def test_python_simplify_sample_subset(self, ts, nsamples):
sub_samples = random.sample(list(ts.samples()), min(nsamples, ts.sample_size))
s = tests.Simplifier(ts, sub_samples)
py_small_ts, py_small_map = s.simplify()
small_ts, small_map = ts.simplify(samples=sub_samples, map_nodes=True)
small_ts.tables.assert_equals(py_small_ts.tables, ignore_provenance=True)
self.verify_simplify(ts, small_ts, sub_samples, small_map)
self.verify_haplotypes(ts, samples=sub_samples)
def test_python_simplify_all_samples(self, ts):
s = tests.Simplifier(ts, ts.samples())
py_full_ts, py_full_map = s.simplify()
full_ts, full_map = ts.simplify(ts.samples(), map_nodes=True)
assert all(py_full_map == full_map)
tsutil.assert_table_collections_equal(
full_ts.tables, py_full_ts.tables, ignore_provenance=True
)
def test_simplify(self):
# check that simplify(big set) -> simplify(subset) equals simplify(subset)
seed = 23
random.seed(seed)
for ts in self.get_wf_sims(seed=seed):
s = tests.Simplifier(ts, ts.samples())
py_full_ts, py_full_map = s.simplify()
full_ts, full_map = ts.simplify(ts.samples(), map_nodes=True)
self.assertTrue(all(py_full_map == full_map))
self.assertTreeSequencesEqual(full_ts, py_full_ts)
for nsamples in [2, 5, 10]:
sub_samples = random.sample(ts.samples(),
min(nsamples, ts.sample_size))
s = tests.Simplifier(ts, sub_samples)
py_small_ts, py_small_map = s.simplify()
small_ts, small_map = ts.simplify(samples=sub_samples,
map_nodes=True)
self.assertTreeSequencesEqual(small_ts, py_small_ts)
self.verify_simplify(ts, small_ts, sub_samples, small_map)
self.verify_haplotypes(ts, samples=sub_samples)