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gdsc and prism annotation warnings

Open Zethson opened this issue 8 months ago • 0 comments

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tests/metadata/test_cell_line.py::test_gdsc_annotation
  /home/zeth/miniconda3/envs/pertpy/lib/python3.13/site-packages/anndata/_core/anndata.py:740: UserWarning: 
  AnnData expects .obs.index to contain strings, but got values like:
      [14, 47, 1124, 952, 14]
  
      Inferred to be: integer
  
    value_idx = self._prep_dim_index(value.index, attr)

tests/metadata/test_cell_line.py::test_prism_annotation
  /home/zeth/PycharmProjects/pertpy/pertpy/metadata/_cell_line.py:198: DtypeWarning: Columns (14,15) have mixed types. Specify dtype option on import or set low_memory=False.
    df = pd.read_csv(drug_response_prism_file_path, index_col=0)[["depmap_id", "name", "ic50", "ec50", "auc"]]

tests/metadata/test_cell_line.py::test_prism_annotation
  /home/zeth/miniconda3/envs/pertpy/lib/python3.13/site-packages/anndata/_core/anndata.py:740: UserWarning: 
  AnnData expects .obs.index to contain strings, but got values like:
      [875, 485, 485, 7, 875]
  
      Inferred to be: integer
  
    value_idx = self._prep_dim_index(value.index, attr)

let's try to resolve these.

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Zethson avatar Apr 28 '25 02:04 Zethson