BUG: scipy 1.15.0 breaking validation

[Bento007]

Description

Here in the code when slicing the X matrix with a Pandas.Series and attribute error is thrown.

single-cell-curation/cellxgene_schema_cli/cellxgene_schema/validate.py

Line 614 in b4b1a5f

n_nonzero = self.adata.X[:, column].count_nonzero()

../cellxgene_schema/validate.py:2092: in validate_adata
    self._deep_check()
../cellxgene_schema/validate.py:2044: in _deep_check
    self._validate_dataframe(component_name)
../cellxgene_schema/validate.py:968: in _validate_dataframe
    self._validate_column(column, column_name, df_name, column_def)
../cellxgene_schema/validate.py:684: in _validate_column
    self._validate_column_feature_is_filtered(column, column_name, df_name)
../cellxgene_schema/validate.py:614: in _validate_column_feature_is_filtered
    n_nonzero = self.adata.X[:, column].count_nonzero()
../.venv/lib/python3.10/site-packages/anndata/_core/sparse_dataset.py:414: in __getitem__
    row_sp_matrix_validated, col_sp_matrix_validated = mtx._validate_indices(
../.venv/lib/python3.10/site-packages/scipy/sparse/_index.py:269: in _validate_indices
    index.extend(ix.nonzero())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = gene_ids-Harvard-Nuclei
ERCC-00002          True
ENSG00000127472    False
ENSG00000142798    False
ENSG00000127603    ...00198938    False
ENSG00000198840    False
ENSG00000198727    False
Name: feature_is_filtered, Length: 136, dtype: bool
name = 'nonzero'

    @final
    def __getattr__(self, name: str):
        """
        After regular attribute access, try looking up the name
        This allows simpler access to columns for interactive use.
        """
        # Note: obj.x will always call obj.__getattribute__('x') prior to
        # calling obj.__getattr__('x').
        if (
            name not in self._internal_names_set
            and name not in self._metadata
            and name not in self._accessors
            and self._info_axis._can_hold_identifiers_and_holds_name(name)
        ):
            return self[name]
>       return object.__getattribute__(self, name)
E       AttributeError: 'Series' object has no attribute 'nonzero'

This failure started occurring with scipy version 1.15.0. Rolling back to scipy version 1.14.1 fixes the issue. There maybe migration steps needs to support the new scipy sparse format see https://docs.scipy.org/doc/scipy/reference/sparse.migration_to_sparray.html#recommended-steps-for-migration