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Merged
jeromekelleher merged 1 commit into from
Dec 15, 2025
Merged

Drop smck hull_offset defaults #2445

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2 changes: 1 addition & 1 deletion docs/ancestry.md
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Expand Up @@ -2259,7 +2259,7 @@ In this example, we use the {class}`SMC(k) <.SmcKApproxCoalescent>` model to run
simulations:
```{code-cell}
ts = msprime.sim_ancestry(4, population_size=10,
model=msprime.SmcKApproxCoalescent(hull_offset=1),
model=msprime.SmcKApproxCoalescent(1),
random_seed=1)
SVG(ts.draw_svg(y_axis=True, time_scale="log_time"))
```
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3 changes: 1 addition & 2 deletions docs/api.md
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Expand Up @@ -21,8 +21,7 @@ for discussion and examples of individual features.
sim_ancestry
SampleSet
StandardCoalescent
SmcApproxCoalescent
SmcPrimeApproxCoalescent
SmcKApproxCoalescent
DiscreteTimeWrightFisher
FixedPedigree
BetaCoalescent
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19 changes: 10 additions & 9 deletions msprime/ancestry.py
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Expand Up @@ -1798,7 +1798,7 @@ class SmcApproxCoalescent(AncestryModel):
This model is implemented using a naive rejection sampling approach
and so it may not be any more efficient to simulate than the
standard Hudson model.
We recommend using the ``SmcKApproxCoalescent(hull_offset=0)`` instead
We recommend using the ``SmcKApproxCoalescent(0)`` instead

The string ``"smc"`` can be used to refer to this model.
"""
Expand All @@ -1822,7 +1822,8 @@ class SmcPrimeApproxCoalescent(AncestryModel):
This model is implemented using a naive rejection sampling approach
and so it may not be any more efficient to simulate than the
standard Hudson model. We recommend using the
``SmcKApproxCoalescent(hull_offset=1)`` instead.
``SmcKApproxCoalescent(1)`` for discrete genomes instead, or
``SmcKApproxCoalescent(1e-14)`` for continous genomes.

The string ``"smc_prime"`` can be used to refer to this model.
"""
Expand All @@ -1845,23 +1846,23 @@ class SmcKApproxCoalescent(ParametricAncestryModel):

Specifically, if the hull_offset is set to 0, then only overlapping genomic
tracts can be joined by a common ancestor event (this is equivalent to the
SMC model). If the hull_offset is set to 1, then overlapping or adjacent
genomic tracts can be joined by a common ancestor (this is equivalent to the
SMC' model). If the hull_offset is set to full the sequence length, then any
segments can share a common ancestor, which is equivalent to the standard Hudson
coalescent.
SMC model). If the hull_offset is set to 1 (for discrete genomes), then
overlapping or adjacent genomic tracts can be joined by a common ancestor
(this is equivalent to the SMC' model). If the hull_offset is set to full
the sequence length, then any segments can share a common ancestor, which
is equivalent to the standard Hudson coalescent.

:param float hull_offset: Determines the maximum distance between genomic tracts
of ancestral material that can be joined by a common ancestor event.
Defaults to 0 (equivalent to the SMC model).

"""

name = "smc_k"

hull_offset: float

# We have to define an __init__ to enforce keyword-only behaviour
def __init__(self, *, duration=None, hull_offset=0.0):
def __init__(self, hull_offset, *, duration=None):
self.duration = duration
self.hull_offset = hull_offset

