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Re: [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 /<<PKGBUILDDIR>>/.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 /<<PKGBUILDDIR>>/.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 <etienne.mollier@mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.

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