bump CIL version to one with SAG/SAGA SVRG/LSVRG (#929) #821
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| name: native | |
| on: | |
| push: | |
| branches: [master] | |
| paths-ignore: | |
| - 'docker/Dockerfile' | |
| - 'docker/*yml' | |
| - '**.md' | |
| - 'VirtualBox/**' | |
| - '.github/workflows/*docker*' | |
| - 'CITATION.cff' | |
| - '.mailmap' | |
| - 'NOTICE.txt' | |
| - 'LICENSE.txt' | |
| pull_request: | |
| branches: [master] | |
| paths-ignore: | |
| - 'docker/Dockerfile' | |
| - 'docker/*yml' | |
| - '**.md' | |
| - 'VirtualBox/**' | |
| - '.github/workflows/*docker*' | |
| - 'CITATION.cff' | |
| - '.mailmap' | |
| - 'NOTICE.txt' | |
| - 'LICENSE.txt' | |
| workflow_dispatch: | |
| inputs: | |
| tmate: | |
| description: Debug with tmate ssh session | |
| type: boolean | |
| default: false | |
| required: true | |
| jobs: | |
| build-test: | |
| runs-on: ${{ matrix.os }} | |
| defaults: {run: {shell: 'bash -el {0}'}} | |
| env: | |
| COMPILER: gcc | |
| BUILD_TYPE: Release | |
| strategy: | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| compiler_version: 9 | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DBUILD_CIL=ON -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON" | |
| DEVEL_BUILD: "OFF" | |
| - os: ubuntu-latest | |
| compiler_version: 9 | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DBUILD_CIL=ON -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_HDF5=OFF -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=OFF" | |
| DEVEL_BUILD: "OFF" | |
| #- os: ubuntu-latest | |
| # compiler_version: 9 | |
| # EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DBUILD_CIL=ON -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON" | |
| # DEVEL_BUILD: "OFF" | |
| - os: ubuntu-latest | |
| compiler_version: 9 | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DBUILD_CIL=ON -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DUSE_SYSTEM_GTest=OFF" | |
| DEVEL_BUILD: "OFF" | |
| - os: ubuntu-latest | |
| compiler_version: 11 | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DBUILD_CIL=ON -DUSE_SYSTEM_Armadillo=OFF -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DUSE_ROOT:BOOL=ON -DUSE_SYSTEM_ROOT=ON -DSIRF_EXTRA_CMAKE_ARGS=-DCMAKE_POLICY_DEFAULT_CMP0074=NEW" # note: SIRF needs CMP0074 with older versions of pre-built ROOT (see below) | |
| DEVEL_BUILD: "ON" | |
| - os: ubuntu-latest | |
| compiler_version: 11 | |
| EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DBUILD_CIL=ON -DUSE_SYSTEM_Armadillo=OFF -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DUSE_ROOT:BOOL=ON -DUSE_SYSTEM_ROOT=ON -DSIRF_EXTRA_CMAKE_ARGS=-DCMAKE_POLICY_DEFAULT_CMP0074=NEW" # note: SIRF needs CMP0074 with older versions of pre-built ROOT (see below) | |
| DEVEL_BUILD: "OFF" | |
| fail-fast: false # don't terminate matrix if one job fails | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - if: contains(matrix.os, fromJSON('["ubuntu","macos"]')) | |
| name: increase disk space | |
| run: sudo .github/workflows/GHA_increase_disk_space.sh | |
| - id: deps | |
| name: install dependencies | |
| working-directory: docker | |
| run: | | |
| sudo ./raw-ubuntu.sh | |
| sudo ./build_system-ubuntu.sh | |
| sudo ./build_essential-ubuntu.sh | |
| sudo ./build_gadgetron-ubuntu.sh | |
| sudo ./build_python-ubuntu.sh | |
| echo "python-version=$(python3 --version | awk '{print $2}')" >> $GITHUB_OUTPUT | |
| - name: optionally install ROOT | |
| env: | |
| EXTRA_BUILD_FLAGS: ${{ matrix.EXTRA_BUILD_FLAGS }} | |
| run: | | |
| sh -ex | |
| if expr match "${EXTRA_BUILD_FLAGS}" ".*-DUSE_SYSTEM_ROOT=ON.*" >/dev/null | |
| then | |
