def test_different_lengths(self):
events = [msprime.PopulationParametersChange(time=1, initial_size=1)] * 10
self.assertFalse(models.demographic_events_equal(events[:1], [], 1))
self.assertFalse(models.demographic_events_equal([], events[:1], 1))
self.assertFalse(models.demographic_events_equal(events, [], 1))
self.assertFalse(models.demographic_events_equal([], events, 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([], events, 1)
def test_different_types(self):
events = [
msprime.PopulationParametersChange(time=1, initial_size=1),
msprime.MigrationRateChange(time=1, rate=1),
msprime.MassMigration(time=1, source=1),
msprime.SimpleBottleneck(time=1)]
for a, b in itertools.combinations(events, 2):
self.assertFalse(models.demographic_events_equal([a], [b], 1))
self.assertFalse(models.demographic_events_equal([b], [a], 1))
self.assertTrue(models.demographic_events_equal([a], [a], 1))
self.assertTrue(models.demographic_events_equal([b], [b], 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([b], [a], 1)
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([a], [b], 1)
def test_different_times(self):
n = 10
e1 = [
msprime.PopulationParametersChange(time=j, initial_size=1)
for j in range(n)]
e2 = [
msprime.PopulationParametersChange(time=j + 1, initial_size=1)
for j in range(n)]
for j in range(1, n):
self.assertFalse(models.demographic_events_equal(e1[:j], e2[:j], 1))
self.assertFalse(models.demographic_events_equal(e2[:j], e1[:j], 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal(e1[:j], e2[:j], 1)
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal(e2[:j], e1[:j], 1)
def test_simple_bottleneck(self):
def f(time=1, population=1, proportion=1):
return msprime.SimpleBottleneck(
time=time, population=population, proportion=proportion)
test_events = [
(f(time=1), f(time=2)),
(f(population=1), f(population=2)),
(f(proportion=1), f(proportion=0.2)),
]
for a, b in test_events:
self.assertFalse(models.demographic_events_equal([a], [b], 1))
self.assertFalse(models.demographic_events_equal([b], [a], 1))
self.assertTrue(models.demographic_events_equal([a], [a], 1))
self.assertTrue(models.demographic_events_equal([b], [b], 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([b], [a], 1)
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([a], [b], 1)
def test_mass_migration(self):
def f(time=1, source=1, dest=1, proportion=1):
return msprime.MassMigration(
time=time, source=source, dest=dest, proportion=proportion)
test_events = [
(f(time=1), f(time=2)),
(f(source=1), f(source=2)),
(f(dest=1), f(dest=2)),
(f(proportion=1), f(proportion=0.2)),
]
for a, b in test_events:
self.assertFalse(models.demographic_events_equal([a], [b], 1))
self.assertFalse(models.demographic_events_equal([b], [a], 1))
self.assertTrue(models.demographic_events_equal([a], [a], 1))
self.assertTrue(models.demographic_events_equal([b], [b], 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([b], [a], 1)
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([a], [b], 1)
def test_migration_rate_change(self):
def f(time=1, rate=1, matrix_index=None):
return msprime.MigrationRateChange(
time=time, rate=rate, matrix_index=matrix_index)
test_events = [
(f(time=1), f(time=2)),
(f(rate=1), f(rate=2)),
(f(matrix_index=[0, 1]), f(matrix_index=[0, 2])),
(f(matrix_index=np.array([0, 1])), f(matrix_index=[0, 2])),
]
for a, b in test_events:
self.assertFalse(models.demographic_events_equal([a], [b], 1))
self.assertFalse(models.demographic_events_equal([b], [a], 1))
self.assertTrue(models.demographic_events_equal([a], [a], 1))
self.assertTrue(models.demographic_events_equal([b], [b], 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([b], [a], 1)
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([a], [b], 1)
def test_population_parameters_change(self):
def f(time=1, initial_size=1, growth_rate=None, population=None):
return msprime.PopulationParametersChange(
time=time, initial_size=initial_size, growth_rate=growth_rate,
population=population)
test_events = [
(f(time=1), f(time=2)),
(f(initial_size=1), f(initial_size=2)),
(f(growth_rate=1), f(growth_rate=2)),
(f(population=1), f(population=2)),
]
for a, b in test_events:
self.assertFalse(models.demographic_events_equal([a], [b], 1))
self.assertFalse(models.demographic_events_equal([b], [a], 1))
self.assertTrue(models.demographic_events_equal([a], [a], 1))
self.assertTrue(models.demographic_events_equal([b], [b], 1))
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([b], [a], 1)
with self.assertRaises(models.UnequalModelsError):
models.verify_demographic_events_equal([a], [b], 1)
