depot/third_party/nixpkgs/pkgs/development/python-modules/scikit-image/default.nix

{ lib
, stdenv
, fetchFromGitHub
, buildPythonPackage
, python
, cython
, pythran
, numpy
, scipy
, matplotlib
, networkx
, six
, pillow
, pywavelets
, dask
, cloudpickle
, imageio
, tifffile
, pytestCheckHook
}:

let
  installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";
  self = buildPythonPackage rec {
    pname = "scikit-image";
    version = "0.19.3";

    src = fetchFromGitHub {
      owner = pname;
      repo = pname;
      rev = "v${version}";
      hash = "sha256-zvXgZdvYycFbbMsBFSqMDzLanEtF9+JuVSQ3AM8/LQk=";
    };

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

    nativeBuildInputs = [ cython pythran ];

    propagatedBuildInputs = [
      cloudpickle
      dask
      imageio
      matplotlib
      networkx
      numpy
      pillow
      pywavelets
      scipy
      six
      tifffile
    ];

    # test suite is very cpu intensive, move to passthru.tests
    doCheck = false;
    nativeCheckInputs = [ pytestCheckHook ];

    # (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::"
    ]);

    # Check cythonized modules
    pythonImportsCheck = [
      "skimage"
      "skimage._shared"
      "skimage.draw"
      "skimage.feature"
      "skimage.restoration"
      "skimage.filters"
      "skimage.future.graph"
      "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";
      license = lib.licenses.bsd3;
      maintainers = with lib.maintainers; [ yl3dy ];
    };
  };
in
  self