[Bioperl-l] Do we need Bio::Root::Object anymore?

Chris Fields cjfields at uiuc.edu
Mon Oct 2 16:52:11 EDT 2006


I have updated the Deprecation page with the Bio::Root::* modules that we
plan on deprecating (note that I have them being removed for rel. 1.5.2).  I
have left out Bio::Root::Storable for now based on Will's response.  

http://www.bioperl.org/wiki/Deprecated_modules

I'll update the DEPRECATED doc in CVS as well.  There is a tentative
schedule for when warnings are added for modules before they are removed.  

In relation to the recent trend for house-cleaning, I noticed that all of
the Bio::Tools::BP* BLAST-related modules all are still present but haven't
been modified or had deprecation warnings added.  BPLite was marked for
deprecation around rel 1.5 since the functionality is present in
Bio::SearchIO, as well as the others.  Judging by the mail list, no one has
used these in quite a while, and everyone has been redirected to use
Bio::SearchIO instead.  Based on that I have added warnings in CVS for
deprecation to BPlite and the related modules BPpsilite and BPbl2seq.

Chris

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Brian Osborne
> Sent: Monday, October 02, 2006 9:14 AM
> To: Sendu Bala; bioperl-l
> Subject: Re: [Bioperl-l] Do we need Bio::Root::Object anymore?
> 
> Sendu,
> 
> No objection but someone should check the scripts in examples/root to make
> sure that they are not used there.
> 
> Brian O.
> 
> 
> On 10/2/06 5:55 AM, "Sendu Bala" <bix at sendu.me.uk> wrote:
> 
> > Torsten Seemann wrote:
> >>>>> I have removed all use/@ISA Bio::Root::Object references from
> >>>>> bioperl-live, except for those in Bio::Root::* itself:
> >>
> >>>> So I'd say they're both relics that can be removed. In fact I was
> >>>> planning on getting rid off all references to both of these modules
> >>>> before you did, so thanks! :)
> >>
> >>> I think they can go. It's probably a pre-1.0 deprecation that somehow
> >>> was never followed through on.
> >>
> >> Today I did a fresh CVS checkout of bioperl-live, and deleted the
> >> following modules and tests, and all tests passed with BIOPERLDEBUG=0
> >>
> >>      * Bio::Root::Err
> >>      * Bio::Root::Global
> >>      * Bio::Root::IOManager
> >>      * Bio::Root::Object
> >>      * Bio::Root::Storable
> >>      * Bio::Root::Utilities  # may be used by third parties?
> >>      * Bio::Root::Vector
> >>      * Bio::Root::Xref
> >>      * t/Root-Utilities.t    # need to keep if we keep Utilities.pm
> >>      * t/RootStorable.t
> >>
> >> Should we schedule for deprecation, or deprecate immediately as Hilmar
> >> suggested they were meant to be deprecated long ago ?
> >
> > I'm happy to get rid of them all straight away. Does anyone object?
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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