* 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
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