Drop metadata schemas on tables.

Closes tskit-dev#2944

python/tests/test_tables.py

@@ -102,12 +102,20 @@ def make_transposed_input_data(self, num_rows):
         cols = self.make_input_data(num_rows)
         return [
             {
-                col: data[j]
-                if len(data) == num_rows
-                else (
-                    bytes(data[cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]])
-                    if "metadata" in col
-                    else data[cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]]
+                col: (
+                    data[j]
+                    if len(data) == num_rows
+                    else (
+                        bytes(
+                            data[
+                                cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]
+                            ]
+                        )
+                        if "metadata" in col
+                        else data[
+                            cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]
+                        ]
+                    )
                 )
                 for col, data in cols.items()
                 if "offset" not in col
@@ -911,6 +919,19 @@ def test_random_metadata(self):
             )
             assert metadatas == unpacked_metadatas
 
+    def test_drop_metadata(self):
+        for num_rows in [1, 10, 100]:
+            input_data = self.make_input_data(num_rows)
+            table_no_meta = self.table_class()
+            table_with_meta = self.table_class()
+            table_with_meta.set_columns(**input_data)
+            del input_data["metadata"]
+            del input_data["metadata_offset"]
+            table_no_meta.set_columns(**input_data)
+            assert not table_no_meta.equals(table_with_meta)
+            table_with_meta.drop_metadata()
+            table_no_meta.assert_equals(table_with_meta)
+
     def test_optional_metadata(self):
         if not getattr(self, "metadata_mandatory", False):
             for num_rows in [0, 10, 100]:

python/tskit/metadata.py

@@ -263,18 +263,18 @@ def required_validator(validator, required, instance, schema):
     "type": "string",
     "pattern": r"^([cbB\?hHiIlLqQfd]|\d*[spx])$",
 }
-struct_meta_schema["definitions"]["root"]["properties"][
-    "binaryFormat"
-] = struct_meta_schema["properties"]["binaryFormat"]
+struct_meta_schema["definitions"]["root"]["properties"]["binaryFormat"] = (
+    struct_meta_schema["properties"]["binaryFormat"]
+)
 # arrayLengthFormat matches regex and has default
 struct_meta_schema["properties"]["arrayLengthFormat"] = {
     "type": "string",
     "pattern": r"^[BHILQ]$",
     "default": "L",
 }
-struct_meta_schema["definitions"]["root"]["properties"][
-    "arrayLengthFormat"
-] = struct_meta_schema["properties"]["arrayLengthFormat"]
+struct_meta_schema["definitions"]["root"]["properties"]["arrayLengthFormat"] = (
+    struct_meta_schema["properties"]["arrayLengthFormat"]
+)
 # index is numeric
 struct_meta_schema["properties"]["index"] = {"type": "number"}
 struct_meta_schema["definitions"]["root"]["properties"]["index"] = struct_meta_schema[
@@ -285,14 +285,14 @@ def required_validator(validator, required, instance, schema):
     "type": "string",
     "default": "utf-8",
 }
-struct_meta_schema["definitions"]["root"]["properties"][
-    "stringEncoding"
-] = struct_meta_schema["properties"]["stringEncoding"]
+struct_meta_schema["definitions"]["root"]["properties"]["stringEncoding"] = (
+    struct_meta_schema["properties"]["stringEncoding"]
+)
 # nullTerminated is a boolean
 struct_meta_schema["properties"]["nullTerminated"] = {"type": "boolean"}
-struct_meta_schema["definitions"]["root"]["properties"][
-    "nullTerminated"
-] = struct_meta_schema["properties"]["nullTerminated"]
+struct_meta_schema["definitions"]["root"]["properties"]["nullTerminated"] = (
+    struct_meta_schema["properties"]["nullTerminated"]
+)
 # noLengthEncodingExhaustBuffer is a boolean
 struct_meta_schema["properties"]["noLengthEncodingExhaustBuffer"] = {"type": "boolean"}
 struct_meta_schema["definitions"]["root"]["properties"][
@@ -722,6 +722,15 @@ def permissive_json():
         """
         return MetadataSchema({"codec": "json"})
 
+    @staticmethod
+    def null():
+        """
+        The null schema which defines no properties and results in raw bytes being returned
+        on accessing metadata column.s
+        no constraints on the properties.
+        """
+        return MetadataSchema(None)
+
 
 # Often many replicate tree sequences are processed with identical schemas, so cache them
 @functools.lru_cache(maxsize=128)
@@ -734,7 +743,7 @@ def parse_metadata_schema(encoded_schema: str) -> MetadataSchema:
     :return: A subclass of AbstractMetadataSchema.
     """
     if encoded_schema == "":
-        return MetadataSchema(schema=None)
+        return MetadataSchema.null()
     else:
         try:
             decoded = json.loads(

python/tskit/tables.py

@@ -794,6 +794,22 @@ def getter(d, k):
             )
         return out
 
+    def drop_metadata(self, keep_schema=False):
+        """
+        Drops all metadata in this table. By default, the schema is also cleared,
+        except if ``keep_schema`` is True.
+
+        :param bool keep_schema: True if the current schema should be kept intact.
+        """
+        if not keep_schema:
+            self.metadata_schema = metadata.MetadataSchema.null()
+        data = {
+            col: getattr(self, col)
+            for col in self.column_names
+            if not col.startswith("metadata")
+        }
+        self.set_columns(**data)
+
 
 class IndividualTable(MetadataTable):
     """