Add test cases for edit extract #31
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| # ================================================================================================== | |
| # Header | |
| # ================================================================================================== | |
| name: CI | |
| on: [push, pull_request] | |
| # ================================================================================================== | |
| # Jobs | |
| # ================================================================================================== | |
| jobs: | |
| ci: | |
| runs-on: ${{ matrix.os }} | |
| # ========================================================================== | |
| # Matrix | |
| # ========================================================================== | |
| strategy: | |
| fail-fast: false | |
| # ------------------------------------------------------- | |
| # matrix | |
| # ------------------------------------------------------- | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#choosing-github-hosted-runners | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| - macos-latest | |
| compiler: | |
| - gcc | |
| - llvm | |
| # ------------------------------------------------------- | |
| # include | |
| # ------------------------------------------------------- | |
| # Instead of a matrix where we only have some combinations that work, and others that do not, | |
| # we just directly opt for a list of all combinations that we actually want to test. | |
| # Easier to reason about, easier to maintain, easier to extend. | |
| # Newer compiler versions are not available on all Ubuntu, so some are excluded. | |
| # Older GCC versions are also not supported by older OSs any more. | |
| # We also currently exclude clang from macos, as it fails with different types of | |
| # linker errors. As this is merely a problem in the setup, we defer solving this for now. | |
| include: | |
| # ------------------------------- | |
| # Ubuntu 22.04 | |
| # ------------------------------- | |
| # Too old | |
| # - os: ubuntu-22.04 | |
| # compiler: gcc-7 | |
| # - os: ubuntu-22.04 | |
| # compiler: gcc-8 | |
| - os: ubuntu-22.04 | |
| compiler: gcc-9 | |
| - os: ubuntu-22.04 | |
| compiler: gcc-10 | |
| - os: ubuntu-22.04 | |
| compiler: gcc-11 | |
| - os: ubuntu-22.04 | |
| compiler: gcc-12 | |
| - os: ubuntu-22.04 | |
| compiler: gcc-13 | |
| # Setup fails | |
| # - os: ubuntu-22.04 | |
| # compiler: gcc-14 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-6 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-7 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-8 | |
| # Weird segfault | |
| # - os: ubuntu-22.04 | |
| # compiler: llvm-9 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-10 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-11 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-12 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-13 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-14 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-15 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-16 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-17 | |
| # Setup fails | |
| # - os: ubuntu-22.04 | |
| # compiler: llvm-18 | |
| # ------------------------------- | |
| # Ubuntu 24.04 | |
| # ------------------------------- | |
| # Too old | |
| # - os: ubuntu-24.04 | |
| # compiler: gcc-7 | |
| # - os: ubuntu-24.04 | |
| # compiler: gcc-8 | |
| - os: ubuntu-24.04 | |
| compiler: gcc-9 | |
| - os: ubuntu-24.04 | |
| compiler: gcc-10 | |
| - os: ubuntu-24.04 | |
| compiler: gcc-11 | |
| - os: ubuntu-24.04 | |
| compiler: gcc-12 | |
| - os: ubuntu-24.04 | |
| compiler: gcc-13 | |
| - os: ubuntu-24.04 | |
| compiler: gcc-14 | |
| # Setup fails | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-6 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-7 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-8 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-9 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-10 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-11 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-12 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-13 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-14 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-15 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-16 | |
| # - os: ubuntu-24.04 | |
| # compiler: llvm-17 | |
| - os: ubuntu-24.04 | |
| compiler: llvm-18 | |
| # ------------------------------- | |
| # MacOS 13 | |
| # ------------------------------- | |
| # Setup fails | |
| # - os: macos-13 | |
| # compiler: gcc-7 | |
| # - os: macos-13 | |
| # compiler: gcc-8 | |
| - os: macos-13 | |
| compiler: gcc-9 | |
| - os: macos-13 | |
| compiler: gcc-10 | |
| - os: macos-13 | |
| compiler: gcc-11 | |
| - os: macos-13 | |
| compiler: gcc-12 | |
| # Weird compiler errors | |
| # - os: macos-13 | |
| # compiler: gcc-13 | |
| - os: macos-13 | |
| compiler: gcc-14 | |
| # Setup fails | |
| # - os: macos-13 | |
| # compiler: llvm-6 | |
| # - os: macos-13 | |
| # compiler: llvm-7 | |
| # - os: macos-13 | |
| # compiler: llvm-8 | |
| # - os: macos-13 | |
| # compiler: llvm-9 | |
| # Weird compiler errors | |
| # - os: macos-13 | |
| # compiler: llvm-10 | |
| # - os: macos-13 | |
| # compiler: llvm-11 | |
| # - os: macos-13 | |
| # compiler: llvm-12 | |
| - os: macos-13 | |
| compiler: llvm-13 | |
| - os: macos-13 | |
| compiler: llvm-14 | |
| - os: macos-13 | |
| compiler: llvm-15 | |
| # Setup fails | |
| # - os: macos-13 | |
| # compiler: llvm-16 | |
| # - os: macos-13 | |
| # compiler: llvm-17 | |
| # - os: macos-13 | |
| # compiler: llvm-18 | |
| # ------------------------------- | |
| # MacOS 14 | |
| # ------------------------------- | |
| # Setup fails for all | |
| # - os: macos-14 | |
| # compiler: gcc-7 | |
| # - os: macos-14 | |
| # compiler: gcc-8 | |
| # - os: macos-14 | |
| # compiler: gcc-9 | |
| # - os: macos-14 | |
| # compiler: gcc-10 | |
| # - os: macos-14 | |
| # compiler: gcc-11 | |
| # - os: macos-14 | |
| # compiler: gcc-12 | |
| # - os: macos-14 | |
| # compiler: gcc-13 | |
| # - os: macos-14 | |
| # compiler: gcc-14 | |
| # - os: macos-14 | |
| # compiler: llvm-6 | |
| # - os: macos-14 | |
| # compiler: llvm-7 | |
| # - os: macos-14 | |
| # compiler: llvm-8 | |
| # - os: macos-14 | |
| # compiler: llvm-9 | |
| # - os: macos-14 | |
| # compiler: llvm-10 | |
| # - os: macos-14 | |
| # compiler: llvm-11 | |
| # - os: macos-14 | |
| # compiler: llvm-12 | |
| # - os: macos-14 | |
| # compiler: llvm-13 | |
| # - os: macos-14 | |
| # compiler: llvm-14 | |
| # - os: macos-14 | |
| # compiler: llvm-15 | |
| # - os: macos-14 | |
| # compiler: llvm-16 | |
| # - os: macos-14 | |
| # compiler: llvm-17 | |
| # - os: macos-14 | |
| # compiler: llvm-18 | |
| # ------------------------------- | |
| # AppleClang | |
| # ------------------------------- | |
| - os: macos-13 | |
| compiler: apple | |
| - os: macos-14 | |
| compiler: apple | |
| - os: macos-15 | |
| compiler: apple | |
| - os: macos-latest | |
| compiler: apple | |
| # ========================================================================== | |
| # Steps | |
| # ========================================================================== | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4.0.0 | |
| # ------------------------------------------------------- | |
| # Setup | |
| # ------------------------------------------------------- | |
| - name: Setup C++ | |
| # Reference: https://github.com/marketplace/actions/setup-cpp-c-c | |
| uses: aminya/setup-cpp@v0.37.0 | |
| if: ${{ matrix.compiler != 'apple' && matrix.os != 'macos-latest' }} | |
| with: | |
| compiler: ${{ matrix.compiler }} | |
| cmake: true | |
| make: true | |
| - name: Setup C++ - AppleClang | |
| if: matrix.compiler == 'apple' | |
| run: | | |
| brew install cmake | |
| # ------------------------------------------------------- | |
| # Dependencies | |
| # ------------------------------------------------------- | |
| - name: Install Dependencies - Ubuntu | |
| if: runner.os == 'linux' | |
