165 lines
4.3 KiB
Nix
165 lines
4.3 KiB
Nix
{ lib
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, stdenv
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, fetchFromGitHub
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, buildPythonPackage
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, python
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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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, 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 = "0.21.0";
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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 = "scikit-image";
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repo = "scikit-image";
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rev = "v${version}";
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hash = "sha256-WJ2WNlcFCEtPr+bV/af6MoBBhbXDpOBEsJu4FmudoIo=";
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};
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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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postPatch = ''
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patchShebangs skimage/_build_utils/{version,cythoner}.py
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substituteInPlace pyproject.toml \
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--replace "numpy==" "numpy>="
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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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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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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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# (1) The package has cythonized modules, whose .so libs will appear only in the wheel, i.e. in nix store;
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# (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;
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# (3) Therefore, tests should be run on the installed package in nix store.
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# See e.g. https://discourse.nixos.org/t/cant-import-cythonized-modules-at-checkphase/14207 on why the following is needed.
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preCheck = ''
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rm -r skimage
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'';
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disabledTestPaths = [
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# 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).
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"${installedPackageRoot}/skimage/filters/rank/tests/test_rank.py"
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];
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pytestFlagsArray = [ "${installedPackageRoot}" "--pyargs" "skimage" ] ++ builtins.map (testid: "--deselect=" + testid) ([
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# These tests require network access
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"skimage/data/test_data.py::test_skin"
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"skimage/data/tests/test_data.py::test_skin"
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"skimage/io/tests/test_io.py::test_imread_http_url"
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"skimage/restoration/tests/test_rolling_ball.py::test_ndim"
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] ++ lib.optionals stdenv.isDarwin [
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# Matplotlib tests are broken inside darwin sandbox
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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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pythonImportsCheck = [
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"skimage"
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"skimage._shared"
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"skimage.draw"
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"skimage.feature"
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"skimage.restoration"
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"skimage.filters"
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"skimage.graph"
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"skimage.io"
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"skimage.measure"
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"skimage.morphology"
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"skimage.transform"
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"skimage.util"
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"skimage.segmentation"
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];
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passthru.tests = {
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all-tests = self.override { doCheck = true; };
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};
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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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};
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in
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self
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