python312Packages.pydicom: 2.4.4 -> 3.0.1; unbreak (#368584)

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

@@ -2,13 +2,13 @@
   lib,
   buildPythonPackage,
   fetchPypi,
-  pythonAtLeast,
   pythonOlder,
   hatchling,
   hatch-vcs,
   numpy,
   packaging,
   importlib-resources,
+  typing-extensions,
   pydicom,
   pillow,
   h5py,
@@ -22,25 +22,28 @@
 
 buildPythonPackage rec {
   pname = "nibabel";
-  version = "5.2.1";
+  version = "5.3.2";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
+  disabled = pythonOlder "3.9";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-tsgLLnKOS8K2XxFC2bjSKHqRAqi/hHfhFe8NgzRVmXU=";
+    hash = "sha256-C9ymUDsceEtEbHRaRUI2fed1bPug1yFDuR+f+3i+Vps=";
   };
 
-  nativeBuildInputs = [
+  build-system = [
     hatchling
     hatch-vcs
   ];
 
-  propagatedBuildInputs = [
-    numpy
-    packaging
-  ] ++ lib.optionals (pythonOlder "3.9") [ importlib-resources ];
+  dependencies =
+    [
+      numpy
+      packaging
+    ]
+    ++ lib.optionals (pythonOlder "3.12") [ importlib-resources ]
+    ++ lib.optionals (pythonOlder "3.13") [ typing-extensions ];
 
   optional-dependencies = rec {
     all = dicom ++ dicomfs ++ minc2 ++ spm ++ zstd;
@@ -65,11 +68,6 @@ buildPythonPackage rec {
     export PATH=$out/bin:$PATH
   '';
 
-  disabledTestPaths = lib.optionals (pythonAtLeast "3.12") [
-    # uses distutils
-    "nisext/tests/test_sexts.py"
-  ];
-
   meta = with lib; {
     homepage = "https://nipy.org/nibabel";
     changelog = "https://github.com/nipy/nibabel/blob/${version}/Changelog";

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

@@ -3,54 +3,59 @@
   stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+  pythonOlder,
   flit-core,
   numpy,
-  pillow,
   pytestCheckHook,
-  pythonOlder,
-  setuptools,
+
+  # optional/test dependencies
+  gdcm,
+  pillow,
+  pylibjpeg,
+  pylibjpeg-libjpeg,
 }:
-
 let
-  pname = "pydicom";
-  version = "2.4.4";
-
-  src = fetchFromGitHub {
-    owner = "pydicom";
-    repo = "pydicom";
-    rev = "refs/tags/v${version}";
-    hash = "sha256-iJE1horEmdL7bKPn+NlZLgmtCbLZCZWQ8NjDBQPzXk8=";
-  };
-
   # 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 = "cbb9b2148bccf0f550e3758c07aca3d0e328e768";
-    hash = "sha256-nF/j7pfcEpWHjjsqqTtIkW8hCEbuQ3J4IxpRk0qc1CQ=";
+    rev = "8da482f208401d63cd63f3f4efc41b6856ef36c7";
+    hash = "sha256-ji7SppKdiszaXs8yCSIPkJj4Ld++XWNw9FuxLoFLfFo=";
   };
 in
-buildPythonPackage {
-  inherit pname version src;
+buildPythonPackage rec {
+  pname = "pydicom";
+  version = "3.0.1";
   pyproject = true;
 
   disabled = pythonOlder "3.10";
 
-  patches = [
-    # backport of https://github.com/pydicom/pydicom/commit/2513a20cc41743a42bdb86f4cbb4873899b7823c
-    ./pillow-10.1.0-compat.patch
-  ];
+  src = fetchFromGitHub {
+    owner = "pydicom";
+    repo = "pydicom";
+    tag = "v${version}";
+    hash = "sha256-SvRevQehRaSp+vCtJRQVEJiC5noIJS+bGG1/q4p7/XU=";
+  };
 
-  nativeBuildInputs = [ flit-core ];
+  build-system = [ flit-core ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     numpy
-    pillow
-    setuptools
   ];
 
-  nativeCheckInputs = [ pytestCheckHook ];
+  optional-dependencies = {
+    pixeldata = [
+      pillow
+      #pyjpegls # not in nixpkgs
+      #pylibjpeg.optional-dependencies.openjpeg # infinite recursion
+      #pylibjpeg.optional-dependencies.rle # not in nixpkgs
+      pylibjpeg-libjpeg
+      gdcm
+    ];
+  };
+
+  nativeCheckInputs = [ pytestCheckHook ] ++ optional-dependencies.pixeldata;
 
   # Setting $HOME to prevent pytest to try to create a folder inside
   # /homeless-shelter which is read-only.
@@ -65,6 +70,14 @@ buildPythonPackage {
     [
       # 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

pkgs/development/python-modules/pydicom/pillow-10.1.0-compat.patch

@@ -1,29 +0,0 @@
-diff --git a/pydicom/pixel_data_handlers/pillow_handler.py b/pydicom/pixel_data_handlers/pillow_handler.py
-index ff781025d..a44eb9a41 100644
---- a/pydicom/pixel_data_handlers/pillow_handler.py
-+++ b/pydicom/pixel_data_handlers/pillow_handler.py
-@@ -119,18 +119,12 @@ def _decompress_single_frame(
-     # space prior to compression, setting the value of "mode" to YCbCr
-     # signals Pillow to not apply any color transformation upon
-     # decompression.
--    if (transfer_syntax in PillowJPEGTransferSyntaxes and
--            photometric_interpretation == 'RGB'):
--        if 'adobe_transform' not in image.info:
--            color_mode = 'YCbCr'
--            image.tile = [(
--                'jpeg',
--                image.tile[0][1],
--                image.tile[0][2],
--                (color_mode, ''),
--            )]
--            image.mode = color_mode
--            image.rawmode = color_mode
-+    if (
-+        transfer_syntax in PillowJPEGTransferSyntaxes
-+        and photometric_interpretation == 'RGB'
-+        and "adobe_transform" not in image.info
-+    ):
-+        image.draft("YCbCr", image.size)
-     return image
- 
- 

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

@@ -9,6 +9,7 @@
   pydicom,
   pylibjpeg-data,
   pylibjpeg-libjpeg,
+  pylibjpeg-openjpeg,
 }:
 
 buildPythonPackage rec {
@@ -29,6 +30,12 @@ buildPythonPackage rec {
 
   dependencies = [ numpy ];
 
+  optional-dependencies = {
+    libjpeg = [ pylibjpeg-libjpeg ];
+    openjpeg = [ pylibjpeg-openjpeg ];
+    #rle = [ pylibjpeg-rle ]; # not in Nixpkgs
+  };
+
   nativeCheckInputs = [
     pytestCheckHook
     pydicom