Build scikit-image v0.24.0

nix/gdsfactory.nix

@@ -13,10 +13,14 @@
 # limitations under the License.
 {
   lib,
+  stdenv,
   buildPythonPackage,
   fetchPypi,
+  fetchFromGitHub,
   setuptools,
   setuptools_scm,
+  python,
+  pythonOlder,
 
   # Python
   matplotlib,
@@ -39,7 +43,6 @@
   freetype-py,
   mapbox-earcut,
   networkx,
-  scikit-image,
   trimesh,
   ipykernel,
   attrs,
@@ -56,6 +59,26 @@
   expat,
   ruamel-yaml,
   jinja2,
+  astropy,
+  cloudpickle,
+  cython,
+  dask,
+  imageio,
+  lazy-loader,
+  meson-python,
+  packaging,
+  pillow,
+  pooch,
+  pyamg,
+  pytestCheckHook,
+  numpydoc,
+  pythran,
+  pywavelets,
+  scikit-learn,
+  simpleitk,
+  six,
+  tifffile,
+  wheel,
 }: let
 
   rectangle-packer = buildPythonPackage rec {
@@ -194,6 +217,143 @@
     doCheck = false;
   };
 
+  installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";
+  scikit-image = buildPythonPackage rec {
+    pname = "scikit-image";
+    version = "0.24.0";
+    format = "pyproject";
+
+    disabled = pythonOlder "3.8";
+
+    src = fetchFromGitHub {
+      owner = "scikit-image";
+      repo = "scikit-image";
+      rev = "refs/tags/v${version}";
+      hash = "sha256-M18y5JBPf3DR7SlJcCf82nG2MzwILg2w1AhJMzZXslg=";
+    };
+
+    postPatch = ''
+      patchShebangs skimage/_build_utils/{version,cythoner}.py
+
+      substituteInPlace pyproject.toml \
+        --replace "numpy==" "numpy>="
+    '';
+
+    nativeBuildInputs = [
+      cython
+      meson-python
+      numpy
+      packaging
+      pythran
+      setuptools
+      wheel
+    ];
+
+    propagatedBuildInputs = [
+      imageio
+      lazy-loader
+      matplotlib
+      networkx
+      numpy
+      packaging
+      pillow
+      pywavelets
+      scipy
+      tifffile
+    ];
+
+    passthru.optional-dependencies = {
+      data = [ pooch ];
+      optional = [
+        astropy
+        cloudpickle
+        dask
+        matplotlib
+        pooch
+        pyamg
+        scikit-learn
+        simpleitk
+      ] ++ dask.optional-dependencies.array;
+    };
+
+    # test suite is very cpu intensive, move to passthru.tests
+    doCheck = false;
+    nativeCheckInputs = [
+      pytestCheckHook
+      numpydoc
+    ];
+
+    # (1) The package has cythonized modules, whose .so libs will appear only in the wheel, i.e. in nix store;
+    # (2) To stop Python from importing the wrong directory, i.e. the one in the build dir, not the one in nix store, `skimage` dir should be removed or renamed;
+    # (3) Therefore, tests should be run on the installed package in nix store.
+
+    # See e.g. https://discourse.nixos.org/t/cant-import-cythonized-modules-at-checkphase/14207 on why the following is needed.
+    preCheck = ''
+      rm -r skimage
+    '';
+
+    disabledTestPaths = [
+      # Requires network access (actually some data is loaded via `skimage._shared.testing.fetch` in the global scope, which calls `pytest.skip` when a network is unaccessible, leading to a pytest collection error).
+      "${installedPackageRoot}/skimage/filters/rank/tests/test_rank.py"
+    ];
+    pytestFlagsArray =
+      [
+        "${installedPackageRoot}"
+        "--pyargs"
+        "skimage"
+      ]
+      ++ builtins.map (testid: "--deselect=" + testid) (
+        [
+          # These tests require network access
+          "skimage/data/test_data.py::test_skin"
+          "skimage/data/tests/test_data.py::test_skin"
+          "skimage/io/tests/test_io.py::test_imread_http_url"
+          "skimage/restoration/tests/test_rolling_ball.py::test_ndim"
+        ]
+        ++ lib.optionals stdenv.isDarwin [
+          # Matplotlib tests are broken inside darwin sandbox
+          "skimage/feature/tests/test_util.py::test_plot_matches"
+          "skimage/filters/tests/test_thresholding.py::TestSimpleImage::test_try_all_threshold"
+          "skimage/io/tests/test_mpl_imshow.py::"
+          # See https://github.com/scikit-image/scikit-image/issues/7061 and https://github.com/scikit-image/scikit-image/issues/7104
+          "skimage/measure/tests/test_fit.py"
+        ]
+        ++ lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [
+          # https://github.com/scikit-image/scikit-image/issues/7104
+          "skimage/measure/tests/test_moments.py"
+        ]
+      );
+
+    # Check cythonized modules
+    pythonImportsCheck = [
+      "skimage"
+      "skimage._shared"
+      "skimage.draw"
+      "skimage.feature"
+      "skimage.restoration"
+      "skimage.filters"
+      "skimage.graph"
+      "skimage.io"
+      "skimage.measure"
+      "skimage.morphology"
+      "skimage.transform"
+      "skimage.util"
+      "skimage.segmentation"
+    ];
+
+    passthru.tests = {
+      all-tests = self.override { doCheck = true; };
+    };
+
+    meta = {
+      description = "Image processing routines for SciPy";
+      homepage = "https://scikit-image.org";
+      changelog = "https://github.com/scikit-image/scikit-image/releases/tag/${lib.removePrefix "refs/tags/" src.rev}";
+      license = lib.licenses.bsd3;
+      maintainers = with lib.maintainers; [ yl3dy ];
+    };
+  };
+
   self = buildPythonPackage rec {
     pname = "gdsfactory";
     format = "pyproject";