def test_reason_for_model_citations(self):
for model in stdpopsim.all_demographic_models():
for citation in model.citations:
assert len(citation.reasons) > 0, (
f"No reason given for '{citation.author}' citation "
f"in model {model.id}"
)
def test_population_config_order_equal(self):
for model in stdpopsim.all_demographic_models():
pop_ids = [pop.id for pop in model.populations]
config_ids = [
config.metadata["id"] for config in model.population_configurations]
for p, c in zip(pop_ids, config_ids):
self.assertEqual(p, c)
def test_population_order(self):
for model in stdpopsim.all_demographic_models():
allow_sample_status = [
int(p.allow_samples) for p in model.populations
]
num_sampling = sum(allow_sample_status)
# All sampling populations must be at the start of the list
self.assertEqual(sum(allow_sample_status[num_sampling:]), 0)
def test_reason_for_model_citations(self):
for model in stdpopsim.all_demographic_models():
for citation in model.citations:
self.assertGreater(
len(citation.reasons),
0,
msg=f"No reason given for '{citation.author}' citation "
f"in model {model.id}",
)
def test_demography_debugger_equal(self):
for model in stdpopsim.all_demographic_models():
ddb1 = model.get_demography_debugger()
ddb2 = msprime.DemographyDebugger(
population_configurations=model.population_configurations,
migration_matrix=model.migration_matrix,
demographic_events=model.demographic_events)
f1 = io.StringIO()
f2 = io.StringIO()
ddb1.print_history(f1)
ddb2.print_history(f2)
self.assertEqual(f1.getvalue(), f2.getvalue())
def test_all_instances(self):
for model in stdpopsim.all_demographic_models():
self.assertIsInstance(model, models.DemographicModel)
self.assertGreater(len(model.id), 0)
self.assertGreater(len(model.description), 0)
self.assertGreater(len(model.long_description), 0)
self.assertGreater(len(model.citations), 0)
self.assertGreater(model.generation_time, 0)
npops = len(model.populations)
self.assertGreater(npops, 0)
self.assertEqual(len(model.population_configurations), npops)
self.assertEqual(len(model.migration_matrix), npops)
self.assertEqual(len(model.migration_matrix[0]), npops)
self.assertIsInstance(model.demographic_events, list)
class TestAllModels:
"""
Tests for registered simulation models.
"""
def test_non_empty(self):
assert len(list(stdpopsim.all_demographic_models())) > 0
@pytest.mark.parametrize("model", stdpopsim.all_demographic_models())
def test_all_instances(self, model):
assert isinstance(model, models.DemographicModel)
assert len(model.id) > 0
assert len(model.description) > 0
assert len(model.long_description) > 0
assert len(model.citations) > 0
assert model.generation_time > 0
model.model.validate()
def test_demography_debugger(self):
for model in stdpopsim.all_demographic_models():
ddb = model.get_demography_debugger()
self.assertIsInstance(ddb, msprime.DemographyDebugger)
def test_known_models(self):
# All models should be equal to themselves.
other_model = models.DemographicModel.empty()
for model in stdpopsim.all_demographic_models():
self.assertTrue(model.equals(model))
self.assertFalse(model.equals(other_model))
def test_non_empty(self):
self.assertGreater(len(list(stdpopsim.all_demographic_models())), 0)
def test_known_models(self):
other_model = msprime.Demography.isolated_model([1])
for model in stdpopsim.all_demographic_models():
model.model.assert_equivalent(model.model)
model.model.assert_equal(model.model)
assert not model.model.is_equivalent(other_model)
def test_non_empty(self):
assert len(list(stdpopsim.all_demographic_models())) > 0
