Fix: Better first_point fix #610
GitHub Actions / JUnit Test Report
failed
Dec 5, 2023 in 0s
221 tests run, 188 passed, 0 skipped, 33 failed.
Annotations
Check failure on line 79 in tests/test_algo.py
github-actions / JUnit Test Report
test_algo.test_TMDApicalAlgo
AssertionError:
Arrays are not almost equal to 6 decimals
Mismatched elements: 3 / 3 (100%)
Max absolute difference: 0.37386951
Max relative difference: 1.83737032
x: array([0.57735, 0.57735, 0.57735])
y: array([0.203481, 0.541099, 0.81597 ])
Raw output
def test_TMDApicalAlgo():
algo, grower = _setup_test(TMDApicalAlgo, SectionGrowerPath)
stop, num_sec = algo.initialize()
expected_stop = {"TMD": TMDStop(bif_id=1, bif=9.7747, term_id=0, term=159.798, ref=0.0)}
assert stop == expected_stop
assert_equal(num_sec, 10)
grower.id = 1
s1, s2 = algo.bifurcate(grower)
assert_equal(algo.apical_section, 1)
_assert_dict_or_array(
s1,
{
"direction": [0.57735, 0.57735, 0.57735],
"process": "major",
"first_point": [1.1, 0.0, 0.0],
"stop": {"TMD": TMDStop(bif_id=2, bif=18.5246, term_id=0, term=159.798, ref=0.0)},
},
)
> _assert_dict_or_array(
s2,
{
"direction": np.array([0.20348076, 0.54109933, 0.81597003]),
"process": "secondary",
"first_point": [1.1, 0.0, 0.0],
"stop": {"TMD": TMDStop(bif_id=2, bif=18.5246, term_id=1, term=124.8796, ref=0.0)},
},
)
tests/test_algo.py:250:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_algo.py:79: in _assert_dict_or_array
assert_array_almost_equal(dict1[key], dict2[key])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f70ef0311c0>, array([0.57735027, 0.57735027, 0.57735027]), array([0.20348076, 0.54109933, 0.81597003]))
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 6 decimals', 'precision': 6, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E Mismatched elements: 3 / 3 (100%)
E Max absolute difference: 0.37386951
E Max relative difference: 1.83737032
E x: array([0.57735, 0.57735, 0.57735])
E y: array([0.203481, 0.541099, 0.81597 ])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
Check failure on line 79 in tests/test_algo.py
github-actions / JUnit Test Report
test_algo.test_TMDGradientAlgo
AssertionError:
Arrays are not almost equal to 6 decimals
Mismatched elements: 3 / 3 (100%)
Max absolute difference: 0.17689627
Max relative difference: 0.4417393
x: array([0.57735, 0.57735, 0.57735])
y: array([0.400454, 0.573604, 0.714573])
Raw output
def test_TMDGradientAlgo():
algo, grower = _setup_test(TMDGradientAlgo, SectionGrowerPath)
stop, num_sec = algo.initialize()
expected_stop = {"TMD": TMDStop(bif_id=1, bif=9.7747, term_id=0, term=159.798, ref=0.0)}
assert stop == expected_stop
assert_equal(num_sec, 10)
s1, s2 = algo.bifurcate(grower)
_assert_dict_or_array(
s1,
{
"direction": [0.57735, 0.57735, 0.57735],
"process": "major",
"first_point": [1.1, 0.0, 0.0],
"stop": {"TMD": TMDStop(bif_id=2, bif=18.5246, term_id=0, term=159.798, ref=0.0)},
},
)
> _assert_dict_or_array(
s2,
{
"direction": np.array([0.400454, 0.573604, 0.714573]),
"process": "major",
"first_point": [1.1, 0.0, 0.0],
"stop": {"TMD": TMDStop(bif_id=2, bif=18.5246, term_id=1, term=124.8796, ref=0.0)},
},
)
tests/test_algo.py:304:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_algo.py:79: in _assert_dict_or_array
assert_array_almost_equal(dict1[key], dict2[key])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f70eeee4b80>, array([0.57735027, 0.57735027, 0.57735027]), array([0.400454, 0.573604, 0.714573]))
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 6 decimals', 'precision': 6, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E Mismatched elements: 3 / 3 (100%)
E Max absolute difference: 0.17689627
E Max relative difference: 0.4417393
E x: array([0.57735, 0.57735, 0.57735])
E y: array([0.400454, 0.573604, 0.714573])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
Check failure on line 297 in tests/test_neuron_functional.py
github-actions / JUnit Test Report
test_neuron_functional.test_breaker_of_tmd_algo
AssertionError:
Arrays are not almost equal to 5 decimals
Mismatched elements: 3 / 3 (100%)
Max absolute difference: 91.49147879
Max relative difference: 2.17589941
x: array([-118.23524, 133.53914, -8.61812], dtype=float32)
y: array([-170.45485, 42.04766, -26.37539])
Raw output
def test_breaker_of_tmd_algo():
"""Test example that could break tmd_algo. Test should fail if problem occurs.
