Merge pull request #63 from tbirdso/bump-itk

ENH: Bump ITK to v5.3.0

.github/workflows/build-test-package.yml

@@ -3,8 +3,9 @@ name: Build, test, package
 on: [push,pull_request]
 
 env:
-  itk-git-tag: "171fb2ba33a87041f99328a2f26612ff33aa9cc8"
-  itk-wheel-tag: "v5.3rc04.post3"
+  itk-git-tag: "v5.3.0"
+  itk-wheel-tag: "v5.3.0"
+  itk-python-package-tag: "03391ad738438661fff40bfe37a7cfabd171b9b1"
   opencl-icd-loader-git-tag: "v2021.04.29"
   opencl-headers-git-tag: "v2021.04.29"
   vkfft-backend: 3
@@ -17,13 +18,13 @@ jobs:
     strategy:
       max-parallel: 3
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-20.04, windows-2022, macos-11]
         include:
           - os: ubuntu-20.04
             c-compiler: "gcc"
             cxx-compiler: "g++"
             cmake-build-type: "MinSizeRel"
-          - os: windows-2019
+          - os: windows-2022
             c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
             cmake-build-type: "Release"
@@ -46,7 +47,7 @@ jobs:
         python -m pip install ninja
 
     - name: Get specific version of CMake, Ninja
-      uses: lukka/get-cmake@v3.18.3
+      uses: lukka/get-cmake@v3.22.2
 
     - name: Download OpenCL-SDK
       if: matrix.os == 'macos-11'
@@ -73,7 +74,7 @@ jobs:
       shell: bash
 
     - name: Install pocl
-      if: matrix.os != 'windows-2019'
+      if: matrix.os != 'windows-2022'
       run: |
         sudo conda config --add channels conda-forge
         sudo conda config --set channel_priority strict
@@ -98,7 +99,7 @@ jobs:
       shell: bash
 
     - name: Build OpenCL-ICD-Loader
-      if: matrix.os != 'windows-2019'
+      if: matrix.os != 'windows-2022'
       run: |
         cd ..
         mkdir OpenCL-ICD-Loader-build
@@ -107,18 +108,18 @@ jobs:
         sudo cmake --build . --target install
 
     - name: Build OpenCL-ICD-Loader
-      if: matrix.os == 'windows-2019'
+      if: matrix.os == 'windows-2022'
       run: |
         cd ..
         mkdir OpenCL-ICD-Loader-build
         cd OpenCL-ICD-Loader-build
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../OpenCL-ICD-Loader
         cmake --build . --target install
       shell: cmd
 
     - name: Build ITK
-      if: matrix.os != 'windows-2019'
+      if: matrix.os != 'windows-2022'
       run: |
         cd ..
         mkdir ITK-build
@@ -127,12 +128,12 @@ jobs:
         ninja
 
     - name: Build ITK
-      if: matrix.os == 'windows-2019'
+      if: matrix.os == 'windows-2022'
       run: |
         cd ..
         mkdir ITK-build
         cd ITK-build
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK
         ninja
       shell: cmd
@@ -196,31 +197,31 @@ jobs:
       shell: bash
 
     - name: Build and test
-      if: matrix.os != 'windows-2019'
+      if: matrix.os != 'windows-2022'
       run: |
         ctest --output-on-failure -j 2 -V -S dashboard.cmake -R "VkFFTBackend"
 
     - name: Build and test
-      if: matrix.os == 'windows-2019'
+      if: matrix.os == 'windows-2022'
       run: |
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         ctest --output-on-failure -j 2 -V -S dashboard.cmake -R "VkFFTBackend"
       shell: cmd
 
   build-windows-opencl-python-packages:
-    runs-on: windows-2019
+    runs-on: windows-2022
     strategy:
       max-parallel: 2
       matrix:
-        python-version-minor: ["7", "8", "9", "10"]
+        python-version-minor: ["7", "8", "9", "10", "11"]
         include:
           - c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
             cmake-build-type: "MinSizeRel"
 
     steps:
     - name: Get specific version of CMake, Ninja
-      uses: lukka/get-cmake@v3.18.3
+      uses: lukka/get-cmake@v3.22.2
 
