Update type ignore comments and fix row indexing

src/sssom/io.py

@@ -156,7 +156,7 @@ def split_file(
     write_tables(splitted, output_directory)
 
 
-@deprecated(  # type:ignore[misc]
+@deprecated(  # type: ignore[untyped-decorator]
     deprecated_in="0.4.3",
     details="This functionality for loading SSSOM metadata from a YAML file is deprecated from the "
     "public API since it has internal assumptions which are usually not valid for downstream users.",

src/sssom/parsers.py

@@ -539,7 +539,7 @@ def _get_mapping_dict(
     # The value could be a string or a list and is handled accordingly via _address_multivalued_slot().
 
     mdict: dict[str, str | list[str]] = {
-        k: _address_multivalued_slot(k, v)
+        k: _address_multivalued_slot(k, v)  # type: ignore[misc, arg-type]
         for k, v in row.to_dict().items()
         if v and pd.notna(v) and k in mapping_slots
     }

src/sssom/validators.py

@@ -208,9 +208,11 @@ def check_strict_curie_format(
 
     for column in entity_reference_slots:
         if column in msdf.df.columns:
-            for index, value in msdf.df[column].to_dict().items():
+            for index, value in enumerate(msdf.df[column], start=1):
                 if pd.notna(value) and "|" in str(value):
-                    message = f"{value} contains a pipe ('|') character (row {index + 1}, column '{column}')."
+                    message = (
+                        f"{value} contains a pipe ('|') character (row {index}, column '{column}')."
+                    )
                     validation_results.append(
                         ValidationResult(
                             type="strict curie test",

src/sssom/writers.py

@@ -192,7 +192,7 @@ def write_json(
         json.dump(data, fh, indent=2)
 
 
-@deprecated(deprecated_in="0.4.7", details="Use write_json() instead")  # type:ignore[misc]
+@deprecated(deprecated_in="0.4.7", details="Use write_json() instead")  # type: ignore[untyped-decorator]
 def write_fhir_json(
     msdf: MappingSetDataFrame, output: PathOrIO, serialisation: str = "fhir_json"
 ) -> None: