[Bioperl-l] deprecated modules

[Jason Stajich]

On Wed, 14 Aug 2002, Steve Chervitz wrote:

> Sounds like a plan to me.  The sooner we reduce Blast parsing to a single
> system, the better (preserving functionality, of course :). Some thoughts:

;)

>
> * The scripts in examples/blast should be re-vamped to use the new system.
> (This exercise should help assure functional preservation).
>
great idea, this goes on the list of must-do before 1.2 release.

> * Go through other files containing code that refers to Bio::Tools::Blast
> (bptutorial.pl, Makefile.PL, SeqFeature.t) and update them.
>
ditto

> * Might be good to have a document we can point people at who wonder how to
> migrate their old scripts to the new system and need extra hand-holding.
>
okay - I'd propose it get written as a HOWTO and put in the doc/howto

> * For archaeologists or folks who need to refer to older modules that are no
> longer in the distribution, you can always access previous releases from
> ftp://bio.perl.org/pub/DIST/
>
Of course and cvs export -r bioperl-release-XXX -d bioperl-XXX
bioperl-live will always work too.

> Steve
>
> --- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> > Bio::Tools::Blast has been deprecated for a while - I'd like to remove it
> > from the trunk.  Additionally I'd like to remove Bio::UnivAln as it too
> > has been deprecated.  Steve and I have agreed that
> > Bio::SearchIO::psiblast, Bio::Search::HSP::BlastHSP
> > Bio::Search::Hit::BlastHit, and Bio::Search::Result::BlastResult will be
> > deprecated in 1.2 assuming we get all the functionality moved over to the
> > SearchIO::blast and XX::GenericXX objects.
> >
> > I can create a DEPRECATED file to list module history like this:
> >
> > # These are modules which are deprecated and later removed from the
> > toolkit
> >
> > Deprecated Modules     Version Deprecated   Version Removed
> > --------------------------------------------------------------
> > Bio::Tools::Blast            1.0	          1.1
> > Bio::Tools::Blast::HSP       1.0		  1.1
> > Bio::Tools::Blast::HTML      1.0		  1.1
> > Bio::Tools::Blast::Sbjct     1.0		  1.1
> >
> > Bio::Tools::WWW		     1.1
> >
> > Bio::UnivAln		     1.0		  1.1
> >
> >
> > My feeling is that BPlite currently still serves a purpose and should stay
> > on the trunk, but it might need some maintence/testing at some point.
> >
> > Shout if you don't want to see this happen.
> >
> > -jason
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
>
> =====
> Steve Chervitz
> sac@bioperl.org
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu