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

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

@@ -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

@@ -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
-    ];
   };
-}
+})