I wonder if this is related to this line in the setup.cfg:

addopts = --flake8 --doctest-modules python bin.src tests

Yep. I double checked the docs and the module arguments aren't needed by the --doctest-modules flag. I think you go ahead and make this change, Krzysztof Findeisen. Do make sure that doctests are still being run.

I think I can see why the line is the way it is; the bug I reported seems to be the least of the various evils:

If I just provide --doctest-modules with no arguments, then pytest gives the following error for each file in bin.src:

../../lsstsw3/stack/Linux64/python_py/1.7.0/lib/python/py-1.7.0-py3.6.egg/py/_path/local.py:688: in pyimport

    raise self.ImportMismatchError(modname, modfile, self)

E   py._path.local.LocalPath.ImportMismatchError: ('dispatch_verify', '[redacted]/devel/verify/bin/dispatch_verify.py', local('[redacted]/devel/verify/bin.src/dispatch_verify.py'))

EDIT: updated to distinguish between scons and pytest

Talking with Tim Jenness, it seems that the best solution is to take --doctest-modules out of the setup.cfg for the reasons above and reintroduce doctests as a separate scons target (implemented in sconsUtils).

Then I propose that Tim Jenness adopt this ticket, since my familiarity with sconsUtils is very limited.

See the discussion in the PR. Generally I want to move to pytest-doctestplus as a general-purpose solution to doctest testing (see also DM-18435), but I'd like an option on the best place to enable the pytest-doctestplus plugin: in individual package's setup.cfg files, or through sconsUtils?

This looks like a good short term fix. We are trying to move to third party conda packages so for now I'd live with the package being part of conda and hope that by the time astropy removes it we will be using conda third parties more widely. The downside to adding it as a mandatory parameter to sconsUtils is that it doesn't seem to always work. I just tried the option in astro_metadata_translator and it breaks badly in the bin.src directory. The work around for that would be to have a switch in the tests/SConscript file to enable doctesting rather than always running it. If we are doing that we may as well be doing it in the setup.cfg file as we have here.

Thanks. I'll keep working on the general solution in DM-18435 .