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{ lib
, stdenv
, fetchFromGitHub
, buildPythonPackage
, python
, pythonOlder
, astropy
, cloudpickle
, cython
, dask
, imageio
, 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 = "0.21.0";
format = "pyproject";
disabled = pythonOlder "3.8";
src = fetchFromGitHub {
owner = "scikit-image";
repo = "scikit-image";
rev = "v${version}";
hash = "sha256-WJ2WNlcFCEtPr+bV/af6MoBBhbXDpOBEsJu4FmudoIo=";
};
patches = [
# https://github.com/scikit-image/scikit-image/pull/7052
# prepare a patch file because the commit contains additional changes
./suppress-deprecation-warning.patch
];
postPatch = ''
patchShebangs skimage/_build_utils/{version,cythoner}.py
'';
nativeBuildInputs = [
cython
meson-python
numpy
packaging
pythran
setuptools
wheel
];
propagatedBuildInputs = [
imageio
lazy-loader
matplotlib
networkx
numpy
packaging
pillow
pywavelets
scipy
tifffile
];
passthru.optional-dependencies = {
data = [
pooch
];
optional = [
astropy
cloudpickle
dask
matplotlib
pooch
pyamg
scikit-learn
simpleitk
] ++ dask.optional-dependencies.array;
};
# test suite is very cpu intensive, move to passthru.tests
doCheck = false;
nativeCheckInputs = [ pytestCheckHook ];
# (1) The package has cythonized modules, whose .so libs will appear only in the wheel, i.e. in nix store;
# (2) To stop Python from importing the wrong directory, i.e. the one in the build dir, not the one in nix store, `skimage` dir should be removed or renamed;
# (3) Therefore, tests should be run on the installed package in nix store.
# See e.g. https://discourse.nixos.org/t/cant-import-cythonized-modules-at-checkphase/14207 on why the following is needed.
preCheck = ''
rm -r skimage
'';
disabledTestPaths = [
# Requires network access (actually some data is loaded via `skimage._shared.testing.fetch` in the global scope, which calls `pytest.skip` when a network is unaccessible, leading to a pytest collection error).
"${installedPackageRoot}/skimage/filters/rank/tests/test_rank.py"
];
pytestFlagsArray = [ "${installedPackageRoot}" "--pyargs" "skimage" ] ++ builtins.map (testid: "--deselect=" + testid) ([
# These tests require network access
"skimage/data/test_data.py::test_skin"
"skimage/data/tests/test_data.py::test_skin"
"skimage/io/tests/test_io.py::test_imread_http_url"
"skimage/restoration/tests/test_rolling_ball.py::test_ndim"
] ++ lib.optionals stdenv.isDarwin [
# Matplotlib tests are broken inside darwin sandbox
"skimage/feature/tests/test_util.py::test_plot_matches"
"skimage/filters/tests/test_thresholding.py::TestSimpleImage::test_try_all_threshold"
"skimage/io/tests/test_mpl_imshow.py::"
] ++ lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [
# https://github.com/scikit-image/scikit-image/issues/7104
"skimage/measure/tests/test_fit.py"
"skimage/measure/tests/test_moments.py"
]);
# Check cythonized modules
pythonImportsCheck = [
"skimage"
"skimage._shared"
"skimage.draw"
"skimage.feature"
"skimage.restoration"
"skimage.filters"
"skimage.graph"
"skimage.io"
"skimage.measure"
"skimage.morphology"
"skimage.transform"
"skimage.util"
"skimage.segmentation"
];
passthru.tests = {
all-tests = self.override { doCheck = true; };
};
meta = {
description = "Image processing routines for SciPy";
homepage = "https://scikit-image.org";
changelog = "https://github.com/scikit-image/scikit-image/releases/tag/${src.rev}";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ yl3dy ];
};
};
in
self
|