python310Packages.scikit-image: 0.19.3 -> 0.21.0
Diff: https://github.com/scikit-image/scikit-image/compare/v0.19.3...v0.21.0 Changelog: https://github.com/scikit-image/scikit-image/releases/tag/v0.21.0
This commit is contained in:
parent
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commit
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@ -1,17 +0,0 @@
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diff --git a/skimage/data/setup.py b/skimage/data/setup.py
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index 528e9c284ce..ba0e155559c 100644
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--- a/skimage/data/setup.py
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+++ b/skimage/data/setup.py
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@@ -11,7 +11,11 @@ def configuration(parent_package='', top_path=None):
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# further notice.
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# Testing data and additional datasets should only
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# be made available via pooch
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- config.add_data_files(*legacy_datasets)
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+ # Nix patch: add ALL images to facilitate testing of a fully-built package
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+ from pathlib import Path
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+ config.add_data_files(
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+ *(path.name for path in Path(__file__).parent.glob("*") if path.suffix != ".py")
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+ )
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# It seems hard to create a consistent hash for README.txt since
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# the line endings keep getting converted
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config.add_data_files('README.txt')
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@ -3,53 +3,98 @@
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, fetchFromGitHub
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, buildPythonPackage
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, python
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, cython
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, pythran
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, numpy
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, scipy
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, matplotlib
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, networkx
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, six
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, pillow
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, pywavelets
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, dask
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, pythonOlder
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, astropy
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, cloudpickle
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, cython
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, dask
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, imageio
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, tifffile
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, lazy-loader
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, matplotlib
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, meson-python
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, networkx
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, numpy
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, packaging
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, pillow
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, pooch
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, pyamg
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, pytestCheckHook
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, pythran
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, pywavelets
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, scikit-learn
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, scipy
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, setuptools
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, simpleitk
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, six
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, tifffile
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, wheel
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}:
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let
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installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";
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self = buildPythonPackage rec {
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pname = "scikit-image";
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version = "0.19.3";
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version = "0.21.0";
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format = "pyproject";
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disabled = pythonOlder "3.8";
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src = fetchFromGitHub {
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owner = pname;
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repo = pname;
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owner = "scikit-image";
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repo = "scikit-image";
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rev = "v${version}";
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hash = "sha256-zvXgZdvYycFbbMsBFSqMDzLanEtF9+JuVSQ3AM8/LQk=";
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hash = "sha256-WJ2WNlcFCEtPr+bV/af6MoBBhbXDpOBEsJu4FmudoIo=";
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};
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patches = [ ./add-testing-data.patch ];
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patches = [
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# https://github.com/scikit-image/scikit-image/pull/7052
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# prepare a patch file because the commit contains additional changes
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./suppress-deprecation-warning.patch
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];
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nativeBuildInputs = [ cython pythran ];
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postPatch = ''
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patchShebangs skimage/_build_utils/{version,cythoner}.py
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'';
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nativeBuildInputs = [
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cython
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meson-python
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numpy
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packaging
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pythran
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setuptools
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wheel
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];
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propagatedBuildInputs = [
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cloudpickle
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dask
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imageio
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lazy-loader
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matplotlib
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networkx
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numpy
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packaging
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pillow
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pywavelets
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scipy
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six
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tifffile
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];
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passthru.optional-dependencies = {
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data = [
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pooch
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];
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optional = [
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astropy
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cloudpickle
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dask
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matplotlib
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pooch
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pyamg
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scikit-learn
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simpleitk
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] ++ dask.optional-dependencies.array;
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};
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# test suite is very cpu intensive, move to passthru.tests
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doCheck = false;
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nativeCheckInputs = [ pytestCheckHook ];
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"skimage/feature/tests/test_util.py::test_plot_matches"
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"skimage/filters/tests/test_thresholding.py::TestSimpleImage::test_try_all_threshold"
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"skimage/io/tests/test_mpl_imshow.py::"
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] ++ lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [
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# https://github.com/scikit-image/scikit-image/issues/7104
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"skimage/measure/tests/test_fit.py"
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"skimage/measure/tests/test_moments.py"
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]);
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# Check cythonized modules
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"skimage.feature"
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"skimage.restoration"
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"skimage.filters"
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"skimage.future.graph"
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"skimage.graph"
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"skimage.io"
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"skimage.measure"
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meta = {
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description = "Image processing routines for SciPy";
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homepage = "https://scikit-image.org";
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changelog = "https://github.com/scikit-image/scikit-image/releases/tag/${src.rev}";
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license = lib.licenses.bsd3;
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maintainers = with lib.maintainers; [ yl3dy ];
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};
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@ -0,0 +1,30 @@
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diff --git a/skimage/exposure/tests/test_exposure.py b/skimage/exposure/tests/test_exposure.py
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index ed8dd6bc8..8ec7d13bf 100644
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--- a/skimage/exposure/tests/test_exposure.py
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+++ b/skimage/exposure/tests/test_exposure.py
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@@ -368,19 +368,16 @@ def test_rescale_nan_warning(in_range, out_range):
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)
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# 2019/11/10 Passing NaN to np.clip raises a DeprecationWarning for
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- # versions above 1.17
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- # TODO: Remove once NumPy removes this DeprecationWarning
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+ # versions above 1.17, "|\A\Z" marks as optional warning
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+ # TODO: Remove once NumPy 1.25.0 is minimal dependency
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numpy_warning_1_17_plus = (
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- "Passing `np.nan` to mean no clipping in np.clip"
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+ "|\\A\\ZPassing `np.nan` to mean no clipping in np.clip"
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)
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- if in_range == "image":
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- exp_warn = [msg, numpy_warning_1_17_plus]
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- else:
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- exp_warn = [msg]
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+ with expected_warnings([msg, numpy_warning_1_17_plus]):
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+ result = exposure.rescale_intensity(image, in_range, out_range)
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- with expected_warnings(exp_warn):
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- exposure.rescale_intensity(image, in_range, out_range)
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+ assert np.all(np.isnan(result))
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@pytest.mark.parametrize(
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