Release v0.6.1 #105
Workflow file for this run
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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 | |
| # ------------------------------------------------------- | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#choosing-github-hosted-runners | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners | |
| matrix: | |
| # Need dummy entries for the matrix to pick up the variables. | |
| # We later set all other combinations that we want explicitly. | |
| 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 MacOS 12 any more. | |
| # Currently, llvm-9 causes weird segfauls on Ubuntu, which do not seem to be our fault, | |
| # but rather a bug in their thread forking, according to valgrind. | |
| # 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. | |
| # 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 20.04 | |
| # ------------------------------- | |
| - os: ubuntu-20.04 | |
| compiler: gcc-7 | |
| - os: ubuntu-20.04 | |
| compiler: gcc-8 | |
| - os: ubuntu-20.04 | |
| compiler: gcc-9 | |
| - os: ubuntu-20.04 | |
| compiler: gcc-10 | |
| # Setup fails | |
| # - os: ubuntu-20.04 | |
| # compiler: gcc-11 | |
| # - os: ubuntu-20.04 | |
| # compiler: gcc-12 | |
| - os: ubuntu-20.04 | |
| compiler: gcc-13 | |
| # Too new | |
| # - os: ubuntu-20.04 | |
| # compiler: gcc-14 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-6 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-7 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-8 | |
| # Weird segfault | |
| # - os: ubuntu-20.04 | |
| # compiler: llvm-9 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-10 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-11 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-12 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-13 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-14 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-15 | |
| # Setup fails | |
| # - os: ubuntu-20.04 | |
| # compiler: llvm-16 | |
| - os: ubuntu-20.04 | |
| compiler: llvm-17 | |
| # Setup fails | |
| # - os: ubuntu-20.04 | |
| # compiler: llvm-18 | |
| # ------------------------------- | |
| # 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 12 | |
| # ------------------------------- | |
| # Setup fails (too old?) | |
| # - os: macos-12 | |
| # compiler: gcc-7 | |
| # - os: macos-12 | |
| # compiler: gcc-8 | |
| - os: macos-12 | |
| compiler: gcc-9 | |
| - os: macos-12 | |
| compiler: gcc-10 | |
| - os: macos-12 | |
| compiler: gcc-11 | |
| - os: macos-12 | |
| compiler: gcc-12 | |
| # Weird compiler errors | |
| # - os: macos-12 | |
| # compiler: gcc-13 | |
| - os: macos-12 | |
| compiler: gcc-14 | |
| # Setup fails | |
| # - 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 | |
| # Weird compiler errors | |
| # - os: macos-12 | |
| # compiler: llvm-12 | |
| - os: macos-12 | |
| compiler: llvm-13 | |
| - os: macos-12 | |
| compiler: llvm-14 | |
| - os: macos-12 | |
| compiler: llvm-15 | |
| # Setup fails | |
| # - os: macos-12 | |
| # compiler: llvm-16 | |
| # - os: macos-12 | |
| # compiler: llvm-17 | |
| # - os: macos-12 | |
| # 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-12 | |
| compiler: apple | |
| - os: macos-13 | |
| compiler: apple | |
| - os: macos-14 | |
| 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 [[ ${{ matrix.os }} != ubuntu-24.04 ]] ; then | |
| sudo apt-get install libtinfo5 | |
| fi | |
| - name: Install Dependencies - MacOS | |
| if: runner.os == 'macos' | |
| # - Install simple dependencies of htslib | |
| # - For our test script, we might need gdate, see https://apple.stackexchange.com/a/47181 | |
| # This is not used at the moment, but we keep it here for the future. | |
| # - switch xcode mode, see https://stackoverflow.com/a/67654877 | |
| run: | | |
| brew install autoconf automake libdeflate | |
| brew install coreutils | |
| if [[ "${{ matrix.compiler }}" == gcc* ]]; then | |
| echo "Patching xcode gcc issues" | |
| sudo xcode-select --switch /Library/Developer/CommandLineTools | |
| fi | |
| # ------------------------------------------------------- | |
| # Configure | |
| # ------------------------------------------------------- | |
| - name: Configure | |
| run: | | |
| # 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 [[ "${{ matrix.os }}" == "ubuntu-latest" ]] && [[ "${{ matrix.compiler }}" == "gcc" ]]; then | |
| if [[ "${{ matrix.os }}" == "ubuntu-latest" ]] ; then | |
| export GRENEDALF_BUILD_STATIC="-DGRENEDALF_BUILD_STATIC=ON" | |
| fi | |
| cmake -S . -B ./build ${GRENEDALF_BUILD_STATIC} | |
| # ------------------------------------------------------- | |
| # Build | |
| # ------------------------------------------------------- | |
| - name: Build | |
| run: | | |
| # Weird workarounds. On some CI builds, this is needed somehow for LLVM under Ubuntu. | |
| if [[ "${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: | | |
| build/**/*.log | |
| # ------------------------------------------------------- | |
| # Upload Binaries | |
| # ------------------------------------------------------- | |
| # We upload the static binaries for the most important systems. | |
| # These are the ones that we want to publish with release versions. | |
| - name: Upload Binaries | |
| # If the Ubuntu binary here is changed, it needs to be changed above as well, | |
| # to enable static building for that version! | |
| # if: ( matrix.os == 'ubuntu-latest' && matrix.compiler == 'gcc' ) || matrix.compiler == 'apple' | |
| if: matrix.os == 'ubuntu-latest' || matrix.compiler == 'apple' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: binary-${{ matrix.os }}-${{ matrix.compiler }} | |
| path: | | |
| bin/grenedalf | |
| # ------------------------------------------------------- | |
| # Test | |
| # ------------------------------------------------------- | |
| # We also run the test case, comparing grenedalf against our independent implementation. | |
| # This covers several OS and compiler combionations, so hopefully good enough. | |
| - name: Python Setup | |
| if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install Test Dependencies | |
| if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' | |
| run: | | |
| # Install the dependencies for the tests | |
| pip install -r test/pip.txt | |
| # Verify the installation | |
| pip list | |
| python --version | |
| - 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 |