[Biopython-dev] Bio.Motif update

[Michiel de Hoon]

OK, thanks! I separated Bio.Motif into Bio.Motif (essentially the same as in Biopython release 1.60) and Bio.motifs (the new code).

Best,
-Michiel.

--- On Sun, 1/20/13, Bartek Wilczynski <bartek at rezolwenta.eu.org> wrote:

> From: Bartek Wilczynski <bartek at rezolwenta.eu.org>
> Subject: Re: [Biopython-dev] Bio.Motif update
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: "BioPython-Dev" <biopython-dev at biopython.org>
> Date: Sunday, January 20, 2013, 5:34 PM
> Hi,
> 
> great job Michiel! It looks very nice overall. As the code
> that will
> be using the new library needs to be changed, I would vote
> for the
> change in the namespace, but given that the userbase of the
> Bio.Motif
> was quite limited, I think it wouldn't cause major problems
> to keep
> the name as is.
> 
> best
> Bartek
> 
> On Sun, Jan 20, 2013 at 8:30 AM, Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> > Dear all,
> >
> > As we discussed previously, I've been going over
> Bio.Motif to update it and make its usage more explicit. I'm
> pretty much done. While I have been uploading my changes to
> the main biopython github repository, this does not mean
> that these changes are final; comments and suggestions for
> changes are welcome.
> >
> > In many cases, there is a difference in the syntax
> between the old Bio.Motif and the new Bio.Motif. For
> example, motif.consensus is a method in the old Bio.Motif,
> but a property in the new Bio.Motif.
> > While I tried to put PendingDeprecationWarnings on all
> changes consistently, there may be some corner cases that I
> missed.
> >
> > For this reason, and also to make the documentation
> more understandable, it may be better to put the new
> Bio.Motif code in a module Bio.motifs, to put the old
> Bio.Motif code back into Bio.Motif (so that Bio.Motif in
> release 1.61 will be identical to the Bio.Motif in release
> 1.60), and (assuming that we are happy with the new
> Bio.motifs modules) put a PendingDeprecationWarning on
> Bio.Motif as a whole. Then in the documentation we'll have
> one chapter on Bio.Motif and one chapter on Bio.motifs. Also
> we'll have one set of tests for Bio.Motif, and one set of
> tests for Bio.motifs.
> >
> > Any objections to creating a separate Bio.motifs
> module?
> >
> > Here you can find the relevant chapter in the current
> documentation on the new Bio.Motif:
> >
> > http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html#htoc190
> >
> > Best,
> > -Michiel
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
> >
> 
> 
> 
> -- 
> Bartek Wilczynski
>