[Biopython-dev] Bio.Motif update

[Peter Cock]

On Fri, Feb 1, 2013 at 2:53 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 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.

Thanks.

>> 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.

Agreed.

>> (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?

I went over the list in the DEPRECATED file last month, but a second
check would be a good idea.

Peter