Correct assert_equals message when tables differ by content and metadata

Author: benjeffery

python/CHANGELOG.rst

@@ -12,6 +12,12 @@
   associated with each individual as a numpy array.
   (:user:`benjeffery`, :pr:`3153`)
 
+
+**Fixes**
+
+- Correct assertion message when tables are compared with metadata ignored.
+  (:user:`benjeffery`, :pr:`3162`, :issue:`3161`)
+  
 --------------------
 [0.6.3] - 2025-04-28
 --------------------

python/tests/test_tables.py

@@ -3758,6 +3758,25 @@ def test_equals_options(self, ts_fixture):
         with pytest.raises(TypeError):
             t1.equals(t2, True)
 
+        # When two tables differ, check that the right reason is given
+        t1 = tskit.TableCollection(sequence_length=1.0)
+        t2 = tskit.TableCollection(sequence_length=1.0)
+        t1.assert_equals(t2)
+        t1.metadata = b""
+        t2.metadata = b"abc"
+        t1.assert_equals(t2, ignore_ts_metadata=True)
+        t1.edges.add_row(0, 1, 0, 1)
+        with pytest.raises(AssertionError, match="EdgeTable number of rows"):
+            t1.assert_equals(t2, ignore_ts_metadata=True)
+        t2.metadata = b""
+        t2.edges.add_row(0, 1, 0, 1, metadata=b"abc")
+        t1.assert_equals(t2, ignore_metadata=True)
+        t1.edges.add_row(0, 1, 0, 1)
+        with pytest.raises(AssertionError, match="EdgeTable number of rows"):
+            t1.assert_equals(t2, ignore_metadata=True)
+        with pytest.raises(AssertionError, match="EdgeTable row 0 differs"):
+            t1.assert_equals(t2)
+
     def test_sequence_length(self):
         for sequence_length in [0, 1, 100.1234]:
             tables = tskit.TableCollection(sequence_length=sequence_length)

python/tskit/tables.py

@@ -3246,7 +3246,7 @@ def assert_equals(
         ):
             return
 
-        if not ignore_metadata or ignore_ts_metadata:
+        if not (ignore_metadata or ignore_ts_metadata):
             super().assert_equals(other)
 
         if not ignore_reference_sequence: