[Biopython-dev] Output of Biopython tests

[Michiel De Hoon]

Peter wrote:
> Michiel De Hoon wrote:
> > 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 now that it's there we can start to use in things 
> like modules that wrap external tools.

That is why I put it in Bio/__init__.py; Bio/GFF/__init__.py is already using
this exception (outside of the testing framework).

> 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).

Thanks! I missed those.

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

At some point, somebody will need to go through the documentation to check if
everything documented there still works with the Biopython in CVS, and to
remove sections in the documentation describing deprecated code. But it's
probably better to wait until after we decide what to do with
test_GenBankFormat.

> 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.
> 
> http://bugzilla.open-bio.org/show_bug.cgi?id=2366

No time to check it. But I'd be happy to rely on your judgement and include
it.

--Michiel.