Otherwise, this grower should run smoothly.
"""
distributions, params = _load_inputs(
join(_path, "bio_distr_breaker.json"), join(_path, "bio_params_breaker.json")
)
np.random.seed(3367155)
N = NeuronGrower(input_distributions=distributions, input_parameters=params)
n = N.grow()
assert_array_equal(N.apical_sections, [10])
> assert_array_almost_equal(
n.sections[118].points[-1],
np.array([-170.45485, 42.04766, -26.375393]),
decimal=5,
)
tests/test_neuron_functional.py:297:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f70eeef4860>, array([-118.235245, 133.53914 , -8.618125], dtype=float32), array([-170.45485 , 42.04766 , -26.375393]))
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 5 decimals', 'precision': 5, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 5 decimals
E
E Mismatched elements: 3 / 3 (100%)
E Max absolute difference: 91.49147879
E Max relative difference: 2.17589941
E x: array([-118.23524, 133.53914, -8.61812], dtype=float32)
E y: array([-170.45485, 42.04766, -26.37539])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
Check failure on line 26 in tests/test_morphmath_bifurcation.py
github-actions / JUnit Test Report
test_morphmath_bifurcation.test_get_bif_directional
AssertionError:
Arrays are not almost equal to 6 decimals
Mismatched elements: 2 / 6 (33.3%)
Max absolute difference: 1.
Max relative difference: 1.
x: array([[0., 1., 0.],
[0., 1., 0.]])
y: array([[0., 1., 0.],
[0., 0., 1.]])Raw output
def test_get_bif_directional():
> assert_array_almost_equal(
_bf.directional([0.0, 1.0, 0.0], [0.0, 0.0, 0.0, np.pi / 2]),
(np.array([0.0, 1.0, 0.0]), np.array([0.0, 0.0, 1.0])),
)
tests/test_morphmath_bifurcation.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f4a92c0d080>, (array([0., 1., 0.]), array([0., 1., 0.])), (array([0., 1., 0.]), array([0., 0., 1.])))
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 6 decimals', 'precision': 6, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E Mismatched elements: 2 / 6 (33.3%)
E Max absolute difference: 1.
E Max relative difference: 1.
E x: array([[0., 1., 0.],
E [0., 1., 0.]])
E y: array([[0., 1., 0.],
E [0., 0., 1.]])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
Check failure on line 48 in tests/test_morphmath_bifurcation.py
github-actions / JUnit Test Report
test_morphmath_bifurcation.test_get_bif_bio_oriented
AssertionError:
Arrays are not almost equal to 6 decimals
Mismatched elements: 2 / 6 (33.3%)
Max absolute difference: 0.70710678
Max relative difference: 1.
x: array([[0., 1., 0.],
[0., 1., 0.]])
y: array([[0. , 1. , 0. ],
[0. , 0.707107, 0.707107]])Raw output
def test_get_bif_bio_oriented():
> assert_array_almost_equal(
_bf.bio_oriented([0.0, 1.0, 0.0], [0.0, 0.0, 0.0, np.pi / 4]),
(
np.array([0.0, 1.0, 0.0]),
np.array([0.0, 1.0 / np.sqrt(2), 1.0 / np.sqrt(2)]),
),
)
tests/test_morphmath_bifurcation.py:48:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f4a90ae8e00>, (array([0., 1., 0.]), array([0., 1., 0.])), (array([0., 1., 0.]), array([0. , 0.70710678, 0.70710678])))
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 6 decimals', 'precision': 6, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E Mismatched elements: 2 / 6 (33.3%)
E Max absolute difference: 0.70710678
E Max relative difference: 1.
E x: array([[0., 1., 0.],
E [0., 1., 0.]])
