distribution" however. I'd prefer
it to be more like this:


   - Bio::Perl -- the core distribution, containing Bio::Root, Bio::Seq,
   BioSeqFeature, Bio::SeqIO and Bio::Annotation
   - Bio::Align -- alignment support
   - Bio::Ontology -- ontology support
   - Bio::Microarray -- microarray support
   - Bio::PopGen -- population genetics
   - Bio::SeqEvolution -- evolutionary biology
   - Bio::Structure -- structures
   - Bio::Tree -- trees

I wonder how many interdependencies there are to disentangle?

In the immediate future, it'd be great to get the regression tests working
100% and do a CPAN release, but this may be easier said than done.

Lincoln


On Mon, Nov 10, 2008 at 4:46 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Lincoln,
>
> 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?
>
> chris
>
>
> 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>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
>


-- 
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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