Fix doctests to work with pytest.

[bdice]

Description

Examples in docstrings were not being tested since the switch to pytest.

This is because the load_tests function is not recognized by pytest, only unittest.

I attempted to use pytest --doctest-modules but that isn't quite what we want, and it appears to only work with pure Python (not Cython) modules.

Instead, I adopted a variation on the strategy proposed in this StackOverflow post:
https://stackoverflow.com/questions/16982514/python-test-discovery-with-doctests-coverage-and-parallelism

Motivation and Context

Ensures that docstrings are runnable. I noticed the issue while reviewing #793.

How Has This Been Tested?

Tests should pass and show output like test_docstrings[freud.box.Box.center].

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds or improves functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation improvement (updates to user guides, docstrings, or developer docs)

Checklist:

• I have read the CONTRIBUTING document.
• My code follows the code style of this project.
• I have updated the documentation (if relevant).
• I have added tests that cover my changes (if relevant).
• All new and existing tests passed.
• I have updated the credits.
• I have updated the Changelog.

[vyasr]

The current error looks to be related to the upload of coverage artifacts I think. FYI, the Windows test is a false positive, the tests actually failed on import but it's reporting a success on this dashboard anyway.

For some reason all doctests are doubled up, with a copy in some *.__test__.* namespaces. I suspect it's related to pytest-dev/pytest#1558, but I've never used this feature of pytest to skip tests before so I'm not sure. It looks like all doctests are somehow being added twice.

[bdice]

@vyasr I couldn’t figure out how the __test__ module attribute is created. The previous tests were also doubled for the same reason. I think it might be a Cython thing. The docstring tests don’t point to line numbers but the __test__ tests do have pyx line info, so it is probably being generated at Cython compilation time.

I’ll look at the failing tests later, I have a lot going on right now. Anyone can feel free to take a look or push to this branch.

[bdice]

I got the doctests to run successfully, but I am seeing an unrelated error in CI from either coverage or pytest-cov. I commented on this related issue to document the problem: nedbat/coveragepy#1160

@glotzerlab/freud-maintainers Since I'm not sure if our code coverage is being reported correctly anyway, I think the next step is to disable coverage/codecov before merging this PR. Thoughts on this? See also: codecov deprecation: glotzerlab/signac#630

[bdice]

The issue upstream in coverage has been fixed:

• get_python_source gets called on shared object file and causes SyntaxError nedbat/coveragepy#1160 (comment)
• nedbat/coveragepy@afe6cf3

This PR can be merged once a new version of coverage is released and we upgrade the pinning. I don't really want to disable coverage in our CI (even though it's not currently working), but that would be another option.

[codecov]

Codecov Report

Merging #802 (1c42014) into master (76b2ced) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #802   +/-   ##
=======================================
  Coverage   55.34%   55.34%           
=======================================
  Files          16       16           
  Lines        2564     2564           
  Branches       34       34           
=======================================
  Hits         1419     1419           
  Misses       1131     1131           
  Partials       14       14           

Impacted Files	Coverage Δ
freud/diffraction.pyx	61.70% <ø> (ø)

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[bdice]

@tommy-waltmann I went ahead and merged this since it affects tests and had been stalled. We want any new PRs to have their documentation examples tested. This was blocked until coverage 6.1 was released, which fixed the failing tests.