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

[Steve Chervitz]

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
>