def _assert_baseline_dataframe(result, force_update=False):
with tempfile.NamedTemporaryFile(mode="w", delete=False) as fp:
result.to_csv(fp.name, index=False)
fp.flush()
baseline_filename = create_baseline(fp.name, force_update=force_update)
pd.testing.assert_frame_equal(
result, pd.read_csv(baseline_filename, dtype=np.RESULT_DTYPES))
def _assert_baseline(result, force_update=False):
with tempfile.NamedTemporaryFile(mode="w", delete=False) as fp:
json.dump(result, fp, indent=4)
baseline_filename = create_baseline(fp.name, force_update=force_update)
with open(baseline_filename) as fp:
assert result == pytest.approx(json.load(fp))
def test_run_seeded(base_data_dir):
try:
sampleUseOfModel.main(["-c", str(base_data_dir / "config.yaml")])
test_data = base_data_dir / "output" / "simple_network_sim" / "outbreak-timeseries" / "data.csv"
baseline = create_baseline(test_data)
test_df = pd.read_csv(test_data)
baseline_df = pd.read_csv(baseline)
pd.testing.assert_frame_equal(
test_df.set_index(["time", "node", "age", "state"]),
baseline_df.set_index(["time", "node", "age", "state"]),
check_like=True,
)
finally:
# TODO; remove this once https://github.com/ScottishCovidResponse/data_pipeline_api/issues/12 is done
(base_data_dir / "access.log").unlink()
def test_stochastic_cli_run(base_data_dir):
try:
sampleUseOfModel.main(["-c", str(base_data_dir / "config_stochastic.yaml")])
h5_file = base_data_dir / "output" / "simple_network_sim" / "outbreak-timeseries" / "data.h5"
csv_file = base_data_dir / "output" / "simple_network_sim" / "outbreak-timeseries" / "data.csv"
hdf5_to_csv.main([str(h5_file), str(csv_file)])
baseline = create_baseline(csv_file)
test_df = pd.read_csv(csv_file)
baseline_df = pd.read_csv(baseline)
pd.testing.assert_frame_equal(
test_df.set_index(["date", "node", "age", "state"]),
baseline_df.set_index(["date", "node", "age", "state"]),
check_like=True,
)
finally:
# TODO; remove this once https://github.com/ScottishCovidResponse/data_pipeline_api/issues/12 is done
(base_data_dir / "access.log").unlink()
h5_file.unlink()
csv_file.unlink()