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 <andr...@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 <andr...@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 >> -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
