[MISC] Add seqan3::multiple_sequence_alignment_result. #93
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| name: SeqAn3 CI | |
| on: [push, pull_request] | |
| env: | |
| CMAKE_VERSION: 3.7.2 | |
| DOXYGEN_VERSION: 1.8.19 | |
| SEQAN3_NO_VERSION_CHECK: 1 | |
| TZ: Europe/Berlin | |
| jobs: | |
| cancel: | |
| name: "Cancel previous runs" | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| build: | |
| needs: cancel | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: "Coverage gcc7" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-7" | |
| cc: "gcc-7" | |
| build: coverage | |
| build_type: Debug | |
| - name: "Unit gcc9 (c++2a) on Linux" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-9" | |
| cc: "gcc-9" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++2a" | |
| - name: "Unit gcc9 (c++2a) on macOS" | |
| os: macos-10.15 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-9" | |
| cc: "gcc-9" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++2a" | |
| - name: "Unit gcc10 (c++17) on Linux" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++17 -fconcepts" | |
| - name: "Unit gcc10 (c++17) on macOS" | |
| os: macos-10.15 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++17 -fconcepts" | |
| - name: "Unit gcc10 (c++20) on Linux" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| build: unit | |
| build_type: Release | |
| - name: "Unit gcc10 (c++20) on macOS" | |
| os: macos-10.15 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| build: unit | |
| build_type: Release | |
| - name: "Unit gcc8 on Linux" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-8" | |
| cc: "gcc-8" | |
| build: unit | |
| build_type: Release | |
| - name: "Unit gcc8 on macOS" | |
| os: macos-10.15 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-8" | |
| cc: "gcc-8" | |
| build: unit | |
| build_type: Release | |
| - name: "Unit gcc7 on Linux" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-7" | |
| cc: "gcc-7" | |
| build: unit | |
| build_type: Release | |
| - name: "Unit gcc7 on macOS" | |
| os: macos-10.15 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-7" | |
| cc: "gcc-7" | |
| build: unit | |
| build_type: Release | |
| - name: "Performance gcc7" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-7" | |
| cc: "gcc-7" | |
| build: performance | |
| build_type: Release | |
| - name: "Header gcc7" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-7" | |
| cc: "gcc-7" | |
| build: header | |
| build_type: Release | |
| - name: "Snippet gcc7" | |
| os: ubuntu-20.04 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| cxx: "g++-7" | |
| cc: "gcc-7" | |
| build: snippet | |
| build_type: Release | |
| - name: "Documentation" | |
| os: ubuntu-20.04 | |
| requires_toolchain: false | |
| requires_ccache: false | |
| build: documentation | |
| steps: | |
| - name: Checkout SeqAn3 | |
| uses: actions/checkout@v2 | |
| with: | |
| path: seqan3 | |
| submodules: true | |
| - name: Checkout SeqAn2 | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: seqan/seqan | |
| ref: develop | |
| path: seqan3/submodules/seqan | |
| - name: Setup CMake | |
| shell: bash | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| OS="Linux" | |
| else | |
| OS="Darwin" | |
| fi | |
| mkdir -p /tmp/cmake-download | |
| wget --no-clobber --quiet --directory-prefix=/tmp/cmake-download/ https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-${OS}-x86_64.tar.gz | |
| tar -C /tmp/ -zxf /tmp/cmake-download/cmake-${CMAKE_VERSION}-${OS}-x86_64.tar.gz | |
| echo "::add-path::/tmp/cmake-${CMAKE_VERSION}-${OS}-x86_64/bin" # Only available in subsequent steps! | |
| - name: Setup Doxygen | |
| if: matrix.build == 'documentation' | |
| shell: bash | |
