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