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16 changes: 8 additions & 8 deletions tests/test_ancestry.py
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Expand Up @@ -3052,7 +3052,7 @@ class TestSMCK:
def test_discrete(self, seed):
tss = msprime.sim_ancestry(
samples=10,
model=msprime.SmcKApproxCoalescent(),
model=msprime.SmcKApproxCoalescent(1),
recombination_rate=0.005,
sequence_length=1000,
random_seed=seed,
Expand All @@ -3064,7 +3064,7 @@ def test_discrete(self, seed):
def test_continuous(self):
tss = msprime.sim_ancestry(
samples=10,
model=msprime.SmcKApproxCoalescent(),
model=msprime.SmcKApproxCoalescent(1),
recombination_rate=0.005,
sequence_length=1000,
num_replicates=10,
Expand All @@ -3086,7 +3086,7 @@ def test_ancient_samples(self):
ts = msprime.sim_ancestry(
initial_state=tables,
population_size=10_000,
model=msprime.SmcKApproxCoalescent(),
model=msprime.SmcKApproxCoalescent(1),
recombination_rate=1e-6,
)
for tree in ts.trees():
Expand All @@ -3098,7 +3098,7 @@ def test_model_switch(self):
population_size=10_000,
model=[
msprime.StandardCoalescent(duration=10),
msprime.SmcKApproxCoalescent(duration=10),
msprime.SmcKApproxCoalescent(1, duration=10),
msprime.StandardCoalescent(),
],
random_seed=10,
Expand All @@ -3114,7 +3114,7 @@ def test_model_switch_high_rec(self):
population_size=10_000,
model=[
msprime.StandardCoalescent(duration=100),
msprime.SmcKApproxCoalescent(),
msprime.SmcKApproxCoalescent(1),
],
random_seed=10,
recombination_rate=1e-4,
Expand All @@ -3129,7 +3129,7 @@ def test_smc_k_plus(self, hull_offset, discrete_genome):
tss = msprime.sim_ancestry(
samples=10,
population_size=10_000,
model=msprime.SmcKApproxCoalescent(hull_offset=hull_offset),
model=msprime.SmcKApproxCoalescent(hull_offset),
random_seed=10,
recombination_rate=1e-5,
sequence_length=100,
Expand All @@ -3149,7 +3149,7 @@ def test_two_pops(self):
ts = msprime.sim_ancestry(
samples={0: 2, 1: 2},
demography=demography,
model=msprime.SmcKApproxCoalescent(),
model=msprime.SmcKApproxCoalescent(1),
random_seed=74024,
recombination_rate=1e-5,
sequence_length=100,
Expand All @@ -3166,7 +3166,7 @@ def test_gc(self):
):
msprime.sim_ancestry(
samples=10,
model=msprime.SmcKApproxCoalescent(),
model=msprime.SmcKApproxCoalescent(1),
sequence_length=100,
gene_conversion_rate=1.0,
gene_conversion_tract_length=5,
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8 changes: 6 additions & 2 deletions tests/test_demography.py
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Expand Up @@ -2521,7 +2521,7 @@ class TestMigrationRecordsSmcPrime(MigrationRecordsMixin):


class TestMigrationRecordsSmcK(MigrationRecordsMixin):
model = msprime.SmcKApproxCoalescent()
model = msprime.SmcKApproxCoalescent(1)


class TestMigrationRecordsDtwf(MigrationRecordsMixin):
Expand Down Expand Up @@ -2576,7 +2576,11 @@ def test_full_arg_migration(self):
self.verify_two_pops_full_arg(ts)

def test_full_arg_migration_smc(self):
for model in ["smc", "smc_prime", msprime.SmcKApproxCoalescent()]:
for model in [
msprime.SmcApproxCoalescent(),
msprime.SmcPrimeApproxCoalescent(),
msprime.SmcKApproxCoalescent(1),
]:
population_configurations = [
msprime.PopulationConfiguration(10),
msprime.PopulationConfiguration(10),
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14 changes: 7 additions & 7 deletions tests/test_models.py
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Expand Up @@ -60,7 +60,7 @@ def test_smc_models(self):
assert repr(model) == repr_s
assert str(model) == repr_s

