def test_decode_errors(self):
with self.assertRaises(ValueError):
pyslim.decode_mutation(2.0)
with self.assertRaises(ValueError):
pyslim.decode_mutation([2.0, 3.0])
with self.assertRaises(ValueError):
pyslim.decode_node(2.0)
with self.assertRaises(ValueError):
pyslim.decode_node([1, 2])
with self.assertRaises(ValueError):
pyslim.decode_individual(3.0)
with self.assertRaises(ValueError):
pyslim.decode_individual([1, 2])
with self.assertRaises(ValueError):
pyslim.decode_population(1.0)
with self.assertRaises(ValueError):
pyslim.decode_population([2, 3])
def test_population_derived_info(self):
for ts in self.get_slim_examples():
for j, pop in enumerate(ts.populations()):
a = ts.tables.populations.metadata_offset[j]
b = ts.tables.populations.metadata_offset[j+1]
raw_md = ts.tables.populations.metadata[a:b]
md = pyslim.decode_population(raw_md)
self.assertEqual(pop.metadata, md)
self.assertEqual(ts.population(j).metadata, 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_decode_already_population(self):
m = pyslim.PopulationMetadata(slim_id=1, selfing_fraction=0.2,
female_cloning_fraction=0.3,
male_cloning_fraction=0.4,
sex_ratio=0.5, bounds_x0=0, bounds_x1=10,
bounds_y0=2, bounds_y1=20, bounds_z0=3,
bounds_z1=30, migration_records=[])
dm = pyslim.decode_population(m)
self.assertEqual(m, dm)
def test_population_metadata(self):
mrs = [pyslim.PopulationMigrationMetadata(source_subpop=j, migration_rate=0.2)
for j in range(3)]
for mr_list in [[], mrs]:
md = pyslim.PopulationMetadata(
slim_id=1, selfing_fraction=0.75, female_cloning_fraction=0.2,
male_cloning_fraction=0.8, sex_ratio=0.6, bounds_x0=-1.0,
bounds_x1=2.0, bounds_y0=0.0, bounds_y1=0.0, bounds_z0=0.0,
bounds_z1=1.0, migration_records=mr_list)
md_bytes = pyslim.encode_population(md)
new_md = pyslim.decode_population(md_bytes)
self.assertEqual(md, new_md)
def test_annotate_populations(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.populations.metadata,
tables.populations.metadata_offset):
dm = pyslim.decode_population(md)
edm = pyslim.encode_population(dm)
self.assertEqual(md, edm)
metadata.append(dm)
pyslim.annotate_population_metadata(new_tables, metadata)
self.assertEqual(tables, new_tables)
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)
pyslim.annotate_individuals(tables, individual_metadata)
# populations
population_metadata = []
for md in msprime.unpack_bytes(tables.populations.metadata,
tables.populations.metadata_offset):
if len(md) > 0:
dp = pyslim.decode_population(md)
edp = pyslim.encode_population(dp)
assert (md == edp)
else:
dp = None
population_metadata.append(dp)
pyslim.annotate_populations(tables, population_metadata)
print(tables)
