[Bioperl-l] bioperl reorganization

Chris Mungall cjm at berkeleybop.org
Thu Jul 23 19:54:13 UTC 2009

OMG it's full of *s.

(and %s. and $s. and @s. and #s...)

On Jul 23, 2009, at 10:16 AM, Mark A. Jensen wrote:

> Open the pod bay doors, BioPerl.
> ----- Original Message ----- From: "Jay Hannah" <jay at jays.net>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Thursday, July 23, 2009 10:11 AM
> Subject: Re: [Bioperl-l] bioperl reorganization
>> 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.
>> j
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