Unverified Commit 50b30f81 authored by kirillrdy's avatar kirillrdy Committed by GitHub
Browse files

python3Packages.nibabel: cleanup, fix on darwin (#480291)

parents 79ccb839 bca3dcb3

pkgs/development/python-modules/nibabel/default.nix

+17 −12
Original line number Diff line number Diff line
@@ -5,17 +5,25 @@ 
  fetchpatch2,

  pythonAtLeast,

  pythonOlder,

  hatchling,



  # build-system

  hatch-vcs,

  hatchling,



  # dependencies

  numpy,

  packaging,

  importlib-resources,

  typing-extensions,



  # optional-dependencies

  pydicom,

  pillow,

  h5py,

  scipy,

  git,



  addBinToPathHook,

  gitMinimal,

  pytest-doctestplus,

  pytest-httpserver,

  pytest-xdist,
@@ -42,8 +50,8 @@ buildPythonPackage (finalAttrs: { 
  ];



  build-system = [

    hatchling

    hatch-vcs

    hatchling

  ];



  dependencies = [
@@ -53,19 +61,20 @@ buildPythonPackage (finalAttrs: { 
  ++ lib.optionals (pythonOlder "3.12") [ importlib-resources ]

  ++ lib.optionals (pythonOlder "3.13") [ typing-extensions ];



  optional-dependencies = rec {

    all = dicom ++ dicomfs ++ minc2 ++ spm ++ zstd;

  optional-dependencies = lib.fix (self: {

    all = self.dicom ++ self.dicomfs ++ self.minc2 ++ self.spm ++ self.zstd;

    dicom = [ pydicom ];

    dicomfs = [ pillow ] ++ dicom;

    dicomfs = [ pillow ] ++ self.dicom;

    minc2 = [ h5py ];

    spm = [ scipy ];

    zstd = [

      # TODO: pyzstd

    ];

  };

  });



  nativeCheckInputs = [

    git

    addBinToPathHook

    gitMinimal

    pytest-doctestplus

    pytest-httpserver

    pytest-xdist
@@ -78,10 +87,6 @@ buildPythonPackage (finalAttrs: { 
    "test_deprecator_maker"

  ];



  preCheck = ''

    export PATH=$out/bin:$PATH

  '';



  meta = {

    homepage = "https://nipy.org/nibabel";

    changelog = "https://github.com/nipy/nibabel/blob/${finalAttrs.version}/Changelog";

pkgs/development/python-modules/pydicom/default.nix

+5 −13
Original line number Diff line number Diff line
@@ -26,7 +26,7 @@ let 
    hash = "sha256-ji7SppKdiszaXs8yCSIPkJj4Ld++XWNw9FuxLoFLfFo=";

  };

in

buildPythonPackage rec {

buildPythonPackage (finalAttrs: {

  pname = "pydicom";

  version = "3.0.1";

  pyproject = true;
@@ -34,7 +34,7 @@ buildPythonPackage rec { 
  src = fetchFromGitHub {

    owner = "pydicom";

    repo = "pydicom";

    tag = "v${version}";

    tag = "v${finalAttrs.version}";

    hash = "sha256-SvRevQehRaSp+vCtJRQVEJiC5noIJS+bGG1/q4p7/XU=";

  };
@@ -60,7 +60,7 @@ buildPythonPackage rec { 
    pytestCheckHook

    writableTmpDirAsHomeHook

  ]

  ++ optional-dependencies.pixeldata;

  ++ finalAttrs.passthru.optional-dependencies.pixeldata;



  passthru.pydicom-data = test_data;
@@ -105,16 +105,8 @@ buildPythonPackage rec { 
    description = "Python package for working with DICOM files";

    mainProgram = "pydicom";

    homepage = "https://pydicom.github.io";

    changelog = "https://github.com/pydicom/pydicom/releases/tag/v${version}";

    changelog = "https://github.com/pydicom/pydicom/releases/tag/${finalAttrs.src.tag}";

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ bcdarwin ];

    badPlatforms = [

      # > 200 tests are failing with errors like:

      # AttributeError: 'FileDataset' object has no attribute 'BitsStored'

      # AttributeError: 'FileDataset' object has no attribute 'Rows'

      # AttributeError: The dataset has no 'Pixel Data', 'Float Pixel Data' or 'Double Float Pixel Data' element, no pixel data to decode

      # pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header.

      lib.systems.inspect.patterns.isDarwin

    ];

  };

}
 
})