Add ref seq equals

Author: benjeffery

python/CHANGELOG.rst

@@ -5,7 +5,10 @@
 **Fixes**
 
 - ``TreeSequence.dump_text`` now prints decoded metadata if there is a schema.
-  (:user:`bejeffery`, :issue:`1860`, :issue:`1527`,
+  (:user:`benjeffery`, :issue:`1860`, :issue:`1527`)
+
+- Add missing ``ReferenceSequence.__eq__`` method.
+  (:user:`benjeffery`, :issue:`2063`, :pr:`2085`)
 
 
 ----------------------

python/tests/test_reference_sequence.py

@@ -148,42 +148,80 @@ def test_repr(self):
         assert repr(refseq).startswith("ReferenceSequence")
 
 
-class TestAssertEquals:
-    def test_success_self(self, ts_fixture):
+class TestEquals:
+    def test_equal_self(self, ts_fixture):
         ts_fixture.reference_sequence.assert_equals(ts_fixture.reference_sequence)
+        assert ts_fixture.reference_sequence == ts_fixture.reference_sequence
+        assert not ts_fixture.reference_sequence != ts_fixture.reference_sequence
+        assert ts_fixture.reference_sequence.equals(ts_fixture.reference_sequence)
 
-    def test_success_empty(self):
+    def test_equal_empty(self):
         tables = tskit.TableCollection(1)
         tables.reference_sequence.assert_equals(tables.reference_sequence)
+        assert tables.reference_sequence == tables.reference_sequence
+        assert tables.reference_sequence.equals(tables.reference_sequence)
 
     @pytest.mark.parametrize("attr", ["url", "data"])
-    def test_fails_attr_missing(self, ts_fixture, attr):
+    def test_unequal_attr_missing(self, ts_fixture, attr):
         t1 = ts_fixture.tables
         d = t1.asdict()
         del d["reference_sequence"][attr]
         t2 = tskit.TableCollection.fromdict(d)
         with pytest.raises(AssertionError, match=attr):
             t1.reference_sequence.assert_equals(t2.reference_sequence)
+        assert t1.reference_sequence != t2.reference_sequence
+        assert not t1.reference_sequence.equals(t2.reference_sequence)
         with pytest.raises(AssertionError, match=attr):
             t2.reference_sequence.assert_equals(t1.reference_sequence)
-
-    def test_fails_metadata_different(self, ts_fixture):
+        assert t2.reference_sequence != t1.reference_sequence
+        assert not t2.reference_sequence.equals(t1.reference_sequence)
+
+    @pytest.mark.parametrize(
+        ("attr", "val"),
+        [
+            ("url", "foo"),
+            ("data", "bar"),
+            ("metadata", {"json": "runs the world"}),
+            ("metadata_schema", tskit.MetadataSchema(None)),
+        ],
+    )
+    def test_different_not_equal(self, ts_fixture, attr, val):
         t1 = ts_fixture.dump_tables()
         t2 = t1.copy()
-        t1.reference_sequence.metadata = {"different": "metadata"}
-        with pytest.raises(AssertionError, match="metadata"):
+        setattr(t1.reference_sequence, attr, val)
+
+        with pytest.raises(AssertionError):
             t1.reference_sequence.assert_equals(t2.reference_sequence)
-        with pytest.raises(AssertionError, match="metadata"):
+        assert t1.reference_sequence != t2.reference_sequence
+        assert not t1.reference_sequence.equals(t2.reference_sequence)
+        with pytest.raises(AssertionError):
             t2.reference_sequence.assert_equals(t1.reference_sequence)
-
-    def test_fails_metadata_schema_different(self, ts_fixture):
+        assert t2.reference_sequence != t1.reference_sequence
+        assert not t2.reference_sequence.equals(t1.reference_sequence)
+
+    @pytest.mark.parametrize(
+        ("attr", "val"),
+        [
+            ("metadata", {"json": "runs the world"}),
+            ("metadata_schema", tskit.MetadataSchema(None)),
+        ],
+    )
+    def test_different_but_ignore(self, ts_fixture, attr, val):
         t1 = ts_fixture.dump_tables()
         t2 = t1.copy()
-        t1.reference_sequence.metadata_schema = tskit.MetadataSchema(None)
-        with pytest.raises(AssertionError, match="schemas"):
+        setattr(t1.reference_sequence, attr, val)
+
+        with pytest.raises(AssertionError):
             t1.reference_sequence.assert_equals(t2.reference_sequence)
-        with pytest.raises(AssertionError, match="schemas"):
+        assert t1.reference_sequence != t2.reference_sequence
+        assert not t1.reference_sequence.equals(t2.reference_sequence)
+        with pytest.raises(AssertionError):
             t2.reference_sequence.assert_equals(t1.reference_sequence)
+        assert t2.reference_sequence != t1.reference_sequence
+        assert not t2.reference_sequence.equals(t1.reference_sequence)
+
+        t2.reference_sequence.assert_equals(t1.reference_sequence, ignore_metadata=True)
+        assert t2.reference_sequence.equals(t1.reference_sequence, ignore_metadata=True)
 
 
 class TestTreeSequenceProperties:

python/tskit/metadata.py

@@ -829,6 +829,12 @@ def metadata_bytes(self) -> Any:
     def nbytes(self) -> int:
         return len(self._ll_object.metadata) + len(self._ll_object.metadata_schema)
 
+    def equals(self, other) -> bool:
+        return (
+            self.metadata == other.metadata
+            and self.metadata_schema == other.metadata_schema
+        )
+
     def assert_equals(self, other: MetadataProvider):
         if self.metadata_schema != other.metadata_schema:
             raise AssertionError(

python/tskit/tables.py

@@ -2773,6 +2773,16 @@ def asdict(self) -> dict:
             "url": self.url,
         }
 
+    def __eq__(self, other):
+        return self.equals(other)
+
+    def equals(self, other, ignore_metadata=False):
+        try:
+            self.assert_equals(other, ignore_metadata)
+            return True
+        except AssertionError:
+            return False
+
     def assert_equals(self, other, ignore_metadata=False):
         if not ignore_metadata:
             super().assert_equals(other)