python312Packages.itk: init at 5.4.0
This commit is contained in:
Ben Darwin
parent
53a541a222
commit
06fc8aa4dc
@ -10,6 +10,8 @@
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fetchFromGitHub,
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fetchpatch,
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cmake,
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castxml,
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swig,
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expat,
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fftw,
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gdcm,
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@ -20,13 +22,21 @@
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libpng,
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libX11,
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libuuid,
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patchelf,
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python ? null,
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numpy ? null,
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xz,
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vtk,
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which,
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zlib,
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Cocoa,
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enablePython ? false,
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}:
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let
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# Python wrapper contains its own VTK support incompatible with MODULE_ITKVtkGlue
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withVtk = !enablePython;
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itkGenericLabelInterpolatorSrc = fetchFromGitHub {
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owner = "InsightSoftwareConsortium";
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repo = "ITKGenericLabelInterpolator";
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@ -47,6 +57,19 @@ let
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rev = "bb896868fc6480835495d0da4356d5db009592a6";
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hash = "sha256-MfaIA0xxA/pzUBSwnAevr17iR23Bo5iQO2cSyknS3o4=";
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};
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# remove after next swig update:
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swigUnstable = swig.overrideAttrs ({
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version = "4.2.1-unstable-2024-08-19";
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src = fetchFromGitHub {
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owner = "swig";
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repo = "swig";
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rev = "5ac5d90f970759fbe705fae551d0743a7c63c67e";
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hash = "sha256-32EFLHpP4l04nqrc8dt4Qsr8deTBqLt8lUlhnNnaIGU=";
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};
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});
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in
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stdenv.mkDerivation {
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@ -77,39 +100,56 @@ stdenv.mkDerivation {
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ln -sr ${itkSimpleITKFiltersSrc} Modules/External/ITKSimpleITKFilters
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'';
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cmakeFlags = [
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"-DBUILD_EXAMPLES=OFF"
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"-DBUILD_SHARED_LIBS=ON"
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"-DITK_FORBID_DOWNLOADS=ON"
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"-DITK_USE_SYSTEM_LIBRARIES=ON" # finds common libraries e.g. hdf5, libpng, libtiff, zlib, but not GDCM, NIFTI, MINC, etc.
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# note ITK_USE_SYSTEM_EIGEN, part of ITK_USE_SYSTEM_LIBRARIES,
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# causes "...-itk-5.2.1/include/ITK-5.2/itkSymmetricEigenAnalysis.h:23:31: fatal error: Eigen/Eigenvalues: No such file or directory"
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# when compiling c3d, but maybe an ITK 5.2/eigen version issue:
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"-DITK_USE_SYSTEM_EIGEN=OFF"
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"-DITK_USE_SYSTEM_GOOGLETEST=OFF" # ANTs build failure due to https://github.com/ANTsX/ANTs/issues/1489
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"-DITK_USE_SYSTEM_GDCM=ON"
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"-DITK_USE_SYSTEM_MINC=ON"
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"-DLIBMINC_DIR=${libminc}/lib/cmake"
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"-DModule_ITKMINC=ON"
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"-DModule_ITKIOMINC=ON"
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"-DModule_ITKIOTransformMINC=ON"
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"-DModule_SimpleITKFilters=ON"
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"-DModule_ITKVtkGlue=ON"
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"-DModule_ITKReview=ON"
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"-DModule_MGHIO=ON"
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"-DModule_AdaptiveDenoising=ON"
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"-DModule_GenericLabelInterpolator=ON"
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];
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cmakeFlags =
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[
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"-DBUILD_EXAMPLES=OFF"
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"-DBUILD_SHARED_LIBS=ON"
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"-DITK_FORBID_DOWNLOADS=ON"
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"-DITK_USE_SYSTEM_LIBRARIES=ON" # finds common libraries e.g. hdf5, libpng, libtiff, zlib, but not GDCM, NIFTI, MINC, etc.
