[Biopython-dev] Bio.Motif update

Peter Cock p.j.a.cock at googlemail.com
Fri Feb 1 14:56:02 UTC 2013

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.


>> 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?

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


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