     - uses: actions/checkout@v2
       with:
@@ -233,6 +234,7 @@ jobs:
         iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/scikit-build/scikit-ci-addons/master/windows/install-python.ps1'))
 
     - name: 'Fetch build dependencies'
+      shell: bash
       run: |
         mv im ../../
         cd ../../im
@@ -242,7 +244,14 @@ jobs:
         7z x doxygen-1.8.11.windows.bin.zip -o/c/P/doxygen -aoa -r
         curl -L "https://data.kitware.com/api/v1/file/5bbf87ba8d777f06b91f27d6/download/grep-win.zip" -o "grep-win.zip"
         7z x grep-win.zip -o/c/P/grep -aoa -r
-      shell: bash
+
+        echo "Updating ITKPythonPackage build scripts to ${{ env.itk-python-package-tag }}"
+        pushd /c/P/IPP
+        git remote add InsightSoftwareConsortium https://github.com/InsightSoftwareConsortium/ITKPythonPackage.git --tags
+        git fetch InsightSoftwareConsortium
+        git checkout ${{ env.itk-python-package-tag }}
+        git status
+        popd
 
     - name: Download OpenCL-ICD-Loader
       run: |
@@ -265,15 +274,15 @@ jobs:
         cd ..
         mkdir OpenCL-ICD-Loader-build
         cd OpenCL-ICD-Loader-build
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../OpenCL-ICD-Loader
         cmake --build . --target install
       shell: cmd
 
     - name: 'Build 🐍 Python 📦 package'
       run: |
         cd ../../im
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
         set PATH=C:\P\grep;%PATH%
         set CC=cl.exe
         set CXX=cl.exe
@@ -291,7 +300,7 @@ jobs:
     strategy:
       max-parallel: 2
       matrix:
-        python-version: ["37", "38", "39", "310"]
+        python-version: ["37", "38", "39", "310", "311"]
 
     steps:
     - uses: actions/checkout@v2
@@ -305,11 +314,19 @@ jobs:
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
         df -h
 
+    - name: 'Fetch build dependencies'
+      shell: bash
+      run: |
+        sudo apt-get install zstd
+        unzstd --version
+
     - name: 'Build 🐍 Python 📦 package'
       run: |
         export ITK_PACKAGE_VERSION=${{ env.itk-wheel-tag }}
-        export TARBALL_SPECIALIZATION="-manylinux_2_28"
-        ./wrapping/dockcross-manylinux-download-cache.sh
+        export ITKPYTHONPACKAGE_TAG=${{ env.itk-python-package-tag }}
+        export MANYLINUX_VERSION="_2_28"
+        echo "Building for manylinux specialization ${MANYLINUX_VERSION}"
+        ./wrapping/dockcross-manylinux-download-cache.sh cp${{ matrix.python-version }}
         ./wrapping/dockcross-manylinux-build-module-wheels-opencl.sh cp${{ matrix.python-version }}
 
     - name: Publish Python package as GitHub Artifact
@@ -331,16 +348,17 @@ jobs:
         sudo xcode-select -s "/Applications/Xcode_13.2.1.app"
 
     - name: Get specific version of CMake, Ninja
-      uses: lukka/get-cmake@v3.18.3
+      uses: lukka/get-cmake@v3.22.2
 
     - name: 'Fetch build script'
       run: |
-        curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/macpython-download-cache-and-build-module-wheels.sh -O
+        curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/${{ env.itk-python-package-tag }}/scripts/macpython-download-cache-and-build-module-wheels.sh -O
         chmod u+x macpython-download-cache-and-build-module-wheels.sh
 
     - name: 'Build 🐍 Python 📦 package'
       run: |
         export ITK_PACKAGE_VERSION=${{ env.itk-wheel-tag }}
+        export ITKPYTHONPACKAGE_TAG=${{ env.itk-python-package-tag }}
         export MACOSX_DEPLOYMENT_TARGET=10.9
         ./macpython-download-cache-and-build-module-wheels.sh
 

