NiftyPET version 2 #831
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build and ctest and recon_test_pack CI | ||
| on: | ||
| push: | ||
| branches: [ master ] | ||
| paths-ignore: | ||
| - '.appveyor.yml' | ||
| - 'CITATION.cff' | ||
| - '**/*.md' | ||
| - '**/*.html' | ||
| - '**/*.htm' | ||
| - '**/*.tex' | ||
| pull_request: | ||
| branches: [ master ] | ||
| paths-ignore: | ||
| - '.appveyor.yml' | ||
| - 'CITATION.cff' | ||
| - '**/*.md' | ||
| - '**/*.html' | ||
| - '**/*.htm' | ||
| - '**/*.tex' | ||
| workflow_dispatch: | ||
| inputs: | ||
| debug_enabled: | ||
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | ||
| required: false | ||
| default: false | ||
| jobs: | ||
| build: | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| matrix: | ||
| include: | ||
| - os: ubuntu-latest | ||
| compiler: gcc | ||
| compiler_version: 9 | ||
| cuda_version: "0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=ON" | ||
| BUILD_TYPE: "Release" | ||
| parallelproj: "ON" | ||
| ROOT: "ON" | ||
| ITK: "OFF" | ||
| - os: ubuntu-latest | ||
| compiler: clang | ||
| #compiler_version: | ||
| cuda_version: "0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=ON" | ||
| BUILD_TYPE: "Release" | ||
| parallelproj: "ON" | ||
| ROOT: "OFF" | ||
| # currently using ITK 5.2 which doesn't like clang 14 | ||
| ITK: "OFF" | ||
| - os: ubuntu-latest | ||
| compiler: gcc | ||
| compiler_version: 10 | ||
| cuda_version: "0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17" | ||
| BUILD_TYPE: "Debug" | ||
| parallelproj: "OFF" | ||
| ROOT: "OFF" | ||
| ITK: "ON" | ||
| - os: ubuntu-latest | ||
| compiler: gcc | ||
| compiler_version: 12 | ||
| cuda_version: "0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14" | ||
| BUILD_TYPE: "RelWithDebInfo" | ||
| parallelproj: "ON" | ||
| ROOT: "OFF" | ||
| ITK: "ON" | ||
| - os: ubuntu-latest | ||
| compiler: gcc | ||
| compiler_version: 12 | ||
| cuda_version: "12.1.0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14" | ||
| BUILD_TYPE: "Release" | ||
| parallelproj: "ON" | ||
| ROOT: "OFF" | ||
| ITK: "ON" | ||
| - os: macOS-latest | ||
| compiler: gcc | ||
| compiler_version: 11 | ||
| cuda_version: "0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | ||
| parallelproj: "OFF" | ||
| BUILD_TYPE: "Debug" | ||
| ROOT: "OFF" | ||
| ITK: "OFF" | ||
| # Currently disabled due to problems with listmode recon, see https://github.com/UCL/STIR/issues/1200 | ||
| #- os: macOS-latest | ||
| # compiler: clang | ||
| # compiler_version: 16 | ||
| # BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | ||
| # parallelproj: "OFF" | ||
| # BUILD_TYPE: "Release" | ||
| # ROOT: "OFF" | ||
| # ITK: "OFF" | ||
| # let's run all of them, as opposed to aborting when one fails | ||
| fail-fast: false | ||
| name: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | ||
| steps: | ||
| - name: disk space | ||
| shell: bash | ||
| run: | | ||
| case ${{matrix.os}} in | ||
| (ubuntu* | macOS*) | ||
| df -h | ||
| # saves about 2GB | ||
| echo removing dotnet | ||
| sudo rm -rf /usr/share/dotnet | ||
| # saves about 10 GB | ||
| echo removing agent_tools | ||
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | ||
| # saves about 10 GB | ||
| echo removing android files | ||
| sudo rm -rf /usr/local/lib/android | ||
| df -h | ||
| ;; | ||
| (windows*) | ||
| # no idea how to do this | ||
| ;; | ||
| esac | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| submodules: recursive | ||
