[Biopython-dev] Biopython 1.59 plans

[João Rodrigues]

Sure, we can look at it afterwards then, it was just a cosmetic issue, it's
annoying to see so many repeated lines.

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



No dia 24 de Fevereiro de 2012 16:45, Peter Cock
<p.j.a.cock at googlemail.com>escreveu:

> On Fri, Feb 24, 2012 at 2:56 PM, João Rodrigues <anaryin at gmail.com> wrote:
> > Hi Peter,
> >
> > In both Linux and Mac all tests ran fine.
> >
>
> Thank you - I would have been surprised if not though. It would
> suggest a gap in the buildbot coverage.
>
> > A remark, when running the tests I get plenty of these warnings:
> >
> > test_FSSP ...
> >
> /Volumes/Home/users/joaor/Software/biopython-1.59/build/lib.macosx-10.6-intel-2.7/Bio/Align/Generic.py:54:
> > BiopythonDeprecationWarning: With the introduction of the
> > MultipleSeqAlignment class in Bio.Align, this base class is deprecated
> and
> > is likely to be removed in a future release of Biopython.
> >   warnings.warn("With the introduction of the MultipleSeqAlignment class
> in
> > Bio.Align, this base class is deprecated and is likely to be removed in a
> > future release of Biopython.", Bio.BiopythonDeprecationWarning)
> >
> > Is there an option not to have the message repeated? It's just cosmetics
> but
> > I thought of asking anyways..
> >
> > Good work,
> >
> > João
>
> I don't think we can alter the repeat when the warning is shown,
> but we can silence it for this test. We should do that (but really
> we should update the FSSP code), likewise the warning for the
> BioSQL feature 'order' thing.
>
> We've got similar code in other tests - the trouble is that the
> warnings module is global and there are subtle interactions
> between test scripts. I think we need to add some cleanup in
> run_tests.py to restore the filters as a fall back.
>
> Do you want to try this (after the release)?
>
> Peter
>