[Bioperl-l] branched for 1.0

[Brian Osborne]

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
>
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