On Wed, Mar 12, 2014 at 01:20:38AM -0400, Éric Araujo wrote:
> Le 05/03/2014 10:31, Andreas Tille a écrit :
> >I have noted another problem: I worked a bit
> >on the tests and noticed that those tests that are including compiled C
> >code are failing. Is there anything in addition I need to do to make
> >the C object code visible to the Python modules?
>
> Can non-DD see the source code somewhere?
Theoretically you should get the code via
debcheckout python-biopython
Unfortunately currently this is a bit broken (I have filed a bug report
about this) since the URL redirector on svn.debian.org needs an explicit
/svn dir after the host name and thus you need to replace
svn co
svn://svn.debian.org/debian-med/trunk/packages/python-biopython/trunk/
python-biopython
by
svn co
svn://svn.debian.org/svn/debian-med/trunk/packages/python-biopython/trunk/
python-biopython
Since debcheckout failed in this step you manually need to get the
source via
apt-get source python-biopython
and replace the debian/ dir in it by the current status in SVN.
> IIUC you have a Python package and C extensions; when running the
> tests during the package build (or is it against the installed
> package?),
It is my exact problem that I'm running the test at package build
time.
> the C extensions are not found. One explanation for that
> could be that the C extensions are built in a “build” directory
> instead of inside the Python package, and thus aren’t readily
> importable. If the build uses distutils/setuptools, there is an
> option to control that:
>
> # file setup.cfg next to setup.py
> [build_ext]
> inplace = 1
This hint sounds promising but setup.py only says
setup_args = {
"name": 'biopython',
"version": __version__,
"author": 'The Biopython Consortium',
"author_email": 'biopyt...@biopython.org',
"url": 'http://www.biopython.org/',
"description": 'Freely available tools for computational molecular
biology.',
"download_url": 'http://biopython.org/DIST/',
"cmdclass": {
"install": install_biopython,
"build_py": build_py_biopython,
"build_ext": build_ext_biopython,
"test": test_biopython,
},
...
Perhaps I could set build_ext_biopython somehow properly? Since I have
no experience with distutils/setuptools a proper patch to the file would
save me some time with experimenting.
Thanks for your comments in any case
Andreas.
--
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