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

[Chris Fields]

I'll add the table from DEPRECATED to the page.  We can add the  
schedule for the modules that are being phased out and modify  
DEPRECATED as needed.

The current list that are still in core (I think):

Deprecated:

Bio::Tools::BPLite (rev 1.5)
Bio::Species (rev 1.5.2)
Bio::Taxonomy* (rev 1.5.2)
Bio::Tools::RestrictionEnzyme (rev 1.5)
Bio::Ontology::SimpleGOEngine (rev 1.5.1)

Soon-to-be:

Bio::Graph* (maybe rev. 1.5.2, waiting on word from Nat Goodman)
Bio::Factory::ResultFactoryI (rev. 1.5.2)
Bio::Factory::HitFactoryI (rev. 1.5.2)
Bio::SeqIO::game (rev. 1.5.2)
Bio::Search::Processor (rev. 1.5.2)
Bio:Root::Object (rev. 1.5.2)


Torsten also pointed out that Bio::Root::Xref has no other modules  
using it:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/12764

so it could be deprecated as well.

Chris


On Sep 30, 2006, at 1:26 AM, Mauricio Herrera Cuadra wrote:

> Chris has already set up this one:
>
> http://bioperl.org/wiki/Deprecated_modules
>
> As you suggest, a deprecation schedule should be added to the last  
> section.
>
> Cheers,
> Mauricio.
>
> Hilmar Lapp wrote:
>> I think they can go. It's probably a pre-1.0 deprecation that somehow
>> was never followed through on.
>>
>> BTW in this context, to avoid (or diminish ...) the same from
>> happening with currently begun deprecations, what setting up a page
>> on the bioperl site that lists deprecations currently in progress and
>> their schedule (e.g., deprecated in rel. >1.5.2, warning in rel.
>>> 1.6.x, removed in rel. >1.7.x).
>>
>> Or does this exist already?
>>
>> 	-hilmar
>>
>> On Sep 29, 2006, at 2:58 AM, Sendu Bala wrote:
>>
>>> Torsten Seemann wrote:
>>>> Chris Fields directed us to a previous post by Hilmar Lapp where
>>>> he was
>>>> organizing the transfer of Bio::Root::Object to Bio::Root:RootI/ 
>>>> Root:
>>>>
>>>> http://bioperl.org/pipermail/bioperl-l/2001-January/004854.html
>>>>
>>>> I have removed all use/@ISA Bio::Root::Object references from
>>>> bioperl-live, except for those in Bio::Root::* itself:
>>>>
>>>> Bio/Root/Err.pm
>>>> Bio/Root/Global.pm
>>>> Bio/Root/IOManager.pm
>>>> Bio/Root/Object.pm
>>>> Bio/Root/RootI.pm
>>>> Bio/Root/Utilities.pm
>>>> Bio/Root/Vector.pm
>>>> Bio/Root/Xref.pm
>>>>
>>>> Can any developers from <= 2001 advise on the role of Object.pm in
>>>> these
>>>> classes?
>>> Well, according to a comment in Bio::Root::Object:
>>>
>>> #
>>> # This object is deprecated as the root of the inheritance tree,
>>> but some
>>> # modules depend on it as a legacy. We issue a deprecation warning
>>> for all
>>> # other modules.
>>> #
>>> my @inheriting_modules = ('Bio::Root::Object',
>>> 			  'Bio::Root::IOManager');
>>>
>>> Nothing seems to use IOManager (except Object), and its also
>>> redundant.
>>> 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! :)
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>
> -- 
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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