[Biopython-dev] Bio.Motif update

[Michiel de Hoon]

Hi Peter and all,

--- On Tue, 1/29/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> We need to say something about this in the NEWS file too.

Done.

> I think it would make sense to add a PendingDeprecationWarning
> to Bio.Motif now.

Done.

> Also, if you feel the new Bio.motifs API isn't quite
> settled yet, adding the new BiopythonExperimentalWarning to
> that makes sense.

I don't expect big changes in the API, so I think we can do without the BiopythonExperimentalWarning. Also we should avoid the situation that Bio.Motif gives a DeprecationWarning, and Bio.Motifs gives a BiopythonExperimentalWarning.

> (And once this is settled, I think we can schedule the
> release)

We should also check whether we can remove deprecated modules, or deprecate modules that are currently declared obsolete. Or has somebody done that already?

Best,
-Michiel