[Biopython-dev] 1.62b test coverage report

[Eric Talevich]

On Wed, Jul 31, 2013 at 12:40 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Wednesday, July 31, 2013, Ben Fulton wrote:
>
> > I ran Ned Batchelder's coverage tool against the 1.62 beta code to see
> how
> > much code is covered by tests. The overall total was 74% which is pretty
> > respectable.
> >
> > I ran the tests on a fairly fresh machine, which meant I had to install a
> > lot of software, some of which I either didn't get installed properly, or
> > the tests are out of date, or there were failures for some other reason.
> I
> > ended up having to skip seven test files:
> >
> > Dialign_Tool
> > EmbossPhylipNew
> > Mafft
> > PopGen_DFDist
> > PopGen_FDist
> > XXMotif
> > phyml
>
>
> I'm pretty sure I have some or all of those setup on at least one
> of my test machines, so with a little more work together we
> can try to resolve those (which may mean updating the docs).
>

I just fixed the error in test_phyml_tool.py, it was a simple one:
https://github.com/biopython/biopython/commit/90da547f0a85c00d3ca300bdf52bdb96ddeb449f


> There were three tests I managed to get running but still had failures:
> >
> > FastTree
> > NCBI_BLAST
> > Prank_too
>

The FastTree test is not based on the unittest framework, so the output
contains the word "Failed" in three places to describe error-handling tests
that worked correctly. Can we see the output for this one? (It works on my
machine.)

The test is also fairly new, so there could be some version-compatibility
issues there too.

Thanks,
Eric