Sheldon McKay | 9 Feb 14:04 2013

Re: [Gmod-gbrowse] BioPerl future

Hi Chris,

This sounds like a good idea.  I think it will eventually allow bioperl to
evolve into a leaner, meaner package that would be more likely to be
adopted by new or isolated bioinformaticians, who tend to be put off by
the size and complexity of bioperl as it now stands.

One question I have is whether the name of branch v1 might be perceived as
a step backward.  How about v2?


On Saturday, February 9, 2013, Fields, Christopher J wrote:

> All,
> (cross-posting to gmod-gbrowse)
> I want to gauge the community's thoughts on a few things.  At the moment I
> think we can safely say that BioPerl 1.x is in maintenance mode.  By
> 'maintenance mode', I mean that we can only do so much with it w/o breaking
> backwards compatibility with old scripts.  We need a way forward so that we
> can address fundamental problems within the core codebase, namely speed.
> I am thinking at the moment of pushing a 'v1' branch next week after I
> make an official announcement, with a new 1.6 release coming out from that
> branch (as already announced, tentatively scheduled for March 1).  That
> frees up master for any code development, removal of modules/cruft, etc.
>  This will open an initial path forward and at least enable us to do more.
>  Make sense?  This of course means that any code reliant on v1 should pull
> from that branch instead of 'master'.
> Thoughts?
> chris
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Sheldon McKay, PhD
Computational Biologist
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Rd
Cold Spring Harbor, NY 11724
(516) 367-5185