[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Michiel de Hoon]

--- On Mon, 1/28/13, Wibowo Arindrarto <w.arindrarto at gmail.com> wrote:
> Hm..in this case (and in light of Eric's points as well), it
> may be ok to drop the string formatting functions in Bio._utils.
> They are used in Bio.Phylo and Bio.SearchIO for now. In Bio.SearchIO
> they are used in multiple submodules, however, so I am still leaning
> on putting them at least on Bio.SearchIO's main directory. They were
> originally in Bio.SearchIO._utils, after all.

I think it's OK to have a _utils submodule inside Bio.SearchIO. Since you are developing and maintaining that module, to a large degree it's up to you how you want to organize your code. For the same reason, for Bio.Phylo it's better to discuss with Eric Talevich first to see what he thinks.

> As for the doctest-related functions, do you propose to move
> them to a specific doctest-related module as well?

For the doctest-related functions, we first need to understand what the purpose is, before deciding how to implement it (and in what module the code should be).

Best,
-Michiel.