E y: array([[0. , 1. , 0. ],
E [0. , 0.707107, 0.707107]])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
Check failure on line 62 in tests/test_morphmath_bifurcation.py
github-actions / JUnit Test Report
test_morphmath_bifurcation.test_get_bif_symmetric
AssertionError:
Arrays are not almost equal to 6 decimals
Mismatched elements: 4 / 6 (66.7%)
Max absolute difference: 0.479426
Max relative difference: 1.
x: array([[0., 0., 1.],
[0., 0., 1.]])
y: array([[ 0. , -0.479426, 0.877583],
[ 0. , 0.479426, 0.877583]])Raw output
def test_get_bif_symmetric():
> assert_array_almost_equal(
_bf.symmetric([0, 0, 1], [1, 1, 1, 1]),
[[0.0, -0.479426, 0.877583], [0.0, 0.479426, 0.877583]],
)
tests/test_morphmath_bifurcation.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7f4a90ae94e0>, (array([0., 0., 1.]), array([0., 0., 1.])), [[0.0, -0.479426, 0.877583], [0.0, 0.479426, 0.877583]])
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 6 decimals', 'precision': 6, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E Mismatched elements: 4 / 6 (66.7%)
E Max absolute difference: 0.479426
E Max relative difference: 1.
E x: array([[0., 0., 1.],
E [0., 0., 1.]])
E y: array([[ 0. , -0.479426, 0.877583],
E [ 0. , 0.479426, 0.877583]])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
Check failure on line 1 in TestBioRatL5Tpc1
github-actions / JUnit Test Report
TestBioRatL5Tpc1.test_skip_rng_and_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a92b76b10>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f4a92b76b10> = diff('/tmp/tmpolpash9itest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params1.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc1 object at 0x7f4a92ce2610>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_skip_rng_and_preprocessin0')
def test_skip_rng_and_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params1_orientation_manager.json",
"expected_bio_rat_L5_TPC_B_with_params1.h5",
"expected_bio_rat_L5_TPC_B_with_params1_persistence_diagram.json",
skip_preprocessing=True,
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:607:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params1_orientation_manager.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params1.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params1_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F4A908FBA40, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_skip_rng_and_preprocessin0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a92b76b10>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f4a92b76b10> = diff('/tmp/tmpolpash9itest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params1.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestPathGrower
github-actions / JUnit Test Report
TestPathGrower.test_skip_rng_and_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55dbd35310>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55dbd35310> = diff('/tmp/tmpa5q3ezo7test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestPathGrower object at 0x7f55dba3c910>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_rng_and_preprocessin0')
def test_skip_rng_and_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_path_params_orientation_manager.json",
"path_grower.h5",
"bio_path_persistence_diagram.json",
skip_preprocessing=True,
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:491:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_path_params_orientation_manager.json'
ref_cell = 'path_grower.h5'
ref_persistence_diagram = 'bio_path_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F55DB8B7D40, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_rng_and_preprocessin0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55dbd35310>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55dbd35310> = diff('/tmp/tmpa5q3ezo7test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestPathGrower
github-actions / JUnit Test Report
TestPathGrower.test_default
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eeeb5390>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f70eeeb5390> = diff('/tmp/tmp880epgfutest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestPathGrower object at 0x7f70ef157010>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_default0')
def test_default(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_path_params.json",
"path_grower.h5",
"bio_path_persistence_diagram.json",
output_dir=tmpdir,
)
tests/test_neuron_functional.py:459:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_path_params.json', ref_cell = 'path_grower.h5'
ref_persistence_diagram = 'bio_path_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_default0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eeeb5390>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f70eeeb5390> = diff('/tmp/tmp880epgfutest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestPathGrower
github-actions / JUnit Test Report
TestPathGrower.test_with_rng
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c850>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c850> = diff('/tmp/tmpincz5kh_test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestPathGrower object at 0x7f70ef1576d0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_with_rng0')
def test_with_rng(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_path_params.json",
"path_grower.h5",
"bio_path_persistence_diagram.json",
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:469:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_path_params.json', ref_cell = 'path_grower.h5'
ref_persistence_diagram = 'bio_path_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F70ECE10640, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_with_rng0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c850>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c850> = diff('/tmp/tmpincz5kh_test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestGradientPathGrower
github-actions / JUnit Test Report
TestGradientPathGrower.test_default
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db7bb990>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55db7bb990> = diff('/tmp/tmpft_vpu2ytest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestGradientPathGrower object at 0x7f55dba3c8d0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_default0')
def test_default(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_gradient_path_params.json",
"gradient_path_grower.h5",
"gradient_path_persistence_diagram.json",
output_dir=tmpdir,
)
