Re: Compiled C modules are not found by test suite (Was: Help needed for python-biopython which splits up modules into two packages per Python version)

[Andreas Tille <andreas@an3as.eu>]

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": 'biopython@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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