Use dict representation for compress and decompress

CHANGELOG.rst

@@ -1,3 +1,9 @@
+--------------------
+[0.1.1] - 2021-04-XX
+--------------------
+
+- Add support for new columns in tskit. (benjeffery, #39, #42).
+
 --------------------
 [0.1.0] - 2019-05-10
 --------------------

requirements/CI-tests-conda.txt

@@ -1,4 +1,5 @@
 humanize==3.4.1
+h5py==3.2.1
 msprime==1.0.0
 pytest==6.2.3
 pytest-cov==2.11.1

requirements/development.txt

@@ -1,6 +1,7 @@
 codecov
 coverage
 flake8
+h5py
 pre-commit
 pytest
 pytest-cov

tests/test_cli.py

@@ -31,7 +31,6 @@
 
 import msprime
 import numpy as np
-import pytest
 import tskit
 
 import tszip
@@ -43,6 +42,9 @@ class TestException(Exception):
     Custom exception we can throw for testing.
     """
 
+    # We don't want pytest to use this as a class to test
+    __test__ = False
+
 
 def capture_output(func, *args, **kwargs):
     """
@@ -189,7 +191,6 @@ def setUp(self):
     def tearDown(self):
         del self.tmpdir
 
-    @pytest.mark.xfail
     def test_simple(self):
         self.assertTrue(self.trees_path.exists())
         self.run_tszip([str(self.trees_path)])
@@ -199,7 +200,6 @@ def test_simple(self):
         ts = tszip.decompress(outpath)
         self.assertEqual(ts.tables, self.ts.tables)
 
-    @pytest.mark.xfail
     def test_suffix(self):
         self.assertTrue(self.trees_path.exists())
         self.run_tszip([str(self.trees_path), "-S", ".XYZasdf"])
@@ -221,7 +221,6 @@ def test_variants_only(self):
         G2 = self.ts.genotype_matrix()
         self.assertTrue(np.array_equal(G1, G2))
 
-    @pytest.mark.xfail
     def test_keep(self):
         self.assertTrue(self.trees_path.exists())
         self.run_tszip([str(self.trees_path), "--keep"])
@@ -231,7 +230,6 @@ def test_keep(self):
         ts = tszip.decompress(outpath)
         self.assertEqual(ts.tables, self.ts.tables)
 
-    @pytest.mark.xfail
     def test_overwrite(self):
         self.assertTrue(self.trees_path.exists())
         outpath = pathlib.Path(str(self.trees_path) + ".tsz")
@@ -255,7 +253,6 @@ def test_no_overwrite(self):
                 f"'{outpath}' already exists; use --force to overwrite"
             )
 
-    @pytest.mark.xfail
     def test_bad_file_format(self):
         self.assertTrue(self.trees_path.exists())
         with open(str(self.trees_path), "w") as f:
@@ -283,7 +280,6 @@ def setUp(self):
     def tearDown(self):
         del self.tmpdir
 
-    @pytest.mark.xfail
     def test_simple(self):
         self.assertTrue(self.compressed_path.exists())
         self.run_decompress([str(self.compressed_path)])
@@ -293,7 +289,6 @@ def test_simple(self):
         ts = tskit.load(str(outpath))
         self.assertEqual(ts.tables, self.ts.tables)
 
-    @pytest.mark.xfail
     def test_suffix(self):
         suffix = ".XYGsdf"
         self.compressed_path = self.compressed_path.with_suffix(suffix)
@@ -306,7 +301,6 @@ def test_suffix(self):
         ts = tskit.load(str(outpath))
         self.assertEqual(ts.tables, self.ts.tables)
 
-    @pytest.mark.xfail
     def test_keep(self):
         self.assertTrue(self.compressed_path.exists())
         self.run_decompress([str(self.compressed_path), "--keep"])
@@ -316,7 +310,6 @@ def test_keep(self):
         ts = tskit.load(str(outpath))
         self.assertEqual(ts.tables, self.ts.tables)
 
-    @pytest.mark.xfail
     def test_overwrite(self):
         self.assertTrue(self.compressed_path.exists())
         outpath = self.trees_path
@@ -346,7 +339,6 @@ def test_decompress_bad_suffix(self):
                 "Compressed file must have 'asdf' suffix"
             )
 
-    @pytest.mark.xfail
     def test_bad_file_format(self):
         self.assertTrue(self.compressed_path.exists())
         with open(str(self.compressed_path), "w") as f:

tests/test_compression.py

@@ -28,7 +28,6 @@
 
 import msprime
 import numpy as np
-import pytest
 import tskit
 import zarr
 
@@ -106,20 +105,17 @@ class RoundTripMixin:
     Set of example tree sequences that we should be able to round trip.
     """
 
