[Bioperl-l] Withdraw Bio::Graphics and Bio::DB::SeqFeature from bioperl distribution?
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
> to package GBrowse 2.00 into debian and rpm packages. Is there any
> if I withdraw Bio::Graphics and Bio::DB::SeqFeature from the bioperl
> distribution and turn them into independent CPAN modules?
> 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
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Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign
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