Merge pull request #1328 from benjeffery/assert_equal

Assert equal for tables and collections

Author: mergify[bot]

python/CHANGELOG.rst

@@ -31,6 +31,9 @@
 - Improve display of tables when ``print``ed, limiting lines set via
   ``tskit.set_print_options`` (:user:`benjeffery`,:issue:`1270`, :pr:`1300`).
 
+- Add ``Table.assert_equals`` and ``TableCollection.assert_equals`` which give an exact
+  report of any differences. (:user:`benjeffery`,:issue:`1076`, :pr:`1328`)
+
 **Fixes**
 
 - Tree sequences were not properly init'd after unpickling

python/tests/test_combinatorics.py

@@ -1233,7 +1233,7 @@ def test_binary_tree(self):
         t1 = msprime.simulate(10, random_seed=1234).first()
         t2 = t1.split_polytomies(random_seed=1234)
         tables = t1.tree_sequence.dump_tables()
-        assert tables.equals(t2.tree_sequence.tables, ignore_provenance=True)
+        tables.assert_equals(t2.tree_sequence.tables, ignore_provenance=True)
 
     def test_bad_method(self):
         tree = tskit.Tree.generate_star(3)
@@ -1405,7 +1405,7 @@ def test_rank_unrank_round_trip(self, n):
         tree2 = tskit.Tree.unrank(n, rank)
         tables1 = tree1.tree_sequence.tables
         tables2 = tree2.tree_sequence.tables
-        assert tables1.equals(tables2, ignore_provenance=True)
+        tables1.assert_equals(tables2, ignore_provenance=True)
 
     def test_kwargs(self):
         tree = self.method(3, tracked_samples=[0, 1])
@@ -1457,7 +1457,7 @@ def test_rank_unrank_round_trip_arity(self, n, arity):
         tree2 = tskit.Tree.unrank(n, rank)
         tables1 = tree1.tree_sequence.tables
         tables2 = tree2.tree_sequence.tables
-        assert tables1.equals(tables2, ignore_provenance=True)
+        tables1.assert_equals(tables2, ignore_provenance=True)
 
     def test_bad_arity(self):
         for arity in [-1, 0, 1]:
@@ -1505,7 +1505,7 @@ def test_rank_unrank_round_trip_seeds(self, seed):
         tree2 = tskit.Tree.unrank(n, rank)
         tables1 = tree1.tree_sequence.tables
         tables2 = tree2.tree_sequence.tables
-        assert tables1.equals(tables2, ignore_provenance=True)
+        tables1.assert_equals(tables2, ignore_provenance=True)
 
 
 class TestGenerateComb(TreeGeneratorTestBase):

python/tests/test_file_format.py

@@ -869,7 +869,7 @@ def test_empty_mutation_time(self):
         # Null out the time column
         t1 = ts1.dump_tables()
         t1.mutations.time = np.full_like(t1.mutations.time, tskit.UNKNOWN_TIME)
-        assert t1 == ts3.tables
+        t1.assert_equals(ts3.tables)
 
     def test_empty_individual_parents(self):
         ts1 = migration_example()
@@ -890,7 +890,7 @@ def test_empty_individual_parents(self):
             ]
             * tables.individuals.num_rows
         )
-        assert tables == ts3.tables
+        tables.assert_equals(ts3.tables)
 
 
 class TestFileFormatErrors(TestFileFormat):

python/tests/test_highlevel.py

@@ -1145,7 +1145,7 @@ def verify_tables_api_equality(self, ts):
         for samples in [None, list(ts.samples()), ts.samples()]:
             tables = ts.dump_tables()
             tables.simplify(samples=samples)
-            assert tables.equals(
+            tables.assert_equals(
                 ts.simplify(samples=samples).tables, ignore_timestamps=True
             )
 

python/tests/test_metadata.py

@@ -1889,11 +1889,11 @@ def test_equality(self):
         tables.metadata_schema = metadata.MetadataSchema(schema)
         assert tables != tables2
         tables2.metadata_schema = metadata.MetadataSchema(schema2)
-        assert tables == tables2
+        tables.assert_equals(tables2)
         tables.metadata = collections.OrderedDict(one="tree", two=5)
         assert tables != tables2
         tables2.metadata = collections.OrderedDict(two=5, one="tree")
-        assert tables == tables2
+        tables.assert_equals(tables2)
 
     def test_fixing_uncanonical(self):
         ts = msprime.simulate(10, random_seed=42)