Do not allow shared memory metagenome search #442
Workflow file for this run
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| name: CI misc | |
| on: | |
| push: | |
| branches: | |
| # Push events to branches matching refs/heads/main | |
| - 'main' | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| group: misc-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| CMAKE_VERSION: 3.16.9 | |
| SEQAN3_NO_VERSION_CHECK: 1 | |
| TZ: Europe/Berlin | |
| defaults: | |
| run: | |
| shell: bash -ex {0} | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: "Documentation" | |
| build: documentation | |
| build_threads: 2 | |
| test_threads: 2 | |
| cmake: 3.16.9 | |
| doxygen: 1.9.4 | |
| requires_toolchain: false | |
| requires_ccache: false | |
| skip_build_tests: true | |
| skip_run_tests: false | |
| - name: "Header gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| build_type: Release | |
| build: header | |
| build_threads: 2 | |
| test_threads: 2 | |
| cmake: 3.16.9 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| skip_build_tests: false | |
| skip_run_tests: true | |
| - name: "Header gcc10" | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| build_type: Release | |
| build: header | |
| build_threads: 2 | |
| test_threads: 2 | |
| cmake: 3.16.9 | |
| requires_toolchain: true | |
| requires_ccache: true | |
| skip_build_tests: false | |
| skip_run_tests: true | |
| steps: | |
| - name: Set repository name | |
| run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| path: ${{ env.REPOSITORY_NAME }} | |
| fetch-depth: 2 | |
| submodules: recursive | |
| - name: Add package source | |
| run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/configure_apt.sh | |
| - name: Install CMake | |
| env: | |
| BUILD: ${{ matrix.build }} | |
| CMAKE_VERSION: ${{ matrix.cmake }} | |
| run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh | |
| - name: Install Doxygen | |
| if: matrix.build == 'documentation' | |
| env: | |
| DOXYGEN_VERSION: ${{ matrix.doxygen }} | |
| run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_doxygen.sh | |
| - name: Install ccache | |
| if: matrix.requires_ccache | |
| run: | | |
| conda install --yes --override-channels --channel conda-forge ccache | |
| sudo ln -s $CONDA/bin/ccache /usr/bin/ccache | |
| - name: Install compiler ${{ matrix.cxx }} | |
| if: matrix.requires_toolchain | |
| run: sudo apt-get install --yes ${{ matrix.cxx }} | |
| - name: Load ccache | |
| if: matrix.requires_ccache | |
| uses: actions/cache@v3 | |
| with: | |
| path: .ccache | |
| key: ${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }} | |
| # Restoring: From current branch, otherwise from base branch, otherwise from any branch. | |
| restore-keys: | | |
| ${{ matrix.name }}-ccache-${{ github.ref }} | |
| ${{ matrix.name }}-ccache-${{ github.base_ref }} | |
| ${{ matrix.name }}-ccache- | |
| - name: Tool versions | |
| run: | | |
| env cmake --version | |
| env doxygen --version || true | |
| env ${{ matrix.cxx }} --version || true | |
| - name: Configure tests | |
| env: | |
| CXX: ${{ matrix.cxx }} | |
| CC: ${{ matrix.cc }} | |
| run: | | |
| mkdir build | |
| cd build | |
| header_test_flag=$(echo "${{ env.REPOSITORY_NAME }}_HEADER_TEST_ONLY" | tr '[:lower:]' '[:upper:]') | |
| cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \ | |
| -D${header_test_flag}=${{ matrix.build == 'header' && 'ON' || 'OFF'}} | |
| if [[ "${{ matrix.build }}" =~ ^(header)$ ]]; then | |
| make -j${{ matrix.build_threads }} gtest_build | |
| fi | |
| - name: Build tests | |
| if: ${{!matrix.skip_build_tests}} | |
| env: | |
| CCACHE_BASEDIR: ${{ github.workspace }} | |
| CCACHE_DIR: ${{ github.workspace }}/.ccache | |
| CCACHE_COMPRESS: true | |
| CCACHE_COMPRESSLEVEL: 12 | |
| CCACHE_MAXSIZE: 75M | |
| CMAKE_BUILD_PARALLEL_LEVEL: ${{ matrix.build_threads }} | |
| run: | | |
| ccache -p || true | |
| cd build | |
| make -k test | |
| ccache -s || true | |
| - name: Run tests | |
| if: ${{!matrix.skip_run_tests}} | |
| run: | | |
| cd build | |
| if [[ "${{ matrix.build }}" =~ ^(documentation)$ ]]; then | |
| make -k -j${{ matrix.test_threads }} doc 2>doxygen_warnings.txt | |
| cat doxygen_warnings.txt | |
| # test ! -s doxygen_warnings.txt | |
| else | |
| ctest . -j${{ matrix.test_threads }} --output-on-failure | |
| fi | |
| - name: Package documentation | |
| if: matrix.build == 'documentation' | |
| continue-on-error: true | |
| run: tar -zcf documentation.tar.gz build | |
| - name: Upload documentation | |
| if: matrix.build == 'documentation' | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: documentation | |
| path: documentation.tar.gz |