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Refactor tests for haploid case with multiallelic sites #140

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Jul 1, 2024
Merged

Refactor tests for haploid case with multiallelic sites #140

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34 changes: 2 additions & 32 deletions tests/lsbase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -287,10 +287,10 @@ def get_ts_multiallelic_n10_no_recomb(self, seed=42):
assert ts.num_sites > 3
return ts

def get_ts_multiallelic_n6(self, seed=42):
def get_ts_multiallelic(self, num_samples, seed=42):
ts = msprime.sim_mutations(
msprime.sim_ancestry(
samples=6,
samples=num_samples,
recombination_rate=1e-4,
sequence_length=40,
population_size=1e4,
Expand All @@ -299,40 +299,10 @@ def get_ts_multiallelic_n6(self, seed=42):
rate=1e-3,
random_seed=seed,
)
assert ts.num_sites > 5
return ts

def get_ts_multiallelic_n8(self, seed=42):
ts = msprime.sim_mutations(
msprime.sim_ancestry(
samples=8,
recombination_rate=1e-4,
sequence_length=20,
population_size=1e4,
random_seed=seed,
),
rate=1e-4,
random_seed=seed,
)
assert ts.num_trees > 15
assert ts.num_sites > 5
return ts

def get_ts_multiallelic_n16(self, seed=42):
ts = msprime.sim_mutations(
msprime.sim_ancestry(
samples=16,
recombination_rate=1e-2,
sequence_length=20,
population_size=1e4,
random_seed=seed,
),
rate=1e-4,
random_seed=seed,
)
assert ts.num_sites > 5
return ts


class ForwardBackwardAlgorithmBase(LSBase):
"""Base for testing forwards-backwards algorithms."""
Expand Down
39 changes: 7 additions & 32 deletions tests/test_api_fb_haploid_multi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,38 +61,13 @@ def test_ts_multiallelic_n10_no_recomb(
self, scale_mutation_rate, include_ancestors
):
ts = self.get_ts_multiallelic_n10_no_recomb()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)

@pytest.mark.parametrize("scale_mutation_rate", [True, False])
@pytest.mark.parametrize("include_ancestors", [True, False])
def test_ts_multiallelic_n6(self, scale_mutation_rate, include_ancestors):
ts = self.get_ts_multiallelic_n6()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)
self.verify(ts, scale_mutation_rate, include_ancestors)

@pytest.mark.parametrize("num_samples", [6, 8, 16])
@pytest.mark.parametrize("scale_mutation_rate", [True, False])
@pytest.mark.parametrize("include_ancestors", [True, False])
def test_ts_multiallelic_n8(self, scale_mutation_rate, include_ancestors):
ts = self.get_ts_multiallelic_n8()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)

@pytest.mark.parametrize("scale_mutation_rate", [True, False])
@pytest.mark.parametrize("include_ancestors", [True, False])
def test_ts_multiallelic_n16(self, scale_mutation_rate, include_ancestors):
ts = self.get_ts_multiallelic_n16()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)
def test_ts_multiallelic_n16(
self, num_samples, scale_mutation_rate, include_ancestors
):
ts = self.get_ts_multiallelic(num_samples)
self.verify(ts, scale_mutation_rate, include_ancestors)
33 changes: 6 additions & 27 deletions tests/test_api_vit_haploid_multi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,32 +50,11 @@ def test_ts_multiallelic_n10_no_recomb(
include_ancestors=include_ancestors,
)

@pytest.mark.parametrize("num_samples", [6, 8, 16])
@pytest.mark.parametrize("scale_mutation_rate", [True, False])
@pytest.mark.parametrize("include_ancestors", [True, False])
def test_ts_multiallelic_n6(self, scale_mutation_rate, include_ancestors):
ts = self.get_ts_multiallelic_n6()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)

@pytest.mark.parametrize("scale_mutation_rate", [True, False])
@pytest.mark.parametrize("include_ancestors", [True, False])
def test_ts_multiallelic_n8(self, scale_mutation_rate, include_ancestors):
ts = self.get_ts_multiallelic_n8()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)

@pytest.mark.parametrize("scale_mutation_rate", [True, False])
@pytest.mark.parametrize("include_ancestors", [True, False])
def test_ts_multiallelic_n16(self, scale_mutation_rate, include_ancestors):
ts = self.get_ts_multiallelic_n16()
self.verify(
ts,
scale_mutation_rate=scale_mutation_rate,
include_ancestors=include_ancestors,
)
def test_ts_multiallelic_n16(
self, num_samples, scale_mutation_rate, include_ancestors
):
ts = self.get_ts_multiallelic(num_samples)
self.verify(ts, scale_mutation_rate, include_ancestors)
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