[Biopython-dev] Output of Biopython tests

Peter biopython-dev at maubp.freeserve.co.uk
Thu Oct 11 20:37:52 UTC 2007

Michiel De Hoon wrote:
>> Perhaps we should introduce a MissingExternalDependency error instead,
>> used for this specific case, and catch that in run_tests.py, while
>> treating ImportError as a real error.
> OK. I added a MissingExternalDependencyError exception to Bio/__init__.py,
> and modified BioSQL, Bio.GFF, and some test scripts accordingly. When
> MissingExternalDependencyError occurs in a test, a warning is printed but it
> is not counted as a failure.

I might have defined the exception within the test framework rather than
Bio/__init__.py, but not that its there we can start to use in things
like modules that wrap external tools.

I've updated Tests/requires_internet.py and Test/requires_wise.py to
match (I don't have wise on my machine which is why I noticed it still
threw an ImportError).

This means run_tests.py now runs without errors using CVS on my 64 bit
Linux machine (bar the mxTextTools 3.0 issue with test_GenBankFormat.py
(bug  2361).

Is there anything I can do to help get things ready for the release of
Biopython 1.44?

If you do have time to give the patch on bug 2366 a check, I think it
would be worth including before the next release.



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