Path: csiph.com!aioe.org!gothmog.csi.it!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.maint.python Subject: Please help auto_test for python-biom-format working Date: Thu, 11 Feb 2016 17:10:02 +0100 Message-ID: X-Original-To: debian-python@lists.debian.org X-Mailbox-Line: From debian-python-request@lists.debian.org Thu Feb 11 16:06:43 2016 Old-Return-Path: X-Amavis-Spam-Status: No, score=-5.001 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, LDO_WHITELIST=-5, MEDS2=2, RP_MATCHES_RCVD=-0.001] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate:hard: -6.1 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.23 (2014-03-12) X-Mailing-List: archive/latest/13527 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/20160211160627.GF7438@an3as.eu Approved: robomod@news.nic.it Lines: 41 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Date: Thu, 11 Feb 2016 17:06:27 +0100 X-Original-Message-ID: <20160211160627.GF7438@an3as.eu> Xref: csiph.com linux.debian.maint.python:8203 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 -- http://fam-tille.de