| # Install ROOT (warning: currently only valid on Ubuntu) | |
| ROOT_file=root_v6.28.12.Linux-ubuntu20-x86_64-gcc9.4.tar.gz | |
| wget https://root.cern/download/"$ROOT_file" | |
| tar -xzf "$ROOT_file" | |
| rm "$ROOT_file" | |
| source root/bin/thisroot.sh | |
| echo ROOT_DIR="$ROOTSYS/cmake" >> $GITHUB_ENV | |
| echo ROOTSYS="$ROOTSYS" >> $GITHUB_ENV | |
| echo | |
| # work-around problem with problem with Vdt for ROOT version pre-6.30.04 as per https://github.com/root-project/root/pull/14178 | |
| echo Vdt_ROOT="$ROOTSYS" >> $GITHUB_ENV | |
| # thisroot modifies the following | |
| case ${{matrix.os}} in | |
| (ubuntu*) | |
| echo LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo PATH="$PATH" >> $GITHUB_ENV | |
| ;; | |
| (macOS*) # future-proof | |
| echo DYLD_FALLBACK_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$DYLD_FALLBACK_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo PATH="$PATH" >> $GITHUB_ENV | |
| ;; | |
| (windows*) # future-proof | |
| echo PATH="${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/bin:$PATH" >> $GITHUB_ENV | |
| ;; | |
| esac | |
| fi | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '${{ steps.deps.outputs.python-version }}' | |
| cache: pip | |
| - name: pip install | |
| working-directory: docker | |
| run: PYTHON_EXECUTABLE=python3 PYTHON_INSTALL_DIR="$HOME/virtualenv" ./user_python-ubuntu.sh | |
| - uses: hendrikmuhs/ccache-action@v1 | |
| with: | |
| key: ${{ matrix.os }}-${{ env.COMPILER }}-${{ matrix.compiler_version }}-${{ env.BUILD_TYPE }}-${{ github.ref_name }}-${{ github.run_id }} | |
| restore-keys: | | |
| ${{ matrix.os }}-${{ env.COMPILER }}-${{ matrix.compiler_version }}-${{ env.BUILD_TYPE }}-${{ github.ref_name }} | |
| ${{ matrix.os }}-${{ env.COMPILER }}-${{ matrix.compiler_version }}-${{ env.BUILD_TYPE }} | |
| append-timestamp: false | |
| - name: export CC CXX | |
| run: | | |
| set -ex | |
| if test '${{ env.COMPILER }}' = clang; then | |
| CC=clang | |
| CXX=clang++ | |
| elif test '${{ env.COMPILER }}' = gcc; then | |
| CC=gcc | |
| CXX=g++ | |
| fi | |
| if test -n '${{ matrix.compiler_version }}'; then | |
| CC=${CC}-${{ matrix.compiler_version }} | |
| CXX=${CXX}-${{ matrix.compiler_version }} | |
| sudo apt install -yq ${CXX} ${CC} | |
| fi | |
| # make available to jobs below | |
| echo "CC=$CC" >> $GITHUB_ENV | |
| echo "CXX=$CXX" >> $GITHUB_ENV | |
| - name: cmake -S . | |
| env: | |
| EXTRA_BUILD_FLAGS: ${{ matrix.EXTRA_BUILD_FLAGS }} | |
| CMAKE_BUILD_TYPE: ${{ env.BUILD_TYPE }} | |
| DEVEL_BUILD: "-DDEVEL_BUILD=${{ matrix.DEVEL_BUILD }}" | |
| run: | | |
| set -ex | |
| export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH" | |
| export superbuild=`pwd` | |
| export BUILD_FLAGS="-DCMAKE_INSTALL_PREFIX=~/install -DPYVER=3 -DUSE_SYSTEM_RocksDB=OFF -DBUILD_TESTING_Gadgetron:BOOL=ON" | |
| source ~/virtualenv/bin/activate | |
| cmake -S ${GITHUB_WORKSPACE} -B ./build ${BUILD_FLAGS} ${EXTRA_BUILD_FLAGS} ${DEVEL_BUILD}; | |
| - name: cmake --build | |
| run: | | |
| source ~/virtualenv/bin/activate | |
| cmake --build ./build -j 2 | |
| # tmate ssh debugging | |
| - if: github.event_name == 'workflow_dispatch' && github.event.inputs.tmate == 'true' | |
| uses: mxschmitt/action-tmate@v3 | |
| timeout-minutes: 15 | |
| - if: failure() | |
| name: Upload build log files for debugging | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build_log_files-${{ matrix.os }}-${{ env.COMPILER }}${{ matrix.compiler_version }}-${{ env.BUILD_TYPE }}-DEVEL=${{ matrix.DEVEL_BUILD }} | |
| path: ${{ github.workspace }}/build/**/*.log | |
| retention-days: 7 | |
| - name: ctest | |
| run: ./docker/ctest_sirf.sh |