CI: SimpleElastix on Github Actions, build wheel attempts.

.circleci/config.yml

@@ -1,7 +1,7 @@
 referenced:
   defaults: &defaults
     docker:
-     - image: circleci/python:3.5-stretch
+     - image: circleci/python:3.6-buster
     working_directory: ~/
     resource_class: medium
   default_environment_keys:  &default_environment
@@ -24,8 +24,8 @@ referenced:
       command: |
         sudo apt-get install -y rsync lua5.3 ccache
         sudo python -m pip install --upgrade pip
-        sudo python -m pip install scikit-ci-addons # Provides "ctest_junit_formatter" add-on
-        sudo python -m pip install cmake==3.13.3
+        sudo python -m pip install scikit-ci-addons lxml # Provides "ctest_junit_formatter" add-on
+        sudo python -m pip install cmake==3.18.*
   generate-hash-step: &generate-hash-step
     run:
       name: Generate external data hash
@@ -54,7 +54,7 @@ referenced:
        command: |
          echo 'export DASHBOARD_MODEL=$( [[ "$CIRCLE_BRANCH" = "master" || "$CIRCLE_BRANCH" = "next"  || "$CIRCLE_BRANCH" = "release" ]] && echo Continuous || echo Experimental )' >> $BASH_ENV
          echo 'export PATH=/usr/lib/ccache:${PATH}' >> $BASH_ENV
-  junit-fotmatting: &junit-fotmatting
+  junit-formatting: &junit-formatting
      run:
        name: Formatting CTest for JUnit
        when: always
@@ -106,7 +106,7 @@ jobs:
           when: always
           command: |
             ccache --show-stats
-      - *junit-fotmatting
+      - *junit-formatting
       - *junit-store-test-results
       - save_cache:
           key: 'ccache-{{ arch }}-{{ .Branch }}-{{ epoch }}'
@@ -123,8 +123,10 @@ jobs:
           root: /home/circleci/SimpleITK-build
           paths:
             - "*"
-  python3.5-and-test:
+  python3.6-and-test:
     <<: *defaults
+    docker:
+      - image: circleci/python:3.6-buster
     environment:
       <<: *default_environment_keys
       CTEST_BUILD_FLAGS: "-j 2"
@@ -157,12 +159,12 @@ jobs:
                         SWIG_EXECUTABLE:PATH=${ROOT_BINARY_DIRECTORY}/Swig/bin/swig
                         BUILD_EXAMPLES:BOOL=ON"
             ctest -V -Ddashboard_source_config_dir:PATH="Wrapping/Python" -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
-      - *junit-fotmatting
+      - *junit-formatting
       - *junit-store-test-results
-  python3.7-and-test:
+  python3.9-and-test:
     <<: *defaults
     docker:
-     - image: circleci/python:3.7-stretch
+     - image: circleci/python:3.9-buster
     environment:
       <<: *default_environment_keys
       CTEST_BUILD_FLAGS: "-j 2"
@@ -195,7 +197,7 @@ jobs:
                         SWIG_EXECUTABLE:PATH=${ROOT_BINARY_DIRECTORY}/Swig/bin/swig
                         BUILD_EXAMPLES:BOOL=ON"
             ctest -V -Ddashboard_source_config_dir:PATH="Wrapping/Python" -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
-      - *junit-fotmatting
+      - *junit-formatting
       - *junit-store-test-results
   r-and-test:
     <<: *defaults
@@ -216,10 +218,6 @@ jobs:
       - run:
           name: Additional Dependencies
           command: |
-            sudo apt-get update -y
-            sudo apt-get -y install dirmngr apt-transport-https software-properties-common
-            sudo apt-key adv --keyserver http://keyserver.ubuntu.com --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
-            sudo add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/debian stretch-cran35/"
             sudo apt-get update -y
             sudo apt-get install -y r-base r-base-dev
       - attach_workspace:
@@ -234,12 +232,12 @@ jobs:
                         SWIG_EXECUTABLE:PATH=${ROOT_BINARY_DIRECTORY}/Swig/bin/swig
                         BUILD_EXAMPLES:BOOL=ON"
             ctest -V -Ddashboard_source_config_dir:PATH="Wrapping/R" -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
-      - *junit-fotmatting
+      - *junit-formatting
       - *junit-store-test-results
   java-and-test:
     <<: *defaults
     docker:
-      - image: circleci/openjdk:8-jdk-stretch
+      - image: circleci/openjdk:8-jdk-buster
     resource_class: medium
     environment:
       <<: *default_environment_keys
@@ -275,7 +273,7 @@ jobs:
                         SWIG_EXECUTABLE:PATH=${ROOT_BINARY_DIRECTORY}/Swig/bin/swig
                         BUILD_EXAMPLES:BOOL=ON"
             ctest -V -Ddashboard_source_config_dir:PATH="Wrapping/Java" -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
-      - *junit-fotmatting
+      - *junit-formatting
       - *junit-store-test-results
   docs:
     <<: *defaults
@@ -325,10 +323,10 @@ workflows:
                  - gh-pages
                  - dashboard
                  - hooks
-      - python3.5-and-test:
+      - python3.6-and-test:
           requires:
             - build-and-test
-      - python3.7-and-test:
+      - python3.9-and-test:
           requires:
             - build-and-test
       - r-and-test:

.github/workflows/Build.yml

@@ -0,0 +1,87 @@
+name: Elastix Python 3.7
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 3
+      matrix:
+        os: [windows-2019]
+        include:
+#           - os: ubuntu-18.04
+#             cmake-build-type: "Release"
+#             ANNLib: "libANNlib-5.0.so"
+#             ANNLib2: "libANNlib-5.0.so.1"
+          - os: windows-2019
+            cmake-build-type: "Release"
+            ANNLib: "ANNlib-5.0.dll"
+#           - os: macos-10.15
+#             cmake-build-type: "Release"
+#             ANNLib: "libANNlib-5.0.1.dylib"
+#             ANNLib2: "libANNlib-5.0.dylib"
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install ninja
+        python -m pip install setuptools
+        python -m pip install scikit-ci-addons
+        python -m pip install wheel
+
+    - name: Get specific version of CMake, Ninja
+      uses: lukka/[email protected]
+
+    - name: Build SimpleElastix Unix
+      if: matrix.os != 'windows-2019'
+      run: |
+        export CXXFLAGS="$CXXFLAGS -fPIC"
+        mkdir SEb
+        cd SEb
+        cmake -DWRAP_LUA:BOOL=OFF -DWRAP_PYTHON:BOOL=ON -DWRAP_JAVA:BOOL=OFF -DWRAP_CSHARP:BOOL=OFF -DWRAP_TCL:BOOL=OFF -DWRAP_R:BOOL=OFF -DWRAP_RUBY:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DSimpleITK_USE_SYSTEM_ITK:BOOL=OFF -DSimpleITK_USE_SYSTEM_ELASTIX:BOOL=OFF -DSimpleITK_4D_IMAGES:BOOL=OFF -v ../SuperBuild &&
+        make --jobs=4
+
+    - name: Build SimpleElastix Windows
+      if: matrix.os == 'windows-2019'
+      shell: cmd
+      run: |
+        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        mkdir SEb
+        cd SEb
+        cmake -DWRAP_LUA:BOOL=OFF -DWRAP_PYTHON:BOOL=ON -DWRAP_JAVA:BOOL=OFF -DWRAP_CSHARP:BOOL=OFF -DWRAP_TCL:BOOL=OFF -DWRAP_R:BOOL=OFF -DWRAP_RUBY:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DSimpleITK_USE_SYSTEM_ITK:BOOL=OFF -DSimpleITK_USE_SYSTEM_ELASTIX:BOOL=OFF -DSimpleITK_4D_IMAGES:BOOL=OFF -v -GNinja ../SuperBuild
+        ninja
+
+    - name: Test SimpleITK
+      run: |
+        ctest -C Release
+
+    - name: Build Wheel
+      run: |
+        cd SEb/SimpleITK-build/Wrapping/Python
+        python setup.py bdist_wheel
+
+    - name: Prepare Artifacts
+      shell: bash
+      run: |
+        mkdir uploads
+        mv SEb/SimpleITK-build/Wrapping/Python/dist uploads
+
+    - name: Publish Artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: "${{ matrix.os }}"
+        path: uploads

