def test_one_event(self):
expected_event = msprime.AncestryModelChange(
time=1.33, model=msprime.StandardCoalescent())
model, events = ancestry._parse_model_arg(["dtwf", (1.33, "hudson")])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == [expected_event]
model, events = ancestry._parse_model_arg(["dtwf", (1.33, None)])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == [expected_event]
model, events = ancestry._parse_model_arg(
["dtwf", (1.33, msprime.StandardCoalescent())])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == [expected_event]
model, events = ancestry._parse_model_arg(["dtwf", expected_event])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == [expected_event]
# We should take a copy of the event.
assert events[0] is not expected_event
model, events = ancestry._parse_model_arg(["dtwf", (None, None)])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == [
msprime.AncestryModelChange(time=None,
model=msprime.StandardCoalescent())
]
def test_two_events(self):
expected_events = [
msprime.AncestryModelChange(time=1,
model=msprime.StandardCoalescent()),
msprime.AncestryModelChange(time=2,
model=msprime.SmcApproxCoalescent()),
]
model, events = ancestry._parse_model_arg(
["dtwf", (1, "hudson"), (2, "smc")])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == expected_events
model, events = ancestry._parse_model_arg(
["dtwf", (1, None), (2, msprime.SmcApproxCoalescent())])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == expected_events
model, events = ancestry._parse_model_arg(
["dtwf", expected_events[0], (2, msprime.SmcApproxCoalescent())])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == expected_events
model, events = ancestry._parse_model_arg(
["dtwf", expected_events[0], (2, msprime.SmcApproxCoalescent())])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == expected_events
assert events[0] is not expected_events[0]
model, events = ancestry._parse_model_arg(["dtwf"] + expected_events)
assert model == msprime.DiscreteTimeWrightFisher()
assert events == expected_events
assert events[0] is not expected_events[0]
assert events[1] is not expected_events[1]
def test_one_event(self):
expected_event = msprime.SimulationModelChange(
time=1.33, model=msprime.StandardCoalescent())
model, events = ancestry._parse_model_arg(["dtwf", (1.33, "hudson")])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
model, events = ancestry._parse_model_arg(["dtwf", (1.33, None)])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
model, events = ancestry._parse_model_arg(
["dtwf", (1.33, msprime.StandardCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [expected_event])
model, events = ancestry._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 = ancestry._parse_model_arg(["dtwf", (None, None)])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(
events,
[
msprime.SimulationModelChange(
time=None, model=msprime.StandardCoalescent())
],
)
def test_two_events(self):
expected_events = [
msprime.SimulationModelChange(time=1,
model=msprime.StandardCoalescent()),
msprime.SimulationModelChange(time=2,
model=msprime.SmcApproxCoalescent()),
]
model, events = ancestry._parse_model_arg(
["dtwf", (1, "hudson"), (2, "smc")])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
model, events = ancestry._parse_model_arg(
["dtwf", (1, None), (2, msprime.SmcApproxCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
model, events = ancestry._parse_model_arg(
["dtwf", expected_events[0], (2, msprime.SmcApproxCoalescent())])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, expected_events)
model, events = ancestry._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 = ancestry._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_single_model(self):
models = ancestry._parse_model_arg("hudson")
assert models == [msprime.StandardCoalescent()]
models = ancestry._parse_model_arg(msprime.StandardCoalescent())
assert models == [msprime.StandardCoalescent()]
models = ancestry._parse_model_arg("dtwf")
assert models == [msprime.DiscreteTimeWrightFisher()]
models = ancestry._parse_model_arg(msprime.DiscreteTimeWrightFisher())
assert models == [msprime.DiscreteTimeWrightFisher()]
def test_one_change(self):
models = ancestry._parse_model_arg(
[msprime.DiscreteTimeWrightFisher(duration=1.33), "hudson"])
assert models == [
msprime.DiscreteTimeWrightFisher(duration=1.33),
msprime.StandardCoalescent(),
]
models = ancestry._parse_model_arg(
[msprime.DiscreteTimeWrightFisher(duration=1.33), None])
assert models == [
msprime.DiscreteTimeWrightFisher(duration=1.33),
msprime.StandardCoalescent(),
]
def test_single_model(self):
model, events = ancestry._parse_model_arg("hudson")
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg(msprime.StandardCoalescent())
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg("dtwf")
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg(
msprime.DiscreteTimeWrightFisher())
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
def test_two_changes(self):
models = ancestry._parse_model_arg([
msprime.DiscreteTimeWrightFisher(duration=1),
msprime.StandardCoalescent(duration=2),
msprime.SmcApproxCoalescent(duration=3),
])
assert models == [
msprime.DiscreteTimeWrightFisher(duration=1),
msprime.StandardCoalescent(duration=2),
msprime.SmcApproxCoalescent(duration=3),
]
def test_single_model_list(self):
model, events = ancestry._parse_model_arg([None])
assert model == msprime.StandardCoalescent()
assert events == []
