def test_node_metadata(self):
md = pyslim.NodeMetadata(slim_id=2,
is_null=False,
genome_type=pyslim.GENOME_TYPE_X)
md_bytes = pyslim.encode_node(md)
new_md = pyslim.decode_node(md_bytes)
self.assertEqual(md, new_md)
def test_node_metadata(self):
md = pyslim.NodeMetadata(slim_id=2,
is_null=False,
genome_type=pyslim.GENOME_TYPE_X)
with self.assertWarns(DeprecationWarning):
md_bytes = pyslim.encode_node(md)
with self.assertWarns(DeprecationWarning):
new_md = pyslim.decode_node(md_bytes)
self.assertEqual(md, new_md)
def test_legacy_errors(self):
defaults = pyslim.default_slim_metadata
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_mutation(defaults('mutation'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_population(defaults('population'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_individual(defaults('individual'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_node(defaults('node'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_mutation(defaults('mutation'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_population(defaults('population'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_individual(defaults('individual'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_node(defaults('node'))
def test_annotate_nodes(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.nodes.metadata,
tables.nodes.metadata_offset):
dm = pyslim.decode_node(md)
edm = pyslim.encode_node(dm)
self.assertEqual(md, edm)
metadata.append(dm)
pyslim.annotate_node_metadata(new_tables, metadata)
self.assertEqual(tables, new_tables)
def test_annotate_nodes(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.nodes.metadata,
tables.nodes.metadata_offset):
with self.assertWarns(DeprecationWarning):
dm = pyslim.decode_node(md)
with self.assertWarns(DeprecationWarning):
edm = pyslim.encode_node(dm)
self.assertEqual(md, edm)
metadata.append(dm)
with self.assertWarns(DeprecationWarning):
pyslim.annotate_node_metadata(new_tables, metadata)
self.assertTableCollectionsEqual(tables, new_tables)
for md in msprime.unpack_bytes(tables.mutations.metadata,
tables.mutations.metadata_offset):
dm = pyslim.decode_mutation(md)
edm = pyslim.encode_mutation(dm)
assert (md == edm)
mut_metadata.append(dm)
pyslim.annotate_mutations(tables, mut_metadata)
# nodes
node_metadata = []
for md in msprime.unpack_bytes(tables.nodes.metadata,
tables.nodes.metadata_offset):
dn = pyslim.decode_node(md)
edn = pyslim.encode_node(dn)
assert (md == edn)
node_metadata.append(dn)
pyslim.annotate_nodes(tables, node_metadata)
# individuals
individual_metadata = []
for md in msprime.unpack_bytes(tables.individuals.metadata,
tables.individuals.metadata_offset):
di = pyslim.decode_individual(md)
edi = pyslim.encode_individual(di)
assert (md == edi)
individual_metadata.append(di)