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Feat: Add boundary context #52

Feat: Add boundary context

Feat: Add boundary context #52

GitHub Actions / JUnit Test Report 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

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@github-actions 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