Arch Linux User Repository

Sorry this fell off my radar. I'm running into some issues testing entshuld's contribution, but will update this today if I'm able to get it built and packaged.

I have some amendments to share

• 1. Allow Python wrappers independent of locale.
• 2. ```makepkg -C``` exists to clean if the user so wishes
• 3. use pkgname and pkgver instead of InsightToolkit

--- a/PKGBUILD
+++ b/PKGBUILD
@@ -23,19 +23,56 @@ optdepends=('python2: build python wrapping'
             'clang: for swig'
        'castxml-git: for ITK')
 makedepends=('cmake' 'git')
-source=("https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${pkgver}/InsightToolkit-${pkgver}.tar.gz")
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${pkgver}/InsightToolkit-${pkgver}.tar.gz")
 sha512sums=('6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7')
+provides=(python-itk=${pkgver})
+conflicts=(python-itk)
+options=(!emptydirs)

-_usepython=false
+safe_flags="-Wp,-D_FORTIFY_SOURCE=2,-D_GLIBCXX_ASSERTIONS"
+safe_flags+=" -fcf-protection -fno-plt"
+safe_flags+=" -fstack-clash-protection -Wformat"
+safe_flags+=" -Werror=format-security"
+generic_flags="-pipe -fno-plt -fPIC -fopenmp"
+generic_flags+=" -march=native"
+generic_flags+=" -mtune=native ${safe_flags}"
+opt_flags="${generic_flags} -O3"
+generic_flags="${generic_flags} -O2"
+
+export COPTFLAGS="${opt_flags}"
+export CXXOPTFLAGS="$COPTFLAGS"
+export FOPTFLAGS="$COPTFLAGS"
+export CPPFLAGS="$generic_flags"
+export CXXFLAGS="$CPPFLAGS"
+export CFLAGS="$generic_flags"
+export FFLAGS="$generic_flags"
+export FCFLAGS="$generic_flags"
+export F90FLAGS="$generic_flags"
+export F77FLAGS="$generic_flags"
+
+export LANG=C
+export OMPI_MCA_opal_cuda_support=0
+export OMPI_MCA_mpi_oversubscribe=0
+
+_usepython=true
+# https://github.com/InsightSoftwareConsortium/ITK/search?q=typeinfo&type=issues
+# https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538?focusedCommentId=27765&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-27765
+# from here: https://github.com/InsightSoftwareConsortium/ITK/issues/1701#issuecomment-598311460
+export LC_ALL=C LANG=C LANGUAGE=C
+
+prepare() {
+  cd "$srcdir"
+  [[ -d InsightToolkit-"${pkgver}" ]] &&
+    mv InsightToolkit-"${pkgver}" "${pkgname}"-"${pkgver}"
+}

 build() {
   cd "$srcdir"
-  rm -rf build
-  mkdir build
-  cd build

-  cmake \
+  cmake -S "${srcdir}/${pkgname}-${pkgver}" \
+    -B "${srcdir}/${pkgname}-${pkgver}"/build \
     -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
     -DBUILD_TESTING:BOOL=OFF \
     -DBUILD_EXAMPLES:BOOL=OFF \
     -DBUILD_SHARED_LIBS:BOOL=ON \
@@ -56,16 +93,25 @@ build() {
     -DITK_USE_SYSTEM_EXPAT:BOOL=ON \
     -DITK_USE_SYSTEM_FFTW:BOOL=ON \
     -DITK_USE_SYSTEM_HDF5:BOOL=ON \
+    -DITK_USE_64BITS_IDS:BOOL=ON \
+    -DITK_LEGACY_REMOVE:BOOL=ON \
     -DModule_ITKIOMINC:BOOL=ON \
     -DModule_ITKIOTransformMINC:BOOL=ON \
-    -DModule_SimpleITKFilters:BOOL=ON \
-    ../InsightToolkit-${pkgver}
+    -DModule_SimpleITKFilters:BOOL=ON

-  make
+  # 4: to your liking
+  make -j4 -s -C "${srcdir}/${pkgname}-${pkgver}"/build
 }

 package() {
-  cd "$srcdir"/build
+  cd "${srcdir}/${pkgname}-${pkgver}"/build
+
+  make -C "${srcdir}"/"${pkgname}-${pkgver}"/build DESTDIR="${pkgdir}" install

-  make DESTDIR="${pkgdir}" install
+  # Based on AUR's itk-git package
+  # (quick fix for https://github.com/InsightSoftwareConsortium/ITK/issues/2960)
+  install -dm755 "${pkgdir}"/usr/lib
+  _pyver=$(python -c 'import sys; print(str(sys.version_info[0]) + "." + str(sys.version_info[1]))')
+  find "${pkgdir}" -type d -name "python${_pyver}" -print0 -quit | xargs -0 mv -vt "${pkgdir}/usr/lib"
+  python -O -m compileall "${pkgdir}/usr/lib"
 }

@m-pilia @crmullins Maybe merge insight-toolkit, itk, and python-itk, and keep only itk and python-itk? I currently maintain itk-git and python-itk-git here.

Hi @crmullins! I was wondering if we could improve a bit the Python distribution of ITK.

The current situation is: the Python wheels can be built from your PKGBUILD but are disabled by default and require manual intervention. There is also a separate package for the Python part only (python-itk, that I maintain) but it does not make sense to build the wheels separately from insight-toolkit, since it is a lot of duplicated build time. (context in this comment).

The best solution would be to turn insight-toolkit into a split package, so that it is possible to build both insight-toolkit and python-itk from the same PKGBUILD.

Hottea has kindly created a split PKGBUILD here. Could you consider updating this package to use Hottea's approach? (pushing the split package will require to delete python-itk first: feel free to nominate my package for deletion because of this reason).

Please add git to makedepends, otherwise it does not build (in a https://wiki.archlinux.org/title/DeveloperWiki:Building_in_a_clean_chroot).

could you please change the dependency from 'hdf5-cpp-fortran' to 'hdf5'? The special cpp/fortran versions doe not exist anymore.

Hi! Could you please add the SimpleITKFilters module to the package (CMake command line flag -DModule_SimpleITKFilters:BOOL=ON)? It is required to build simpleitk version >=2.0.

Hi, it would be great if you could add the Generic Label Interpolator flag to the build process: https://itk.org/Doxygen/html/group__GenericLabelInterpolator.html

This is necessary for ITK to be used by ANTs: https://github.com/ANTsX/ANTs/issues/817