.github/workflows/BuildPython38.yml

@@ -0,0 +1,85 @@
+name: Elastix Python 3.8
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 3
+      matrix:
+        os: [macos-10.15, ubuntu-18.04, windows-2019]
+        include:
+          - os: ubuntu-18.04
+            cmake-build-type: "Release"
+            ANNLib: "libANNlib-5.0.so"
+            ANNLib2: "libANNlib-5.0.so.1"
+          - os: windows-2019
+            cmake-build-type: "Release"
+            ANNLib: "ANNlib-5.0.dll"
+          - os: macos-10.15
+            ANNLib: "libANNlib-5.0.1.dylib"
+            ANNLib2: "libANNlib-5.0.dylib"
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install ninja
+        python -m pip install setuptools
+        python -m pip install scikit-ci-addons
+        python -m pip install wheel
+    - name: Get specific version of CMake, Ninja
+      uses: lukka/[email protected]
+
+    - name: Build SimpleElastix Unix
+      if: matrix.os != 'windows-2019'
+      run: |
+        export CXXFLAGS="$CXXFLAGS -fPIC"
+        mkdir SEb
+        cd SEb
+        cmake -DWRAP_LUA:BOOL=OFF -DWRAP_PYTHON:BOOL=ON -DWRAP_JAVA:BOOL=OFF -DWRAP_CSHARP:BOOL=OFF -DWRAP_TCL:BOOL=OFF -DWRAP_R:BOOL=OFF -DWRAP_RUBY:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DSimpleITK_USE_SYSTEM_ITK:BOOL=OFF -DSimpleITK_USE_SYSTEM_ELASTIX:BOOL=OFF -DSimpleITK_4D_IMAGES:BOOL=OFF -v ../SuperBuild &&
+        make --jobs=4
+
+    - name: Build SimpleElastix Windows
+      if: matrix.os == 'windows-2019'
+      shell: cmd
+      run: |
+        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        mkdir SEb
+        cd SEb
+        cmake -DWRAP_LUA:BOOL=OFF -DWRAP_PYTHON:BOOL=ON -DWRAP_JAVA:BOOL=OFF -DWRAP_CSHARP:BOOL=OFF -DWRAP_TCL:BOOL=OFF -DWRAP_R:BOOL=OFF -DWRAP_RUBY:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DSimpleITK_USE_SYSTEM_ITK:BOOL=OFF -DSimpleITK_USE_SYSTEM_ELASTIX:BOOL=OFF -DSimpleITK_4D_IMAGES:BOOL=OFF -v -GNinja ../SuperBuild
+        ninja
+
+    - name: Test SimpleITK
+      run: |
+        ctest -C Release
+
+
+    - name: Build Wheel
+      run: |
+        cd SEb/SimpleITK-build/Wrapping/Python
+        python setup.py bdist_wheel
+
+    - name: Prepare Artifacts
+      shell: bash
+      run: |
+        mkdir uploads
+        mv SEb/SimpleITK-build/Wrapping/Python/dist uploads
+    - name: Publish Artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: "${{ matrix.os }}"
+        path: uploads

.github/workflows/BuildPython39.yml

@@ -0,0 +1,85 @@
+name: Elastix Python 3.9
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 3
+      matrix:
+        os: [macos-10.15, ubuntu-18.04, windows-2019]
+        include:
+          - os: ubuntu-18.04
+            cmake-build-type: "Release"
+            ANNLib: "libANNlib-5.0.so"
+            ANNLib2: "libANNlib-5.0.so.1"
+          - os: windows-2019
+            cmake-build-type: "Release"
+            ANNLib: "ANNlib-5.0.dll"
+          - os: macos-10.15
+            cmake-build-type: "Release"
+            ANNLib: "libANNlib-5.0.1.dylib"
+            ANNLib2: "libANNlib-5.0.dylib"
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.9
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install ninja
+        python -m pip install setuptools
+        python -m pip install scikit-ci-addons
+        python -m pip install wheel
+    - name: Get specific version of CMake, Ninja
+      uses: lukka/[email protected]
+
+    - name: Build SimpleElastix Unix
+      if: matrix.os != 'windows-2019'
+      run: |
+        export CXXFLAGS="$CXXFLAGS -fPIC"
+        mkdir SEb
+        cd SEb
+        cmake -DWRAP_LUA:BOOL=OFF -DWRAP_PYTHON:BOOL=ON -DWRAP_JAVA:BOOL=OFF -DWRAP_CSHARP:BOOL=OFF -DWRAP_TCL:BOOL=OFF -DWRAP_R:BOOL=OFF -DWRAP_RUBY:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DSimpleITK_USE_SYSTEM_ITK:BOOL=OFF -DSimpleITK_USE_SYSTEM_ELASTIX:BOOL=OFF -DSimpleITK_4D_IMAGES:BOOL=OFF -v ../SuperBuild &&
+        make --jobs=4
+
+    - name: Build SimpleElastix Windows
+      if: matrix.os == 'windows-2019'
+      shell: cmd
+      run: |
+        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+        mkdir SEb
+        cd SEb
+        cmake -DWRAP_LUA:BOOL=OFF -DWRAP_PYTHON:BOOL=ON -DWRAP_JAVA:BOOL=OFF -DWRAP_CSHARP:BOOL=OFF -DWRAP_TCL:BOOL=OFF -DWRAP_R:BOOL=OFF -DWRAP_RUBY:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DSimpleITK_USE_SYSTEM_ITK:BOOL=OFF -DSimpleITK_USE_SYSTEM_ELASTIX:BOOL=OFF -DSimpleITK_4D_IMAGES:BOOL=OFF -v -GNinja ../SuperBuild
+        ninja
+
+    - name: Test SimpleITK
+      run: |
+        ctest -C Release
+
+    - name: Build Wheel
+      run: |
+        cd SEb/SimpleITK-build/Wrapping/Python
+        python setup.py bdist_wheel
+
+    - name: Prepare Artifacts
+      shell: bash
+      run: |
+        mkdir uploads
+        mv SEb/SimpleITK-build/Wrapping/Python/dist uploads
+    - name: Publish Artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: "${{ matrix.os }}"
+        path: uploads