Fix dump_text

Author: benjeffery

python/CHANGELOG.rst

@@ -1,3 +1,13 @@
+----------------------
+[0.4.0] - 2022-0X-XX
+----------------------
+
+**Fixes**
+
+- ``TreeSequence.dump_text`` now prints decoded metadata if there is a schema.
+  (:user:`bejeffery`, :issue:`1860`, :issue:`1527`,
+
+
 ----------------------
 [0.4.0] - 2021-12-10
 ----------------------

python/tests/conftest.py

@@ -42,7 +42,7 @@ def test_something(self, ts_fixture):
 import pytest
 from pytest import fixture
 
-import tskit
+from . import tsutil
 
 
 def pytest_addoption(parser):
@@ -108,74 +108,7 @@ def ts_fixture():
     """
     A tree sequence with data in all fields
     """
-    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(name="D", initial_size=500)
-    demography.add_population(name="E", initial_size=100)
-    demography.add_population_split(time=1000, derived=["A", "B"], ancestral="C")
-    ts = msprime.sim_ancestry(
-        samples={"A": 10, "B": 10},
-        demography=demography,
-        sequence_length=5,
-        random_seed=42,
-        recombination_rate=1,
-        record_migrations=True,
-        record_provenance=True,
-    )
-    ts = msprime.sim_mutations(ts, rate=0.001, random_seed=42)
-    tables = ts.dump_tables()
-    # Add locations to individuals
-    individuals_copy = tables.individuals.copy()
-    tables.individuals.clear()
-    for i, individual in enumerate(individuals_copy):
-        tables.individuals.append(
-            individual.replace(flags=i, location=[i, i + 1], parents=[i - 1, i - 1])
-        )
-    # Ensure all columns have unique values
-    nodes_copy = tables.nodes.copy()
-    tables.nodes.clear()
-    for i, node in enumerate(nodes_copy):
-        tables.nodes.append(
-            node.replace(
-                flags=i,
-                time=node.time + 0.00001 * i,
-                individual=i % len(tables.individuals),
-                population=i % len(tables.populations),
-            )
-        )
-    tables.migrations.add_row(left=0, right=1, node=21, source=1, dest=3, time=1001)
-
-    # Add metadata
-    for name, table in tables.name_map.items():
-        if name != "provenances":
-            table.metadata_schema = tskit.MetadataSchema.permissive_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.permissive_json()
-    tables.metadata = "Test metadata"
-    tables.time_units = "Test time units"
-
-    tables.reference_sequence.metadata_schema = tskit.MetadataSchema.permissive_json()
-    tables.reference_sequence.metadata = "Test reference metadata"
-    tables.reference_sequence.data = "A" * int(ts.sequence_length)
-    # NOTE: it's unclear whether we'll want to have this set at the same time as
-    # 'data', but it's useful to have something in all columns for now.
-    tables.reference_sequence.url = "http://example.com/a_reference"
-
-    # Add some more rows to provenance to have enough for testing.
-    for _ in range(3):
-        tables.provenances.add_row(record="A")
-
-    return tables.tree_sequence()
+    return tsutil.all_fields_ts()
 
 
 @fixture(scope="session")