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Fix read-only error in NaN reorder test under pandas >=3 #85

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Marius1311 merged 1 commit into from
Jun 9, 2026
Merged

Fix read-only error in NaN reorder test under pandas >=3 #85

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11 changes: 8 additions & 3 deletions tests/model/test_obs_beautifier.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,14 @@ def test_reorder_categories_with_nan_values(self, cell_annotator_single):
adata = cell_annotator.adata

# Set up initial annotations with a NaN value
adata.obs["leiden"] = adata.obs["leiden"].map({"0": "B cells", "1": "T cells"}).astype("category")
# Add a NaN value
adata.obs.loc[adata.obs.index[0], "leiden"] = np.nan
leiden = adata.obs["leiden"].map({"0": "B cells", "1": "T cells"}).astype("category")
# Inject a NaN via a writable copy + full-column reassignment rather than an in-place
# `.loc` write. anndata subsetting (here sc.pp.filter_cells in the fixture) leaves obs
# backing arrays read-only, and pandas >=3 refuses in-place mutation of them
# ("ValueError: assignment destination is read-only"). Reassigning the column avoids it.
leiden = leiden.copy()
leiden.iloc[0] = np.nan
adata.obs["leiden"] = leiden

nan_count_before = adata.obs["leiden"].isna().sum()
assert nan_count_before > 0
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