On Tue, Nov 19, 2019 at 9:43 AM Andreas Tille <andr...@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
