Merge pull request #89 from KamitaniLab/origin/myaokai/fix_preproc #111

TestBdata.test_metadata_add_get_where AssertionError: Arrays are not equal (shapes (0, 18), (10,) mismatch) x: array([], shape=(0, 18), dtype=float64) y: array([0.751006, 0.640369, 0.284991, 0.839797, 0.849895, 0.90571 , 0.562591, 0.149279, 0.45419 , 0.580267])

test (3.9): tests/evals/test_metrics.py#L72

TestMetrics.test_2d FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d.pkl.gz'

test (3.9): tests/evals/test_metrics.py#L88

TestMetrics.test_2d_nan FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d-nan.pkl.gz'

test (3.9): tests/test_mri.py#L23

TestMri.test_add_load_epi_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.9): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.9): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0002 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.9)

Process completed with exit code 1.

Error code: `import-untyped`: bdpy/util/info.py#L13

Library stubs not installed for "yaml"

Error code: `arg-type`: bdpy/util/info.py#L24

Argument 1 to "md5" has incompatible type "str"; expected "Buffer"

Error code: `import-untyped`: bdpy/fig/tile_images.py#L5

Skipping analyzing "matplotlib.pyplot": module is installed, but missing library stubs or py.typed marker

Error code: `import-untyped`: bdpy/fig/tile_images.py#L5

Skipping analyzing "matplotlib": module is installed, but missing library stubs or py.typed marker

Error code: `import-untyped`: bdpy/fig/tile_images.py#L6

Skipping analyzing "matplotlib.gridspec": module is installed, but missing library stubs or py.typed marker

Error code: `var-annotated`: bdpy/util/utils.py#L48

Need type annotation for "group_vector" (hint: "group_vector: List[<type>] = ...")

Error code: `assignment`: bdpy/util/utils.py#L64

Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "List[Any]")

Error code: `union-attr`: bdpy/util/utils.py#L118

Item "List[Any]" of "Union[List[Any], ndarray[Any, Any]]" has no attribute "ndim"

Error code: `call-overload`: bdpy/util/utils.py#L119

No overload variant of "__getitem__" of "list" matches argument type "List[Any]"

Error code: `call-overload`: bdpy/util/utils.py#L121

No overload variant of "__getitem__" of "list" matches argument type "Tuple[List[Any], slice]"

test (3.10): tests/bdata/test_bdata.py#L88

TestBdata.test_metadata_add_get_where AssertionError: Arrays are not equal (shapes (0, 18), (10,) mismatch) x: array([], shape=(0, 18), dtype=float64) y: array([0.27812 , 0.732599, 0.976756, 0.24563 , 0.591236, 0.969363, 0.328211, 0.14038 , 0.563627, 0.047644])

test (3.10): tests/evals/test_metrics.py#L72

TestMetrics.test_2d FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d.pkl.gz'

test (3.10): tests/evals/test_metrics.py#L88

TestMetrics.test_2d_nan FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d-nan.pkl.gz'

test (3.10): tests/test_mri.py#L23

TestMri.test_add_load_epi_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.10): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.10): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0002 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.10)

Process completed with exit code 1.

test (3.11): tests/bdata/test_bdata.py#L88

TestBdata.test_metadata_add_get_where AssertionError: Arrays are not equal (shapes (0, 18), (10,) mismatch) x: array([], shape=(0, 18), dtype=float64) y: array([0.961081, 0.648758, 0.796687, 0.017611, 0.209054, 0.96669 , 0.593904, 0.550181, 0.495267, 0.71384 ])

test (3.11): tests/evals/test_metrics.py#L72

TestMetrics.test_2d FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d.pkl.gz'

test (3.11): tests/evals/test_metrics.py#L88

TestMetrics.test_2d_nan FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d-nan.pkl.gz'

test (3.11): tests/test_mri.py#L23

TestMri.test_add_load_epi_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.11): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.11): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0002 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.11)

Process completed with exit code 1.

test (3.8): tests/bdata/test_bdata.py#L88

TestBdata.test_metadata_add_get_where AssertionError: Arrays are not equal (shapes (0, 18), (10,) mismatch) x: array([], shape=(0, 18), dtype=float64) y: array([0.040054, 0.532655, 0.495909, 0.784464, 0.594638, 0.799516, 0.966128, 0.278253, 0.381451, 0.698548])

test (3.8): tests/evals/test_metrics.py#L72

TestMetrics.test_2d FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d.pkl.gz'

test (3.8): tests/evals/test_metrics.py#L88

TestMetrics.test_2d_nan FileNotFoundError: [Errno 2] No such file or directory: 'data/testdata-2d-nan.pkl.gz'

test (3.8): tests/test_mri.py#L23

TestMri.test_add_load_epi_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.8): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0001 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.8): tests/test_mri.py#L23

TestMri.test_get_roiflag_pass0002 FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/bdpy/bdpy/tests/data/mri/epi.mat'

test (3.8)

Process completed with exit code 1.

lint

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

test (3.9)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-python@v4, MishaKav/pytest-coverage-comment@v1.1.47. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

type-check

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-python@v4. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

type-check: bdpy/util/utils.py#L119

Possible overload variants:

type-check: bdpy/util/utils.py#L121

Possible overload variants:

type-check: bdpy/dataset/utils.py#L11

Hint: "python3 -m pip install types-tqdm"

type-check: bdpy/dataset/utils.py#L11

(or run "mypy --install-types" to install all missing stub packages)

type-check: bdpy/dataset/utils.py#L11

See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports

Error code: `annotation-unchecked`: bdpy/dataform/features.py#L382

By default the bodies of untyped functions are not checked, consider using --check-untyped-defs