| - name: set_compiler_variables | ||
| shell: bash | ||
| run: | | ||
| set -ex | ||
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | ||
| CC="clang" | ||
| CXX="clang++" | ||
| elif test 'XX${{ matrix.compiler }}' = 'XXgcc'; then | ||
| CC="gcc" | ||
| CXX="g++" | ||
| fi | ||
| if test 'XX${{ matrix.compiler_version }}' != 'XX'; then | ||
| CC=${CC}-${{ matrix.compiler_version }} | ||
| CXX=${CXX}-${{ matrix.compiler_version }} | ||
| fi | ||
| if test 'XX${{ matrix.os }}' = 'XXmacOS-latest'; then | ||
| # need to force XCode version for the moment due to a linker bug | ||
| # see https://github.com/UCL/STIR/issues/1103 | ||
| echo DEVELOPER_DIR="/Applications/Xcode_14.1.app/Contents/Developer" >> $GITHUB_ENV | ||
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | ||
| brew install llvm@${{ matrix.compiler_version }} | ||
| if test XX${HOMEBREW_PREFIX} = XX; then | ||
| HOMEBREW_PREFIX=/usr/local | ||
| fi | ||
| LDFLAGS="-L$HOMEBREW_PREFIX/opt/llvm/lib/c++ -Wl,-rpath,$HOMEBREW_PREFIX/opt/llvm/lib/c++" | ||
| # make available to jobs below | ||
| echo LDFLAGS="$LDFLAGS" >> $GITHUB_ENV | ||
| CC="$HOMEBREW_PREFIX/opt/llvm/bin/clang" | ||
| CXX="$HOMEBREW_PREFIX/opt/llvm/bin/clang++" | ||
| fi | ||
| fi | ||
| export CC CXX | ||
| # make available to jobs below | ||
| echo CC="$CC" >> $GITHUB_ENV | ||
| echo CXX="$CXX" >> $GITHUB_ENV | ||
| - if: ${{ ! matrix.cuda_version == '0' }} | ||
| uses: Jimver/cuda-toolkit@v0.2.11 | ||
| id: cuda-toolkit | ||
| with: | ||
| cuda: ${{ matrix.cuda_version }} | ||
| linux-local-args: '["--toolkit"]' | ||
| - name: install_dependencies | ||
| shell: bash | ||
| run: | | ||
|
Check failure on line 178 in .github/workflows/build-test.yml
|
||
| set -ex | ||
| # We will install some external dependencies here | ||
| CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | ||
| case ${{matrix.os}} in | ||
| (ubuntu*) | ||
| sudo apt update | ||
| # install compiler | ||
| if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | ||
| # package is called clang, need libomp-dev for OpenMP support | ||
| sudo apt install $CC libomp-dev | ||
| else | ||
| sudo apt install $CXX | ||
| fi | ||
| # other dependencies | ||
| sudo apt install libboost-dev libhdf5-serial-dev swig python3-dev nlohmann-json3-dev | ||
| if test "${{matrix.ITK}}XX" == "ONXX"; then | ||
| sudo apt install libinsighttoolkit5-dev | ||
| fi | ||
| # free up some disk space | ||
| sudo apt clean | ||
| PYTHON_EXECUTABLE=$(which python3) | ||
| ;; | ||
| (macOS*) | ||
| brew install boost swig python nlohmann-json | ||
| PYTHON_EXECUTABLE=$(which python3) | ||
| ;; | ||
| (windows*) | ||
| # this compiles the whole thing so takes ages | ||
| vcpkg install boost-core hdf5 nlohmann-json | ||
| # swig is preinstalled and is currently not in vcpcg | ||
| vcpkg list | ||
| PYTHON_EXECUTABLE=$(which python3) | ||
| ;; | ||
| esac | ||
| echo PYTHON_EXECUTABLE="$PYTHON_EXECUTABLE" >> $GITHUB_ENV | ||
| ${PYTHON_EXECUTABLE} -m venv ${GITHUB_WORKSPACE}/my-env | ||
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | ||
| #python -m pip install -U pip | ||
| case ${{matrix.os}} in | ||
| (macOS*) | ||
| # attempt to get round buggy Accelerate builds, see https://github.com/numpy/numpy/issues/15947 | ||
| # but it didn't work, so commented out | ||
| # brew install openblas | ||
| # export OPENBLAS=$(brew --prefix openblas) | ||
| #python -m pip install --no-cache-dir --no-binary numpy numpy # avoid the cached .whl! | ||
