[Biopython-dev] [Bug 2749] Proposal: a template for biopython's unittests

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Feb 4 16:16:37 UTC 2009


------- Comment #3 from bsouthey at gmail.com  2009-02-04 11:16 EST -------
(In reply to comment #1)
> The current view from the Biopython developers is that we don't want to depend
> on nose for running our unit tests (nose is not installed automatically as part
> of python).  This has been discussed on the mailing list, so I won't repeat
> myself here.

Also, the test framework must support Python 2.3 while Biopython supports it. 

Really I find that the huge diversity in Biopython prevents a 'single' template
that is sufficiently easy to follow. I do not like the splitting that test into
setups for each 'subtest' followed by a general test. This starts to get rather
difficult to read and manage when you have modules like the sequence object
involve many different tasks that require a separate setup for each test as
well as the actual test. A related problem is that certain tests may require a
specific exception for a specific situation.

Another problem is that some of the tests are very similar for the same module
(say Logistic regression or testing alphabets in reading sequences into a Seq
object) so it makes more sense to do what numpy does
(http://projects.scipy.org/scipy/numpy/wiki/TestingGuidelines ) where the same
test function is used with different inputs. I would like to easily add a new
test case to an existing test like Numpy has a test case class that is separate
from the actual tests.

Just few cents,

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