# Tuples are also accepted as input.
model, events = ancestry._parse_model_arg((None, ))
assert model == msprime.StandardCoalescent()
assert events == []
model, events = ancestry._parse_model_arg(["hudson"])
assert model == msprime.StandardCoalescent()
assert events == []
model, events = ancestry._parse_model_arg(
[msprime.StandardCoalescent()])
assert model == msprime.StandardCoalescent()
assert events == []
model, events = ancestry._parse_model_arg(["dtwf"])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == []
model, events = ancestry._parse_model_arg(
[msprime.DiscreteTimeWrightFisher()])
assert model == msprime.DiscreteTimeWrightFisher()
assert events == []
def test_single_model_list(self):
model, events = ancestry._parse_model_arg([None])
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
# Tuples are also accepted as input.
model, events = ancestry._parse_model_arg((None, ))
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg(["hudson"])
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg(
[msprime.StandardCoalescent()])
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg(["dtwf"])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
model, events = ancestry._parse_model_arg(
[msprime.DiscreteTimeWrightFisher()])
self.assertEqual(model, msprime.DiscreteTimeWrightFisher())
self.assertEqual(events, [])
def test_errors(self):
with pytest.raises(ValueError, match="at least one AncestryModel"):
ancestry._parse_model_arg([])
for bad_model in ["X", ["X"]]:
with pytest.raises(ValueError, match="Model 'X' unknown"):
ancestry._parse_model_arg(bad_model)
# Anything that's not a list or tuple is interpreted as a model
with pytest.raises(TypeError,
match="Ancestry model must be a string or"):
ancestry._parse_model_arg({})
def test_errors(self):
with pytest.raises(ValueError):
ancestry._parse_model_arg([])
with pytest.raises(ValueError):
ancestry._parse_model_arg("X")
# Anything that's not a list or tuple is interpreted as a model
with pytest.raises(TypeError):
ancestry._parse_model_arg({})
for bad_model_change_type in [None, "str", {}]:
with pytest.raises(TypeError):
ancestry._parse_model_arg([None, bad_model_change_type])
for bad_model_change_tuple in [[], [1, None, None]]:
with pytest.raises(ValueError):
ancestry._parse_model_arg(["hudson", bad_model_change_tuple])
for bad_time in ["sdf", [], {}]:
with pytest.raises(ValueError):
ancestry._parse_model_arg(["hudson", (bad_time, "hudson")])
for bad_model_type in [[], {}]:
with pytest.raises(TypeError):
ancestry._parse_model_arg(["hudson", (1, bad_model_type)])
def test_none(self):
model, events = ancestry._parse_model_arg(None)
assert model == msprime.StandardCoalescent()
assert events == []
def test_none(self):
model, events = ancestry._parse_model_arg(None)
self.assertEqual(model, msprime.StandardCoalescent())
self.assertEqual(events, [])
