Deprecate .A attributes of sparse matrix in Sijie july24 fix
#691
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chansigit
approved these changes
Jul 10, 2024
| @@ -443,5 +443,5 @@ def sctransform( | |||
| X_squared = adata.X.copy() | |||
| X_squared.data **= 2 | |||
| variance = X_squared.mean(0) - np.square(adata.X.mean(0)) | |||
| adata.var["sct_score"] = variance.toarray().ravel() if sp.issparse(variance) else variance.ravel() | |||
| adata.var["sct_score"] = variance.A1 | |||
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can you please double check if this line would work properly if variance is a sparse matrix
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since you've validated variance is not sparse, i've no additional comments
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Replace
.Awithtoarray()since SciPy 1.14.0 removed.Aattributes for sparse matrix objects.