[Bioperl-l] bioperl reorganization

Mark A. Jensen maj at fortinbras.us
Thu Jul 23 10:16:07 EDT 2009

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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