Feat: Add boundary context #52
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failed
Dec 11, 2024 in 0s
86 tests run, 85 passed, 0 skipped, 1 failed.
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Check failure on line 123 in tests/test_synthesize_morphologies.py
github-actions / JUnit Test Report
test_synthesize_morphologies.test_synthesize_no_thicknesses
ValueError: region_structure file not found at /home/runner/work/region-grower/region-grower/tests/data/region_structure_no_thicknesses.yaml.
Raw output
tmpdir = local('/home/runner/work/region-grower/region-grower/.tox/min_versions/tmp/test_synthesize_no_thicknesses0')
small_O1_path = '/home/runner/work/region-grower/region-grower/.tox/min_versions/tmp/atlas_small_O10'
input_cells = local('/home/runner/work/region-grower/region-grower/.tox/min_versions/tmp/test_synthesize_no_thicknesses0/input_cells.mvd3')
axon_morph_tsv = local('/home/runner/work/region-grower/region-grower/.tox/min_versions/tmp/test_synthesize_no_thicknesses0/axon_morphs.tsv')
def test_synthesize_no_thicknesses(
tmpdir,
small_O1_path,
input_cells,
axon_morph_tsv,
): # pylint: disable=unused-argument
"""Test morphology synthesis."""
tmp_folder = Path(tmpdir)
args = create_args(
False,
tmp_folder,
input_cells,
small_O1_path,
None,
None,
800,
DATA / "region_structure_no_thicknesses.yaml",
)
> synthesizer = SynthesizeMorphologies(**args)
tests/test_synthesize_morphologies.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
region_grower/synthesize_morphologies.py:322: in __init__
self.atlas = AtlasHelper(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <region_grower.atlas_helper.AtlasHelper object at 0x7f12db4857c0>
atlas = <voxcell.nexus.voxelbrain.LocalAtlas object at 0x7f12db485250>
region_structure_path = PosixPath('/home/runner/work/region-grower/region-grower/tests/data/region_structure_no_thicknesses.yaml')
def __init__(self, atlas: Atlas, region_structure_path: str):
"""The AtlasHelper constructor.
Args:
atlas: the atlas
region_structure_path: path to region structure yaml file
"""
self.atlas = atlas
if region_structure_path is not None and Path(region_structure_path).exists():
with open(region_structure_path, "r", encoding="utf-8") as region_file:
self.region_structure = yaml.safe_load(region_file)
self.region_structure_base_path = Path(region_structure_path).parent
else:
> raise ValueError(f"region_structure file not found at {region_structure_path}.")
E ValueError: region_structure file not found at /home/runner/work/region-grower/region-grower/tests/data/region_structure_no_thicknesses.yaml.
region_grower/atlas_helper.py:47: ValueError
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