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

Hilmar Lapp hlapp at gmx.net
Fri Sep 29 16:46:06 EDT 2006


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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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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