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

Lincoln Stein lincoln.stein at gmail.com
Mon Nov 10 18:10:09 EST 2008

Hi Sendu,

Thanks for pointing me to the thread; I'm sorry I missed it at the time. The
idea of splitting bioperl into 900 individual modules is a terrible idea but
I'm not advocating that. I'm just advocating splitting it into a half dozen
modules that are divided according to the* de facto *maintainer. For
example, Gabriel becomes the maintainer of Bio::PhyloNetwork.


On Mon, Nov 10, 2008 at 5:59 PM, Sendu Bala <bix at sendu.me.uk> wrote:

> Dan Bolser wrote:
>> Sorry for the potentially dumb question, but why have an overall
>> release cycle at all?
>> BioPerl is so large and diverse, asking for a new 'release' is almost
>> like asking for 'the next release of CPAN'. Can't inter-module
>> dependencies just be handled in the same way as in the rest of CPAN,
>> with everything released asynchronously? Is BioPerl just too tightly
>> woven for that to happen?
> Doing that is considered a Bad Idea (TM):
> http://www.nntp.perl.org/group/perl.modules/2007/07/msg55160.html
> (especially Adam Kennedy's postings of 4/07)
> (It just so happens that we discuss Bio::Graphics as an example of the
> problem)
> As for Lincoln's desire to pull Bio::Graphics out, as Chris described that
> was more or less the kind of plan we had in mind. We'd have probably ended
> up splitting it out into its own little package so that it could be updated
> and released on its own cycle, with the latest version of it always
> compatible and tested with the latest core package and any other split-off
> Bio package it might depend on. In our plan Bio::Graphics would still have
> belonged to Bioperl-ML on CPAN, but I can understand the desire for Lincoln
> to have full direct control over those modules again.

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>

More information about the Bioperl-l mailing list