[Bioperl-l] Priorities for a bioperl-1.6 release

Chris Fields cjfields at uiuc.edu
Wed Feb 13 14:11:34 EST 2008


On Feb 13, 2008, at 12:32 PM, Brian Osborne wrote:

> Chris,
>
> You should be careful about the names of these packages. For  
> example, Bio::Biblio and Bio::Restriction are not "in development"  
> as the term bioperl-dev implies. They're tried and true. And there  
> may be sets of modules that are experimental in "bioperl-dev", of  
> course. Is it possible to have 2 packages, "dev" and "tools"? Or  
> something along those lines?
>
> Calling things by the wrong names leads to confusion, witness the  
> Bioperl newcomers who would install an antiquated version 1.4  
> because it was labelled 'stable'.
>
> BIO

I agree the name 'dev' is misleading.  'tools' or 'extras' sounds  
better, maybe using 'dev' for experimental implementations, such as  
Jason's SeqFeature::Slim or my SeqIO driver/handler modules.  The  
problem with the two namespaces you mention is lack of maintenance and  
documentation, though I agree they're stable (so maybe in those cases  
maintenance isn't an issue).

We do need to clean up documentation issues with those classes as well  
as many more (mine included); POD/test coverage will help out there.

chris



More information about the Bioperl-l mailing list