[Bioperl-l] branched for 1.0

[Jason Stajich]

Steve C needed to rewrite his code without UnivAln - I guess it didn't get
done.  I have similar code that does this in GenericHSP but creates
SimpleAlign.  It is a very simple switchover.

This reminds me, Steve, we never were able to merge SearchIO psiblast.pm
with blast.pm - I am concerned that we have a very confusing set of
objects there, I am more inclined to mark psiblast as experimental or not
include it.

-jason

On Thu, 14 Mar 2002, Brian Osborne wrote:

> Colleagues,
>
> UnivAln has been removed from branch-1.0, as you know. It's still required
> by Bio/Tools/Blast/HSP.pm, probably not a problem since the Tools/Blast
> group of modules is destined to vanish. However, it's also required by the
> get_aln method of Search/HSP/BlastHSP.pm.
>
> I have to assume that this is a bug, so I'll submit it. Your thoughts?
>
> Brian O.
>
> ----- Original Message -----
> From: "Jason Stajich" <jason@cgt.mc.duke.edu>
> To: "Bioperl" <bioperl-l@bioperl.org>
> Sent: Sunday, March 10, 2002 1:02 PM
> Subject: [Bioperl-l] branched for 1.0
>
>
> >
> > I've tagged and branched the code for 1.0.  This means if you have bug
> > fixes to check in you will need to do it twice or else merge your changes
> > from the branch onto the trunk.
> >
> > To do this, you will need two checkouts of the bioperl code:
> > The branch
> > % cvs -d :ext:MYNAME@bio.perl.org:/home/repository/bioperl co -r
> > branch-1-0-0 -d branch-1.0 bioperl-live
> > The -d branch-1.0 will checkout the code in a diretory of that name to
> > help you distinguish.
> >
> > The normal, main-trunk code:
> > % cvs -d :ext:MYNAME@bio.perl.org:/home/repository/bioperl co bioperl-live
> >
> > apply fix and check-ins in both directories
> >
> > ( I realize now that I made a boo-boo and named the branch branch-1-0-0
> >   instead of branch-1-0-0 but hopefully we can all live with that or I
> >   can sed s/branch-1-0-0/branch-1-0/ in the repository)
> >
> > Anyone who is doing any major bioperl coding should have both the main
> > trunk and the branch code checked out and should apply any bugfixes to
> > both branches.
> >
> > A note about branches.
> >
> > It is very important for us to maintain a stable release of bioperl, so
> > nothing should be checked into the branch that changes the API of the
> > toolkit.  We'd like to go to the release schedule of at least 1 major
> > releases a year.  This may get improved to more than one if we have an
> > active developer base and are able to move the toolkit towards new
> > directions.  The bottom line: New modules and major functionality
> > additions should be confined to the main-trunk and the branch should be
> > left with only bug fixes.
> >
> > The Core will hopefully draft a "State of the Onion"-like announcement of
> > where we think Bioperl should be going in the next 6-9 months and anyone
> > is more than welcome to describe what new functionality they are
> > interested in.  I think that some of the future directions include:
> >
> >  * Remote application execution
> >  * Assemblies
> >  * more structure support
> >  * Alignment / Tree building expansion
> >  * more EMBOSS output parsers to map to bioperl objects
> >
> > If you've been sitting on the sidelines and any of these (or your own pet
> > project) interest you and you'd like to help, speak up!
> >
> > I'll have the 1.0alpha2-rc tarball out on the site by tonight or monday
> > morning.
> >
> > Going to be distracted by college basketball for a little while!
> >
> > -jason
> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu