[Debian-med-packaging] [Help] Please help auto_test for python-biom-format working

[Olivier Sallou]

On 02/15/2016 10:45 AM, Andreas Tille wrote:
> Hi folks,
>
> Python team stayed silent about this issue.  Any idea from our side?
>
> Kind regards
>
>        Andreas.
>
> ----- Forwarded message from Andreas Tille <andreas at an3as.eu> -----
>
> Date: Thu, 11 Feb 2016 17:06:27 +0100
> From: Andreas Tille <andreas at an3as.eu>
> To: debian-python at lists.debian.org
> Subject: Please help auto_test for python-biom-format working
>
> Hi,
>
> I tried to get the dh_auto_test for python-biom-format[1] working but it
> seems my way to copy the test data to the right place is not doing the
> trick.  There are always errors like
>
> dh_auto_test
> I: pybuild base:184: cd /build/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose tests
> .......E.E......                                                                                                                                                                                                  EEE........................................................................................................................................................................................................................................S.............
> ======================================================================
> ERROR: Correctly subsets samples in a hdf5 table
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/dist-packages/numpy/testing/decorators.py", line 147, in skipper_func
>     return f(*args, **kwargs)
>   File "/build/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build/tests/test_cli/test_subset_table.py", line 82, in test_subset_observations_hdf5
>     json_table_str=None)
>   File "biom/cli/table_subsetter.py", line 135, in _subset_table
>     with biom_open(hdf5_biom) as f:
>   File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
>     return self.gen.next()
>   File "biom/util.py", line 440, in biom_open
>     if os.path.getsize(fp) == 0:
>   File "/usr/lib/python2.7/genericpath.py", line 57, in getsize
>     return os.stat(filename).st_size
> OSError: [Errno 2] No such file or directory: 'test_data/test.biom'
>
>
> despite I did copy the test_data into {build_dir}.
>
> Any help would be welcome.
I think it expects test_data to be in working directory.

Olivier
> Kind regards
>
>      Andreas.
>
>
> [1] git://anonscm.debian.org/debian-med/python-biom-format.git
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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