[Bioperl-l] Bio::*Taxonomy* changes

[Hilmar Lapp]

How do you mean 'process'? You create a new module, and then you  
deprecate the ones you're phasing out. If possible you rewrite the  
implementation to use the new module.

Not sure this answers your question?

	-hilmar

On Jul 27, 2006, at 10:06 AM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> I don't think the top-level or sub-directory matters at all and I  
>> don't
>> want anybody to get used to the notion that that may imply anything
>> (except possibly better thought-out structure for the sub-directory
>> level). For instance RichSeq is what all rich annotation sequence  
>> format
>> parsers return, yet it is in a sub-directory.
>
> Well, I'm not aware that I've ever used a RichSeq ;). But your  
> point is
> taken.
>
>
>> I don't any real objection to Bio::Taxon though if that's what you'd
>> like to name it - although, what will happen to the Bio::Taxonomy
>> hierarchy then? Phased out?
>
> At the moment it seems to me that the Bio::Taxonomy modules (excluding
> Node) aren't really usable. Jason wrote a comment in t/TaxonTree.t  
> which
> tests Taxon and Tree:
>
> ## I am pretty sure this module is going the way of the dodo bird so
> ## I am not sure how much work to put into fixing the tests/module
>
> FactoryI is strange (it isn't intended to work like any other Bioperl
> factory) and there are no implementers of it, while Taxonomy.pm itself
> would be redundant after my Node changes and has implementation  
> issues,
> though it may make more sense to some people.
>
> My vote is phase out.
>
>
> What is the actual process involved in renaming a module in Bioperl?
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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