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# note ITK_USE_SYSTEM_EIGEN, part of ITK_USE_SYSTEM_LIBRARIES,
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# causes "...-itk-5.2.1/include/ITK-5.2/itkSymmetricEigenAnalysis.h:23:31: fatal error: Eigen/Eigenvalues: No such file or directory"
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# when compiling c3d, but maybe an ITK 5.2/eigen version issue:
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"-DITK_USE_SYSTEM_EIGEN=OFF"
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"-DITK_USE_SYSTEM_GOOGLETEST=OFF" # ANTs build failure due to https://github.com/ANTsX/ANTs/issues/1489
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"-DITK_USE_SYSTEM_GDCM=ON"
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"-DITK_USE_SYSTEM_MINC=ON"
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"-DLIBMINC_DIR=${libminc}/lib/cmake"
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"-DModule_ITKMINC=ON"
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"-DModule_ITKIOMINC=ON"
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"-DModule_ITKIOTransformMINC=ON"
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"-DModule_SimpleITKFilters=ON"
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"-DModule_ITKReview=ON"
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"-DModule_MGHIO=ON"
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"-DModule_AdaptiveDenoising=ON"
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"-DModule_GenericLabelInterpolator=ON"
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]
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++ lib.optionals enablePython [
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"-DITK_WRAP_PYTHON=ON"
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"-DITK_USE_SYSTEM_CASTXML=ON"
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"-DITK_USE_SYSTEM_SWIG=ON"
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"-DPY_SITE_PACKAGES_PATH=${placeholder "out"}/${python.sitePackages}"
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]
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++ lib.optionals withVtk [ "-DModule_ITKVtkGlue=ON" ];
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nativeBuildInputs = [
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cmake
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xz
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];
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buildInputs = [
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libX11
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libuuid
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vtk
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] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
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nativeBuildInputs =
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[
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cmake
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xz
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]
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++ lib.optionals enablePython [
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castxml
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swigUnstable
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which
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];
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buildInputs =
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[
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libX11
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libuuid
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]
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++ lib.optionals stdenv.isDarwin [ Cocoa ]
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++ lib.optionals enablePython [ python ]
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++ lib.optionals withVtk [ vtk ];
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# Due to ITKVtkGlue=ON and the additional dependencies needed to configure VTK 9
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# (specifically libGL and libX11 on Linux),
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# it's now seemingly necessary for packages that configure ITK to
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@ -130,12 +170,30 @@ stdenv.mkDerivation {
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libpng
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libtiff
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zlib
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] ++ vtk.propagatedBuildInputs;
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] ++ lib.optionals withVtk vtk.propagatedBuildInputs ++ lib.optionals enablePython [ numpy ];
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postInstall = lib.optionalString enablePython ''
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substitute \
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${./itk.egg-info} \
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$out/${python.sitePackages}/itk-${version}.egg-info \
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--subst-var-by ITK_VER "${version}"
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'';
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# remove forbidden reference to /build which occur when building the Python wrapping
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# (also remove a copy of itkTestDriver with incorrect permissions/RPATH):
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preFixup = lib.optionals enablePython ''
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rm $out/${python.sitePackages}/itk/itkTestDriver
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find $out/${python.sitePackages}/itk -type f -name '*.so*' -exec \
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patchelf {} --shrink-rpath --allowed-rpath-prefixes "$NIX_STORE" \;
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'';
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meta = {
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description = "Insight Segmentation and Registration Toolkit";
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homepage = "https://www.itk.org";
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license = lib.licenses.asl20;
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maintainers = with lib.maintainers; [ bcdarwin ];
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# aarch64-linux Python wrapping fails with "error: unknown type name '_Float128'" and similar;
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# compilation runs slowly and times out on Darwin
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platforms = with lib.platforms; if enablePython then [ "x86_64-linux" ] else unix;
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};
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}
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5
pkgs/development/libraries/itk/itk.egg-info
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5
pkgs/development/libraries/itk/itk.egg-info
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@ -0,0 +1,5 @@
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Metadata-Version: 2.1
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Name: itk
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Version: @ITK_VER@
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Summary: Insight Segmentation and Registration Toolkit
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Platform: UNKNOWN
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@ -6206,6 +6206,12 @@ self: super: with self; {
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itanium-demangler = callPackage ../development/python-modules/itanium-demangler { };
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itk = toPythonModule (pkgs.itk.override {
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inherit python numpy;
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enablePython = true;
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});
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item-synchronizer = callPackage ../development/python-modules/item-synchronizer { };
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itemadapter = callPackage ../development/python-modules/itemadapter { };
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@ -14477,7 +14483,7 @@ self: super: with self; {
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simplehound = callPackage ../development/python-modules/simplehound { };
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simpleitk = callPackage ../development/python-modules/simpleitk {
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inherit (pkgs) simpleitk;
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inherit (pkgs) itk simpleitk;
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};
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simplejson = callPackage ../development/python-modules/simplejson { };
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