[Bioperl-l] deprecated modules

[Peter Kos]

Hi,

Bio::Tools::Blast has been deprecated for a while - but it still 
works.

I hope good old scripts will be easy to adjust to work with the new 
set of modules.

What is the benefit from removing them? Will they cause problem with 
respect to the self-compatibility and homogeneity of the whole 
toolset in later versions?
I would feel that it may be enough to state clearly that they are 
deprecated so that new scripts should not use them. If these modules 
do not cause too much trouble for you, I would not mind wasting that 
much diskspace. Even now I store the whole Bioperl, although lots of 
the modules will never be necessary for me, and I am happy to have 
all of them under my fingertip, just in case.
There may be hundreds if not thousands of scripts using the 
deprecated modules worldwide, and they may later cause problems on 
machines with only brand-new installations of Bioperl.

I also understand that redundancy may lead to confusion, but 
TIMTOWTDI, as the Camel says.

Cheers
Peter

On Thursday, August 15, 2002 3:22 AM, Jason Stajich 
[SMTP: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
>

..................................................................  
..........
Peter B. Kos
(RITE)
kos@rite.or.jp