[Biopython-dev] 1.62b test coverage report

Peter Cock p.j.a.cock at googlemail.com
Wed Jul 31 07:40:24 UTC 2013

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 the tests are out of date, or there were failures for some other reason.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).

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

A few more details here would be very good - what versions of
the tools did you have and what error did the tests give?

(I just fixed a warning from new options added in BLAST
2.2.28+ committed yesterday)

> You can look at the report on my website at
> http://benfulton.net/BioPython162_Coverage/ . Please let me know if you
> have comments or questions, or can tell me what I did wrong on the above
> tests :)

Thanks Ben - some of the modules with zero or low coverage
are deprecated so don't worry me - others though probably
do need to be looked at.

Would anyone like to make a priority list? This would then
be something we can point volunteers at who ask for
suggestions of something they can contribute?



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