[Bioperl-l] moving Bio::Tools::Run, 1.1 release plans

[Lincoln Stein]

I'm also making some changes to the Bio::Graphics module to add regression 
tests and to speed up the bumping of colliding features.

Lincoln

On Sunday 23 June 2002 09:01 pm, Jason Stajich wrote:
> Here are the plans regarding splitting the Bio::Tools::Run subdir off into
> its own cvs repository.
>
>
> In order to preserve all of the history for Bio::Tools::Run and not
> break the past branches, I will plan to lift the whole directory into a
> new cvs module called bioperl-run.  When releases are done we'll be sure
> and bring this back in as well as I'll add it to the cvs alias
> (bioperl_all) which will make a directory called 'run'.  Once we are
> confident that this works I will then plan to 'cvs remove' all the files
> in bioperl-live/Bio/Tools/Run.  Now it is important before we start the
> move that everyone commit all of their project files in the Bio/Tools/Run
> directory or else you'll need to checkout the new bioperl-run module and
> copy your working files over.  I'm going to say that Tuesday is the day
> for the move -speak up if that is a problem.  You'll need to have all of
> your changes checked in, or you'll need to handle making a fresh checkout
> and copying your changes over to the directory structure.
>
>
> This copy + cvs remove in bioperl-live will allow the older branches to
> work so we don't have to worry about pulling out old versions.  It will
> continue to eat up disk space, but I think with the new server coming
> online by Aug 1 (fingers crossed) we should be quite fine.  Along those
> lines, Chris please let us know what the timeline looks like for the move
> to the new developer-only box so we can start to plan for this.
>
>
>
> 1.1 release
> -----------
> I would like to plan on putting out a developer release of bioperl (1.1)
> before BOSC, so in the next 2-3 weeks depending on the outstanding
> projects.  There are a bunch of changes and bug fixes on the trunk that
> aren't on the branch including the Pise, PAML, RepeatMasker, and TRIBE
> wrappers.  I was informed of, and fixed, some bugs in the SearchIO FastA
> parser. There is also the new SeqFeature::Collection object to handle
> storage of lots of SequenceFeatures and fast retrieval of subsets defined
> by location.  Hopefully will have it implement part of the DasI interface.
>
>
> I'm also changing the object creation model for the Bio::SearchIO parsers
> so it is factory based to facilitate implementing the hmmer parser and
> other classes that will get written.  This is very much in the spirit that
> SteveC defined for his psiblast + statemachine but the API is little
> different.
>
>
> It would be great to get the coordinate mapper that Heikki has described
> in.  I've also not been able to work on the
> FeatureAggregator/SemanticMapper as of late, but don't let me initial
> proposal to work on it keep anyone away from taking a stab at it.  I hope
> to get back to it soon if no one else does want to work on it.
>
>
> -jason

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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