| python -m pip install numpy | ||
| ;; | ||
| (*) | ||
| python -m pip install numpy | ||
| ;; | ||
| esac | ||
| python -m pip install pytest | ||
| if test "${{matrix.parallelproj}}XX" == "ONXX"; then | ||
| git clone --depth 1 --branch v1.3.7 https://github.com/gschramm/parallelproj | ||
| mkdir parallelproj/build | ||
| cd parallelproj/build | ||
| if test ! "${{matrix.cuda_version}}" == "0"; then | ||
| extra_args="-DSKIP_CUDA_LIB:BOOL=ON" | ||
| fi | ||
| cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} "${extra_args}" | ||
| cmake --build . --target install --config Release | ||
| cd ../.. | ||
| fi | ||
| # Install NiftyPET | ||
| if test ! "${{matrix.cuda_version}}" == "0"; then | ||
| export PATHTOOLS=${GITHUB_WORKSPACE}/NiftyPET_tools | ||
| export HMUDIR=${GITHUB_WORKSPACE}/mmr_hardwareumaps | ||
| python -m pip install "nipet>=2" | ||
| niftypet_cmake_prefix=${{python -c "from niftypet.nipet import cmake_prefix; print(cmake_prefix)"}} | ||
| echo NiftyPET_PREFIX="$niftypet_cmake_prefix" >> $GITHUB_ENV | ||
| fi | ||
| # Install ROOT (warning: currently only valid on Ubuntu) | ||
| if test "${{matrix.ROOT}}XX" == "ONXX"; then | ||
| wget https://root.cern/download/root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz | ||
| tar -xzvf root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz | ||
| source root/bin/thisroot.sh | ||
| fi | ||
| # we'll install some dependencies with shared libraries, so need to let the OS know | ||
| # thisroot.sh also modified the path, so save that for the recon_test_pack | ||
| case ${{matrix.os}} in | ||
| (ubuntu*) | ||
| echo LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | ||
| echo PATH="$PATH" >> $GITHUB_ENV | ||
| ;; | ||
| (macOS*) | ||
| echo DYLD_FALLBACK_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$DYLD_FALLBACK_LIBRARY_PATH" >> $GITHUB_ENV | ||
| echo PATH="$PATH" >> $GITHUB_ENV | ||
| ;; | ||
| (windows*) | ||
| echo PATH="${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/bin:$PATH" >> $GITHUB_ENV | ||
| ;; | ||
| esac | ||
| - name: ccache | ||
| uses: hendrikmuhs/ccache-action@v1 | ||
| with: | ||
| key: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }} | ||
| max-size: "2G" | ||
| - name: configure | ||
| shell: bash | ||
| env: | ||
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | ||
| BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }} | ||
| run: | | ||
| set -ex | ||
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | ||
| #export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH" | ||
| cmake --version | ||
| if test "XX$CC" != "XX"; then | ||
| $CC --version | ||
| $CXX --version | ||
| fi | ||
| CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | ||
| # make available to jobs below | ||
| echo CMAKE_INSTALL_PREFIX="$CMAKE_INSTALL_PREFIX" >> $GITHUB_ENV | ||
| EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`" | ||
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}" | ||
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_PREFIX_DIR=${NiftyPET_PREFIX}" | ||
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON" | ||
| EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/src" | ||
| echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS" | ||
| mkdir build | ||
| cd build | ||
| cmake -S .. ${BUILD_FLAGS} ${EXTRA_BUILD_FLAGS} | ||
| # report disk space | ||
| case ${{matrix.os}} in | ||
| (ubuntu* | macOS*) | ||
| df -h | ||
| ;; | ||
| (windows*) | ||
| # no idea how to do this | ||
