Unverified Commit dba8a3ef authored by Mario Rodas's avatar Mario Rodas Committed by GitHub
Browse files

Merge pull request #265927 from bcdarwin/itk-unvendor 

itk: unvendor some of the dependencies
parents b56dc6be dc16ee70

pkgs/development/libraries/gdcm/default.nix

+2 −0
Original line number Diff line number Diff line
@@ -76,6 +76,8 @@ stdenv.mkDerivation rec { 
    "TestSCUValidation"

    # errors because 3 classes not wrapped:

    "TestWrapPython"

  ] ++ lib.optionals (stdenv.isAarch64 && stdenv.isLinux) [

    "TestRescaler2"

  ];



  checkPhase = ''

pkgs/development/libraries/itk/generic.nix

+32 −11
Original line number Diff line number Diff line 
{ version, rev, sourceSha256 }:



{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper

, pkg-config, libX11, libuuid, xz, vtk, Cocoa }:

{ lib, stdenv, fetchFromGitHub, cmake

, expat, fftw, gdcm, hdf5-cpp, libjpeg, libminc, libtiff, libpng

, libX11, libuuid, xz, vtk, zlib, Cocoa }:



let

  itkGenericLabelInterpolatorSrc = fetchFromGitHub {
@@ -41,8 +42,6 @@ stdenv.mkDerivation { 
    substituteInPlace CMake/ITKSetStandardCompilerFlags.cmake  \

      --replace "-march=corei7" ""  \

      --replace "-mtune=native" ""

    substituteInPlace Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/libopenjp2.pc.cmake.in  \

      --replace "@OPENJPEG_INSTALL_LIB_DIR@" "@OPENJPEG_INSTALL_FULL_LIB_DIR@"

    ln -sr ${itkGenericLabelInterpolatorSrc} Modules/External/ITKGenericLabelInterpolator

    ln -sr ${itkAdaptiveDenoisingSrc} Modules/External/ITKAdaptiveDenoising

    ln -sr ${itkSimpleITKFiltersSrc} Modules/External/ITKSimpleITKFilters
@@ -52,6 +51,15 @@ stdenv.mkDerivation { 
    "-DBUILD_EXAMPLES=OFF"

    "-DBUILD_SHARED_LIBS=ON"

    "-DITK_FORBID_DOWNLOADS=ON"

    "-DITK_USE_SYSTEM_LIBRARIES=ON"  # finds common libraries e.g. hdf5, libpng, libtiff, zlib, but not GDCM, NIFTI, MINC, etc.

    # note ITK_USE_SYSTEM_EIGEN, part of ITK_USE_SYSTEM_LIBRARIES,

    # causes "...-itk-5.2.1/include/ITK-5.2/itkSymmetricEigenAnalysis.h:23:31: fatal error: Eigen/Eigenvalues: No such file or directory"

    # when compiling c3d, but maybe an ITK 5.2/eigen version issue:

    "-DITK_USE_SYSTEM_EIGEN=OFF"

    "-DITK_USE_SYSTEM_GOOGLETEST=OFF"  # ANTs build failure due to https://github.com/ANTsX/ANTs/issues/1489

    "-DITK_USE_SYSTEM_GDCM=ON"

    "-DITK_USE_SYSTEM_MINC=ON"

    "-DLIBMINC_DIR=${libminc}/lib/cmake"

    "-DModule_ITKMINC=ON"

    "-DModule_ITKIOMINC=ON"

    "-DModule_ITKIOTransformMINC=ON"
@@ -63,8 +71,12 @@ stdenv.mkDerivation { 
    "-DModule_GenericLabelInterpolator=ON"

  ];



  nativeBuildInputs = [ cmake xz makeWrapper ];

  buildInputs = [ libX11 libuuid vtk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];

  nativeBuildInputs = [ cmake xz ];

  buildInputs = [

    libX11

    libuuid

    vtk

  ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];

  # Due to ITKVtkGlue=ON and the additional dependencies needed to configure VTK 9

  # (specifically libGL and libX11 on Linux),

  # it's now seemingly necessary for packages that configure ITK to
@@ -72,11 +84,20 @@ stdenv.mkDerivation { 
  # These deps were propagated from VTK 9 in https://github.com/NixOS/nixpkgs/pull/206935,

  # so we simply propagate them again from ITK.

  # This admittedly is a hack and seems like an issue with VTK 9's CMake configuration.

  propagatedBuildInputs = vtk.propagatedBuildInputs;



  postInstall = ''

    wrapProgram "$out/bin/h5c++" --prefix PATH ":" "${pkg-config}/bin"

  '';

  propagatedBuildInputs = [

    # The dependencies we've un-vendored from ITK, such as GDCM, must be propagated,

    # otherwise other software built against ITK fails to configure since ITK headers

    # refer to these previously vendored libraries:

    expat

    fftw

    gdcm

    hdf5-cpp

    libjpeg

    libminc

    libpng

    libtiff

    zlib

  ] ++ vtk.propagatedBuildInputs;



  meta = {

    description = "Insight Segmentation and Registration Toolkit";