Fix AnalysisBase.run misreading numpy boolean frame masks - #5480
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The boolean-mask detection in _setup_computation_groups checked isinstance(obj, bool), which misses np.bool_ elements. A numpy boolean array passed via frames= was therefore used as integer indices and the analysis silently ran on the wrong frames. Include np.bool_ in the type check so numpy masks are handled like Python boolean lists. Fixes MDAnalysis#5472.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #5480 +/- ##
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Coverage 93.87% 93.87%
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Files 182 182
Lines 22522 22522
Branches 3206 3206
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This appears to be an AI-generated duplicate of PR #5476 ; furthermore, our standard template was ignored and replaced with generated content. Therefore, I am closing this PR. |
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5476 covers the same boolean-mask path and has merged. |
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Summary
Fixes #5472.
AnalysisBase.run(frames)accepted a NumPy boolean array but treated it as integer frame indices because the mask detection in_setup_computation_groupsusedisinstance(obj, bool), which does not matchnp.bool_elements. With a mask like[True, False, True, False], the Python list form correctly selected frames 0 and 2 while the equivalentnp.bool_array silently ran the analysis on frames[1, 0, 1, 0].The type check now accepts
np.bool_, so NumPy boolean masks behave identically to Python boolean lists. The trajectory-level__getitem__incoordinates/base.pyalready handles both cases. This was the remaining unconverted site in the analysis path.Changes
package/MDAnalysis/analysis/base.py: includenp.bool_in the mask-detection isinstance check.testsuite/MDAnalysisTests/analysis/test_base.py: added the NumPy-bool-array parametrization (same expected frames as the existing bool-list case) to bothtest_frame_sliceandtest_frame_slice_parallel.Verification
Verification used a 4-frame MEMORY trajectory via
AnalysisFromFunction. Pre-change the mask produced the wrong frame sequence, and post-change it matches the Python-list result. The fulltest_base.pysuite reports 100 passed.Fixes #5472.
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