[Debian-med-packaging] Bug#944242: Test issues with BioPython 1.75

[Peter Cock]

On Tue, Nov 19, 2019 at 9:43 AM Andreas Tille <andreas at an3as.eu> wrote:
>
> Hi Peter,
>
> I'd like to give you credit as the fastest upstream answering a
> question. ;-)  Thanks a lot for it!

Lucky timing.

> On Tue, Nov 19, 2019 at 09:17:17AM +0000, Peter Cock wrote:
> > Curious - do you have the Python 2.7 version and build details?
>
> I've attached the full build log.

Thanks - I'v had a quick look. There must be something different to
how the build or installed directories are setup - our TravisCI tests
do not pick up the C modules at all.

> > Missing docstrings are unfortunate (and in this case they are in C
> > code which is a bit different), but ultimately this is harmless. What
> > puzzles me is what has triggered this, that we fail to see it on our
> > own testing.
>
> Hmmm, you say its harmless but its breaking the build of the Debian
> package anyway.  So it would be good to have some means against it.

I mean I would not worry about this particular test failing - and would
consider whitelisting this test acceptable.

Without yet being able to reproduce this and test it, does this work?:

https://github.com/peterjc/biopython/commit/5af680b5043c9f160a19e4bb0deab0ccc271280d

If not, we could explicitly exclude the C modules from testing, maybe here:

https://github.com/biopython/biopython/blob/biopython-175/Tests/run_tests.py#L151

i.e. Add "Bio/KDTree/_CKDTree" etc to EXCLUDE_DOCTEST_MODULES
(with the proviso that to date I've only used this with Python modules,
you might need to include the .so extension?)

> Since you are asking about the 2.7 version:  We need to get rid of
> Python2 as soon as all reverse depends of biopython are ported to
> Python3 (or removed from Debian).  This might take some time but if
> we could move this kind of doc string generation to be done by Python3
> this would be some step in the right direction.

Do you have a list of things still depending on Biopython & Python 2.7
handy? We're discussing when exactly to drop Python 2.7 support -
with a final compatible release in December 2019 or January 2020
looking most likely.

Peter