Fixed #1175 Migrate tests/test_aamp_motifs.py to npt.assert_allclose

[viknesh-ai]

Fixed #1175

Continuing the file-by-file split from #1178 — this one covers tests/test_aamp_motifs.py. Will open the next file's PR once this one merges.

assert_almost_equal only checks a fixed absolute tolerance and NumPy's docs recommend assert_allclose instead. Eight call sites in this file, three different wrinkles:

• Two calls compare the left/right argument order backwards relative to the actual, desired convention (right/out is always the stumpy-computed value in this file, left is either a hand-derived expected value or the naive helper's output) — flipped both.
• Four calls compare against aamp_match/naive_aamp_match output, which mixes a float distance with an int index and so comes back dtype=object — same issue as test_aamp.py, same fix: cast both sides to float64 before comparing, since the values are always numeric.
• The original decimal= values weren't all the same (4, 6, and the implicit default of 7), so I kept each site's original tolerance rather than flattening everything to 1.5e-07 — translated decimal=4/decimal=6 to atol=1.5e-04/atol=1.5e-06 respectively, and the two unlabeled ones to atol=1.5e-07 per the usual convention.

Also ran the file across five random seeds (JIT disabled, CUDA simulated, matching test.sh coverage) since test_data in this file draws from unseeded rng.RNG — wanted to make sure the tolerances hold up beyond just the one seed I happened to run with.

Update: per review, also renamed every left/right variable to ref_/cmp_ (naive output = ref, stumpy-computed output = cmp), and flipped the npt.assert_array_equal argument order to match the same actual, desired convention as assert_allclose.

To Do List

Standing checklist from @seanlaw for this migration, applies to every file in the split - status below is for test_aamp_motifs.py:

• Each test file correctly replaces all uses of npt.assert_almost_equal with its equivalent npt.assert_allclose
• When rtol=0 for npt.assert_allclose, simply omit this parameter and value since this is the default
• Ensure that npt.assert_allclose(actual, desired) always has the stumpy computed value as actual and the naive computation as desired
• Use atol=1.5e-07 rather than atol=1.5*10**-07
• Eventually, replace the ugly 1.5*10**-config.STUMPY_TEST_PRECISION with config.STUMPY_TEST_PRECISION = 1.5e-07 (in config.py) - tracked as a follow-up, not part of this per-file migration
• Use cmp instead of comp - n/a for this file, it never used comp naming to begin with
• Rename naive outputs to ref_ and stumpy-computed outputs to cmp_ (applies to npt.assert_array_equal too, not just npt.assert_allclose) - this file originally used left/right, all renamed

Pull Request Checklist

Below is a simple checklist but please do not hesitate to ask for assistance!

• Read our Contributing Guide
• Referenced a Github issue (or create one if one doesn't already exist)
• Read and reviewed all of the comments in the Github issue that you've referenced (along with cross-referenced issues/pull requests) to ensure that the issue still requires a pull request
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• Left a meaningful comment on the original Github issue to discuss the detailed approach for your contribution and received confirmation from the maintainers before proceeding with this pull request
• Forked, cloned, and checked out the newest version of the code
• Created a new branch
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• Installed flake8 (i.e., python -m pip install flake8 or conda install -c conda-forge flake8)
• Installed pytest-cov (i.e., python -m pip install pytest-cov or conda install -c conda-forge pytest-cov)
• Ran black --exclude=".*\.ipynb" --extend-exclude=".venv" --diff ./ in the root stumpy directory
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[gitnotebooks]

Review these changes at https://app.gitnotebooks.com/stumpy-dev/stumpy/pull/1181

[viknesh-ai]

@seanlaw next file in the split — same conventions as #1178. Ready for review whenever you have time.

[seanlaw]

@viknesh-ai Looks good to me. Ready to merge?

[viknesh-ai]

@viknesh-ai Looks good to me. Ready to merge?

Yeah It’s Ready to merge!