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

[Stefan Kirov]

Heikki,
Sorry for the delay. I think I need  a week (maybe 10 days) to add some 
minor stuff to SiteMatrix module, nothing critical. I plan to add new 
parsers, extend mast parser to read section III (which is a bit messy 
for parsing), allow to write the PSM in some generic format (swissprot I 
guess) and probably one or two scripts. However this is not going to 
happen within the next month, so I guess this can wait for the next 
release. I am using the modules heavily, so I hope it will be useful for 
other people too.
Stefan

Heikki Lehvaslaiho wrote:

>Todd,
>
>That's good news. I was afraid that there are still big chunks of code 
>unwritten.
>
>So what you are saying is that SVG in Bio::Graphics is ready for other people 
>to start testing and using it in their code. Go for it! Bug reports to Todd.
>
>	-Heikki  
>
>On Monday 24 Nov 2003 TT:47, Todd Harris wrote:
>  
>
>>Hi Heikki -
>>
>>Re: SVG support for Bio::Graphics
>>
>>This is now essentially done.  I've released the GD::SVG module to CPAN and
>>implemented support for most features of GD that Bio::Graphics employs. I
>>would very much like to see this a part of 1.4.
>>
>>You can check out the output from the examples/biographics in SVG at
>>http://toddot.net/projects/GD-SVG/index.shtml#examples
>>
>>What remains:
>>   - detailed survey of glyphs to ensure that they render in png and svg
>>     identically.
>>   - more extensive testing
>>   - more supported features in GD::SVG (not required for bp 1.4 release).
>>   - adding in SVG information to full documentation
>>
>>It should be no problem to finish the testing within a week (or two, given
>>thanksgiving gorging and recovery this week for some of us).
>>
>>todd
>>
>>    
>>
>>>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"
>>>      
>>>
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>>    
>>
>
>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
USA
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov