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Fix: Better first_point fix #604

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Fix: Better first_point fix

Fix: Better first_point fix #604

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

See this annotation in the file changed.

@github-actions 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: 0.57735
Max relative difference: 1.
 x: array([0, 1, 0])
 y: array([0.57735, 0.57735, 0.57735])
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)},
            },
        )

tests/test_algo.py:240: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
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 0x7f635b9c14e0>, array([0, 1, 0]), [0.57735, 0.57735, 0.57735])
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: 0.57735
E           Max relative difference: 1.
E            x: array([0, 1, 0])
E            y: array([0.57735, 0.57735, 0.57735])

/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError

Check failure on line 79 in tests/test_algo.py

See this annotation in the file changed.

@github-actions 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: 0.57735
Max relative difference: 1.
 x: array([0, 1, 0])
 y: array([0.57735, 0.57735, 0.57735])
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)},
            },
        )

tests/test_algo.py:294: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
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 0x7f635b890b80>, array([0, 1, 0]), [0.57735, 0.57735, 0.57735])
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: 0.57735
E           Max relative difference: 1.
E            x: array([0, 1, 0])
E            y: array([0.57735, 0.57735, 0.57735])

/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

See this annotation in the file changed.

@github-actions 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: 165.69951562
Max relative difference: 3.15924248
 x: array([ -4.75533, 174.88641,  -9.35779], 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 0x7f635b893ba0>, array([ -4.7553344, 174.88641  ,  -9.357793 ], 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: 165.69951562
E           Max relative difference: 3.15924248
E            x: array([ -4.75533, 174.88641,  -9.35779], 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

See this annotation in the file changed.

@github-actions 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 0x7fe39737c680>, (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 1 in TestBioRatL5Tpc1

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc1.test_skip_rng_and_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7fe3973ba2d0>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe3973ba2d0> = diff('/tmp/tmpw441ojcatest_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 0x7fe3975d3a90>
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 0x7FE397319740, 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 0x7fe3973ba2d0>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe3973ba2d0> = diff('/tmp/tmpw441ojcatest_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 132 in tests/test_neuron_functional.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_neuron_functional.test_axon_grower 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635ba07e50>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635ba07e50> = diff('/tmp/tmpvfzpgvbatest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_axon_grower_absolute.h5')
 +    where '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_axon_grower_absolute.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'test_axon_grower_absolute.h5')
Raw output 
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_axon_grower0')

    def test_axon_grower(tmpdir):
        """Test axon grower, which should only grow trunks with 1 section to allow later axon grafting.
    
        The num_seg value in the parameters is set to 999 but only 1 segment should be synthesized.
        """
    
        _test_full(
            "radial_distances",
            "axon_trunk_distribution.json",
            "axon_trunk_parameters.json",
            "test_axon_grower.h5",
            None,
            output_dir=tmpdir / "default",
        )
        _test_full(
            "radial_distances",
            "axon_trunk_distribution.json",
            "axon_trunk_parameters.json",
            "test_axon_grower.h5",
            None,
            rng_or_seed=build_random_generator(0),
            output_dir=tmpdir / "rng",
        )
        _test_full(
            "radial_distances",
            "axon_trunk_distribution.json",
            "axon_trunk_parameters_orientation_manager.json",
            "test_axon_grower.h5",
            None,
            skip_preprocessing=True,
            output_dir=tmpdir / "skip_preprocessing",
        )
        _test_full(
            "radial_distances",
            "axon_trunk_distribution.json",
            "axon_trunk_parameters_orientation_manager.json",
            "test_axon_grower.h5",
            None,
            rng_or_seed=build_random_generator(0),
            skip_preprocessing=True,
            output_dir=tmpdir / "rng_and_skip_preprocessing",
        )
    
>       _test_full(
            "radial_distances",
            "axon_trunk_distribution.json",
            "axon_trunk_parameters_absolute.json",
            "test_axon_grower_absolute.h5",
            None,
            output_dir=tmpdir / "default_absolute",
        )

tests/test_neuron_functional.py:366: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

feature = 'radial_distances'
distributions = {'apical_dendrite': {}, 'axon': {'num_trees': {'data': {'bins': [1], 'weights': [1]}}, 'trunk': {'absolute_elevation_d...292436, 1.566630375543904, 2.9393430149240416], 'weights': [4, 3, 1, 1, 2]}}}}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'axon_trunk_parameters_absolute.json'
ref_cell = 'test_axon_grower_absolute.h5', ref_persistence_diagram = None
rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_axon_grower0/default_absolute')

    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 0x7f635ba07e50>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635ba07e50> = diff('/tmp/tmpvfzpgvbatest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_axon_grower_absolute.h5')
E            +    where '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_axon_grower_absolute.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'test_axon_grower_absolute.h5')

tests/test_neuron_functional.py:132: AssertionError

Check failure on line 1 in TestPathGrower

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestPathGrower.test_skip_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed5ab50>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed5ab50> = diff('/tmp/tmpi4yrdg_vtest_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 0x7f1e1efab450>
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_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-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 0x7f1e1ed5ab50>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed5ab50> = diff('/tmp/tmpi4yrdg_vtest_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 132 in tests/test_neuron_functional.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_neuron_functional.test_basic_grower 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635b979ad0>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b979ad0> = diff('/tmp/tmpc2lqb78mtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_trunk_grower.h5')
 +    where '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_trunk_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'test_trunk_grower.h5')
Raw output 
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_basic_grower0')

    def test_basic_grower(tmpdir):
>       _test_full(
            "radial_distances",
            "bio_trunk_distribution.json",
            "trunk_parameters.json",
            "test_trunk_grower.h5",
            None,
            output_dir=tmpdir / "default",
        )

tests/test_neuron_functional.py:405: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

feature = 'radial_distances'
distributions = {'apical_dendrite': {'filtration_metric': 'trunk_length', 'min_bar_length': 1.0, 'num_trees': {'data': {'bins': [1], '...292436, 1.566630375543904, 2.9393430149240416], 'weights': [4, 3, 1, 1, 2]}}}}, 'diameter': {'method': 'uniform'}, ...}
parameters = 'trunk_parameters.json', ref_cell = 'test_trunk_grower.h5'
ref_persistence_diagram = None, rng_or_seed = None, skip_preprocessing = False
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_basic_grower0/default')

    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 0x7f635b979ad0>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b979ad0> = diff('/tmp/tmpc2lqb78mtest_grower/test_output_neuron_.h5', '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_trunk_grower.h5')
E            +    where '/home/runner/work/NeuroTS/NeuroTS/tests/data/test_trunk_grower.h5' = join('/home/runner/work/NeuroTS/NeuroTS/tests/data', 'test_trunk_grower.h5')

tests/test_neuron_functional.py:132: AssertionError

Check failure on line 446 in tests/test_neuron_functional.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_neuron_functional.test_basic_grower_with_generator 

AssertionError: 
Arrays are not almost equal to 6 decimals

Mismatched elements: 12 / 12 (100%)
Max absolute difference: 4.68638051
Max relative difference: 78.82940394
 x: array([[-0.511599,  9.385795,  7.817605],
       [-9.209658,  3.399985,  2.019685],
       [ 8.413467,  3.845892,  4.346673],
       [-1.759138, 12.613012,  0.826259]])
 y: array([[ -0.731235,   7.604229,  11.173798],
       [-13.377433,  -1.286395,   2.933682],
       [ 11.861422,  -0.049414,   6.127999],
       [ -2.380422,  12.54182 ,   1.118073]])
Raw output 
def test_basic_grower_with_generator():
        distributions, params = _load_inputs(
            join(_path, "bio_trunk_distribution.json"),
            join(_path, "trunk_parameters.json"),
        )
        expected_pts = [
            [-0.7312348484992981, 7.604228973388672, 11.173797607421875],
            [-13.377432823181152, -1.2863954305648804, 2.9336819648742676],
            [11.861421585083008, -0.049414388835430145, 6.1279988288879395],
            [-2.3804218769073486, 12.54181957244873, 1.118072748184204],
        ]
    
        rng = np.random.default_rng(0)
        rng_or_seeds = [0, rng]
    
        for rng_or_seed in rng_or_seeds:
            n = NeuronGrower(
                input_distributions=distributions,
                input_parameters=params,
                rng_or_seed=rng_or_seed,
            ).grow()
            assert len(n.root_sections) == 4
>           assert_array_almost_equal(
                [i.points[-1].tolist() for i in n.root_sections],
                expected_pts,
            )

tests/test_neuron_functional.py:446: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/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 0x7f635b925760>, [[-0.5115991234779358, 9.385794639587402, 7....421585083008, -0.049414388835430145, 6.1279988288879395], [-2.3804218769073486, 12.54181957244873, 1.118072748184204]])
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: 12 / 12 (100%)
E           Max absolute difference: 4.68638051
E           Max relative difference: 78.82940394
E            x: array([[-0.511599,  9.385795,  7.817605],
E                  [-9.209658,  3.399985,  2.019685],
E                  [ 8.413467,  3.845892,  4.346673],
E                  [-1.759138, 12.613012,  0.826259]])
E            y: array([[ -0.731235,   7.604229,  11.173798],
E                  [-13.377433,  -1.286395,   2.933682],
E                  [ 11.861422,  -0.049414,   6.127999],
E                  [ -2.380422,  12.54182 ,   1.118073]])

/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/contextlib.py:81: AssertionError

Check failure on line 1 in TestPathGrower

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestPathGrower.test_default 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635ba3c210>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635ba3c210> = diff('/tmp/tmpg9tke98ztest_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 0x7f635bb33450>
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 0x7f635ba3c210>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635ba3c210> = diff('/tmp/tmpg9tke98ztest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestPathGrower.test_with_rng 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635b8f4490>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b8f4490> = diff('/tmp/tmpbgq42d2stest_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 0x7f635bb33ed0>
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 0x7F63577F0640, 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 0x7f635b8f4490>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b8f4490> = diff('/tmp/tmpbgq42d2stest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestPathGrower.test_skip_rng_and_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed60350>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed60350> = diff('/tmp/tmpr951244ftest_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 0x7f1e1efabb50>
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 0x7F1E1ED82C40, 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 0x7f1e1ed60350>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed60350> = diff('/tmp/tmpr951244ftest_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 TestBioRatL5Tpc2

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc2.test_default 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7fe397532d50>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe397532d50> = diff('/tmp/tmpbz7_gilatest_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 0x7fe3975d16d0>
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 0x7fe397532d50>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe397532d50> = diff('/tmp/tmpbz7_gilatest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc4.test_default 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635b861190>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b861190> = diff('/tmp/tmpdlsdqgr4test_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 0x7f635bb1d590>
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 0x7f635b861190>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b861190> = diff('/tmp/tmpdlsdqgr4test_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestGradientPathGrower.test_default 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed1d6d0>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed1d6d0> = diff('/tmp/tmpfk36s7sotest_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 0x7f1e1efb0a50>
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 0x7f1e1ed1d6d0>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed1d6d0> = diff('/tmp/tmpfk36s7sotest_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 TestGradientPathGrower

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestGradientPathGrower.test_with_rng 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed5ba90>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed5ba90> = diff('/tmp/tmp1vosqg7rtest_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 0x7f1e1efb1110>
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 0x7F1E1ED82B40, 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 0x7f1e1ed5ba90>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ed5ba90> = diff('/tmp/tmp1vosqg7rtest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc2.test_with_rng 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7fe3972fdf10>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe3972fdf10> = diff('/tmp/tmpsikis4aotest_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 0x7fe3975d12d0>
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 0x7FE397319040, 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 0x7fe3972fdf10>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe3972fdf10> = diff('/tmp/tmpsikis4aotest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc4.test_with_rng 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635b8c8d10>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b8c8d10> = diff('/tmp/tmpe0mufgtntest_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 0x7f635bb1e810>
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 0x7F635B947540, 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 0x7f635b8c8d10>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b8c8d10> = diff('/tmp/tmpe0mufgtntest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestGradientPathGrower.test_skip_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1efdec10>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1efdec10> = diff('/tmp/tmphb9yqym3test_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 0x7f1e1efb1890>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw3/test_skip_preprocessing1')

    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_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 0x7f1e1efdec10>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1efdec10> = diff('/tmp/tmphb9yqym3test_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 TestGradientPathGrower

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestGradientPathGrower.test_skip_rng_and_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ecef150>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ecef150> = diff('/tmp/tmphsin0llltest_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 0x7f1e1efaa310>
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 0x7F1E1ED32240, 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 0x7f1e1ecef150>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1ecef150> = diff('/tmp/tmphsin0llltest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc2.test_skip_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7fe3950e4650>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe3950e4650> = diff('/tmp/tmpypzhw2smtest_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 0x7fe3975d0090>
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 0x7fe3950e4650>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe3950e4650> = diff('/tmp/tmpypzhw2smtest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc4.test_skip_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635782c550>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635782c550> = diff('/tmp/tmpca6bwgnwtest_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 0x7f635bb1fed0>
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_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_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 0x7f635782c550>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635782c550> = diff('/tmp/tmpca6bwgnwtest_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

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc1.test_default 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f1e1cadfd50>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1cadfd50> = diff('/tmp/tmpjcoht39dtest_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 0x7f1e1efb1850>
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 0x7f1e1cadfd50>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f1e1cadfd50> = diff('/tmp/tmpjcoht39dtest_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 TestBioRatL5Tpc4

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc4.test_skip_rng_and_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7f635b8d4090>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b8d4090> = diff('/tmp/tmpql92idbutest_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 0x7f635b9a4350>
tmpdir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/test_skip_rng_and_preprocessin0')

    def test_skip_rng_and_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,
            rng_or_seed=build_random_generator(0),
            output_dir=tmpdir,
        )

tests/test_neuron_functional.py:745: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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 = RandomState(MT19937) at 0x7F635B945740, skip_preprocessing = True
output_dir = local('/home/runner/work/NeuroTS/NeuroTS/.tox/py311/tmp/popen-gw0/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 0x7f635b8d4090>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7f635b8d4090> = diff('/tmp/tmpql92idbutest_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 TestBioRatL5Tpc2

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

TestBioRatL5Tpc2.test_skip_rng_and_preprocessing 

AssertionError: assert not <morph_tool.morphio_diff.DiffResult object at 0x7fe397383550>
 +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe397383550> = diff('/tmp/tmp3pg6b2ogtest_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 0x7fe3995a9790>
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 0x7FE39731A240, 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 0x7fe397383550>
E            +  where <morph_tool.morphio_diff.DiffResult object at 0x7fe397383550> = diff('/tmp/tmp3pg6b2ogtest_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
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