read_metadata: add dtype for METADATA_DATE_COLUMN

Avoid Pandas type inference for the date column because it could contain incomplete year only dates that get inferred as int.
nextstrain · May 26, 2023 · def0840 · def0840
1 parent bd4b5d8
commit def0840
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/augur/io/metadata.py b/augur/io/metadata.py
@@ -111,7 +111,10 @@ def read_metadata(metadata_file, delimiters=DEFAULT_DELIMITERS, id_columns=DEFAU
     # of having its type inferred. This latter argument allows users to provide
     # numerical ids that don't get converted to numbers by pandas.
     kwargs["index_col"] = index_col
-    kwargs["dtype"] = {index_col: "string"}
+    kwargs["dtype"] = {
+        index_col: "string",
+        METADATA_DATE_COLUMN: "string"
+    }
 
     return pd.read_csv(
         metadata_file,