def test_environment(self):
# Basic environment should be the same as tskit.
d_tszip = provenance.get_provenance_dict({})
d_tskit = tskit.provenance.get_provenance_dict()
self.assertEqual(d_tszip["environment"]["os"],
d_tskit["environment"]["os"])
self.assertEqual(d_tszip["environment"]["python"],
d_tskit["environment"]["python"])
def test_provenance(self):
ts = msprime.simulate(10, random_seed=1)
for variants_only in [True, False]:
tszip.compress(ts, self.path, variants_only=variants_only)
with zarr.ZipStore(str(self.path), mode='r') as store:
root = zarr.group(store=store)
self.assertEqual(
root.attrs["provenance"],
provenance.get_provenance_dict(
{"variants_only": variants_only}))
def test_parameters(self):
for params in [{}, {"a": "a"}, {"a": {"a": 1}}]:
d = provenance.get_provenance_dict(params)["parameters"]
self.assertEqual(d, params)
def test_sofware(self):
software = provenance.get_provenance_dict({})["software"]
self.assertEqual(software, {
"name": "tszip",
"version": tszip.__version__
})
def test_libraries(self):
libs = provenance.get_provenance_dict({})["environment"]["libraries"]
self.assertEqual(libs["tskit"]["version"], tskit.__version__)
self.assertEqual(libs["zarr"]["version"], zarr.__version__)
self.assertEqual(libs["numcodecs"]["version"], numcodecs.__version__)
def test_schema_validates(self):
for params in [{}, {"a": "a"}, {"a": {"a": 1}}]:
d = provenance.get_provenance_dict(params)
tskit.validate_provenance(d)