[Bioperl-l] branched for 1.0

[Jason Stajich]

Scratch that - I just did this, should be fixed.  very simple.

On Thu, 14 Mar 2002, Jason Stajich wrote:

> 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
> > >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu