[FIX] Exact search: lower bound for error rate (#18) #124
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| name: CI on Linux | ||
| on: | ||
| push: | ||
| branches: | ||
| - 'main' | ||
| pull_request: | ||
| workflow_dispatch: | ||
| concurrency: | ||
| group: coverage-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: ${{ github.event_name != 'push' }} | ||
| env: | ||
| CMAKE_VERSION: 3.16.9 | ||
| SEQAN3_NO_VERSION_CHECK: 1 | ||
| SHARG_NO_VERSION_CHECK: 1 | ||
| TZ: Europe/Berlin | ||
| defaults: | ||
| run: | ||
| shell: bash -ex {0} | ||
| jobs: | ||
| build: | ||
| name: ${{ matrix.name }} | ||
| runs-on: ubuntu-20.04 | ||
| timeout-minutes: 120 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| # - name: "Coverage gcc10" | ||
| # cxx: "g++-10" | ||
| # cc: "gcc-10" | ||
| # build_type: Coverage | ||
| steps: | ||
| - name: Set repository name | ||
| run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV | ||
| # How many commits do we need to fetch to also fetch the branch point? | ||
| - name: Get fetch depth | ||
| id: fetch_depth | ||
| run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT | ||
| - name: Checkout | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| path: ${{ env.REPOSITORY_NAME }} | ||
| fetch-depth: ${{ steps.fetch_depth.outputs.depth }} | ||
| submodules: recursive | ||
| - name: Add package source | ||
| run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/configure_apt.sh | ||
| - name: Install CMake | ||
| run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh | ||
| - name: Install 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 }} | ||
| run: sudo apt-get install --yes ${{ matrix.cxx }} | ||
| - name: Install gcovr | ||
| env: | ||
| CC: ${{ matrix.cc }} | ||
| run: | | ||
| sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100 | ||
| pip install gcovr==5.0 | ||
| - name: Load ccache | ||
| uses: actions/cache@v3 | ||
| 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: ${{ matrix.cc }} | ||
| run: | | ||
| mkdir build | ||
| cd build | ||
| cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | ||
| -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" | ||
| make -j2 gtest_build | ||
| - name: Build application | ||
| env: | ||
| CCACHE_BASEDIR: ${{ github.workspace }} | ||
| CCACHE_DIR: ${{ github.workspace }}/.ccache | ||
| CCACHE_COMPRESS: true | ||
| CCACHE_COMPRESSLEVEL: 12 | ||
| CCACHE_MAXSIZE: 525M | ||
| CCACHE_IGNOREOPTIONS: "-fprofile-abs-path" | ||
| run: | | ||
| ccache -z | ||
| cd build | ||
| make -k -j2 | ||
| ccache -sv | ||
| - name: Build tests | ||
| env: | ||
| CCACHE_BASEDIR: ${{ github.workspace }} | ||
| CCACHE_DIR: ${{ github.workspace }}/.ccache | ||
| CCACHE_COMPRESS: true | ||
| CCACHE_COMPRESSLEVEL: 12 | ||
| CCACHE_MAXSIZE: 525M | ||
| CCACHE_IGNOREOPTIONS: "-fprofile-abs-path" | ||
| run: | | ||
| ccache -z | ||
| cd build | ||
| make -k -j2 api_test cli_test | ||
| ccache -sv | ||
| - name: Run tests | ||
| run: | | ||
| cd build | ||
| ctest . -j2 --output-on-failure | ||
| - name: Generate coverage report | ||
| run: | | ||
| gcovr --gcov-executable ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/gcov.sh \ | ||
| --root ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/test/coverage \ | ||
| ${{ github.workspace }}/build \ | ||
| --filter ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/include \ | ||
| --filter ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/src \ | ||
| --exclude-lines-by-pattern '^\s*$' \ | ||
| --exclude-lines-by-pattern '^\s*};$' \ | ||
| --exclude-lines-by-pattern '^.*GCOVR_EXCL_LINE.*$' \ | ||
| --exclude-unreachable-branches \ | ||
| --exclude-throw-branches \ | ||
| -j 2 \ | ||
| --xml \ | ||
| --output ${{ github.workspace }}/build/coverage_report.xml | ||
| - name: Submit coverage report | ||
| uses: codecov/codecov-action@v3 | ||
| with: | ||
| files: ${{ github.workspace }}/build/coverage_report.xml | ||
| root_dir: ${{ github.workspace }}/${{ env.REPOSITORY_NAME }} | ||
