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Deprecate RandomState (using names only) #3372

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merged 1 commit into from
Nov 19, 2024

Deprecate RandomState (using names only)

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Merged

Deprecate RandomState (using names only) #3372

Deprecate RandomState (using names only)
092237a
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Azure Pipelines / scverse.scanpy failed Nov 18, 2024 in 26m 59s

Build #20241118.2 had test failures

1 errors / 2 warnings

Details

Tests

  • Failed: 24 (0.26%)
  • Passed: 8,593 (92.70%)
  • Other: 653 (7.04%)
  • Total: 9,270
Code coverage

  • 9849 of 12907 line covered (76.31%)

Annotations

Check failure on line 4789 in Build log

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

Build log #L4789 

Bash exited with code '1'.

Check failure on line 1 in tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-None-None]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-None-None] 

@pytest.mark.parametrize(
        ("array_type", "zero_center", "svd_solver", "warn_pat_expected"),
        [
            pytest.param(
                array_type.values[0],
                zero_center,
                svd_solver,
                warn_pat_expected,
                marks=(
                    array_type.marks
                    if xfail_reason is None
                    else [pytest.mark.xfail(reason=xfail_reason)]
                ),
                id=(
                    f"{array_type.id}-{'zero_center' if zero_center else 'no_zero_center'}-"
                    f"{svd_solver or svd_solver_type}-{'xfail' if xfail_reason else warn_pat_expected}"
                ),
            )
            for array_type in ARRAY_TYPES
            for zero_center in [True, False]
            for svd_solver_type in [None, "valid", "invalid"]
            for svd_solver, warn_pat_expected, xfail_reason in gen_pca_params(
                array_type=array_type.values[0],
                zero_center=zero_center,
                svd_solver_type=svd_solver_type,
            )
        ],
    )
    def test_pca_warnings(
        *,
        array_type: ArrayType,
        zero_center: bool,
        svd_solver: SVDSolver,
        warn_pat_expected: str | None,
    ):
        A = array_type(A_list).astype("float32")
        adata = AnnData(A)
    
        if warn_pat_expected is not None:
            with pytest.warns((UserWarning, FutureWarning), match=warn_pat_expected):
                warnings.filterwarnings(
                    "ignore", r".*Using a dense eigensolver instead of LOBPCG", UserWarning
                )
                sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)
            return
    
        warnings.simplefilter("error")
        warnings.filterwarnings(
            "ignore", "pkg_resources is deprecated as an API", DeprecationWarning
        )
>       sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)

tests/test_pca.py:240: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/scanpy/preprocessing/_pca/__init__.py:345: in pca
    from dask_ml.decomposition import PCA
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/__init__.py:2: in <module>
    from dask_ml.model_selection import _normalize  # noqa: F401
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/__init__.py:9: in <module>
    from ._search import GridSearchCV, RandomizedSearchCV, check_cv, compute_n_splits
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

    from __future__ import absolute_import, division, print_function
    
    import logging
    import numbers
    from collections import defaultdict
    from itertools import repeat
    from multiprocessing import cpu_count
    from operator import getitem
    
    import dask
    import numpy as np
    import packaging.version
    from dask.base import tokenize
    from dask.delayed import delayed
    from dask.distributed import as_completed
    from dask.utils import derived_from
    from sklearn import model_selection
    from sklearn.base import BaseEstimator, MetaEstimatorMixin, clone, is_classifier
    from sklearn.exceptions import NotFittedError
    from sklearn.model_selection._search import BaseSearchCV
    from sklearn.model_selection._split import (
        BaseShuffleSplit,
        KFold,
        LeaveOneGroupOut,
        LeaveOneOut,
        LeavePGroupsOut,
        LeavePOut,
        PredefinedSplit,
        StratifiedKFold,
        _BaseKFold,
        _CVIterableWrapper,
    )
    from sklearn.pipeline import FeatureUnion, Pipeline
>   from sklearn.utils._tags import _safe_tags
E   ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.p
Raw output 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/_search.py:34: ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.py)

Check failure on line 1 in tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-auto-None]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-auto-None] 

