[Bioperl-l] Developers: what do you want to fix before 1.4 release?

[Heikki Lehvaslaiho]

Jason,

If everyone were to raise to a challenge like you...!

Thanks,
		-Heikki

On Tuesday 25 Nov 2003 TT:06, Jason Stajich wrote:
> > P.S.1. Other open bugs related to SearchIO are: 1416, 1418, 1468, 1558
>
> Happy pre-Thanksgiving ....
>
> 1558 - Fixed.
> 1416 - Fixed. good enough, I can't reproduce it
> 1418 - Fixed. I think it works, I have started just using Guy's GFF output
>        but I think it all matches up with parse from his VULGAR
>        strings
>
> Not quite there:
> 1468 - It seems to work okay now.  Everything except printing the
>        Statistics in the BLAST way.
>        Something that can be done without too much work I think.
>
> > P.S.2. Also thanks for spotting the wrong URL.
> >
> > On Tuesday 25 Nov 2003 TT:10, Steve Chervitz wrote:
> > > On Nov 24, 2003, at 2:04 PM, Jason Stajich wrote:
> > > > I am fixing up blast parsing to get the gapped, ungapped, and
> > > > frame-specific lambda,kappa, entropy from the reports for those who
> > > > want
> > > > this.  I will also try and make sure we are getting more of the
> > > > parameters
> > > > from the reports into the Result objects.
> > > >
> > > > Presumably we had talked about remove SearchIO/psiblast.pm from 1.4
> > > > release - not sure if that is still a good idea.
> > >
> > > I'm fine with this. There are a few example scripts that are pointing
> > > at psiblast.pm. We'll have to make sure they work with blast.pm.
> > >
> > > SearchIO/psiblast.pm depends on some modules in Bio::Tools that can
> > > probably also go away (Bio::Tools::StateMachine::*) since these modules
> > > aren't being used by any other Bioperl modules. There may be external
> > > code that depends on them, but not too likely. If there's interest, I
> > > could contribute them separately to CPAN.
> > >
> > > Steve
> > >
> > > > I also have some more work on the PopGen objects to make sure all the
> > > > numbers are correct for some of the implemented tests.
> > > >
> > > > -jason
> > > >
> > > > On Mon, 24 Nov 2003, Heikki Lehvaslaiho wrote:
> > > >> With developer snapshot 1.3.03 out last Friday, I'd like to hear
> > > >> from bioperl
> > > >> developers what they'd like to accomplish before 1.4 comes out.
> > > >>
> > > >> At this stage, I'd rather not see major new features added; there
> > > >> will not be
> > > >> time to test them properly.
> > > >>
> > > >> I'd especially like to hear from
> > > >> * Lincoln Stein / Todd Harris about the SVG timetable
> > > >> * Stefan Kirov about Bio::Matrix::PSM modules
> > > >> * anyone else about their pet modules and bugs
> > > >>
> > > >> I'll give you three choices:
> > > >>
> > > >> 1. You've got a fix/enhancement under way and you can give me
> > > >> timetable
> > > >> for it to be in.
> > > >>
> > > >> 2. There is a bug that need to be fixed before the release but you
> > > >> do not know how to do it.  Let's discuss that now!
> > > >>
> > > >> 3. Your modules are not ready for release and you do not have time
> > > >> to work on your code. That means that they will need to be excluded
> > > >> from the release.
> > > >>
> > > >> I am pretty happy with the current status of bioperl CVS tree. Tests
> > > >> pass, but there still are bugs in bugzilla. I urge anyone and
> > > >> everyone to have a look at the bugzilla and see what they think of
> > > >> the bugs still
> > > >> there.
> > > >>
> > > >> Realistically, we have couple of weeks time to get the fixes in.
> > > >> Then a
> > > >> week to wait to make sure everyone has time to make sure that
> > > >> everything
> > > >> works.
> > > >>
> > > >> 	-Heikki "Let's push 1.4 out"
> > > >
> > > > --
> > > > Jason Stajich
> > > > Duke University
> > > > jason at cgt.mc.duke.edu
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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