[Bioperl-l] branched for 1.0
Thu, 14 Mar 2002 17:40:39 -0500 (EST)
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
On Thu, 14 Mar 2002, Brian Osborne wrote:
> 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" <firstname.lastname@example.org>
> To: "Bioperl" <email@example.com>
> 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
> > firstname.lastname@example.org
> > _______________________________________________
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