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Simplify the smck OOA verification and refactor smck verifications fix 2462, 2463 #2468

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Merged
jeromekelleher merged 1 commit into from
Jan 27, 2026
Merged

Simplify the smck OOA verification and refactor smck verifications fix 2462, 2463 #2468

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17 changes: 6 additions & 11 deletions verification.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4528,9 +4528,10 @@ def test_smc_num_trees(self):
pyplot.close("all")


class SmckvsSMCK(Test):
class SmcKTest(Test):
"""
Tests for the SMC(k) approximation coalescent against the SMC(k) model.
Tests for the SMCK model.
SMC(0) is compared against rejection sampling SMC (SmcApproxCoalescent).
"""

models = {
Expand Down Expand Up @@ -4653,12 +4654,6 @@ def _run(self, **kwargs):
self.plot_SmcKApprox_smcK_stats(df)
self.plot_tree_intervals(df)


class SmcKTest(SmckvsSMCK):
"""
Tests for the SMC(0) model against rejection sampling.
"""

def test_smc_k_oldest_time(self):
"""
Runs the check for number of trees using the CLI.
Expand Down Expand Up @@ -4950,7 +4945,7 @@ def test_smck_vs_smckapprox_multiple_bottleneck(self):
)

def test_out_of_africa_migration_model(self):
s_no = 10
s_no = 1
samples = {
"YRI": s_no,
"CEU": s_no,
Expand All @@ -4960,7 +4955,7 @@ def test_out_of_africa_migration_model(self):
"ANC": s_no,
}
recombination_map = msprime.RateMap(
position=[0, 100, 500, 900, 1200, 1500, 2000],
position=[0, 50, 250, 450, 600, 750, 1000],
rate=[0.00001, 0, 0.0002, 0.00005, 0, 0.001],
)

Expand All @@ -4972,7 +4967,7 @@ def test_out_of_africa_migration_model(self):
discrete_genome=True,
demography=msprime.Demography._ooa_model(),
record_migrations=True,
num_replicates=50,
num_replicates=20,
model=model_cls,
)

Expand Down