CI #60
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| # ================================================================================================== | |
| # Header | |
| # ================================================================================================== | |
| name: CI | |
| on: [push, pull_request] | |
| # ================================================================================================== | |
| # Jobs | |
| # ================================================================================================== | |
| jobs: | |
| # ========================================================================== | |
| # CI Matrix | |
| # ========================================================================== | |
| ci: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| # ------------------------------------------------------- | |
| # matrix | |
| # ------------------------------------------------------- | |
| matrix: | |
| os: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#choosing-github-hosted-runners | |
| - ubuntu-20.04 | |
| - ubuntu-22.04 | |
| - macos-11 | |
| - macos-12 | |
| compiler: | |
| - gcc-7 | |
| - gcc-8 | |
| - gcc-9 | |
| - gcc-10 | |
| - gcc-11 | |
| - gcc-12 | |
| - gcc-13 | |
| - llvm-5 | |
| - llvm-6 | |
| - llvm-7 | |
| - llvm-8 | |
| - llvm-9 | |
| - llvm-10 | |
| - llvm-11 | |
| - llvm-12 | |
| - llvm-13 | |
| # ------------------------------------------------------- | |
| # exclude | |
| # ------------------------------------------------------- | |
| exclude: | |
| # Newer GCC versions are not available on all Ubuntu | |
| - os: ubuntu-20.04 | |
| compiler: gcc-12 | |
| - os: ubuntu-20.04 | |
| compiler: gcc-13 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-13 | |
| # Older GCC versions are not supported by Ubuntu any more | |
| - os: ubuntu-22.04 | |
| compiler: gcc-7 | |
| - os: ubuntu-22.04 | |
| compiler: gcc-8 | |
| # llvm-9 causes weird segfauls on Ubuntu, which do not seem to be our fault. | |
| # Need to investiage further at some point. We used setup-cpp locally to install | |
| # the very same version of llvm-9, and got tons of segfauls for all kind of functions... | |
| - os: ubuntu-20.04 | |
| compiler: llvm-9 | |
| - os: ubuntu-22.04 | |
| compiler: llvm-9 | |
| # 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. | |
| # Wildcards do not work here, so we have to list them all... :-( | |
| - os: macos-11 | |
| compiler: llvm-5 | |
| - os: macos-11 | |
| compiler: llvm-6 | |
| - os: macos-11 | |
| compiler: llvm-7 | |
| - os: macos-11 | |
| compiler: llvm-8 | |
| - os: macos-11 | |
| compiler: llvm-9 | |
| - os: macos-11 | |
| compiler: llvm-10 | |
| - os: macos-11 | |
| compiler: llvm-11 | |
| - os: macos-11 | |
| compiler: llvm-12 | |
| - os: macos-11 | |
| compiler: llvm-13 | |
| - os: macos-12 | |
| compiler: llvm-5 | |
| - os: macos-12 | |
| compiler: llvm-6 | |
| - os: macos-12 | |
| compiler: llvm-7 | |
| - os: macos-12 | |
| compiler: llvm-8 | |
| - os: macos-12 | |
| compiler: llvm-9 | |
| - os: macos-12 | |
| compiler: llvm-10 | |
| - os: macos-12 | |
| compiler: llvm-11 | |
| - os: macos-12 | |
| compiler: llvm-12 | |
| - os: macos-12 | |
| compiler: llvm-13 | |
| # ------------------------------------------------------- | |
| # include | |
| # ------------------------------------------------------- | |
| include: | |
| # We test AppleClang as well, as a special case. | |
| # - os: macos-10.15 | |
| # compiler: apple | |
| - os: macos-11 | |
| compiler: apple | |
| - os: macos-12 | |
| compiler: apple | |
| # ========================================================================== | |
| # Steps | |
| # ========================================================================== | |
| steps: | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| # ------------------------------------------------------- | |
| # Setup | |
| # ------------------------------------------------------- | |
| - name: Setup C++ | |
| # Reference: https://github.com/marketplace/actions/setup-cpp-c-c | |
| uses: aminya/[email protected] | |
| if: matrix.compiler != 'apple' | |
| with: | |
| compiler: ${{ matrix.compiler }} | |
| cmake: true | |
| # ------------------------------------------------------- | |
| # Dependencies | |
| # ------------------------------------------------------- | |
| - name: Install Dependencies - Ubuntu | |
| if: runner.os == 'linux' | |
| # 1: htslib dependencies, see https://github.com/samtools/htslib/blob/develop/INSTALL | |
| # 2: clang on ubuntu 22 is not properly set up, we need libtinfo5, | |
| # see https://github.com/aminya/setup-cpp/issues/149 | |
| run: | | |
| sudo apt-get install autoconf automake zlib1g-dev libbz2-dev liblzma-dev | |
| sudo apt-get install libtinfo5 | |
| - name: Install Dependencies - MacOS | |
| if: runner.os == 'macos' | |
| # - Install simple dependencies of htslib | |
| # - For our test script, we might need gdate, see https://apple.stackexchange.com/a/47181 | |
| # This is not used at the moment, but we keep it here for the future. | |
| # - switch xcode mode, see https://stackoverflow.com/a/67654877 | |
| run: | | |
| brew install autoconf automake libdeflate | |
| brew install coreutils | |
| if [[ "${{ matrix.compiler }}" == gcc* ]]; then | |
| echo "Patching xcode gcc issues" | |
| sudo xcode-select --switch /Library/Developer/CommandLineTools | |
| fi | |
| # ------------------------------------------------------- | |
| # Configure | |
| # ------------------------------------------------------- | |
| - name: Configure | |
| run: | | |
| # 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 | |
| export GRENEDALF_BUILD_STATIC="" | |
| if [[ "${{ matrix.os }}" == "ubuntu-22.04" ]] && [[ "${{ matrix.compiler }}" == "gcc-13" ]]; then | |
| export GRENEDALF_BUILD_STATIC="-DGRENEDALF_BUILD_STATIC=ON" | |
| fi | |
| cmake -S . -B ./build ${GRENEDALF_BUILD_STATIC} | |
| # ------------------------------------------------------- | |
| # Build & Test | |
| # ------------------------------------------------------- | |
| - name: Build | |
| # Below we use a workaround for LLVM as configured by setup-cpp, which clashes with htslib: | |
| # https://github.com/samtools/htslib/issues/1527 and | |
| # https://github.com/aminya/setup-cpp/issues/145 | |
| run: | | |
| if [[ ! -z "${LLVM_PATH}" ]]; then | |
| export LDFLAGS=`echo ${LDFLAGS} | sed 's/"//g'` | |
| export CPPFLAGS=`echo ${CPPFLAGS} | sed 's/"//g'` | |
| fi | |
| # Need to set the xcode patch here as well, as job steps don't keep status. | |
| if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then | |
| echo "Patching xcode gcc issues" | |
| sudo xcode-select --switch /Library/Developer/CommandLineTools | |
| fi | |
| cmake --build ./build -- -j 2 | |
| - name: Upload Logs | |
| if: always() | |
| uses: actions/[email protected] | |
| with: | |
| name: logs-${{ matrix.os }}-${{ matrix.compiler }} | |
| path: | | |
| build/**/*.log | |
| # ------------------------------------------------------- | |
| # Upload Binaries | |
| # ------------------------------------------------------- | |
| - name: Upload Binaries | |
| if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: binary-${{ matrix.os }} | |
| path: | | |
| bin/grenedalf |