172 lines
4.5 KiB
Nix
172 lines
4.5 KiB
Nix
{
|
|
lib,
|
|
stdenv,
|
|
fetchFromGitHub,
|
|
buildPythonPackage,
|
|
python,
|
|
pythonOlder,
|
|
astropy,
|
|
cloudpickle,
|
|
cython,
|
|
dask,
|
|
imageio,
|
|
lazy-loader,
|
|
matplotlib,
|
|
meson-python,
|
|
networkx,
|
|
numpy,
|
|
packaging,
|
|
pillow,
|
|
pooch,
|
|
pyamg,
|
|
pytestCheckHook,
|
|
numpydoc,
|
|
pythran,
|
|
pywavelets,
|
|
scikit-learn,
|
|
scipy,
|
|
setuptools,
|
|
simpleitk,
|
|
tifffile,
|
|
wheel,
|
|
}:
|
|
|
|
let
|
|
installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";
|
|
self = buildPythonPackage rec {
|
|
pname = "scikit-image";
|
|
version = "0.22.0";
|
|
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 =
|
|
[
|
|
"${installedPackageRoot}"
|
|
"--pyargs"
|
|
"skimage"
|
|
]
|
|
++ builtins.map (testid: "--deselect=" + testid) (
|
|
[
|
|
# These tests require network access
|
|
"skimage/data/test_data.py::test_skin"
|
|
"skimage/data/tests/test_data.py::test_skin"
|
|
"skimage/io/tests/test_io.py::test_imread_http_url"
|
|
"skimage/restoration/tests/test_rolling_ball.py::test_ndim"
|
|
]
|
|
++ lib.optionals stdenv.hostPlatform.isDarwin [
|
|
# Matplotlib tests are broken inside darwin sandbox
|
|
"skimage/feature/tests/test_util.py::test_plot_matches"
|
|
"skimage/filters/tests/test_thresholding.py::TestSimpleImage::test_try_all_threshold"
|
|
"skimage/io/tests/test_mpl_imshow.py::"
|
|
# See https://github.com/scikit-image/scikit-image/issues/7061 and https://github.com/scikit-image/scikit-image/issues/7104
|
|
"skimage/measure/tests/test_fit.py"
|
|
]
|
|
++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
|
|
# https://github.com/scikit-image/scikit-image/issues/7104
|
|
"skimage/measure/tests/test_moments.py"
|
|
]
|
|
);
|
|
|
|
# Check cythonized modules
|
|
pythonImportsCheck = [
|
|
"skimage"
|
|
"skimage._shared"
|
|
"skimage.draw"
|
|
"skimage.feature"
|
|
"skimage.restoration"
|
|
"skimage.filters"
|
|
"skimage.graph"
|
|
"skimage.io"
|
|
"skimage.measure"
|
|
"skimage.morphology"
|
|
"skimage.transform"
|
|
"skimage.util"
|
|
"skimage.segmentation"
|
|
];
|
|
|
|
passthru.tests = {
|
|
all-tests = self.override { doCheck = true; };
|
|
};
|
|
|
|
meta = {
|
|
description = "Image processing routines for SciPy";
|
|
homepage = "https://scikit-image.org";
|
|
changelog = "https://github.com/scikit-image/scikit-image/releases/tag/${lib.removePrefix "refs/tags/" src.rev}";
|
|
license = lib.licenses.bsd3;
|
|
maintainers = with lib.maintainers; [ yl3dy ];
|
|
};
|
|
};
|
|
in
|
|
self
|