-    @pytest.mark.xfail
     def test_small_msprime_no_recomb(self):
         ts = msprime.simulate(10, mutation_rate=2, random_seed=2)
         self.assertGreater(ts.num_sites, 2)
         self.verify(ts)
 
-    @pytest.mark.xfail
     def test_small_msprime_recomb(self):
         ts = msprime.simulate(10, recombination_rate=2, mutation_rate=2, random_seed=2)
         self.assertGreater(ts.num_sites, 2)
         self.assertGreater(ts.num_trees, 2)
         self.verify(ts)
 
-    @pytest.mark.xfail
     def test_small_msprime_migration(self):
         ts = msprime.simulate(
             population_configurations=[
@@ -137,7 +133,6 @@ def test_small_msprime_migration(self):
         self.assertGreater(ts.num_trees, 2)
         self.verify(ts)
 
-    @pytest.mark.xfail
     def test_small_msprime_top_level_metadata(self):
         ts = msprime.simulate(10, recombination_rate=2, mutation_rate=2, random_seed=2)
         self.assertGreater(ts.num_sites, 2)
@@ -151,15 +146,16 @@ def test_small_msprime_top_level_metadata(self):
         tables.metadata = {"my_int": 1234}
         self.verify(tables.tree_sequence())
 
-    @pytest.mark.xfail
     def test_small_msprime_individuals_metadata(self):
         ts = msprime.simulate(10, recombination_rate=1, mutation_rate=2, random_seed=2)
         self.assertGreater(ts.num_sites, 2)
         self.assertGreater(ts.num_trees, 2)
         tables = ts.dump_tables()
         tables.nodes.clear()
         for j, node in enumerate(ts.nodes()):
-            tables.individuals.add_row(flags=j, location=[j] * j, metadata=b"x" * j)
+            tables.individuals.add_row(
+                flags=j, location=[j] * j, parents=[j - 1] * j, metadata=b"x" * j
+            )
             tables.nodes.add_row(
                 flags=node.flags,
                 population=node.population,
@@ -169,6 +165,7 @@ def test_small_msprime_individuals_metadata(self):
             )
         tables.populations.clear()
         tables.populations.add_row(metadata=b"X" * 1024)
+        tables.sort()
         self.verify(tables.tree_sequence())
 
     def test_small_msprime_complex_mutations(self):
@@ -200,6 +197,33 @@ def test_mutation_parent_example(self):
         tables.mutations.add_row(site=0, node=0, parent=0, derived_state="A")
         self.verify(tables.tree_sequence())
 
+    def test_all_fields(self):
+        demography = msprime.Demography()
+        demography.add_population(name="A", initial_size=10_000)
+        demography.add_population(name="B", initial_size=5_000)
+        demography.add_population(name="C", initial_size=1_000)
+        demography.add_population_split(time=1000, derived=["A", "B"], ancestral="C")
+        ts = msprime.sim_ancestry(
+            samples={"A": 1, "B": 1}, demography=demography, random_seed=42
+        )
+        ts = msprime.sim_mutations(ts, rate=1, random_seed=42)
+        tables = ts.dump_tables()
+        for name, table in tables.name_map.items():
+            if name not in ["provenances", "edges"]:
+                table.metadata_schema = tskit.MetadataSchema({"codec": "json"})
+                metadatas = [f'{{"foo":"n_{name}_{u}"}}' for u in range(len(table))]
+                metadata, metadata_offset = tskit.pack_strings(metadatas)
+                table.set_columns(
+                    **{
+                        **table.asdict(),
+                        "metadata": metadata,
+                        "metadata_offset": metadata_offset,
+                    }
+                )
+        tables.metadata_schema = tskit.MetadataSchema({"codec": "json"})
+        tables.metadata = "Test metadata"
+        self.verify(tables.tree_sequence())
+
 
 class TestGenotypeRoundTrip(unittest.TestCase, RoundTripMixin):
     """

tests/test_legacy.py

@@ -0,0 +1,37 @@
+# MIT License
+#
+# Copyright (c) 2021 Tskit Developers
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+"""
+Tests for files from previous releases.
+"""
+import pathlib
+
+import tskit
+
+import tszip
+
+
+class Testv1:
+    def test_decompress(self):
+        files = pathlib.Path(__file__).parent / "files"
+        ts = tszip.decompress(files / "1.0.0.trees.tsz")
+        ts2 = tskit.load(files / "1.0.0.trees")
+        assert ts == ts2