[Debian-med-packaging] Bug#747494: python3-biopython: Does not use C implementations of cpairwise2 functions

[Andreas Tille]

Hi Peter,

many thanks for this information.  Since I'd like to reward the user
reporting the bug as fast as possible and to send the message that we
really care about our users I applied the fix right now and uploaded
the package.

Kind regards

       Andreas.

On Fri, May 09, 2014 at 01:36:32PM +0100, Peter Cock wrote:
> Hi Andreas,
> 
> This was reported directly to Biopython and fixed two months ago:
> https://github.com/biopython/biopython/pull/299
> https://github.com/biopython/biopython/commit/daf3e3b5ba317fbbea1f7eebae3c5f8b06a40d6b
> 
> If you want to apply the one line fix to Biopython 1.63 for the Debian
> Python 3 package, that would be great. Otherwise (under Python 3)
> the optimised C code is never used, just the pure Python fallback.
> 
> (Note I'm hoping we can get Biopython 1.64 out later this month.)
> 
> On a separate note, is there a mechanism to alert upstream projects
> (in this case Biopython) when a bug is reported in the Debian package?
> 
> Thanks,
> 
> Peter
> 
> 
> On Fri, May 9, 2014 at 12:55 PM, Andreas Tille <andreas at an3as.eu> wrote:
> > Hi,
> >
> > while I have just closed this bug report since I assumed it was a wrong
> > usage of the import statement I would like to forward this issue to
> > upstream Biopython developers anyway.  It seems there are cases when
> > cpairwise2 is not used and things might work slower than necessary.
> >
> > I just forward this for your consideration to make sure that everything
> > works as expected from your side.
> >
> > Kind regards
> >
> >         Andreas.
> >
> > On Fri, May 09, 2014 at 01:32:37PM +0200, Jakub Wilk wrote:
> >> * Andreas Tille <andreas at an3as.eu>, 2014-05-09, 13:15:
> >> >thanks for your bug report.  I think this should work out of the
> >> >box but I personally not comfortable with cpython to know how this
> >> >could be fixed.  I keep the Debian Python list in CC - perhaps
> >> >they might have some helpful advise.
> >>
> >> The relvant code in Bio/pairwaise2.py is:
> >>
> >> # Try and load C implementations of functions.  If I can't,
> >> # then just ignore and use the pure python implementations.
> >> try:
> >>    from cpairwise2 import rint, _make_score_matrix_fast
> >> except ImportError:
> >>    pass
> >>
> >> But in Python 3 imports as always absolute, unless explicitly
> >> requested, so the import fails, and this code snippet is no-op.
> >> Changing the import line to:
> >>
> >>    from .cpairwise2 import rint, _make_score_matrix_fast
> >>
> >> should do the trick.
> >>
> >> Before:
> >> $ python3 -c 'from Bio.pairwise2 import rint; print(rint.__module__)'
> >> Bio.pairwise2
> >>
> >> After:
> >> $ python3 -c 'from Bio.pairwise2 import rint; print(rint.__module__)'
> >> Bio.cpairwise2
> >>
> >> >It seems this module is not affected by the test suite since this
> >> >runs fine.
> >>
> >> Yeah, as the code comment says, if the import fails, everything(?)
> >> still works, just slower.
> >>
> >> --
> >> Jakub Wilk
> >>
> 

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