[Biopython-dev] [Bug 3043] test_NCBI_BLAST_tools fails

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http://bugzilla.open-bio.org/show_bug.cgi?id=3043





------- Comment #4 from mdehoon at ims.u-tokyo.ac.jp  2010-04-06 09:39 EST -------
(In reply to comment #3)
> To address this issue in the short
> term, I've made this abort the test with a missing external dependency error
> (so that run_tests.py will skip it) with what I hope is a clear and not too
> scary error message.
> 
Sorry but I don't think this test is useful. If the test succeeds, all we know
is that the user's Blast has the same options as the developer's Blast. But it
doesn't actually test Bio.Blast.Applications. For many users, the test will
generate a MissingDependencyError; as we've seen, even for the same version
Blast may have different options. But the Blast dependency is not actually
missing, and most like Bio.Blast.Applications works correctly even if some
options were added to Blast. 

> We don't have "full" test suite do we? That would be useful, and we could do
> things like require larger test files to be present (which we can track in the
> repository but not ship) or generated, or assume a particular BLAST database
> will be installed.
> 
That would be useful. We could have a biopython/Developer directory in the
repository with all the tests we want to run before making a release.


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