tests/test_neuron_functional.py:529:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_gradient_path_params.json'
ref_cell = 'gradient_path_grower.h5'
ref_persistence_diagram = 'gradient_path_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_default0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db7bb990>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55db7bb990> = diff('/tmp/tmpft_vpu2ytest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc2
github-actions / JUnit Test Report
TestBioRatL5Tpc2.test_default
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a92c1ce90>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f4a92c1ce90> = diff('/tmp/tmpf3hbeykstest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc2 object at 0x7f4a92ce2a10>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_default0')
def test_default(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params2.json",
"expected_bio_rat_L5_TPC_B_with_params2.h5",
"expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json",
output_dir=tmpdir,
)
tests/test_neuron_functional.py:621:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params2.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params2.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_default0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a92c1ce90>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f4a92c1ce90> = diff('/tmp/tmpf3hbeykstest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestPathGrower
github-actions / JUnit Test Report
TestPathGrower.test_skip_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eccb4210>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f70eccb4210> = diff('/tmp/tmpddd6l8ldtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestPathGrower object at 0x7f70ef157d90>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_skip_preprocessing0')
def test_skip_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_path_params_orientation_manager.json",
"path_grower.h5",
"bio_path_persistence_diagram.json",
skip_preprocessing=True,
output_dir=tmpdir,
)
tests/test_neuron_functional.py:480:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_path_params_orientation_manager.json'
ref_cell = 'path_grower.h5'
ref_persistence_diagram = 'bio_path_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_skip_preprocessing0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eccb4210>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f70eccb4210> = diff('/tmp/tmpddd6l8ldtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestGradientPathGrower
github-actions / JUnit Test Report
TestGradientPathGrower.test_with_rng
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db7ab2d0>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55db7ab2d0> = diff('/tmp/tmprzsp0cn7test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestGradientPathGrower object at 0x7f55db901390>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_with_rng0')
def test_with_rng(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_gradient_path_params.json",
"gradient_path_grower.h5",
"gradient_path_persistence_diagram.json",
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:539:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_gradient_path_params.json'
ref_cell = 'gradient_path_grower.h5'
ref_persistence_diagram = 'gradient_path_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F55DB84BE40, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_with_rng0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db7ab2d0>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55db7ab2d0> = diff('/tmp/tmprzsp0cn7test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc4
github-actions / JUnit Test Report
TestBioRatL5Tpc4.test_default
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70ecc9f5d0>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f70ecc9f5d0> = diff('/tmp/tmpyxmiftintest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params4.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc4 object at 0x7f70ef16e650>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_default1')
def test_default(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params4.json",
"expected_bio_rat_L5_TPC_B_with_params4.h5",
"expected_bio_rat_L5_TPC_B_with_params4_persistence_diagram.json",
output_dir=tmpdir,
)
tests/test_neuron_functional.py:713:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params4.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params4.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params4_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_default1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70ecc9f5d0>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f70ecc9f5d0> = diff('/tmp/tmpyxmiftintest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params4.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestGradientPathGrower
github-actions / JUnit Test Report
TestGradientPathGrower.test_skip_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db9aa110>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55db9aa110> = diff('/tmp/tmprzwa_ocbtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestGradientPathGrower object at 0x7f55db94f650>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_preprocessing0')
def test_skip_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_gradient_path_params_orientation_manager.json",
"gradient_path_grower.h5",
"gradient_path_persistence_diagram.json",
skip_preprocessing=True,
output_dir=tmpdir,
)
tests/test_neuron_functional.py:550:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_gradient_path_params_orientation_manager.json'
ref_cell = 'gradient_path_grower.h5'
ref_persistence_diagram = 'gradient_path_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_preprocessing0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db9aa110>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55db9aa110> = diff('/tmp/tmprzwa_ocbtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc2
github-actions / JUnit Test Report
TestBioRatL5Tpc2.test_with_rng
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a9084bf10>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f4a9084bf10> = diff('/tmp/tmplll0498xtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc2 object at 0x7f4a92ce30d0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_with_rng0')
def test_with_rng(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params2.json",
"expected_bio_rat_L5_TPC_B_with_params2.h5",
"expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json",
