[Bioperl-l] SearchIO speed up

Hilmar Lapp hlapp at gmx.net
Mon Aug 14 10:35:36 EDT 2006

Don't complicate things more than they need to, please. The  
experimental branch should be solely for things for which you aren't  
sure whether they are going to work at all, and for API changes for  
which the consequences across the board may be significant and  
difficult to fully anticipate (e.g. the late-breaking and still  
haunting SeqFeatureI changes before 1.5.0 should have gone on an  
experimental branch first to see how they will behave).

It should never be a requirement to merge commits from the main trunk  
to an experimental branch (or commit twice for developers).

Quite frankly the changes Sendu described for me wouldn't have  
warranted an experimental branch, they didn't sound like changing API  
signature or API behavior.


On Aug 14, 2006, at 10:01 AM, Chris Fields wrote:

> Sendu,
> Sounds good.  We need to make sure that commits to bioperl-live also
> get committed to the experimental branch, correct?  Or at lease make
> sure bioperl-live commits are merged into experimental (and not vice-
> versa)?
> Chris
> On Aug 14, 2006, at 6:43 AM, Sendu Bala wrote:
>> Chris Fields wrote:
>>> Here's a couple of  suggestions to get around that if you want to  
>>> get
>>> the code out there for testing:
>>> Could this be CVS-tagged to an experimental bioperl branch instead?
>>> It could be merged back to the main branch once everybody gets to  
>>> try
>>> it out, and you could commit changes to the branch (tests, scripts,
>>> etc) along the way based on suggestions.  Think of this as a test-
>>> drive for a new Bioperl release.
>> I have created branch 'branch-experimental' and committed the
>> changes there.
>> Please test by checking out the experimental branch:
>> cvs co -d experimental -r branch-experimental bioperl-live
>> I'll probably end up writing a new pull/chunk parser for BLAST, but
>> these changes will still speed up the other SearchIO modules. So test
>> the speed-up on different kinds of report as well.
>> The experimental branch should be used for trying out major
>> implementation changes that have the potential to break important and
>> substantial parts of bioperl. Everything else should continue to be
>> committed to HEAD until the 1.6 branch emerges (sometime next year).
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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