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

[Andreas Tille]

Hi Peter,

On Tue, Nov 19, 2019 at 10:03:25AM +0000, Peter Cock wrote:
> > I'd like to give you credit as the fastest upstream answering a
> > question. ;-)  Thanks a lot for it!
> 
> Lucky timing.

Anyway:  Thanks a lot.
 
> > 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.

Hmmm, I'd love to re-implement this for the Debian package.
 
> > 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

Unfortunately this does not work. :-(  I tried it in the packaging commit

   https://salsa.debian.org/med-team/python-biopython/commit/bb94263daca0cd51968305805e444d0254c01c48

> 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

Neither works this

   https://salsa.debian.org/med-team/python-biopython/commit/e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8

> 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?)

I'm not sure what you want to tell me with the last phrase in brackets.
 
> > 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?

As far as I interpret

    apt-cache rdepends python-biopython

it is

   srst2
   seqsero
   prime-phylo
   nanopolish

nothing that I would mind to crash for some time span.  If it can not be
ported it will be removed anyway.  So if you decide to drop Python2
support that would set a clear signal.  If it is the safest means to
get rid of the above trouble I'm all for it.

> 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.

Sounds sensible.

Kind regards

    Andreas. 

-- 
http://fam-tille.de