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Re: RFS: q2-sample-classifier

Hi Steffen,

Steffen Möller, on 2020-12-02 14:51:35 +0100:
> https://salsa.debian.org/med-team/q2-sample-classifier.git/
> Well ... lintian clean, cowbuilder needs to wait for qiime,
> please kindly cross-check to make that I have not messed anything up too
> badly.

As is, the build time test suite was choking on py.test, so I
begun working on a small patch against the Makefile to rename
this py.test-3 and build depend on "python3-pytest <!nocheck>".
However when adding a few more test dependencies[1], I hit that
wall, where registration of the q2 modules seems to be expected:

		make -j6 test
	make[1]: Entering directory '/<<PKGBUILDDIR>>'
	============================= test session starts ==============================
	platform linux -- Python 3.9.1rc1, pytest-4.6.11, py-1.9.0, pluggy-0.13.0
	rootdir: /<<PKGBUILDDIR>>
	collected 0 items / 6 errors
	==================================== ERRORS ====================================
	_________ ERROR collecting q2_sample_classifier/tests/test_actions.py __________
	ImportError while importing test module '/<<PKGBUILDDIR>>/q2_sample_classifier/tests/test_actions.py'.
	Hint: make sure your test modules/packages have valid Python names.
	q2_sample_classifier/tests/test_actions.py:13: in <module>
	    from qiime2.plugins import sample_classifier
	E   ImportError: cannot import name 'sample_classifier' from 'qiime2.plugins' (/usr/lib/python3/dist-packages/qiime2/plugins.py)

[1] namely build time test dependencies are : python3-distutils,
    q2-types and qiime.

Maybe the debian/rules will need an:

	# FIXME: test delayed to autopkgtest

and the package will need an autopkgtest which executes
py.test-3 on the installed module distribution, a bit similar to
what qiime and q2-types are doing at the moment?

I didn't have anything to push, I'm not sure how you would wish
to move forward on this one.

> Many thanks,
> Steffen (hoping ITPs also count for the calendar)
> We should actually think of some Xmas / New Year Promises packaging
> story, like comparing the microbiome of the present, the past and the
> future. The age-effect comparing with the past is obvious (drinking
> mostly milk, parental priming in the very early days). That "future"
> thingy is more real than what the wider public is yet aware of, for one
> there is our immune system that is changing, but there is also
> nutritional genomics so we are not completely out of control.  Anybody
> feeling creative?

Sounds interesting, but I'm not sure I understood your idea?  :)

Kind Regards,
Étienne Mollier <etienne.mollier@mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/1, please excuse my verbosity.

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