Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

(feat): seurat v3 with dask #3340

Draft
wants to merge 6 commits into
base: main
Choose a base branch
from

(fix): use `.any()` to prevent erroneous computation

f83e3f3
Select commit
Loading
Failed to load commit list.
Draft

(feat): seurat v3 with dask #3340

(fix): use `.any()` to prevent erroneous computation
f83e3f3
Select commit
Loading
Failed to load commit list.
Azure Pipelines / scverse.scanpy failed Nov 13, 2024 in 28m 31s

Build #20241113.3 had test failures

3 errors / 3 warnings

Details

Tests

  • Failed: 16 (0.21%)
  • Passed: 6,787 (91.17%)
  • Other: 641 (8.61%)
  • Total: 7,444
Code coverage

  • 9876 of 12921 line covered (76.43%)

Annotations

Check failure on line 1921 in Build log

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

Build log #L1921 

Bash exited with code '132'.

Check failure on line 2554 in Build log

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

Build log #L2554 

Bash exited with code '1'.

Check failure on line 2573 in Build log

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

Build log #L2573 

Bash exited with code '1'.

Check failure on line 1 in tests/test_utils.py::test_check_nonnegative_integers[poisson-float64-dask_array_dense]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_utils.py::test_check_nonnegative_integers[poisson-float64-dask_array_dense] 

array_type = <function as_dense_dask_array at 0x7fca2bf92b60>
array_value = array([[2., 0., 0., ..., 1., 0., 0.],
       [1., 0., 2., ..., 2., 2., 2.],
       [0., 0., 0., ..., 1., 1., 0.],
       ...,
       [0., 4., 0., ..., 0., 1., 0.],
       [0., 0., 0., ..., 2., 0., 1.],
       [2., 1., 2., ..., 3., 2., 1.]])
expected = True

    @pytest.mark.parametrize("array_type", ARRAY_TYPES)
    @pytest.mark.parametrize(
        ("array_value", "expected"),
        [
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.float64),
                True,
                id="poisson-float64",
            ),
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.uint32),
                True,
                id="poisson-uint32",
            ),
            pytest.param(np.random.normal(size=(100, 100)), False, id="normal"),
            pytest.param(np.array([[0, 0, 0], [0, -1, 0], [0, 0, 0]]), False, id="middle"),
        ],
    )
    def test_check_nonnegative_integers(array_type, array_value, expected):
        X = array_type(array_value)
    
        received = check_nonnegative_integers(X)
        if isinstance(X, DaskArray):
>           assert isinstance(received, DaskArray)
E           assert False
E            +  where False = isinstance(np.True_, DaskArray)

tests/test_utils.py:186: AssertionError
Raw output 
/home/vsts/work/1/s/tests/test_utils.py:186: assert False

Check failure on line 1 in tests/test_utils.py::test_check_nonnegative_integers[poisson-float64-dask_array_sparse]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_utils.py::test_check_nonnegative_integers[poisson-float64-dask_array_sparse] 

array_type = <function as_sparse_dask_array at 0x7fca2bf92c00>
array_value = array([[2., 0., 0., ..., 1., 0., 0.],
       [1., 0., 2., ..., 2., 2., 2.],
       [0., 0., 0., ..., 1., 1., 0.],
       ...,
       [0., 4., 0., ..., 0., 1., 0.],
       [0., 0., 0., ..., 2., 0., 1.],
       [2., 1., 2., ..., 3., 2., 1.]])
expected = True

