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

[Heikki Lehvaslaiho]

Steve,

Thanks for offering to clean the SearchIO modules. Could you also see that 
this bug:
	http://bugzilla.bioperl.org/show_bug.cgi?id=1419
gets closed and obsolete modules removed from cvs.

Thanks,

	-Heikki


P.S.1. Other open bugs related to SearchIO are: 1416, 1418, 1468, 1558

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
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
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