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fixed cpairwise2 import issue under python3 #299

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merged 1 commit into from Mar 15, 2014

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newgene
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@newgene newgene commented Mar 14, 2014

In Python v3.3.2, original line 881

from cpairwise2 import rint, _make_score_matrix_fast

failed to import cpairwise2, which causes much slower python functions were used silently.

Relative import should be used here for python 2.x and python 3 compatibility:

from .cpairwise2 import rint, _make_score_matrix_fast

Another possible fix is using the explicit path:

from Bio.cpairwise2 import rint, _make_score_matrix_fast

@peterjc peterjc merged commit daf3e3b into biopython:master Mar 15, 2014
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peterjc commented Mar 15, 2014

Thanks - we missed that during the Python 3 migration work (the pure-Python fallback hid the problem).

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peterjc commented May 9, 2014

N.B. Later reported as a bug in the Debian package for Biopython 1.63, http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=747494

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