Re: Help needed for python-biopython which splits up modules into two packages per Python version
Hi,
On Tue, Mar 04, 2014 at 05:26:51PM +0100, Piotr Ożarowski wrote:
> [Andreas Tille, 2014-03-04]
> > I tried to work on python-biopython which according to authors request
> > supports also Python3 and so I tried to put this into the packaging at
> >
> > svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/
>
> ^ this one is not anonymous, this one is:
>
> svn://anonscm.debian.org/svn/debian-med/trunk/packages/python-biopython/trunk/
>
> (which is weird, I was sure it's the other way around)
You are remembering right and I even opened a bug on alioth:
https://alioth.debian.org/tracker/index.php?func=detail&aid=314620
(and there is a thread about this on debian-devel[1])
In *any* case it is fine if you do some non-annonymous checkout via
svn+ssh and commit since any DD has commit permissions in Debian Med
repositories.
> > The problem is that I seem to have messed up the debian/*.install files
> > in a way that Python2 packages will be moved to the python3 package and
> > the other way around - but I have no idea why. I seem to need those
> > install files since the other method to simply put
> >
> > export PYBUILD_DESTDIR_python2=debian/python-biopython/
> > export PYBUILD_DESTDIR_python3=debian/python3-biopython/
>
> FTR: this requires less typing:
>
> export PYBUILD_NAME=biopython
>
> anyway, you cannot mix .install files and pybuild's DESTDIR, dh_install
> will not find files already installed in the final location AFAIR
>
> > into debian/rules does not separate the Bio module from BioSQL (and I
> > have no idea how to do this properly).
>
> you can force pybuild to move BioSQL files to a different location
> (hint: --ext-dest-dir & --ext-pattern or equivalent PYBUILD_* vars)
> but IMO it's cleaner to use *.install files for that
Hmmm, you say *.install files are cleaner - but this exactly is my
problem since the *.install files do a really bad job in this case and
mix up the Python versions. I do not have the slightest idea why.
> > 2. Tests are not run. Log just says
> >
> > dh_auto_test -O--buildsystem=pybuild
> > pybuild --test -i python{version} -p 2.7 --dir .
> > I: pybuild base:170: cd /tmp/buildd/python-biopython-1.63/.pybuild/pythonX.Y_2.7/build; python2.7 -m unittest discover -v
>
> another pybuild example (without magic PYBUILD_* vars this time):
>
> override_dh_auto_test:
> dh_auto_test -- --test --system=custom --test-args='env PYTHONPATH={build_dir} {interpreter} setup.py test'
>
> (pybuild didn't detect that it should simply invoke setup.py's test
> because "test_suite" is not declared in setup.py. Standards... eh, why
> there are some many of them in Python distutils world?)
Well, tests are running now and besides some URL download errors the
tests are running into some UnicodeDecodeErrors (which are my most
hated errors in Python - but that's another topic).
> PS please add "X-Python-Version: >= 3.3" in debian/control, this module
> doesn't work with 3.2
Done in SVN (with Barrys correction) and I also fixed the missing
dependency issue thanks to the hint from Dmitry. But the problem
with the broken install files remains and I most probably failed
to understand the hint you tried to give.
Kind regards
Andreas.
[1] https://lists.debian.org/debian-devel/2014/03/msg00028.html
--
http://fam-tille.de
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