TreeSequence.tables returns ImmutableTableCollection

Author: benjeffery

python/lwt_interface/dict_encoding_testlib.py

@@ -132,7 +132,7 @@ def verify(self, tables):
 
     def test_simple(self):
         ts = msprime.simulate(10, mutation_rate=1, random_seed=2)
-        self.verify(ts.tables)
+        self.verify(ts.dump_tables())
 
     def test_empty(self):
         tables = tskit.TableCollection(sequence_length=1)
@@ -152,7 +152,7 @@ def test_sequence_length(self):
         ts = msprime.simulate(
             10, recombination_rate=0.1, mutation_rate=1, length=0.99, random_seed=2
         )
-        self.verify(ts.tables)
+        self.verify(ts.dump_tables())
 
     def test_migration(self):
         pop_configs = [msprime.PopulationConfiguration(5) for _ in range(2)]
@@ -164,7 +164,7 @@ def test_migration(self):
             record_migrations=True,
             random_seed=1,
         )
-        self.verify(ts.tables)
+        self.verify(ts.dump_tables())
 
     def test_example(self, tables):
         tables.metadata_schema = tskit.MetadataSchema(

python/tests/test_genotypes.py

@@ -863,7 +863,7 @@ def test_nonbinary_trees(self):
     def test_acgt_mutations(self):
         ts = msprime.simulate(10, mutation_rate=10)
         assert ts.num_sites > 0
-        tables = ts.tables
+        tables = ts.dump_tables()
         sites = tables.sites
         mutations = tables.mutations
         sites.set_columns(
@@ -883,23 +883,23 @@ def test_acgt_mutations(self):
 
     def test_fails_multiletter_mutations(self):
         ts = msprime.simulate(10, random_seed=2)
-        tables = ts.tables
+        tables = ts.dump_tables()
         tables.sites.add_row(0, "ACTG")
         tsp = tables.tree_sequence()
         with pytest.raises(TypeError):
             list(tsp.haplotypes())
 
     def test_fails_deletion_mutations(self):
         ts = msprime.simulate(10, random_seed=2)
-        tables = ts.tables
+        tables = ts.dump_tables()
         tables.sites.add_row(0, "")
         tsp = tables.tree_sequence()
         with pytest.raises(TypeError):
             list(tsp.haplotypes())
 
     def test_nonascii_mutations(self):
         ts = msprime.simulate(10, random_seed=2)
-        tables = ts.tables
+        tables = ts.dump_tables()
         tables.sites.add_row(0, chr(169))  # Copyright symbol
         tsp = tables.tree_sequence()
         with pytest.raises(TypeError):

python/tests/test_highlevel.py

@@ -1292,7 +1292,7 @@ def verify_edgesets(self, ts):
                     tskit.Edge(edgeset.left, edgeset.right, edgeset.parent, child)
                 )
         # squash the edges.
-        t = ts.dump_tables().nodes.time
+        t = ts.tables.nodes.time
         new_edges.sort(key=lambda e: (t[e.parent], e.parent, e.child, e.left))
 
         squashed = []
@@ -1916,24 +1916,20 @@ def test_load_tables(self, ts):
         with pytest.raises(
             _tskit.LibraryError, match="Table collection must be indexed"
         ):
-            assert tskit.TreeSequence.load_tables(tables).dump_tables().has_index()
+            assert tskit.TreeSequence.load_tables(tables).tables.has_index()
 
         # Tables not in tc, but rebuilt
-        assert (
-            tskit.TreeSequence.load_tables(tables, build_indexes=True)
-            .dump_tables()
-            .has_index()
-        )
+        assert tskit.TreeSequence.load_tables(
+            tables, build_indexes=True
+        ).tables.has_index()
 
         tables.build_index()
         # Tables in tc, not rebuilt
-        assert (
-            tskit.TreeSequence.load_tables(tables, build_indexes=False)
-            .dump_tables()
-            .has_index()
-        )
+        assert tskit.TreeSequence.load_tables(
+            tables, build_indexes=False
+        ).tables.has_index()
         # Tables in tc, and rebuilt
-        assert tskit.TreeSequence.load_tables(tables).dump_tables().has_index()
+        assert tskit.TreeSequence.load_tables(tables).tables.has_index()
 
     @pytest.mark.parametrize("ts", tsutil.get_example_tree_sequences())
     def test_html_repr(self, ts):
@@ -1958,14 +1954,14 @@ def test_bad_provenance(self, ts_fixture):
         assert "Could not parse provenance" in ts._repr_html_()
 
     def test_provenance_summary_html(self, ts_fixture):
-        tables = ts_fixture.tables
+        tables = ts_fixture.dump_tables()
         for _ in range(20):
             # Add a row with isotimestamp
             tables.provenances.add_row("foo", "bar")
         assert "... 15 more" in tables.tree_sequence()._repr_html_()
 
     def test_html_repr_limit(self, ts_fixture):
-        tables = ts_fixture.tables
+        tables = ts_fixture.dump_tables()
         d = {n: n for n in range(50)}
         d[0] = "N" * 200
         tables.metadata = d
@@ -2656,7 +2652,8 @@ def verify_tables_api_equality(self, ts):
             tables = ts.dump_tables()
             tables.simplify(samples=samples)
             tables.assert_equals(
-                ts.simplify(samples=samples).tables, ignore_timestamps=True
+                ts.simplify(samples=samples).dump_tables(),
+                ignore_timestamps=True,
             )
 
     @pytest.mark.parametrize("ts", tsutil.get_example_tree_sequences())
@@ -4012,7 +4009,7 @@ def test_first_last(self):
 
     def test_eq_different_tree_sequence(self):
         ts = msprime.simulate(4, recombination_rate=1, length=2, random_seed=42)
-        copy = ts.tables.tree_sequence()
+        copy = ts.dump_tables().tree_sequence()
         for tree1, tree2 in zip(ts.aslist(), copy.aslist()):
             assert tree1 != tree2
 

python/tests/test_ibd.py

@@ -275,7 +275,7 @@ def test_within_between_mutually_exclusive(self, ts):
 
     @pytest.mark.parametrize("ts", example_ts())
     def test_tables_interface(self, ts):
-        ibd_tab = ts.tables.ibd_segments(store_segments=True)
+        ibd_tab = ts.dump_tables().ibd_segments(store_segments=True)
         ibd_ts = ts.ibd_segments(store_segments=True)
         assert ibd_tab == ibd_ts