@pytest.mark.parametrize(
        ("array_type", "zero_center", "svd_solver", "warn_pat_expected"),
        [
            pytest.param(
                array_type.values[0],
                zero_center,
                svd_solver,
                warn_pat_expected,
                marks=(
                    array_type.marks
                    if xfail_reason is None
                    else [pytest.mark.xfail(reason=xfail_reason)]
                ),
                id=(
                    f"{array_type.id}-{'zero_center' if zero_center else 'no_zero_center'}-"
                    f"{svd_solver or svd_solver_type}-{'xfail' if xfail_reason else warn_pat_expected}"
                ),
            )
            for array_type in ARRAY_TYPES
            for zero_center in [True, False]
            for svd_solver_type in [None, "valid", "invalid"]
            for svd_solver, warn_pat_expected, xfail_reason in gen_pca_params(
                array_type=array_type.values[0],
                zero_center=zero_center,
                svd_solver_type=svd_solver_type,
            )
        ],
    )
    def test_pca_warnings(
        *,
        array_type: ArrayType,
        zero_center: bool,
        svd_solver: SVDSolver,
        warn_pat_expected: str | None,
    ):
        A = array_type(A_list).astype("float32")
        adata = AnnData(A)
    
        if warn_pat_expected is not None:
            with pytest.warns((UserWarning, FutureWarning), match=warn_pat_expected):
                warnings.filterwarnings(
                    "ignore", r".*Using a dense eigensolver instead of LOBPCG", UserWarning
                )
                sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)
            return
    
        warnings.simplefilter("error")
        warnings.filterwarnings(
            "ignore", "pkg_resources is deprecated as an API", DeprecationWarning
        )
>       sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)

tests/test_pca.py:240: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/scanpy/preprocessing/_pca/__init__.py:345: in pca
    from dask_ml.decomposition import PCA
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/__init__.py:2: in <module>
    from dask_ml.model_selection import _normalize  # noqa: F401
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/__init__.py:9: in <module>
    from ._search import GridSearchCV, RandomizedSearchCV, check_cv, compute_n_splits
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

    from __future__ import absolute_import, division, print_function
    
    import logging
    import numbers
    from collections import defaultdict
    from itertools import repeat
    from multiprocessing import cpu_count
    from operator import getitem
    
    import dask
    import numpy as np
    import packaging.version
    from dask.base import tokenize
    from dask.delayed import delayed
    from dask.distributed import as_completed
    from dask.utils import derived_from
    from sklearn import model_selection
    from sklearn.base import BaseEstimator, MetaEstimatorMixin, clone, is_classifier
    from sklearn.exceptions import NotFittedError
    from sklearn.model_selection._search import BaseSearchCV
    from sklearn.model_selection._split import (
        BaseShuffleSplit,
        KFold,
        LeaveOneGroupOut,
        LeaveOneOut,
        LeavePGroupsOut,
        LeavePOut,
        PredefinedSplit,
        StratifiedKFold,
        _BaseKFold,
        _CVIterableWrapper,
    )
    from sklearn.pipeline import FeatureUnion, Pipeline
>   from sklearn.utils._tags import _safe_tags
E   ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.p
Raw output 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/_search.py:34: ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.py)

Check failure on line 1 in tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-full-None]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-full-None] 

@pytest.mark.parametrize(
        ("array_type", "zero_center", "svd_solver", "warn_pat_expected"),
        [
            pytest.param(
                array_type.values[0],
                zero_center,
                svd_solver,
                warn_pat_expected,
                marks=(
                    array_type.marks
                    if xfail_reason is None
                    else [pytest.mark.xfail(reason=xfail_reason)]
                ),
                id=(
                    f"{array_type.id}-{'zero_center' if zero_center else 'no_zero_center'}-"
                    f"{svd_solver or svd_solver_type}-{'xfail' if xfail_reason else warn_pat_expected}"
                ),
            )
            for array_type in ARRAY_TYPES
            for zero_center in [True, False]
            for svd_solver_type in [None, "valid", "invalid"]
            for svd_solver, warn_pat_expected, xfail_reason in gen_pca_params(
                array_type=array_type.values[0],
                zero_center=zero_center,
                svd_solver_type=svd_solver_type,
            )
        ],
    )
    def test_pca_warnings(
        *,
        array_type: ArrayType,
        zero_center: bool,
        svd_solver: SVDSolver,
        warn_pat_expected: str | None,
    ):
        A = array_type(A_list).astype("float32")
        adata = AnnData(A)
    
        if warn_pat_expected is not None:
            with pytest.warns((UserWarning, FutureWarning), match=warn_pat_expected):
                warnings.filterwarnings(
                    "ignore", r".*Using a dense eigensolver instead of LOBPCG", UserWarning
                )
                sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)
            return
    
        warnings.simplefilter("error")
        warnings.filterwarnings(
            "ignore", "pkg_resources is deprecated as an API", DeprecationWarning
        )
>       sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)

tests/test_pca.py:240: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/scanpy/preprocessing/_pca/__init__.py:345: in pca
    from dask_ml.decomposition import PCA
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/__init__.py:2: in <module>
    from dask_ml.model_selection import _normalize  # noqa: F401
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/__init__.py:9: in <module>
    from ._search import GridSearchCV, RandomizedSearchCV, check_cv, compute_n_splits
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