.github/workflows/test-gpu.yml

@@ -3,7 +3,7 @@ name: Test GPU
 on: [pull_request]
 
 env:
-  itk-git-tag: "171fb2ba33a87041f99328a2f26612ff33aa9cc8"
+  itk-git-tag: "abf5fa10522a36bc51f42f20f426a622f42ed90d"
 
 jobs:
   build-test-gpu:
@@ -30,7 +30,7 @@ jobs:
     - uses: actions/checkout@v2
 
     - name: Get specific version of CMake, Ninja
-      uses: lukka/get-cmake@v3.18.3
+      uses: lukka/get-cmake@v3.22.2
 
     - name: Download OpenCL-ICD-Loader
       run: |

setup.py

@@ -12,7 +12,7 @@
 
 setup(
     name="itk-vkfft",
-    version="0.1.9",
+    version="0.2.0",
     author="Insight Software Consortium",
     author_email="itk+community@discourse.itk.org",
     packages=["itk"],
@@ -42,5 +42,5 @@
     license="Apache",
     keywords="ITK InsightToolkit",
     url=r"https://itk.org/",
-    install_requires=[r"itk>=5.3rc04.post3"],
+    install_requires=[r"itk>=5.3.0"],
 )

wrapping/dockcross-manylinux-build-module-wheels-opencl.sh

@@ -7,11 +7,14 @@
 # For example,
 #
 #   scripts/dockcross-manylinux-build-module-wheels.sh cp39
+#
+# Forked from
+# https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master/scripts/dockcross-manylinux-build-module-wheels.sh
 
 # Generate dockcross scripts
 
-MANYLINUX_VERSION="_2_28"
-IMAGE_TAG=20220715-9ce3707
+MANYLINUX_VERSION=${MANYLINUX_VERSION:=_2_28}
+IMAGE_TAG=${IMAGE_TAG:=20221108-102ebcc}
 OPENCL_ICD_LOADER_TAG=v2021.04.29
 OPENCL_HEADERS_TAG=v2021.04.29
 
@@ -20,6 +23,12 @@ chmod u+x /tmp/dockcross-manylinux-x64
 
 script_dir=$(cd $(dirname $0) || exit 1; pwd)
 
+mkdir -p $(pwd)/tools
+chmod 777 $(pwd)/tools
+# Build wheels
+mkdir -p dist
+
+# Build OpenCL-ICD-Loader before ITKVkFFTBackend
 if ! test -d ./OpenCL-ICD-Loader; then
   git clone https://github.com/KhronosGroup/OpenCL-ICD-Loader
   pushd OpenCL-ICD-Loader
@@ -40,8 +49,12 @@ if ! test -d ./OpenCL-ICD-Loader; then
 fi
 
 # Build wheels
-mkdir -p dist
-DOCKER_ARGS="-v $(pwd)/dist:/work/dist/ -v $script_dir/../ITKPythonPackage:/ITKPythonPackage -v $(pwd)/tools:/tools -v $(pwd)/OpenCL-ICD-Loader/inc/CL:/usr/include/CL -v $(pwd)/OpenCL-ICD-Loader-build/libOpenCL.so.1.2:/usr/lib64/libOpenCL.so.1 -v $(pwd)/OpenCL-ICD-Loader-build/libOpenCL.so.1.2:/usr/lib64/libOpenCL.so"
+DOCKER_ARGS="-v $(pwd)/dist:/work/dist/ -v $script_dir/../ITKPythonPackage:/ITKPythonPackage -v $(pwd)/tools:/tools"
+DOCKER_ARGS+=" -v $(pwd)/OpenCL-ICD-Loader/inc/CL:/usr/include/CL"
+DOCKER_ARGS+=" -v $(pwd)/OpenCL-ICD-Loader-build/libOpenCL.so.1.2:/usr/lib64/libOpenCL.so.1"
+DOCKER_ARGS+=" -v $(pwd)/OpenCL-ICD-Loader-build/libOpenCL.so.1.2:/usr/lib64/libOpenCL.so"
+DOCKER_ARGS+=" -e MANYLINUX_VERSION"
+
 /tmp/dockcross-manylinux-x64 \
   -a "$DOCKER_ARGS" \
   "/ITKPythonPackage/scripts/internal/manylinux-build-module-wheels.sh" "$@"

