[Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and undef/die

Chris Fields cjfields at uiuc.edu
Wed Sep 20 15:22:17 EDT 2006


Dave, 

There is a small bit about what to have in POD in biodesign.pod, which is no
longer in the core.  I think most of it can be found in the wiki under
'Advanced BioPerl'.  

http://www.bioperl.org/wiki/Advanced_BioPerl

There is a link to the older version of it:

http://bioperl.org/Core/Latest/biodesign.html

There is also an Emacs template, which I haven't toyed around with.  I use
ActiveState Komodo, which runs on Mac OS X and WinXP.  Yes, I am pathetic...

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: David Messina [mailto:dmessina at wustl.edu]
> Sent: Wednesday, September 20, 2006 2:01 PM
> To: Hilmar Lapp
> Cc: Chris Fields; Sendu Bala; bioperl-l; Torsten Seemann
> Subject: Re: [Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and
> undef/die
> 
> On Sep 20, 2006, at 10:10 AM, Hilmar Lapp wrote:
> 
> > I wasn't even aware that that was a 'requirement'
> 
> AFAIK, there wasn't any previously agreed upon set of standards for
> the BioPerl docs, although most modules follow a remarkably
> consistent layout.
> 
> With the Deobfuscator, it helps to enforce a little more uniformity
> for ease of parsing. And since I haven't publicized any of these
> issues until yesterday, it's hardly your fault that you weren't
> aware. :)
> 
> It may not happen before 1.5.2, but at some point I intend to write
> up a little guide which describes the de facto standard that BioPerl
> modules follow (maybe Mauricio has already thought about this?). If
> there is agreement on these as a small set of guidelines, we can add
> it to the developer instructions so that people writing new modules
> will be aware.
> 
> -Dave



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