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

[Sendu Bala]

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?