[Bioperl-l] bioperl reorganization

Jay Hannah jay at jays.net
Thu Jul 23 10:11:26 EDT 2009

On Jul 17, 2009, at 10:26 PM, Chris Fields wrote:
>> If Bio::Foo::Bar is abandoned by all distributions, a new copy of  
>> that dist is flagged DEPRECATED ("in favor of Bio::Fooer::Bar"),  
>> and pushed to CPAN. That clues everyone in that development has  
>> stopped and where they should go instead. For example:
>>  http://search.cpan.org/~mramberg/Catalyst-Plugin-FormValidator-0.03/
> Okay, but seems kinda crufty.  I do think there is some talk of  
> removing such modules from the active CPAN, as they would always be  
> available as part of BackPAN, but I haven't seen movement along  
> those lines.

DEPRECATED modules can be removed from PAUSE after 6 months or 1 year  
or 50 years or whatever. Better to have it explicitly flagged and  
sitting out there than not flagged, misleading new users seeking  
solutions on CPAN. Eventually completely gone.

> Yes, I have to say it has been very nice with Moose, though I wish  
> MooseX::Declare and MooseX::Method::Signatures would move out of  
> alpha (probably will happen around the first stable release of perl6).

Indeed. A current CPAN is no magic bullet for every development  
dilemma. It's just better than a stagnant one.  :)

There's still plenty of tactical argument and jockeying in Catalyst  
and Moose. Like any healthy and active open source project populated  
by energetic people.

On Jul 17, 2009, at 10:31 PM, Chris Fields wrote:
> I think both of you made very good arguments.  Will have to  
> nickname you guys the IRC Mob.

Oooo... I like it! I'll sketch up some tattoo designs.  :)

On Jul 18, 2009, at 11:10 AM, Mark A. Jensen wrote:
> http://www.bioperl.org/wiki/Module_Connectivity

Wow. That's awesome.  :)

> My guess is that the NumDependencies values (which move fastest in  
> the Degree sum and create the sawtooth pattern) reflect  
> dependencies among the modules within the clusters. Wouldn't that  
> be cool? I don't think this works, but the data could certainly be  
> cajoled into giving us this.

Can the data be cajoled into proving that we've already split up  
BioPerl, so we can avoid all that SVN drudgery?  :)

BioPerl became self aware on August 17, 2009.


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