[FEATURE] Layout can be computed on minimizers. #174
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Coverage | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| pull_request: | |
| types: | |
| - unlabeled | |
| workflow_dispatch: | |
| concurrency: | |
| group: coverage-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: false | |
| env: | |
| SHARG_NO_VERSION_CHECK: 1 | |
| TZ: Europe/Berlin | |
| defaults: | |
| run: | |
| shell: bash -Eexuo pipefail {0} | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| include: | |
| - name: "gcc13" | |
| compiler: "gcc-13" | |
| build_type: Coverage | |
| steps: | |
| # How many commits do we need to fetch to also fetch the branch point? | |
| - name: Get fetch depth | |
| id: fetch_depth | |
| run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: ${{ steps.fetch_depth.outputs.depth }} | |
| submodules: recursive | |
| - name: Setup toolchain | |
| uses: seqan/actions/setup-toolchain@main | |
| with: | |
| compiler: ${{ matrix.compiler }} | |
| ccache_size: 200M | |
| - name: Install CMake | |
| uses: seqan/actions/setup-cmake@main | |
| with: | |
| cmake: 3.18.6 | |
| - name: Install gcovr | |
| run: | | |
| sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100 | |
| pip install gcovr==6.0 | |
| - name: Configure tests | |
| run: | | |
| mkdir build | |
| cd build | |
| cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_CXX_FLAGS="-Werror -Wno-interference-size" \ | |
| -DCHOPPER_NATIVE_BUILD=OFF | |
| make -j2 gtest_build | |
| - name: Build tests | |
| env: | |
| CCACHE_IGNOREOPTIONS: "-fprofile-abs-path" | |
| run: | | |
| ccache -z | |
| cd build | |
| make -k -j2 api_test cli_test display_layout measure_hyperloglog | |
| ccache -sv | |
| - name: Run tests | |
| run: | | |
| cd build | |
| ctest . -j2 --output-on-failure | |
| - name: Generate coverage report | |
| run: | | |
| gcovr --gcov-executable ${{ github.workspace }}/lib/seqan3/.github/workflows/scripts/gcov.sh \ | |
| --root ${{ github.workspace }}/test/coverage \ | |
| ${{ github.workspace }}/build \ | |
| --filter ${{ github.workspace }}/include \ | |
| --filter ${{ github.workspace }}/src \ | |
| --exclude ${{ github.workspace }}/src/util \ | |
| --exclude-lines-by-pattern '^\s*$' \ | |
| --exclude-lines-by-pattern '^\s*};$' \ | |
| --exclude-lines-by-pattern '^.*GCOVR_EXCL_LINE.*$' \ | |
| --exclude-unreachable-branches \ | |
| --exclude-throw-branches \ | |
| --exclude-noncode-lines \ | |
| -j 2 \ | |
| --xml \ | |
| --output ${{ github.workspace }}/build/coverage_report.xml | |
| - name: Submit coverage build | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ${{ github.workspace }}/build/coverage_report.xml | |
| fail_ci_if_error: false |