biopython/biopython — pull request #299 by newgene (2014-03-14 20:20:12+00:00)
Title: fixed cpairwise2 import issue under python3

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