[Bioperl-l] bioperl-dev or branch?

Robert Buels rmb32 at cornell.edu
Fri May 22 18:27:15 UTC 2009

Chris Fields wrote:
> We trust our vcs.  I do wish others would use branches more often, but 
> that's not the problem I'm worried about.  Core is simply bloated with 
> unmaintained (albeit possibly useful) code.

Yes, when you put it that way, it makes more sense.  It was sounding to 
me like people were using bioperl-dev as an excuse to not branch when 
appropriate, which caused me to get out my flamethrower.  Thanks for 
putting the discussion back on the larger, stickier core issue, which 
seems to be that of apportioning scarce maintenance resources.

Abstractly, it would seem that the natural solution to this would be to 
separate the current "really big lump" distributions into smaller 
distributions of single-maintainer or small-team size, roughly sorted by 
functionality.  By making the parts of bioperl more loosely coupled, 
even if one couldn't fix it, one could at least say something like (for 
example) 'Bio-TypedSeqFeature' is not currently maintained.

In recent years, the CPAN toolchain has had a lot of rough edges 
smoothed out, so smaller distributions linked together with dependencies 
should actually be quite a bit easier for users to manage now than was 
the case in the past.

Is this what you're getting at cjf?


P.S. A big reorg like this is not too bad to do with svn, particularly 
if the code you're moving around is not changing very fast.  Like if 
it's unmaintained.  ;-)  Mostly I think you'd want to do it with moves 
and renames of directories directly in the repository, not in a working 

P.P.S. I'm willing to help with all of this, of course, now that I've 
found where I put my good-software-citizen-that-helps-out hat.

Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

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