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scanorama fails due to deprecation warning for csr_matrix #247

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KaiWaldrant opened this issue Oct 6, 2023 · 0 comments
Closed

scanorama fails due to deprecation warning for csr_matrix #247

KaiWaldrant opened this issue Oct 6, 2023 · 0 comments
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batch_integration relates to task batch_integration bug Something isn't working external issue is related to an external package/software

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@KaiWaldrant
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Describe the bug
The scanorama components fail due to namespace deprecation of csr_matrix:

/usr/local/lib/python3.10/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead
  if not is_categorical_dtype(df_full[k]):
/usr/local/lib/python3.10/site-packages/scanorama/scanorama.py:378: DeprecationWarning: Please use `csr_matrix` from the `scipy.sparse` namespace, the `scipy.sparse.csr` namespace is deprecated.
  elif issubclass(type(ds), scipy.sparse.csr.csr_matrix):
.command.sh: line 81:   143 Illegal instruction     (core dumped) python -B "$tempscript"

Additional context
The scanorama package should be updated to fix this issue.

@KaiWaldrant KaiWaldrant added bug Something isn't working batch_integration relates to task batch_integration external issue is related to an external package/software labels Oct 6, 2023
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Labels
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