| # 1: htslib dependencies, see https://github.com/samtools/htslib/blob/develop/INSTALL | |
| # 2: clang on ubuntu 22 is not properly set up, we need libtinfo5, | |
| # see https://github.com/aminya/setup-cpp/issues/149 | |
| run: | | |
| sudo apt-get install autoconf automake zlib1g-dev libbz2-dev liblzma-dev | |
| if [[ ${{ matrix.os }} != ubuntu-24.04 ]] && [[ ${{ matrix.os }} != ubuntu-latest ]] ; then | |
| sudo apt-get install libtinfo5 | |
| fi | |
| - name: Install Dependencies - MacOS | |
| if: runner.os == 'macos' | |
| # - Install simple dependencies of htslib | |
| # - For our test script, we might need gdate, see https://apple.stackexchange.com/a/47181 | |
| # This is not used at the moment, but we keep it here for the future. | |
| # - switch xcode mode, see https://stackoverflow.com/a/67654877 | |
| run: | | |
| brew install autoconf automake libdeflate | |
| brew install coreutils | |
| if [[ "${{ matrix.compiler }}" == gcc* ]]; then | |
| echo "Patching xcode gcc issues" | |
| sudo xcode-select --switch /Library/Developer/CommandLineTools | |
| fi | |
| # ------------------------------------------------------- | |
| # Configure | |
| # ------------------------------------------------------- | |
| - name: Configure | |
| run: | | |
| # Deactivate OpenMP on MacOS for now. Causes way too much trouble. | |
| export GENESIS_USE_OPENMP=ON | |
| if [[ "${RUNNER_OS}" == "macOS" ]]; then export GENESIS_USE_OPENMP=OFF; fi | |
| # Need to set the xcode patch here as well, as job steps don't keep status. | |
| if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then | |
| echo "Patching xcode gcc issues" | |
| sudo xcode-select --switch /Library/Developer/CommandLineTools | |
| fi | |
| # For static builds, set the according CMake option | |
| # Deactivated for now, as static building with OpenMP is not possible. | |
| # Will have to wait for gappa to use the genesis ThreadPool instead. | |
| export GAPPA_BUILD_STATIC="" | |
| # if [[ "${{ matrix.os }}" == "ubuntu-22.04" ]] && [[ "${{ matrix.compiler }}" == "gcc-13" ]]; then | |
| # export GAPPA_BUILD_STATIC="-DGAPPA_BUILD_STATIC=ON" | |
| # fi | |
| cmake -S . -B ./build -DGENESIS_USE_OPENMP=${GENESIS_USE_OPENMP} ${GAPPA_BUILD_STATIC} | |
| # ------------------------------------------------------- | |
| # Build | |
| # ------------------------------------------------------- | |
| - name: Build | |
| run: | | |
| # Weird workarounds. On some CI builds, this is needed somehow for LLVM under Ubuntu. | |
| if [[ "${RUNNER_OS}" != "macOS" ]] && [[ ! -f /usr/bin/gmake ]]; then | |
| sudo ln -s /usr/bin/make /usr/bin/gmake | |
| fi | |
| # Need to set the xcode patch here as well, as job steps don't keep status. | |
| if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then | |
| echo "Patching xcode gcc issues" | |
| sudo xcode-select --switch /Library/Developer/CommandLineTools | |
| fi | |
| cmake --build ./build -- -j 2 | |
| - name: Upload Logs | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: logs-${{ matrix.os }}-${{ matrix.compiler }} | |
| path: | | |
| test/log | |
| test/out | |
| build/**/*.log | |
| # ------------------------------------------------------- | |
| # Upload Binaries | |
| # ------------------------------------------------------- | |
| - name: Upload Binaries | |
| if: matrix.compiler == 'apple' | |
| # if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: binary-${{ matrix.os }} | |
| path: | | |
| bin/gappa | |
| # ------------------------------------------------------- | |
| # Test | |
| # ------------------------------------------------------- | |
| - name: Run Test | |
| if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' | |
| run: | | |
| cd ./test | |
| ./run.sh | |
| cd .. | |
| # We need to manually compress the test result files here, as there are many files, | |
| # and we run into https://github.com/actions/upload-artifact/issues/485 | |
| tar -czf ./test.tar.gz ./test | |
| - name: Upload Tests | |
| if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-${{ matrix.os }}-${{ matrix.compiler }} | |
| path: | | |
| # test | |
| ./test.tar.gz |