109 lines
3.1 KiB
Nix
109 lines
3.1 KiB
Nix
{
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lib,
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stdenv,
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buildPythonPackage,
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fetchFromGitHub,
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flit-core,
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numpy,
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pytestCheckHook,
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# optional/test dependencies
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gdcm,
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pillow,
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pylibjpeg-libjpeg,
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writableTmpDirAsHomeHook,
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}:
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let
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# Pydicom needs pydicom-data to run some tests. If these files aren't downloaded
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# before the package creation, it'll try to download during the checkPhase.
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test_data = fetchFromGitHub {
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owner = "pydicom";
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repo = "pydicom-data";
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rev = "8da482f208401d63cd63f3f4efc41b6856ef36c7";
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hash = "sha256-ji7SppKdiszaXs8yCSIPkJj4Ld++XWNw9FuxLoFLfFo=";
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};
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in
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buildPythonPackage rec {
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pname = "pydicom";
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version = "3.0.1";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "pydicom";
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repo = "pydicom";
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tag = "v${version}";
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hash = "sha256-SvRevQehRaSp+vCtJRQVEJiC5noIJS+bGG1/q4p7/XU=";
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};
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build-system = [ flit-core ];
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dependencies = [
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numpy
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];
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optional-dependencies = {
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pixeldata = [
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pillow
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#pyjpegls # not in nixpkgs
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#pylibjpeg.optional-dependencies.openjpeg # infinite recursion
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#pylibjpeg.optional-dependencies.rle # not in nixpkgs
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pylibjpeg-libjpeg
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gdcm
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];
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};
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nativeCheckInputs = [
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pytestCheckHook
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writableTmpDirAsHomeHook
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] ++ optional-dependencies.pixeldata;
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# Setting $HOME to prevent pytest to try to create a folder inside
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# /homeless-shelter which is read-only.
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# Linking pydicom-data dicom files to $HOME/.pydicom/data
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preCheck = ''
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mkdir -p $HOME/.pydicom/
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ln -s ${test_data}/data_store/data $HOME/.pydicom/data
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'';
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disabledTests =
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[
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# tries to remove a dicom inside $HOME/.pydicom/data/ and download it again
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"test_fetch_data_files"
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# test_reference_expl{,_binary}[parametric_map_float.dcm] tries to download that file for some reason even though it's present in test-data
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"test_reference_expl"
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"test_reference_expl_binary"
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# slight error in regex matching
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"test_no_decoders_raises"
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"test_deepcopy_bufferedreader_raises"
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]
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++ lib.optionals stdenv.hostPlatform.isAarch64 [
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# https://github.com/pydicom/pydicom/issues/1386
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"test_array"
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]
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++ lib.optionals stdenv.hostPlatform.isDarwin [
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# flaky, hard to reproduce failure outside hydra
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"test_time_check"
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];
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pythonImportsCheck = [ "pydicom" ];
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meta = {
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description = "Python package for working with DICOM files";
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mainProgram = "pydicom";
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homepage = "https://pydicom.github.io";
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changelog = "https://github.com/pydicom/pydicom/releases/tag/v${version}";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ bcdarwin ];
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badPlatforms = [
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# > 200 tests are failing with errors like:
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# AttributeError: 'FileDataset' object has no attribute 'BitsStored'
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# AttributeError: 'FileDataset' object has no attribute 'Rows'
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# AttributeError: The dataset has no 'Pixel Data', 'Float Pixel Data' or 'Double Float Pixel Data' element, no pixel data to decode
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# pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header.
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lib.systems.inspect.patterns.isDarwin
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];
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};
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}
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