| run: | | |
| sudo apt-get install texlive-font-utils ghostscript texlive-latex-extra graphviz libclang-9-dev libclang-cpp9 # graphviz for dot, latex to parse formulas, libclang for doxygen | |
| mkdir -p /tmp/doxygen-download | |
| wget --no-clobber --quiet --directory-prefix=/tmp/doxygen-download/ https://sourceforge.net/projects/doxygen/files/rel-${DOXYGEN_VERSION}/doxygen-${DOXYGEN_VERSION}.linux.bin.tar.gz | |
| tar -C /tmp/ -zxf /tmp/doxygen-download/doxygen-${DOXYGEN_VERSION}.linux.bin.tar.gz | |
| echo "::add-path::/tmp/doxygen-${DOXYGEN_VERSION}/bin" # Only available in subsequent steps! | |
| - name: Add package source | |
| if: matrix.requires_toolchain && runner.os == 'Linux' | |
| shell: bash | |
| run: sudo add-apt-repository --yes ppa:ubuntu-toolchain-r/ppa && sudo apt-get update | |
| - name: Install ccache | |
| if: matrix.requires_ccache | |
| shell: bash | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| sudo apt-get install --yes ccache | |
| else | |
| brew install --force-bottle ccache | |
| fi | |
| - name: Install compiler ${{ matrix.cxx }} | |
| if: matrix.requires_toolchain | |
| shell: bash | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| sudo apt-get install --yes ${{ matrix.cxx }} | |
| else | |
| brew install --force-bottle $(echo "${{ matrix.cxx }}" | sed "s/++-/cc@/g") | |
| fi | |
| - name: Install lcov | |
| if: matrix.build == 'coverage' | |
| shell: bash | |
| run: | | |
| sudo apt-get install --yes lcov | |
| sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/gcov-7 100 | |
| - name: Prepare ccache | |
| if: matrix.requires_ccache | |
| id: ccache_prepare | |
| shell: cmake -P {0} | |
| run: | | |
| string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S") | |
| message("::set-output name=timestamp::${current_date}") | |
| - name: Load ccache | |
| if: matrix.requires_ccache | |
| uses: actions/[email protected] | |
| with: | |
| path: .ccache | |
| key: ${{ matrix.name }}-ccache-${{ steps.ccache_prepare.outputs.timestamp }} | |
| restore-keys: | | |
| ${{ matrix.name }}-ccache- | |
| - name: Configure tests | |
| env: | |
| CXX: ${{ matrix.cxx }} | |
| CC: ${{ matrix.cc }} | |
| shell: bash | |
| run: | | |
| mkdir seqan3-build | |
| cd seqan3-build | |
| cmake ../seqan3/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" | |
| if [[ "${{ matrix.build }}" =~ ^(unit|header|snippet|coverage)$ ]]; then | |
| make gtest_project | |
| fi | |
| if [[ "${{ matrix.build }}" =~ ^(performance)$ ]]; then | |
| make gbenchmark_project | |
| fi | |
| - name: Build tests | |
| env: | |
| CCACHE_BASEDIR: ${{ github.workspace }} | |
| CCACHE_DIR: ${{ github.workspace }}/.ccache | |
| CCACHE_COMPRESS: true | |
| CCACHE_COMPRESSLEVEL: 6 | |
| CCACHE_MAXSIZE: 5G | |
| shell: bash | |
| run: | | |
| ccache -p || true | |
| cd seqan3-build | |
| make -k -j2 | |
| ccache -s || true | |
| - name: Run tests | |
| shell: bash | |
| run: | | |
| cd seqan3-build | |
| if [[ "${{ matrix.build }}" =~ ^(coverage)$ ]]; then | |
| : ; else | |
| if [[ "${{ matrix.build }}" =~ ^(snippet)$ ]]; then | |
| ctest . --output-on-failure]; else | |
| ctest . -j2 --output-on-failure | |
| fi | |
| fi | |
| - name: Submit coverage build | |
| if: matrix.build == 'coverage' | |
| shell: bash | |
| run: bash <(curl -s https://codecov.io/bash) -f ./seqan3-build/seqan3_coverage -R ./seqan3 || echo 'Codecov failed to upload' | |
| - name: Package documentation | |
| if: matrix.build == 'documentation' | |
| continue-on-error: true | |
| run: tar -zcf documentation.tar.gz seqan3-build | |
| - name: Upload documentation | |
| if: matrix.build == 'documentation' | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: documentation | |
| path: documentation.tar.gz |