Bug#974839: [Help] Test failures in q2-feature-classifier
Hi Andreas, Andreas Tille, on 2021-01-27 21:42:41 +0100: > I think, if the test might pass without this option we could go with > this or even remove those tests temporarily and discuss the issue with > upstream without pressure of an open RC bug (which is unrelated). I would vote against skipping this test, as it shows the underlying code is not functional. I reinforced a bit my patch, given that the initial implementation was rather fragile and pushed another iteration. I'm fine about `dch -r` the package and upload tomorrow to close presently open bugs, if there are no objections; I see I have DM permissions on this one. There is an ever growing breadcrumb of patches not forwarded upstream behind me, I think I'll have to spend some time forwarding them appropriately, at the end of the week hopefully. Have a good evening, -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/0, please excuse my verbosity. signature.asc Description: PGP signature
Bug#974839: [Help] Test failures in q2-feature-classifier
Hi Étienne, On Wed, Jan 27, 2021 at 07:58:51PM +0100, Étienne Mollier wrote: > > Your guess is right; setting the PYTHONPATH to the build > directory allows most tests to run. There were a couple of > tests which then still failed to execute with the following > symptom though: > > Command: vsearch --search_exact > /<>/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/data/se-dna-sequences.fasta > --id 0.8 --query_cov 0.8 --strand both --maxaccepts 10 --maxrejects 0 --db > /<>/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/data/se-dna-sequences.fasta > --threads 1 --output_no_hits --blast6out /tmp/tmpomuor76d > > - Captured stderr call > - > Fatal error: Invalid options to command search_exact > Invalid option(s): --id --maxaccepts --maxrejects --query_cov > The valid options for the search_exact command are: --alnout --biomout > --blast6out --bzip2_decompress --db --dbmask --dbmatched --dbnotmatched > --fasta_width --fastapairs --gzip_decompress --hardmask --log --match > --matched --maxhits --maxqsize --maxqt --maxseqlength --maxsizeratio --maxsl > --mincols --minqt --minseqlength --minsizeratio --minsl --mintsize --mismatch > --mothur_shared_out --no_progress --notmatched --notrunclabels --otutabout > --output_no_hits --qmask --quiet --relabel --relabel_keep --relabel_md5 > --relabel_self --relabel_sha1 --rowlen --samheader --samout --self --sizein > --sizeout --strand --threads --top_hits_only --uc --uc_allhits --userfields > --userout --xee --xsize > > I believe this is not caught by upstream because their CI seems > to stick to vsearch <= 2.7.0. I could devise a patch to remove > the use of invalid options with search_exact. It is sufficient > to enable the test suite to pass through and pushed changes to > Salsa[1]. However I am unsure whether just skipping invalid > options is the right way to go, or if there are some other > options that might need setting instead. Are there people at > ease with vsearch use around ? I think, if the test might pass without this option we could go with this or even remove those tests temporarily and discuss the issue with upstream without pressure of an open RC bug (which is unrelated). As always: Thanks a lot for your work on this Andreas. > [1] https://salsa.debian.org/med-team/q2-feature-classifier -- http://fam-tille.de
Bug#974839: [Help] Test failures in q2-feature-classifier
Hi Andreas, Andreas Tille, on 2021-01-23 08:09:20 +0100: > E ImportError: cannot import name 'feature_classifier' from > 'qiime2.plugins' (/usr/lib/python3/dist-packages/qiime2/plugins.py) > _ ERROR collecting > .pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_cutter.py _ > ... > > My guess is that this is some simple (PYTHON)PATH issue but I'm busy > with real life this weekend and it would be great to have another > RC bug off the table. Your guess is right; setting the PYTHONPATH to the build directory allows most tests to run. There were a couple of tests which then still failed to execute with the following symptom though: Command: vsearch --search_exact /<>/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/data/se-dna-sequences.fasta --id 0.8 --query_cov 0.8 --strand both --maxaccepts 10 --maxrejects 0 --db /<>/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/data/se-dna-sequences.fasta --threads 1 --output_no_hits --blast6out /tmp/tmpomuor76d - Captured stderr call - Fatal error: Invalid options to command search_exact Invalid option(s): --id --maxaccepts --maxrejects --query_cov The valid options for the search_exact command are: --alnout --biomout --blast6out --bzip2_decompress --db --dbmask --dbmatched --dbnotmatched --fasta_width --fastapairs --gzip_decompress --hardmask --log --match --matched --maxhits --maxqsize --maxqt --maxseqlength --maxsizeratio --maxsl --mincols --minqt --minseqlength --minsizeratio --minsl --mintsize --mismatch --mothur_shared_out --no_progress --notmatched --notrunclabels --otutabout --output_no_hits --qmask --quiet --relabel --relabel_keep --relabel_md5 --relabel_self --relabel_sha1 --rowlen --samheader --samout --self --sizein --sizeout --strand --threads --top_hits_only --uc --uc_allhits --userfields --userout --xee --xsize I believe this is not caught by upstream because their CI seems to stick to vsearch <= 2.7.0. I could devise a patch to remove the use of invalid options with search_exact. It is sufficient to enable the test suite to pass through and pushed changes to Salsa[1]. However I am unsure whether just skipping invalid options is the right way to go, or if there are some other options that might need setting instead. Are there people at ease with vsearch use around ? [1] https://salsa.debian.org/med-team/q2-feature-classifier Kind Regards, -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. signature.asc Description: PGP signature
Bug#974839: [Help] Test failures in q2-feature-classifier
Hi, thanks to Nilesh and ftpmaster finally the needed dependencies for q2-feature-classifier are available. Unfortunately when I tried to build the package there where some test failures in autopkgtest: ... test session starts == platform linux -- Python 3.9.1+, pytest-6.0.2, py-1.10.0, pluggy-0.13.0 rootdir: /build/q2-feature-classifier-2020.11.1 plugins: cov-2.10.1 collected 0 items / 5 errors ERRORS _ ERROR collecting .pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_classifier.py _ ImportError while importing test module '/build/q2-feature-classifier-2020.11.1/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_classifier.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.9/importlib/__init__.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) q2_feature_classifier/tests/test_classifier.py:14: in from qiime2.plugins import feature_classifier E ImportError: cannot import name 'feature_classifier' from 'qiime2.plugins' (/usr/lib/python3/dist-packages/qiime2/plugins.py) _ ERROR collecting .pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_consensus_assignment.py _ ImportError while importing test module '/build/q2-feature-classifier-2020.11.1/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_consensus_assignment.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.9/importlib/__init__.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) q2_feature_classifier/tests/test_consensus_assignment.py:12: in from qiime2.plugins import feature_classifier E ImportError: cannot import name 'feature_classifier' from 'qiime2.plugins' (/usr/lib/python3/dist-packages/qiime2/plugins.py) _ ERROR collecting .pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_custom.py _ ImportError while importing test module '/build/q2-feature-classifier-2020.11.1/.pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_custom.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.9/importlib/__init__.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) q2_feature_classifier/tests/test_custom.py:12: in from qiime2.plugins import feature_classifier E ImportError: cannot import name 'feature_classifier' from 'qiime2.plugins' (/usr/lib/python3/dist-packages/qiime2/plugins.py) _ ERROR collecting .pybuild/cpython3_3.9/build/q2_feature_classifier/tests/test_cutter.py _ ... My guess is that this is some simple (PYTHON)PATH issue but I'm busy with real life this weekend and it would be great to have another RC bug off the table. Kind regards Andreas. -- http://fam-tille.de
