[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.
>
>> 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)

Hi Michiel,

Rather than having two (very similar) chapters in the Tutorial for
the old Bio.Motif and new Bio.motifs modules, I've downgraded
the old chapter to just a section of the new chapter:

https://github.com/biopython/biopython/commit/ee5cccf6bc661befc924cb7fc2a422c07f3eeee1

There is still a lot of redundant content - would you be able to
shorten this? Or can we just cut it and refer anyone interested
to the tutorial shipped with Biopython 1.60 instead?

I think a summary of the differences  be more useful, to help people
convert from the old module to the new motifs module.

Also, what is the point of the Bio.motifs.create function? Is there
a reason not to initialise a Motif object directly?

Thanks,

Peter