| ;; | ||
| esac | ||
| - name: build | ||
| shell: bash | ||
| env: | ||
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | ||
| run: | | ||
| cd ${GITHUB_WORKSPACE}/build; | ||
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | ||
| cmake --build . -j 2 --config ${BUILD_TYPE}} --target install | ||
| - name: ctest | ||
| shell: bash | ||
| env: | ||
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | ||
| run: | | ||
| cd ${GITHUB_WORKSPACE}/build | ||
| # don't run all of them in Debug mode as it takes too long | ||
| if test ${BUILD_TYPE} = Debug; then | ||
| EXCLUDE="-E test_data_processor_projectors|test_export_array|test_ArcCorrection|test_blocks_on_cylindrical_projectors" | ||
| fi | ||
| ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE} | ||
| - name: recon_test_pack | ||
| shell: bash | ||
| env: | ||
| BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }} | ||
| BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | ||
| run: | | ||
| set -ex; | ||
| PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | ||
| cd ${GITHUB_WORKSPACE}/recon_test_pack | ||
| ./run_tests.sh --nointbp | ||
| # don't run all of them in Debug mode as it takes too long | ||
| if test ${BUILD_TYPE} != Debug; then | ||
| ./run_test_simulate_and_recon.sh | ||
| ./run_test_listmode_recon.sh | ||
| ./run_test_simulate_and_recon_with_motion.sh | ||
| ./run_scatter_tests.sh | ||
| ./run_test_zoom_image.sh | ||
| ./run_ML_norm_tests.sh | ||
| if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi | ||
| ./run_tests_modelling.sh | ||
| cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT | ||
| ./run_SPECT_tests.sh | ||
| fi | ||
| - name: Upload log files for debugging | ||
| uses: actions/upload-artifact@v3 | ||
| if: failure() | ||
| with: | ||
| name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | ||
| path: ${{ github.workspace }}/recon_test_pack/**/*.log | ||
| retention-days: 7 | ||
| # Enable tmate debugging of manually-triggered workflows if the input option was provided | ||
| - name: Setup tmate session if triggered | ||
| uses: mxschmitt/action-tmate@v3 | ||
| timeout-minutes: 15 | ||
| if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }} | ||
| - name: examples | ||
| shell: bash | ||
| run: | | ||
| set -ex; | ||
| PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | ||
| # Run examples to see if they work | ||
| cd ${GITHUB_WORKSPACE}/examples/PET_simulation | ||
| ./run_simulation.sh 1> /dev/null | ||
| # Run the Demo executables | ||
| EXE_LOC=${GITHUB_WORKSPACE}/build/src/examples/C++ | ||
| cd ${GITHUB_WORKSPACE}/examples/C++/src | ||
| generate_image generate_image.par | ||
| forward_project sino.hs image.hv small.hs | ||
| # Cannot test demo1 or demo2 as they require interactivity. Piping does not work. | ||
| ${EXE_LOC}/demo3 demo.par --display_off | ||
| ${EXE_LOC}/demo3 demoPM.par --display_off | ||
| ${EXE_LOC}/demo4_obj_fun demo4_obj_fun.par | ||
| ${EXE_LOC}/demo5_line_search demo5_line_search.par | ||
| - name: Python | ||
| shell: bash | ||
| run: | | ||
| set -ex | ||
| source ${GITHUB_WORKSPACE}/my-env/bin/activate | ||
| # Run Python tests, making sure we're using the correct Python interpreter | ||
| which python | ||
| export PYTHONPATH=${CMAKE_INSTALL_PREFIX}/python | ||
| cd ${GITHUB_WORKSPACE}/src | ||
| case ${{matrix.os}} in | ||
| (macOS*) | ||
| echo skipping pytest due to numpy problem for now. | ||
| ;; | ||
| (*) | ||
| python -m pytest . | ||
| ;; | ||
| esac | ||