model = msprime.SmcKApproxCoalescent()
model = msprime.SmcKApproxCoalescent(0.0)
repr_s = "SmcKApproxCoalescent(duration=None, hull_offset=0.0)"
assert repr(model) == repr_s
assert str(model) == repr_s
Expand Down Expand Up @@ -144,7 +144,7 @@ def test_model_instances(self):
msprime.StandardCoalescent(),
msprime.SmcApproxCoalescent(),
msprime.SmcPrimeApproxCoalescent(),
msprime.SmcKApproxCoalescent(),
msprime.SmcKApproxCoalescent(1),
msprime.DiscreteTimeWrightFisher(),
msprime.FixedPedigree(),
msprime.SweepGenicSelection(
Expand Down Expand Up @@ -332,11 +332,11 @@ def test_sweep_genic_selection(self):
msprime.SweepGenicSelection(1)

def test_smck_coalescent(self):
model = msprime.SmcKApproxCoalescent()
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@jeromekelleher jeromekelleher Dec 15, 2025

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Should resinstate this test to check that it raises a TypeError (or whatever it is)

# mandatory positional argument
with pytest.raises(TypeError):
        msprime.SmcKApproxCoalescent()

assert model.duration is None
assert model.hull_offset == 0.0

model = msprime.SmcKApproxCoalescent(hull_offset=1.1)
with pytest.raises(TypeError, match="hull_offset"):
model = msprime.SmcKApproxCoalescent()

model = msprime.SmcKApproxCoalescent(1.1)
assert model.duration is None
assert model.hull_offset == 1.1

Expand Down Expand Up @@ -471,7 +471,7 @@ def test_dirac_coalescent_parameters(self):

def test_smck_coalescent_parameters(self):
for hull_offset in [0.01, 10.0, 0.99]:
model = msprime.SmcKApproxCoalescent(hull_offset=hull_offset)
model = msprime.SmcKApproxCoalescent(hull_offset)
assert model.hull_offset == hull_offset
d = model._as_lowlevel()
assert d == {"name": "smc_k", "hull_offset": hull_offset, "duration": None}
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12 changes: 6 additions & 6 deletions verification.py
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Expand Up @@ -4535,7 +4535,7 @@ class SmckvsSmcKApproxCoalescent(Test):
"""

models = {
"SmcKApprox": msprime.SmcKApproxCoalescent(),
"SmcKApprox": msprime.SmcKApproxCoalescent(hull_offset=0.0),
"smc": msprime.SmcApproxCoalescent(),
}

Expand Down Expand Up @@ -4955,9 +4955,9 @@ def test_gc_tract_length_smc(self):
Runs the check for the mean length of gene conversion tracts.
"""
models = {
"Hudson": msprime.SmcApproxCoalescent(),
"SMC": msprime.SmcKApproxCoalescent(),
"SMCK": msprime.StandardCoalescent(),
"SMC": msprime.SmcApproxCoalescent(),
"SMCK": msprime.SmcKApproxCoalescent(hull_offset=0.0),
"Hudson": msprime.StandardCoalescent(),
}
num_replicates = 10
n = 10
Expand Down Expand Up @@ -5053,7 +5053,7 @@ def test_smc_k_num_trees_gc(self):

models_to_run = [
(msprime.SmcApproxCoalescent(), "msprime (hudson)"),
(msprime.SmcKApproxCoalescent(), "smc"),
(msprime.SmcApproxCoalescent(), "smc"),
(msprime.SmcPrimeApproxCoalescent(), "smc_prime"),
(msprime.SmcKApproxCoalescent(hull_offset=0.0), "smc_k(0)"),
(msprime.SmcKApproxCoalescent(hull_offset=1.0), "smc_k(1)"),
Expand Down Expand Up @@ -5618,7 +5618,7 @@ def test_above_root_smck(self):
samples=10,
sequence_length=100,
recombination_rate=0.1,
model=msprime.SmcKApproxCoalescent(),
model=msprime.SmcKApproxCoalescent(hull_offset=0.0),
num_replicates=300,
)

Expand Down