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:631:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params2.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params2.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F4A92BF8640, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_with_rng0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a9084bf10>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f4a9084bf10> = diff('/tmp/tmplll0498xtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestGradientPathGrower
github-actions / JUnit Test Report
TestGradientPathGrower.test_skip_rng_and_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55d7497dd0>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55d7497dd0> = diff('/tmp/tmplwnxy2gvtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')Raw output
self = <tests.test_neuron_functional.TestGradientPathGrower object at 0x7f55dba537d0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_rng_and_preprocessin1')
def test_skip_rng_and_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_distribution.json",
"bio_gradient_path_params_orientation_manager.json",
"gradient_path_grower.h5",
"gradient_path_persistence_diagram.json",
skip_preprocessing=True,
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:561:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],...665, 0.02188742478139427], [265.46654445080054, 0, nan, nan, nan, nan]]], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'bio_gradient_path_params_orientation_manager.json'
ref_cell = 'gradient_path_grower.h5'
ref_persistence_diagram = 'gradient_path_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F55DB84B640, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_rng_and_preprocessin1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55d7497dd0>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55d7497dd0> = diff('/tmp/tmplwnxy2gvtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/gradient_path_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'gradient_path_grower.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc4
github-actions / JUnit Test Report
TestBioRatL5Tpc4.test_with_rng
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70ec8f5390>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f70ec8f5390> = diff('/tmp/tmpcvaix3ritest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params4.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc4 object at 0x7f70ef16ed10>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_with_rng1')
def test_with_rng(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params4.json",
"expected_bio_rat_L5_TPC_B_with_params4.h5",
"expected_bio_rat_L5_TPC_B_with_params4_persistence_diagram.json",
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:723:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params4.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params4.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params4_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F70ECE11240, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_with_rng1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70ec8f5390>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f70ec8f5390> = diff('/tmp/tmpcvaix3ritest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params4.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc1
github-actions / JUnit Test Report
TestBioRatL5Tpc1.test_default
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db824d90>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55db824d90> = diff('/tmp/tmpwfj3pd32test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params1.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc1 object at 0x7f55dba53dd0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_default1')
def test_default(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params1.json",
"expected_bio_rat_L5_TPC_B_with_params1.h5",
"expected_bio_rat_L5_TPC_B_with_params1_persistence_diagram.json",
output_dir=tmpdir,
)
tests/test_neuron_functional.py:575:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params1.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params1.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params1_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_default1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55db824d90>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55db824d90> = diff('/tmp/tmpwfj3pd32test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params1.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc2
github-actions / JUnit Test Report
TestBioRatL5Tpc2.test_skip_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a902e4e90>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f4a902e4e90> = diff('/tmp/tmpjstpo84htest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc2 object at 0x7f4a92ce3790>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_skip_preprocessing0')
def test_skip_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params2_orientation_manager.json",
"expected_bio_rat_L5_TPC_B_with_params2.h5",
"expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json",
skip_preprocessing=True,
output_dir=tmpdir,
)
tests/test_neuron_functional.py:642:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params2_orientation_manager.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params2.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_skip_preprocessing0')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a902e4e90>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f4a902e4e90> = diff('/tmp/tmpjstpo84htest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc4
github-actions / JUnit Test Report
TestBioRatL5Tpc4.test_skip_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c210>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c210> = diff('/tmp/tmpnshpyy31test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params4.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc4 object at 0x7f70ef16f3d0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_skip_preprocessing1')
def test_skip_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params4_orientation_manager.json",
"expected_bio_rat_L5_TPC_B_with_params4.h5",
"expected_bio_rat_L5_TPC_B_with_params4_persistence_diagram.json",
skip_preprocessing=True,
output_dir=tmpdir,
)
tests/test_neuron_functional.py:734:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params4_orientation_manager.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params4.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params4_persistence_diagram.json'
