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