    @pytest.mark.parametrize("array_type", ARRAY_TYPES)
    @pytest.mark.parametrize(
        ("array_value", "expected"),
        [
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.float64),
                True,
                id="poisson-float64",
            ),
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.uint32),
                True,
                id="poisson-uint32",
            ),
            pytest.param(np.random.normal(size=(100, 100)), False, id="normal"),
            pytest.param(np.array([[0, 0, 0], [0, -1, 0], [0, 0, 0]]), False, id="middle"),
        ],
    )
    def test_check_nonnegative_integers(array_type, array_value, expected):
        X = array_type(array_value)
    
        received = check_nonnegative_integers(X)
        if isinstance(X, DaskArray):
>           assert isinstance(received, DaskArray)
E           assert False
E            +  where False = isinstance(np.True_, DaskArray)

tests/test_utils.py:186: AssertionError
Raw output 
/home/vsts/work/1/s/tests/test_utils.py:186: assert False

Check failure on line 1 in tests/test_utils.py::test_check_nonnegative_integers[poisson-uint32-dask_array_dense]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_utils.py::test_check_nonnegative_integers[poisson-uint32-dask_array_dense] 

array_type = <function as_dense_dask_array at 0x7fca2bf92b60>
array_value = array([[1, 3, 2, ..., 1, 2, 1],
       [4, 0, 2, ..., 2, 1, 1],
       [1, 0, 1, ..., 0, 2, 1],
       ...,
       [1, 1, 0, ..., 1, 0, 1],
       [1, 0, 1, ..., 1, 0, 0],
       [1, 1, 1, ..., 0, 0, 0]], dtype=uint32)
expected = True

    @pytest.mark.parametrize("array_type", ARRAY_TYPES)
    @pytest.mark.parametrize(
        ("array_value", "expected"),
        [
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.float64),
                True,
                id="poisson-float64",
            ),
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.uint32),
                True,
                id="poisson-uint32",
            ),
            pytest.param(np.random.normal(size=(100, 100)), False, id="normal"),
            pytest.param(np.array([[0, 0, 0], [0, -1, 0], [0, 0, 0]]), False, id="middle"),
        ],
    )
    def test_check_nonnegative_integers(array_type, array_value, expected):
        X = array_type(array_value)
    
        received = check_nonnegative_integers(X)
        if isinstance(X, DaskArray):
>           assert isinstance(received, DaskArray)
E           assert False
E            +  where False = isinstance(np.True_, DaskArray)

tests/test_utils.py:186: AssertionError
Raw output 
/home/vsts/work/1/s/tests/test_utils.py:186: assert False

Check failure on line 1 in tests/test_utils.py::test_check_nonnegative_integers[poisson-uint32-dask_array_sparse]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_utils.py::test_check_nonnegative_integers[poisson-uint32-dask_array_sparse] 

array_type = <function as_sparse_dask_array at 0x7fca2bf92c00>
array_value = array([[1, 3, 2, ..., 1, 2, 1],
       [4, 0, 2, ..., 2, 1, 1],
       [1, 0, 1, ..., 0, 2, 1],
       ...,
       [1, 1, 0, ..., 1, 0, 1],
       [1, 0, 1, ..., 1, 0, 0],
       [1, 1, 1, ..., 0, 0, 0]], dtype=uint32)
expected = True

    @pytest.mark.parametrize("array_type", ARRAY_TYPES)
    @pytest.mark.parametrize(
        ("array_value", "expected"),
        [
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.float64),
                True,
                id="poisson-float64",
            ),
            pytest.param(
                np.random.poisson(size=(100, 100)).astype(np.uint32),
                True,
                id="poisson-uint32",
            ),
            pytest.param(np.random.normal(size=(100, 100)), False, id="normal"),
            pytest.param(np.array([[0, 0, 0], [0, -1, 0], [0, 0, 0]]), False, id="middle"),
        ],
    )
    def test_check_nonnegative_integers(array_type, array_value, expected):
        X = array_type(array_value)
    
        received = check_nonnegative_integers(X)
        if isinstance(X, DaskArray):
>           assert isinstance(received, DaskArray)
E           assert False
E            +  where False = isinstance(np.True_, DaskArray)

tests/test_utils.py:186: AssertionError
Raw output 
/home/vsts/work/1/s/tests/test_utils.py:186: assert False
View more details on Azure Pipelines