Ok, continuing my shotgunning of the list with BLAST stuff...
With Marek's refactoring of the BLAST tests and addition of a bunch of
BLAST parsing tests, the base test runner class for BLAST tests should
no longer skip all tests when blast isn't present. I've moved the check
& the resulting SkipTest raises into the specific tests, under branch
'blast_skip':
http://github.com/ctb/pygr/commits/blast_skip
It turns out that 10 of the 19 tests can be run without blastall or
formatdb being present; all 19 tests are skipped without this patch.
http://github.com/ctb/pygr/commit/52edb20ef93792a872c1c60a0082a9bf18e8f191#diff-1
--
Note also that the testutil.blast_enabled() function didn't cache its
results, so I've also fixed that.
http://github.com/ctb/pygr/commit/52edb20ef93792a872c1c60a0082a9bf18e8f191#diff-2
--
Finally, I don't entirely understand how the formatdb stuff is working;
see
http://github.com/ctb/pygr/commit/52edb20ef93792a872c1c60a0082a9bf18e8f191#diff-0
for my quizzical comment where the OSError from failing to run formatdb
is caught. I think it doesn't matter... but I'm not sure.
cheers,
--titus
--
C. Titus Brown, c...@msu.edu
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