Merge pull request #249674 from natsukium/skimage/update

python310Packages.scikit-image: 0.19.3 -> 0.21.0

pkgs/development/python-modules/scikit-image/add-testing-data.patch

@@ -1,17 +0,0 @@
-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')

pkgs/development/python-modules/scikit-image/default.nix

@@ -3,53 +3,98 @@
 , fetchFromGitHub
 , buildPythonPackage
 , python
-, cython
-, pythran
-, numpy
-, scipy
-, matplotlib
-, networkx
-, six
-, pillow
-, pywavelets
-, dask
+, pythonOlder
+, astropy
 , cloudpickle
+, cython
+, dask
 , imageio
-, tifffile
+, lazy-loader
+, matplotlib
+, meson-python
+, networkx
+, numpy
+, packaging
+, pillow
+, pooch
+, pyamg
 , pytestCheckHook
+, pythran
+, pywavelets
+, scikit-learn
+, scipy
+, setuptools
+, simpleitk
+, six
+, tifffile
+, 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
+    ];
 
-    nativeBuildInputs = [ cython pythran ];
+    postPatch = ''
+      patchShebangs skimage/_build_utils/{version,cythoner}.py
+    '';
+
+    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 ];
@@ -78,6 +123,10 @@ let
       "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
@@ -88,7 +137,6 @@ let
       "skimage.feature"
       "skimage.restoration"
       "skimage.filters"
-      "skimage.future.graph"
       "skimage.graph"
       "skimage.io"
       "skimage.measure"
@@ -105,6 +153,7 @@ let
     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 ];
     };

pkgs/development/python-modules/scikit-image/suppress-deprecation-warning.patch

@@ -0,0 +1,30 @@
+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(