    from __future__ import absolute_import, division, print_function
    
    import logging
    import numbers
    from collections import defaultdict
    from itertools import repeat
    from multiprocessing import cpu_count
    from operator import getitem
    
    import dask
    import numpy as np
    import packaging.version
    from dask.base import tokenize
    from dask.delayed import delayed
    from dask.distributed import as_completed
    from dask.utils import derived_from
    from sklearn import model_selection
    from sklearn.base import BaseEstimator, MetaEstimatorMixin, clone, is_classifier
    from sklearn.exceptions import NotFittedError
    from sklearn.model_selection._search import BaseSearchCV
    from sklearn.model_selection._split import (
        BaseShuffleSplit,
        KFold,
        LeaveOneGroupOut,
        LeaveOneOut,
        LeavePGroupsOut,
        LeavePOut,
        PredefinedSplit,
        StratifiedKFold,
        _BaseKFold,
        _CVIterableWrapper,
    )
    from sklearn.pipeline import FeatureUnion, Pipeline
>   from sklearn.utils._tags import _safe_tags
E   ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.p
Raw output 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/_search.py:34: ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.py)

Check failure on line 1 in tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-randomized-None]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_pca.py::test_pca_warnings[dask_array_dense-zero_center-randomized-None] 

@pytest.mark.parametrize(
        ("array_type", "zero_center", "svd_solver", "warn_pat_expected"),
        [
            pytest.param(
                array_type.values[0],
                zero_center,
                svd_solver,
                warn_pat_expected,
                marks=(
                    array_type.marks
                    if xfail_reason is None
                    else [pytest.mark.xfail(reason=xfail_reason)]
                ),
                id=(
                    f"{array_type.id}-{'zero_center' if zero_center else 'no_zero_center'}-"
                    f"{svd_solver or svd_solver_type}-{'xfail' if xfail_reason else warn_pat_expected}"
                ),
            )
            for array_type in ARRAY_TYPES
            for zero_center in [True, False]
            for svd_solver_type in [None, "valid", "invalid"]
            for svd_solver, warn_pat_expected, xfail_reason in gen_pca_params(
                array_type=array_type.values[0],
                zero_center=zero_center,
                svd_solver_type=svd_solver_type,
            )
        ],
    )
    def test_pca_warnings(
        *,
        array_type: ArrayType,
        zero_center: bool,
        svd_solver: SVDSolver,
        warn_pat_expected: str | None,
    ):
        A = array_type(A_list).astype("float32")
        adata = AnnData(A)
    
        if warn_pat_expected is not None:
            with pytest.warns((UserWarning, FutureWarning), match=warn_pat_expected):
                warnings.filterwarnings(
                    "ignore", r".*Using a dense eigensolver instead of LOBPCG", UserWarning
                )
                sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)
            return
    
        warnings.simplefilter("error")
        warnings.filterwarnings(
            "ignore", "pkg_resources is deprecated as an API", DeprecationWarning
        )
>       sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)

tests/test_pca.py:240: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/scanpy/preprocessing/_pca/__init__.py:345: in pca
    from dask_ml.decomposition import PCA
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/__init__.py:2: in <module>
    from dask_ml.model_selection import _normalize  # noqa: F401
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/__init__.py:9: in <module>
    from ._search import GridSearchCV, RandomizedSearchCV, check_cv, compute_n_splits
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

    from __future__ import absolute_import, division, print_function
    
    import logging
    import numbers
    from collections import defaultdict
    from itertools import repeat
    from multiprocessing import cpu_count
    from operator import getitem
    
    import dask
    import numpy as np
    import packaging.version
    from dask.base import tokenize
    from dask.delayed import delayed
    from dask.distributed import as_completed
    from dask.utils import derived_from
    from sklearn import model_selection
    from sklearn.base import BaseEstimator, MetaEstimatorMixin, clone, is_classifier
    from sklearn.exceptions import NotFittedError
    from sklearn.model_selection._search import BaseSearchCV
    from sklearn.model_selection._split import (
        BaseShuffleSplit,
        KFold,
        LeaveOneGroupOut,
        LeaveOneOut,
        LeavePGroupsOut,
        LeavePOut,
        PredefinedSplit,
        StratifiedKFold,
        _BaseKFold,
        _CVIterableWrapper,
    )
    from sklearn.pipeline import FeatureUnion, Pipeline
>   from sklearn.utils._tags import _safe_tags
E   ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.p
Raw output 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/dask_ml/model_selection/_search.py:34: ImportError: cannot import name '_safe_tags' from 'sklearn.utils._tags' (/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/sklearn/utils/_tags.py)
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