Merge pull request #249674 from natsukium/skimage/update

diff --git a/skimage/data/setup.py b/skimage/data/setup.py

index 528e9c284ce..ba0e155559c 100644

--- a/skimage/data/setup.py

+++ b/skimage/data/setup.py

@@ -11,7 +11,11 @@ def configuration(parent_package='', top_path=None):

     # further notice.

     # Testing data and additional datasets should only

     # be made available via pooch

-    config.add_data_files(*legacy_datasets)

+    # Nix patch: add ALL images to facilitate testing of a fully-built package

+    from pathlib import Path

+    config.add_data_files(

+        *(path.name for path in Path(__file__).parent.glob("*") if path.suffix != ".py")

+    )

     # It seems hard to create a consistent hash for README.txt since

     # the line endings keep getting converted

     config.add_data_files('README.txt')

, fetchFromGitHub

, buildPythonPackage

, python

, pythonOlder

, astropy

, cloudpickle

, cython

, pythran

, numpy

, scipy

, dask

, imageio

, lazy-loader

, matplotlib

, meson-python

, networkx

, six

, numpy

, packaging

, pillow

, pooch

, pyamg

, pytestCheckHook

, pythran

, pywavelets

, dask

, cloudpickle

, imageio

, scikit-learn

, scipy

, setuptools

, simpleitk

, six

, tifffile

, pytestCheckHook

, wheel

}:

let

  installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";

  self = buildPythonPackage rec {

    pname = "scikit-image";

    version = "0.19.3";

    version = "0.21.0";

    format = "pyproject";

    disabled = pythonOlder "3.8";

    src = fetchFromGitHub {

      owner = pname;

      repo = pname;

      owner = "scikit-image";

      repo = "scikit-image";

      rev = "v${version}";

      hash = "sha256-zvXgZdvYycFbbMsBFSqMDzLanEtF9+JuVSQ3AM8/LQk=";

      hash = "sha256-WJ2WNlcFCEtPr+bV/af6MoBBhbXDpOBEsJu4FmudoIo=";

    };

    patches = [ ./add-testing-data.patch ];

    patches = [

      # https://github.com/scikit-image/scikit-image/pull/7052

      # prepare a patch file because the commit contains additional changes

      ./suppress-deprecation-warning.patch

    ];

    postPatch = ''

      patchShebangs skimage/_build_utils/{version,cythoner}.py

    '';

    nativeBuildInputs = [ cython pythran ];

    nativeBuildInputs = [

      cython

      meson-python

      numpy

      packaging

      pythran

      setuptools

      wheel

    ];

    propagatedBuildInputs = [

      cloudpickle

      dask

      imageio

      lazy-loader

      matplotlib

      networkx

      numpy

      packaging

      pillow

      pywavelets

      scipy

      six

      tifffile

    ];

    passthru.optional-dependencies = {

      data = [

        pooch

      ];

      optional = [

        astropy

        cloudpickle

        dask

        matplotlib

        pooch

        pyamg

        scikit-learn

        simpleitk

      ] ++ dask.optional-dependencies.array;

    };

    # test suite is very cpu intensive, move to passthru.tests

    doCheck = false;

    nativeCheckInputs = [ pytestCheckHook ];

      "skimage/feature/tests/test_util.py::test_plot_matches"

      "skimage/filters/tests/test_thresholding.py::TestSimpleImage::test_try_all_threshold"

      "skimage/io/tests/test_mpl_imshow.py::"

    ] ++ lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [

      # https://github.com/scikit-image/scikit-image/issues/7104

      "skimage/measure/tests/test_fit.py"

      "skimage/measure/tests/test_moments.py"

    ]);

    # Check cythonized modules

      "skimage.feature"

      "skimage.restoration"

      "skimage.filters"

      "skimage.future.graph"

      "skimage.graph"

      "skimage.io"

      "skimage.measure"

    meta = {

      description = "Image processing routines for SciPy";

      homepage = "https://scikit-image.org";

      changelog = "https://github.com/scikit-image/scikit-image/releases/tag/${src.rev}";

      license = lib.licenses.bsd3;

      maintainers = with lib.maintainers; [ yl3dy ];

    };

diff --git a/skimage/exposure/tests/test_exposure.py b/skimage/exposure/tests/test_exposure.py

index ed8dd6bc8..8ec7d13bf 100644

--- a/skimage/exposure/tests/test_exposure.py

+++ b/skimage/exposure/tests/test_exposure.py

@@ -368,19 +368,16 @@ def test_rescale_nan_warning(in_range, out_range):

     )

     # 2019/11/10 Passing NaN to np.clip raises a DeprecationWarning for

-    # versions above 1.17

-    # TODO: Remove once NumPy removes this DeprecationWarning

+    # versions above 1.17, "|\A\Z" marks as optional warning

+    # TODO: Remove once NumPy 1.25.0 is minimal dependency

     numpy_warning_1_17_plus = (

-        "Passing `np.nan` to mean no clipping in np.clip"

+        "|\\A\\ZPassing `np.nan` to mean no clipping in np.clip"

     )

-    if in_range == "image":

-        exp_warn = [msg, numpy_warning_1_17_plus]

-    else:

-        exp_warn = [msg]

+    with expected_warnings([msg, numpy_warning_1_17_plus]):

+        result = exposure.rescale_intensity(image, in_range, out_range)

-    with expected_warnings(exp_warn):

-        exposure.rescale_intensity(image, in_range, out_range)

+    assert np.all(np.isnan(result))

 @pytest.mark.parametrize(