def test_two_events(self):
expected_events = [
msprime.SimulationModelChange(time=1,
model=msprime.StandardCoalescent()),
msprime.SimulationModelChange(time=2,
model=msprime.SmcApproxCoalescent()),
]
model, events = msprime.parse_model_arg(
["dtwf", (1, "hudson"), (2, "smc")])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
model, events = msprime.parse_model_arg(
["dtwf", (1, None), (2, msprime.SmcApproxCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
model, events = msprime.parse_model_arg(
["dtwf", expected_events[0], (2, msprime.SmcApproxCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
model, events = msprime.parse_model_arg(
["dtwf", expected_events[0], (2, msprime.SmcApproxCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
self.assertIsNot(events[0], expected_events[0])
model, events = msprime.parse_model_arg(["dtwf"] + expected_events)
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
self.assertIsNot(events[0], expected_events[0])
self.assertIsNot(events[1], expected_events[1])
def test_one_event(self):
expected_event = msprime.SimulationModelChange(
time=1.33, model=msprime.StandardCoalescent())
model, events = msprime.parse_model_arg(["dtwf", (1.33, "hudson")])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
model, events = msprime.parse_model_arg(["dtwf", (1.33, None)])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
model, events = msprime.parse_model_arg(
["dtwf", (1.33, msprime.StandardCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
model, events = msprime.parse_model_arg(["dtwf", expected_event])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
# We should take a copy of the event.
self.assertIsNot(events[0], expected_event)
model, events = msprime.parse_model_arg(["dtwf", (None, None)])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(
events,
[
msprime.SimulationModelChange(
time=None, model=msprime.StandardCoalescent())
],
)
def test_single_model(self):
model, events = msprime.parse_model_arg("hudson")
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg(msprime.StandardCoalescent())
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg("dtwf")
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg(
msprime.DiscreteTimeWrightFisher())
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
def test_single_model_list(self):
model, events = msprime.parse_model_arg([None])
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
# Tuples are also accepted as input.
model, events = msprime.parse_model_arg((None, ))
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg(["hudson"])
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg([msprime.StandardCoalescent()])
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg(["dtwf"])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
model, events = msprime.parse_model_arg(
[msprime.DiscreteTimeWrightFisher()])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
def test_errors(self):
with self.assertRaises(ValueError):
msprime.parse_model_arg([])
with self.assertRaises(ValueError):
msprime.parse_model_arg("X")
# Anything that's not a list or tuple is interpreted as a model
with self.assertRaises(TypeError):
msprime.parse_model_arg({})
for bad_model_change_type in [None, "str", {}]:
with self.assertRaises(TypeError):
msprime.parse_model_arg([None, bad_model_change_type])
for bad_model_change_tuple in [[], [1, None, None]]:
with self.assertRaises(ValueError):
msprime.parse_model_arg(["hudson", bad_model_change_tuple])
for bad_time in ["sdf", [], {}]:
with self.assertRaises(ValueError):
msprime.parse_model_arg(["hudson", (bad_time, "hudson")])
for bad_model_type in [[], {}]:
with self.assertRaises(TypeError):
msprime.parse_model_arg(["hudson", (1, bad_model_type)])
def test_none(self):
model, events = msprime.parse_model_arg(None)
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])