Adjust num of parts to accomodate number of frames #4710
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* Investigate rdkit issue * Update azure-pipelines.yml * fix numpy 2.0 import block * fix imports
- fix MDAnalysis#4680 - PCA explicitly marked as not parallelizable (at least not with simple split-apply-combine) - add tests - update CHANGELOG
Linter Bot Results:Hi @yuxuanzhuang! Thanks for making this PR. We linted your code and found the following: Some issues were found with the formatting of your code.
Please have a look at the Please note: The |
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#4682 will pass with this fix. |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4710 +/- ##
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- Coverage 93.54% 93.53% -0.02%
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Files 173 185 +12
Lines 21434 22505 +1071
Branches 3981 3983 +2
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+ Hits 20051 21049 +998
- Misses 929 1002 +73
Partials 454 454 ☔ View full report in Codecov by Sentry. |
| warnings.warn(f"Set to {n_parts} parts to match the total number " | ||
| "of frames being analyzed") |
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| warnings.warn(f"Set to {n_parts} parts to match the total number " | |
| "of frames being analyzed") | |
| warnings.warn(f"Set 'n_parts' to {n_parts} to match the total number " | |
| "of frames being analyzed") |
I think it's a bit clearer what is being tone this way? Feel free to ignore if you disagree.
| def test_reset_n_parts_to_n_frames(u): | ||
| # Issue #4685 | ||
| a = FrameAnalysis(u.trajectory) |
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| def test_reset_n_parts_to_n_frames(u): | |
| # Issue #4685 | |
| a = FrameAnalysis(u.trajectory) | |
| def test_reset_n_parts_to_n_frames(u): | |
| """ | |
| Issue #4685 | |
| https://github.com/MDAnalysis/mdanalysis/issues/4685 | |
| """ | |
| a = FrameAnalysis(u.trajectory) |
| def test_reset_n_parts_to_n_frames(u): | ||
| # Issue #4685 | ||
| a = FrameAnalysis(u.trajectory) | ||
| with pytest.warns(UserWarning, match='Set to'): |
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| with pytest.warns(UserWarning, match='Set to'): | |
| with pytest.warns(UserWarning, match="Set 'n_parts' to"): |
The change suggested above makes the test also a bit more specific.
Fixes #4685
Changes made in this Pull Request:
n_partsto the total number of frames being analyzed ifn_partsis bigger.PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4710.org.readthedocs.build/en/4710/