rng_or_seed = None, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_skip_preprocessing1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c210>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f70eef5c210> = diff('/tmp/tmpnshpyy31test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params4.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params4.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc1
github-actions / JUnit Test Report
TestBioRatL5Tpc1.test_with_rng
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55d7496dd0>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f55d7496dd0> = diff('/tmp/tmp5s2blio8test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params1.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc1 object at 0x7f55dba535d0>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_with_rng1')
def test_with_rng(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params1.json",
"expected_bio_rat_L5_TPC_B_with_params1.h5",
"expected_bio_rat_L5_TPC_B_with_params1_persistence_diagram.json",
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:585:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params1.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params1.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params1_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F55D74F9240, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_with_rng1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f55d7496dd0>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f55d7496dd0> = diff('/tmp/tmp5s2blio8test_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params1.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params1.h5')
tests/test_neuron_functional.py:132: AssertionError
Check failure on line 1 in TestBioRatL5Tpc2
github-actions / JUnit Test Report
TestBioRatL5Tpc2.test_skip_rng_and_preprocessing
AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a90a27910>
+ where <morph_tool.morphio_diff.DiffResult object at 0x7f4a90a27910> = diff('/tmp/tmpljy3s0sotest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
+ where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')Raw output
self = <tests.test_neuron_functional.TestBioRatL5Tpc2 object at 0x7f4a92ce3e90>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_skip_rng_and_preprocessin1')
def test_skip_rng_and_preprocessing(self, tmpdir):
> _test_full(
"path_distances",
"bio_rat_L5_TPC_B_distribution.json",
"params2_orientation_manager.json",
"expected_bio_rat_L5_TPC_B_with_params2.h5",
"expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json",
skip_preprocessing=True,
rng_or_seed=build_random_generator(0),
output_dir=tmpdir,
)
tests/test_neuron_functional.py:653:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = 'path_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'path_distances', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1],....4106653615432989, 0.5277795547616266, -0.18579814237229897], ...], ...], ...}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'params2_orientation_manager.json'
ref_cell = 'expected_bio_rat_L5_TPC_B_with_params2.h5'
ref_persistence_diagram = 'expected_bio_rat_L5_TPC_B_with_params2_persistence_diagram.json'
rng_or_seed = RandomState(MT19937) at 0x7F4A92BFB140, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw1/test_skip_rng_and_preprocessin1')
def _test_full(
feature,
distributions,
parameters,
ref_cell,
ref_persistence_diagram,
rng_or_seed=None,
skip_preprocessing=False,
output_dir=None,
):
distributions, params = _load_inputs(join(_path, distributions), join(_path, parameters))
if rng_or_seed is None:
np.random.seed(0)
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
skip_preprocessing=skip_preprocessing,
).grow()
else:
n = NeuronGrower(
input_distributions=distributions,
input_parameters=params,
rng_or_seed=rng_or_seed,
skip_preprocessing=skip_preprocessing,
).grow()
with TemporaryDirectory("test_grower") as folder:
out_neuron = join(folder, "test_output_neuron_.h5")
n.write(out_neuron)
# For checking purposes, we can output the cells as swc
if output_dir is not None:
if not os.path.exists(output_dir):
os.mkdir(output_dir)
n.write(join(output_dir, basename(ref_cell)))
if ref_persistence_diagram is not None:
# Load with TMD and extract radial persistence
n0 = tmd.io.load_neuron(out_neuron)
actual_persistence_diagram = tmd.methods.get_persistence_diagram(
n0.apical_dendrite[0], feature=feature
)
if output_dir is not None:
with open(
join(output_dir, basename(ref_persistence_diagram)), "w", encoding="utf-8"
) as f:
json.dump(actual_persistence_diagram, f, sort_keys=True, indent=2)
with open(join(_path, ref_persistence_diagram), encoding="utf-8") as f:
expected_persistence_diagram = json.load(f)
assert_close_persistent_diagram(
actual_persistence_diagram, expected_persistence_diagram
)
> assert not diff(out_neuron, join(_path, ref_cell))
E AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f4a90a27910>
E + where <morph_tool.morphio_diff.DiffResult object at 0x7f4a90a27910> = diff('/tmp/tmpljy3s0sotest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5')
E + where '/home/runner/work/NeuroTS/NeuroTS/tests/data/expected_bio_rat_L5_TPC_B_with_params2.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'expected_bio_rat_L5_TPC_B_with_params2.h5')
tests/test_neuron_functional.py:132: AssertionError
github-actions / JUnit Test Report
test_rotation.test_rotate_vector
AssertionError:
Arrays are not almost equal to 6 decimals
Mismatched elements: 3 / 3 (100%)
Max absolute difference: 0.706011
Max relative difference: 2.40148781
x: array([1., 1., 1.])
y: array([0.293989, 1.240039, 1.172976])
Raw output
def test_rotate_vector():
> assert_array_almost_equal(
test_module.rotate_vector([1, 1, 1], [2, 3, 4], 2),
[0.293989, 1.240039, 1.172976],
)
tests/test_rotation.py:32:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: in inner
return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_array_almost_equal.<locals>.compare at 0x7fa89c27e160>, array([1., 1., 1.]), [0.293989, 1.240039, 1.172976])
kwds = {'err_msg': '', 'header': 'Arrays are not almost equal to 6 decimals', 'precision': 6, 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
> return func(*args, **kwds)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E Mismatched elements: 3 / 3 (100%)
E Max absolute difference: 0.706011
E Max relative difference: 2.40148781
E x: array([1., 1., 1.])
E y: array([0.293989, 1.240039, 1.172976])
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError
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