[Biopython-dev] [Bug 3043] test_NCBI_BLAST_tools fails

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





------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2010-04-06 15:29 EST -------
(In reply to comment #4)
> (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. 

Do you agree this check would be useful as part of a "developer's extended
test suite"? The idea being that it will hopefully catch when the NCBI adds
or removes a BLAST+ switch. We would then update the wrapper and/or white list
the change in the test.

> > 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.

I had been thinking something like Tests/dev_test_XXX.py and Tests/dev/XXX
for any files required - but your suggestion of a new top level directory
would make the manifest and setup.py work easier.

Peter


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