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

[Andreas Tille]

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.

Kind regards

     Andreas.


[1] git://anonscm.debian.org/debian-med/python-biom-format.git

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