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{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,
flit-core,
numpy,
pytestCheckHook,
# optional/test dependencies
gdcm,
pillow,
pydicom,
pyjpegls,
pylibjpeg,
pylibjpeg-libjpeg,
writableTmpDirAsHomeHook,
}:
let
# Pydicom needs pydicom-data to run some tests. If these files aren't downloaded
# before the package creation, it'll try to download during the checkPhase.
test_data = fetchFromGitHub {
owner = "pydicom";
repo = "pydicom-data";
rev = "8da482f208401d63cd63f3f4efc41b6856ef36c7";
hash = "sha256-ji7SppKdiszaXs8yCSIPkJj4Ld++XWNw9FuxLoFLfFo=";
};
in
buildPythonPackage (finalAttrs: {
pname = "pydicom";
version = "3.0.1";
pyproject = true;
src = fetchFromGitHub {
owner = "pydicom";
repo = "pydicom";
tag = "v${finalAttrs.version}";
hash = "sha256-SvRevQehRaSp+vCtJRQVEJiC5noIJS+bGG1/q4p7/XU=";
};
build-system = [ flit-core ];
dependencies = [
numpy
];
optional-dependencies = {
pixeldata = [
pillow
pyjpegls
pylibjpeg
pylibjpeg-libjpeg
gdcm
]
++ pylibjpeg.optional-dependencies.openjpeg
++ pylibjpeg.optional-dependencies.rle;
};
nativeCheckInputs = [
pytestCheckHook
writableTmpDirAsHomeHook
]
++ finalAttrs.passthru.optional-dependencies.pixeldata;
passthru.pydicom-data = test_data;
doCheck = false; # circular dependency
passthru.tests.pytest = pydicom.overridePythonAttrs {
doCheck = true;
};
# Setting $HOME to prevent pytest to try to create a folder inside
# /homeless-shelter which is read-only.
# Linking pydicom-data dicom files to $HOME/.pydicom/data
preCheck = ''
mkdir -p $HOME/.pydicom/
ln -s ${test_data}/data_store/data $HOME/.pydicom/data
'';
disabledTests = [
# tries to remove a dicom inside $HOME/.pydicom/data/ and download it again
"test_fetch_data_files"
# test_reference_expl{,_binary}[parametric_map_float.dcm] tries to download that file for some reason even though it's present in test-data
"test_reference_expl"
"test_reference_expl_binary"
# slight error in regex matching
"test_no_decoders_raises"
"test_deepcopy_bufferedreader_raises"
]
++ lib.optionals stdenv.hostPlatform.isAarch64 [
# https://github.com/pydicom/pydicom/issues/1386
"test_array"
]
++ lib.optionals stdenv.hostPlatform.isDarwin [
# flaky, hard to reproduce failure outside hydra
"test_time_check"
];
pythonImportsCheck = [ "pydicom" ];
meta = {
description = "Python package for working with DICOM files";
mainProgram = "pydicom";
homepage = "https://pydicom.github.io";
changelog = "https://github.com/pydicom/pydicom/releases/tag/${finalAttrs.src.tag}";
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ bcdarwin ];
};
})
|
