Fix mypy CI errors in sample_metadata.py (dtype typing for pd.read_csv)

Author: mohamed-laarej

malariagen_data/anoph/sample_metadata.py

@@ -1,6 +1,18 @@
 import io
 from itertools import cycle
-from typing import Any, Callable, Dict, List, Mapping, Optional, Sequence, Tuple, Union
+from typing import (
+    Any,
+    Callable,
+    Dict,
+    List,
+    Mapping,
+    Optional,
+    Sequence,
+    Tuple,
+    Union,
+    Hashable,
+    cast,
+)
 
 import ipyleaflet  # type: ignore
 import numpy as np
@@ -148,9 +160,11 @@ def _parse_general_metadata(
             }
 
             # Convert string dtypes to actual dtypes
-            dtype = {col: dtype_map.get(dtype[col], str) for col in dtype}
+            dtype_fixed: Mapping[Hashable, Union[str, np.dtype, type]] = {
+                col: dtype_map.get(dtype[col], str) for col in dtype
+            }
 
-            df = pd.read_csv(io.BytesIO(data), dtype=dtype, na_values="")
+            df = pd.read_csv(io.BytesIO(data), dtype=dtype_fixed, na_values="")
 
             # Ensure all column names are lower case.
             df.columns = [c.lower() for c in df.columns]  # type: ignore
@@ -470,7 +484,12 @@ def _parse_aim_metadata(
         if isinstance(data, bytes):
             # Parse CSV data.
             df = pd.read_csv(
-                io.BytesIO(data), dtype=self._aim_metadata_dtype, na_values=""
+                io.BytesIO(data),
+                dtype=cast(
+                    Mapping[Hashable, Union[str, type, np.dtype]],
+                    self._aim_metadata_dtype,
+                ),
+                na_values="",
             )
 
             # Ensure all column names are lower case.