[Bioperl-l] 0.7 release: Evaluating every module

[Jason Stajich]

Hilmar - I'm happy to serve as point on this.  I'll wiki up a list of all
the modules and who is responsible for them.  

Once we establish our minimal requirements we can have a checklist for
each module so we can be sure every module has been looked at.

-Jason

On Mon, 13 Nov 2000, Ewan Birney wrote:

> 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
> > -------------------------------------------------------------
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> 

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/