[Biopython-dev] Biopython 1.59 plans

[Peter Cock]

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