Feat: Add a nexus access point converter and improve CLI #83
GitHub Actions / JUnit Test Report
failed
Nov 16, 2023 in 0s
20 tests run, 18 passed, 0 skipped, 2 failed.
Annotations
Check failure on line 34 in .tox/py310/lib/python3.10/site-packages/dask/tests/test_cli.py
github-actions / JUnit Test Report
test_cli.test_compute_currents
AssertionError:
Not equal to tolerance rtol=1e-05, atol=0
Mismatched elements: 2 / 2 (100%)
Max absolute difference: 78.24665844
Max relative difference: 1.
x: array([0., 0.])
y: array([-78.246658, -78.047578])
Raw output
cli_runner = <click.testing.CliRunner object at 0x7f789b8bdde0>
tmpdir = local('/home/runner/work/emodel-generalisation/emodel-generalisation/.tox/py310/tmp/test_compute_currents0')
def test_compute_currents(cli_runner, tmpdir):
"""Test cli compute_currents."""
# fmt: off
response = cli_runner.invoke(
tested.cli,
[
"compute_currents",
"--input-path", str(DATA / "sonata_v6.h5"),
"--output-path", str(tmpdir / "sonata_currents.h5"),
"--morphology-path", str(DATA / "morphologies"),
"--protocol-config-path", str(DATA / "protocol_config.yaml"),
"--hoc-path", str(DATA / "hoc"),
"--parallel-lib", None,
# "--debug-csv-path", "debug.csv" # use this to debug
],
)
# fmt: on
assert response.exit_code == 0
df = CellCollection().load_sonata(tmpdir / "sonata_currents.h5").as_dataframe()
> npt.assert_allclose(
df["@dynamics:resting_potential"].to_list(),
[-78.24665843577513, -78.04757822491321],
rtol=1e-5,
)
tests/test_cli.py:34:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_allclose.<locals>.compare at 0x7f789b414430>, array([0., 0.]), array([-78.24665844, -78.04757822]))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-05, atol=0', 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Not equal to tolerance rtol=1e-05, atol=0
E
E Mismatched elements: 2 / 2 (100%)
E Max absolute difference: 78.24665844
E Max relative difference: 1.
E x: array([0., 0.])
E y: array([-78.246658, -78.047578])
/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/contextlib.py:79: AssertionError
Check failure on line 153 in .tox/py310/lib/python3.10/site-packages/dask/tests/test_cli.py
github-actions / JUnit Test Report
test_cli.test_adapt
assert 1.1 == 2.0
Raw output
cli_runner = <click.testing.CliRunner object at 0x7f789b43df00>
tmpdir = local('/home/runner/work/emodel-generalisation/emodel-generalisation/.tox/py310/tmp/test_adapt0')
def test_adapt(cli_runner, tmpdir):
"""Test cli adapt."""
# fmt: off
response = cli_runner.invoke(
tested.cli,
[
"adapt",
"--input-node-path", str(DATA / "sonata_v6.h5"),
"--output-node-path", str(tmpdir / "sonata_v6_adapted.h5"),
"--morphology-path", str(DATA / "morphologies"),
"--config-path", str(DATA / "config"),
"--final-path", str(DATA / "final.json"),
"--local-dir", str(tmpdir / 'local'),
"--output-hoc-path", str(tmpdir / "hoc"),
"--parallel-lib", None,
],
)
# fmt: on
assert response.exit_code == 0
df = pd.read_csv(tmpdir / "local" / "adapt_df.csv")
# df.to_csv(DATA / "adapt_df.csv", index=None)
expected_df = pd.read_csv(DATA / "adapt_df.csv")
> assert df.loc[0, "ais_scaler"] == expected_df.loc[0, "ais_scaler"]
E assert 1.1 == 2.0
tests/test_cli.py:153: AssertionError
Loading