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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Sat Sep 30 02:26:20 EDT 2006


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! :)
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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>>
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM


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