Fix pandas Series used as numpy array index#435
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Newer pandas versions removed .nonzero() from Series, causing AttributeError when a Series boolean mask is used to index arrays. - tutorial_utils.py: add .values to Series comparison before array indexing - run_colocation.py: add .values to obs column comparison - plot_expected_vs_obs.py: wrap var_names comparison in np.array() Fixes #424 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
Fixes #424 -
AttributeError: 'Series' object has no attribute 'nonzero'Newer pandas versions removed
.nonzero()from Series objects. When a pandas Series boolean mask is used directly to index numpy/sparse arrays, it fails. The fix is to convert to numpy arrays first.Changes across 3 files:
docs/notebooks/tutorial_utils.py: Add.valuestoslide.var["SYMBOL"] == genes[j]comparisoncell2location/run_colocation.py: Add.valuestosp_data.obs[...] == scomparisoncell2location/plt/plot_expected_vs_obs.py: Wrapdata.var_names == geneinnp.array()This supersedes #425 by fixing all similar occurrences in the codebase, not just the one in tutorial_utils.py.
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