Clean up some low-hanging warnings in test suite #310

ajjackson · 2024-07-24T10:48:42Z

Spglib 2.5 deprecation warnings; when caused by Euphonic, we can solve the compatibility issue by converting to a dict. When caused by a dependency, suppress the warning.
Filter out expected warnings from certain tests in a more systematic way
Avoid a Matplotlib warning when calling tight_layout() on a plot with a colourbar... by not doing that.
Replace noisy implicit filling of masked values with NaN with explicit filling

There is a divide-by-zero warning which I think has its roots in nasty pint/spectroscopy units hackery. That is not just an artifact and should be dealt with in a separate PR.

Spglib 2.5 introduces dataclasses for many of its data objects, and raises a DeprecationWarning if you try to use it as a dictionary. That's very nice, but we'd like to support a range of versions, so for now we convert the new classes to a dict. We can migrate when these versions of Spglib are more established.

Maybe when seekpath fixes this we can bump both version requirements?

The warning was still raised in the main test. In order to suppress this without suppressing unexpected warnings, we may as well check it raised correctly. The other test is then fully redundant.

Otherwise a warning is raised.

github-actions · 2024-07-24T11:10:33Z

Test Results

22 files ± 0 22 suites ±0 29m 53s ⏱️ -29s
1 048 tests - 2 1 042 ✅ - 2 6 💤 ±0 0 ❌ ±0
10 420 runs - 20 10 357 ✅ - 20 63 💤 ±0 0 ❌ ±0

Results for commit bbf31ca. ± Comparison against base commit 8c87ed6.

This pull request removes 37 and adds 35 tests. Note that renamed tests count towards both.

euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesCalculateDosMap ‑ test_calculate_dos_map[NaCl-NaCl_band_yaml_from_phonopy_qpoint_frequencies.json-ebins2-NaCl_band_yaml_dos_map.json]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesCalculateDosMap ‑ test_calculate_dos_map[quartz-quartz_bandstructure_cv_only_qpoint_frequencies.json-ebins0-quartz_bandstructure_dos_map.json]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesCalculateDosMap ‑ test_calculate_dos_map[quartz-quartz_bandstructure_cv_only_qpoint_frequencies.json-ebins1-quartz_bandstructure_dos_map_uneven_bins.json]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesGetDispersion ‑ test_get_dispersion[NaCl-NaCl_band_yaml_from_phonopy_qpoint_frequencies.json-NaCl_band_yaml_dispersion.json]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesGetDispersion ‑ test_get_dispersion[quartz-quartz_bandstructure_cv_only_qpoint_frequencies.json-quartz_bandstructure_cv_only_dispersion.json]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesGetDispersion ‑ test_get_dispersion[quartz-quartz_bandstructure_qpoint_frequencies.json-quartz_bandstructure_dispersion.json]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args0-methane_pdos_index_1.json-methane_pdos_index_1_1meV_gauss_broaden.json]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args1-quartz_666_dos.json-quartz_666_1meV_gauss_broaden_dos.json]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args2-quartz_666_dos.json-quartz_666_1meV_gauss_broaden_dos.json]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args3-quartz_666_dos.json-quartz_666_1meV_lorentz_broaden_dos.json]
…

euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesCalculateDosMap ‑ test_calculate_dos_map[NaCl-NaCl_band_yaml_from_phonopy_qpoint_frequencies.json-ebins2-NaCl_band_yaml_dos_map.json-context2]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesCalculateDosMap ‑ test_calculate_dos_map[quartz-quartz_bandstructure_cv_only_qpoint_frequencies.json-ebins0-quartz_bandstructure_dos_map.json-context0]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesCalculateDosMap ‑ test_calculate_dos_map[quartz-quartz_bandstructure_cv_only_qpoint_frequencies.json-ebins1-quartz_bandstructure_dos_map_uneven_bins.json-context1]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesGetDispersion ‑ test_get_dispersion[NaCl-NaCl_band_yaml_from_phonopy_qpoint_frequencies.json-NaCl_band_yaml_dispersion.json-context2]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesGetDispersion ‑ test_get_dispersion[quartz-quartz_bandstructure_cv_only_qpoint_frequencies.json-quartz_bandstructure_cv_only_dispersion.json-context1]
euphonic_test.test_qpoint_frequencies.TestQpointFrequenciesGetDispersion ‑ test_get_dispersion[quartz-quartz_bandstructure_qpoint_frequencies.json-quartz_bandstructure_dispersion.json-context0]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args0-methane_pdos_index_1.json-methane_pdos_index_1_1meV_gauss_broaden.json-context0]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args1-quartz_666_dos.json-quartz_666_1meV_gauss_broaden_dos.json-context1]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args2-quartz_666_dos.json-quartz_666_1meV_gauss_broaden_dos.json-context2]
euphonic_test.test_spectrum1d.TestSpectrum1DMethods ‑ test_broaden[args3-quartz_666_dos.json-quartz_666_1meV_lorentz_broaden_dos.json-context3]
…

♻️ This comment has been updated with latest results.

To deal with broadening bin warnings, this uses an elegant approach to error/warning "expectations" suggested by the pytest docs. We find that different warning messages are raised by ostensibly the same problem, depending on the code path. That's not ideal, but can stay for now. A unit-strip warning in test_mul is also fixed.

Testing separately results in an un-caught warning. May as well check in one place.

- use "context" as name; the word "expected" appears enough already - use dummy context manager does_not_raise to simplify implementation in test_util

ajjackson added 7 commits July 24, 2024 10:57

Suppress Spglib 2.5 deprecation warning raised by seekpath

e8a0e7f

Maybe when seekpath fixes this we can bump both version requirements?

Catch warning during intensity-map broadening test

a1de124

Integrate warning check into main test for optimise_dipole_parameter

5edbbc6

The warning was still raised in the main test. In order to suppress this without suppressing unexpected warnings, we may as well check it raised correctly. The other test is then fully redundant.

Call to tight_layout() raises warning but seems to be unnecessary

a605cb2

Explicitly fill masked array values with NaN

8bcd317

Otherwise a warning is raised.

Account for warning raised in TestGetQptLabels

c9140bc

ajjackson added 4 commits July 24, 2024 15:07

Add warning checks to test_qpoint_frequencies

dfe4e1f

Integrate warning check to spectrum1d broadening test

3863e1f

Testing separately results in an un-caught warning. May as well check in one place.

Make warning checks in test suite more consistent

7cc01e8

- use "context" as name; the word "expected" appears enough already - use dummy context manager does_not_raise to simplify implementation in test_util

ajjackson marked this pull request as ready for review July 24, 2024 15:02

Tidy up, try to get codacy off my back

bbf31ca

ajjackson added the nice to have Not urgently required, but would be an improvement label Jul 24, 2024

ajjackson added this to the v1.4.0 milestone Jul 24, 2024

ajjackson merged commit 75fe42e into master Jul 24, 2024
15 checks passed

ajjackson deleted the warnings-cleanup branch December 12, 2024 16:41

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Clean up some low-hanging warnings in test suite #310

Clean up some low-hanging warnings in test suite #310

ajjackson commented Jul 24, 2024 •

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Clean up some low-hanging warnings in test suite #310

Clean up some low-hanging warnings in test suite #310

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