Merge pull request #73 from h-2/gcc13 #244
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| name: Linux CI | |
| on: | |
| push: | |
| branches: | |
| # Push events to branches matching refs/heads/master | |
| - 'main' | |
| # Push events to branches matching refs/heads/release* | |
| - 'release*' | |
| # Trigger after PR was unlabeled | |
| pull_request: | |
| # Enables a manual trigger, may run on any branch | |
| workflow_dispatch: | |
| concurrency: | |
| group: linux-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| TZ: Europe/Berlin | |
| defaults: | |
| run: | |
| shell: bash -ex {0} | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os == '' && 'ubuntu-22.04' || matrix.os }} | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: "Unit clang16 + clang-tidy" | |
| cxx: "clang++-16" | |
| cc: "clang-16" | |
| pkg: "clang-16 clang-tidy-16 g++-12" | |
| build: clang_tidy | |
| build_type: Debug | |
| - name: "Unit gcc10 Debug" | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| pkg: "gcc-10 g++-10" | |
| build: unit | |
| build_type: Debug | |
| - name: "Unit gcc11 Release" | |
| cxx: "g++-11" | |
| cc: "gcc-11" | |
| pkg: "gcc-11 g++-11" | |
| build: unit | |
| build_type: Release | |
| - name: "Unit gcc12 ASAN+UBSAN" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| pkg: "gcc-12 g++-12" | |
| build: unit | |
| build_type: Debug | |
| cxx_flags: "-fsanitize=address,undefined" | |
| - name: "Unit gcc13 Debug" | |
| cxx: "g++-13" | |
| cc: "gcc-13" | |
| pkg: "gcc-13 g++-13" | |
| build: unit | |
| build_type: Debug | |
| - name: "Integration gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| pkg: "gcc-12 g++-12" | |
| build: integration | |
| build_type: Debug | |
| - name: "Documentation" | |
| pkg: "doxygen" | |
| build: documentation | |
| build_type: Debug | |
| version: 1.9.6 | |
| - name: "Clang Format" | |
| pkg: "clang-format-16" | |
| build: clang_format | |
| build_type: Debug | |
| - name: "Coverage gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| pkg: "gcc-12 g++-12" | |
| build: coverage | |
| build_type: Debug | |
| - name: "Snippet gcc10" | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| pkg: "gcc-10 g++-10" | |
| build: snippet | |
| build_type: Debug | |
| - name: "Snippet gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| pkg: "gcc-12 g++-12" | |
| build: snippet | |
| build_type: Release | |
| - name: "Snippet Clang-16" | |
| cxx: "clang++-16" | |
| cc: "clang-16" | |
| pkg: "clang-16 g++-12" | |
| build: snippet | |
| build_type: Release | |
| - name: "Performance gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| pkg: "gcc-12 g++-12" | |
| build: performance | |
| build_type: Release | |
| - name: "Header gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| pkg: "gcc-12 g++-12" | |
| build: header | |
| build_type: Release | |
| steps: | |
| - name: Checkout BioC++ | |
| uses: actions/checkout@v2 | |
| with: | |
| path: biocpp-core | |
| fetch-depth: 2 | |
| submodules: true | |
| #- name: Checkout SeqAn2 | |
| #uses: actions/checkout@v2 | |
| #with: | |
| #repository: seqan/seqan | |
| #ref: develop | |
| #path: biocpp-core/submodules/seqan | |
| #fetch-depth: 2 | |
| - name: Configure APT (llvm) | |
| continue-on-error: true | |
| if: contains(matrix.pkg, 'clang') | |
| run: | | |
| sudo apt-add-repository --no-update --yes "deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-16 main" | |
| wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key|sudo apt-key add - | |
| - name: Configure APT | |
| continue-on-error: true | |
| run: | | |
| echo 'APT::Acquire::Retries "5";' | sudo tee -a /etc/apt/apt.conf.d/80-retries > /dev/null | |
| sudo add-apt-repository --no-update --yes ppa:ubuntu-toolchain-r/ppa | |
| sudo add-apt-repository --no-update --yes ppa:ubuntu-toolchain-r/test | |
| sudo apt-get update | |
| - name: Install CMake | |
| run: sudo apt-get install --yes cmake | |
| - name: Install ccache | |
| run: sudo apt-get install --yes ccache | |
| - name: Install compiler/tool ${{ matrix.pkg }} | |
| run: sudo apt-get install --yes ${{ matrix.pkg }} | |
| - name: Install doxygen | |
| if: matrix.build == 'documentation' | |
| run: | | |
| sudo apt-get install --yes texlive-font-utils ghostscript texlive-latex-extra graphviz | |
| mkdir -p /tmp/doxygen-download | |
| wget --retry-connrefused --waitretry=30 --read-timeout=30 --timeout=30 --tries=20 --no-clobber --quiet --directory-prefix=/tmp/doxygen-download/ https://github.com/doxygen/doxygen/releases/download/Release_$(echo ${{ matrix.version }} | sed -e 's/\./_/g')/doxygen-${{ matrix.version }}.linux.bin.tar.gz | |
| tar -C /tmp/ -zxf /tmp/doxygen-download/doxygen-${{ matrix.version }}.linux.bin.tar.gz | |
| echo "/tmp/doxygen-${{ matrix.version }}/bin" >> $GITHUB_PATH # Only available in subsequent steps! | |
| - name: Install gcovr | |
| if: matrix.build == 'coverage' | |
| env: | |
| CC: ${{ matrix.cc }} | |
| run: | | |
| sudo apt-get install --yes gcovr | |
| sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100 | |
| - name: Load ccache | |
| if: matrix.build != 'documentation' | |
| uses: actions/cache@v2 | |
| with: | |
| path: .ccache | |
| key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }} | |
| # Restoring: From current branch, otherwise from base branch, otherwise from any branch. | |
| restore-keys: | | |
| ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }} | |
| ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.base_ref }} | |
| ${{ runner.os }}-${{ matrix.name }}-ccache- | |
| - name: Tool versions | |
| run: | | |
| env cmake --version | |
| env ${{ matrix.cxx }} --version | |
| - name: Configure tests | |
| env: | |
| CXX: ${{ matrix.cxx }} | |
| CC: ${{ matrix.cc }} | |
| run: | | |
| mkdir biocpp-core-build | |
| cd biocpp-core-build | |
| cmake ../biocpp-core/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE="${{ matrix.build_type }}" -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" | |
| - name: Build tests | |
| env: | |
| CCACHE_BASEDIR: ${{ github.workspace }} | |
| CCACHE_DIR: ${{ github.workspace }}/.ccache | |
| CCACHE_COMPRESS: true | |
| CCACHE_COMPRESSLEVEL: 12 | |
| CCACHE_MAXSIZE: ${{ matrix.build == 'coverage' && '525M' || '75M' }} | |
| CCACHE_IGNOREOPTIONS: "-fprofile-abs-path" | |
| run: | | |
| ccache -z | |
| cd biocpp-core-build | |
| make -k -j2 | |
| ccache -sv | |
| - name: Run tests | |
| if: ${{ matrix.build != 'coverage' && matrix.build != 'clang_format' }} | |
| run: | | |
| cd biocpp-core-build | |
| ctest . -j2 --output-on-failure | |
| - name: Submit coverage build | |
| if: matrix.build == 'coverage' | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| files: ${{ github.workspace }}/biocpp-core-build/biocpp_coverage.xml | |
| root_dir: ${{ github.workspace }}/biocpp-core |