[Bioperl-l] 0.7 release: Evaluating every module

Ewan Birney birney@ebi.ac.uk
Mon, 13 Nov 2000 20:31:32 +0000 (GMT)

On Mon, 13 Nov 2000, Hilmar Lapp wrote:

> Jason Stajich wrote:
> > 
> > I would like to propose that we have a checklist and go through the
> > standards for every module.  As we establish a minimal documentation,
> > perhaps RootI compliance, and standardization of subroutine POD, this will
> > give us an opportunity for all the code to get a lookover before we
> > certify as an 0.7 release.
> I second this proposal, a minimal review before a release is certainly
> beneficial. As always, the point is who's going to do this: as a supporter
> I must count me myself in; anyone else willing to help? (Anyone supporting
> it will automatically be counted :-)
> Jason, does it make sense if you take over this subject, or shall I
> coordinate it?

Happy to be considered a supporter, and happy to do my time in reviewing
code. However, I don't think we will be able to tease out the Root::Object
from the blast code, and we can't remove the code (backward compatibility)
even though we have BPLite in.

I will sign up for doing Bio::Seq, Bio::PrimarySeq, Bio::SimpleAlign,
Bio::LoctableSeq and the Bio::Annotation::* set of modules to make them
Bio::Root::Object free...

I'd like to hear steve's or peter's (vh) view on this in  case we are
screwing them - does anyone object to this?

> > Also some modules - the Bio::Search::* specifically have been unfinished
> > for quite some time.  I've communicated with Aaron and he suggested they
> > either be finished or removed from the tree.  I think a Bio::SearchIO in
> > the AlignIO/SeqIO spirit for processing search results (blast,fasta,HMMER)
> > would be interesting, but obviously not contained in this release.
> > However, decisions should be made if we are going to continue to include
> > incomplete modules in a release.
> > 
> My vote goes for abandoning incomplete stuff from a release; that's what
> the development trunk is for. By incomplete I mean modules that are not yet
> usable in a meaningful way. It confuses potential users of the package who
> may waste their time in trying to figure out whether that module is able to
> solve their problem -- only to find out that it's not working yet.

I agree completely hilmar. Not sure if these should be removed from teh
trunk completely, or removed on the branch before the first release off
the branch...

 > 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420