wrapping/dockcross-manylinux-download-cache.sh

@@ -2,20 +2,55 @@
 
 # This module should be pulled and run from an ITKModule root directory to generate the Linux python wheels of this module,
 # it is used by the circle.yml file contained in ITKModuleTemplate: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate
+#
+# Forked from
+# https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master/scripts/dockcross-manylinux-download-cache-and-build-module-wheels.sh
 
-curl https://data.kitware.com/api/v1/file/592dd8068d777f16d01e1a92/download -o zstd-1.2.0-linux.tar.gz
-gunzip -d zstd-1.2.0-linux.tar.gz
-tar xf zstd-1.2.0-linux.tar
+# -----------------------------------------------------------------------
 
+# Verifies that unzstd binary is available to decompress ITK build archives.
+unzstd_exe=`(which unzstd)`
+
+if [[ -z ${unzstd_exe} ]]; then
+  echo "ERROR: can not find required binary 'unzstd' "
+  exit 255
+fi
+
+# Expect unzstd > v1.3.2, see discussion in `dockcross-manylinux-build-tarball.sh`
+${unzstd_exe} --version
+
+# -----------------------------------------------------------------------
+# Fetch build archive
+
+TARBALL_SPECIALIZATION="-manylinux${MANYLINUX_VERSION:=_2_28}"
 TARBALL_NAME="ITKPythonBuilds-linux${TARBALL_SPECIALIZATION}.tar"
-curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.3rc04.post2}/${TARBALL_NAME}.zst -O
-./zstd-1.2.0-linux/bin/unzstd ${TARBALL_NAME}.zst -o ${TARBALL_NAME}
-echo "Extracting all files"
-tar xf ${TARBALL_NAME}
+curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.3.0}/${TARBALL_NAME}.zst -O
+
+${unzstd_exe} --long=31 ${TARBALL_NAME}.zst -o ${TARBALL_NAME}
+if [ "$#" -lt 1 ]; then
+  echo "Extracting all files";
+  tar xf ${TARBALL_NAME}
+else
+  echo "Extracting files relevant for: $1";
+  tar xf ${TARBALL_NAME} ITKPythonPackage/scripts/
+  tar xf ${TARBALL_NAME} ITKPythonPackage/ITK-source/
+  tar xf ${TARBALL_NAME} ITKPythonPackage/oneTBB-prefix/
+  tar xf ${TARBALL_NAME} --wildcards ITKPythonPackage/ITK-$1*
+fi
 rm ${TARBALL_NAME}
 
-mkdir tools
-curl https://data.kitware.com/api/v1/file/5c0aa4b18d777f2179dd0a71/download -o doxygen-1.8.11.linux.bin.tar.gz
-tar -xvzf doxygen-1.8.11.linux.bin.tar.gz -C tools
+# Optional: Update build scripts
+if [[ -n ${ITKPYTHONPACKAGE_TAG} ]]; then
+  echo "Updating build scripts to ${ITKPYTHONPACKAGE_ORG:=InsightSoftwareConsortium}/ITKPythonPackage@${ITKPYTHONPACKAGE_TAG}"
+  git clone "https://github.com/${ITKPYTHONPACKAGE_ORG}/ITKPythonPackage.git" "IPP-tmp"
+  pushd IPP-tmp/
+  git checkout "${ITKPYTHONPACKAGE_TAG}"
+  git status
+  popd
+
+  rm -rf ITKPythonPackage/scripts/
+  cp -r IPP-tmp/scripts ITKPythonPackage/
+  rm -rf IPP-tmp/
+fi
 
 cp -a ITKPythonPackage/oneTBB-prefix ./