list, not Sequence

Author: petrelharp

python/tests/test_tables.py

@@ -24,7 +24,6 @@
 Test cases for the low-level tables used to transfer information
 between simulations and the tree sequence.
 """
-import collections.abc
 import dataclasses
 import io
 import json
@@ -1127,7 +1126,7 @@ def verify_metadata_vector(self, table, key, dtype, default_value=9999):
         if dtype is not None:
             assert md_vec.dtype == np.dtype(dtype)
         assert len(md_vec) == table.num_rows
-        if not isinstance(key, collections.abc.Sequence):
+        if not isinstance(key, list):
             key = [key]
         for x, row in zip(md_vec, table):
             md = row.metadata
@@ -1170,10 +1169,10 @@ def test_metadata_vector_nodefault(self):
         ms = tskit.MetadataSchema({"codec": "json"})
         table.metadata_schema = ms
         metadata_list = [
-            {"a": 4, "u": [1, 2]},
-            {"a": 10, "u": [3, 4]},
-            {"a": -3, "b": {"c": 1}, "u": [5, 6]},
-            {"a": 1},
+            {"abc": 4, "u": [1, 2]},
+            {"abc": 10, "u": [3, 4]},
+            {"abc": -3, "b": {"c": 1}, "u": [5, 6]},
+            {"abc": 1},
         ]
         for md in metadata_list:
             table.add_row(
@@ -1182,10 +1181,16 @@ def test_metadata_vector_nodefault(self):
                     "metadata": md,
                 }
             )
+        # first the totally obvious test
+        md_vec = table.metadata_vector("abc")
+        assert np.all(np.equal(md_vec, [d["abc"] for d in metadata_list]))
+        # now automated ones
         for dtype in [None, "int", "float", "object"]:
-            self.verify_metadata_vector(table, key="a", dtype=dtype, default_value=9999)
             self.verify_metadata_vector(
-                table, key=["a"], dtype=dtype, default_value=9999
+                table, key="abc", dtype=dtype, default_value=9999
+            )
+            self.verify_metadata_vector(
+                table, key=["abc"], dtype=dtype, default_value=9999
             )
 
     def test_metadata_vector(self):
@@ -1208,6 +1213,19 @@ def test_metadata_vector(self):
                     "metadata": md,
                 }
             )
+        # first the totally obvious test
+        md_vec = table.metadata_vector("abc", default_value=0)
+        assert np.all(
+            np.equal(
+                md_vec,
+                [
+                    d["abc"] if (d is not None and "abc" in d) else 0
+                    for d in metadata_list
+                ],
+            )
+        )
+
+        # now some automated ones
         for dtype in [None, "int", "float", "object"]:
             self.verify_metadata_vector(table, key="abc", dtype=dtype, default_value=-1)
             self.verify_metadata_vector(

python/tskit/tables.py

@@ -617,7 +617,7 @@ def getter(d, k):
                     d.get(k, default_value) if isinstance(d, Mapping) else default_value
                 )
 
-        if isinstance(key, collections.abc.Sequence):
+        if isinstance(key, list):
             out = np.array(
                 [
                     reduce(