Bump nf-core/setup-nextflow from 1 to 2 #868
Workflow file for this run
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| 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 -Eeuxo pipefail {0} | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: "gcc13" | |
| compiler: "gcc-13" | |
| build: coverage | |
| build_type: Coverage | |
| cxx_flags: "-std=c++23" | |
| steps: | |
| # How many commits do we need to fetch to also fetch the branch point? | |
| - name: Get fetch depth | |
| id: fetch_depth | |
| run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| path: raptor | |
| fetch-depth: ${{ steps.fetch_depth.outputs.depth }} | |
| submodules: true | |
| - name: Setup toolchain | |
| uses: seqan/actions/setup-toolchain@main | |
| with: | |
| compiler: ${{ matrix.compiler }} | |
| ccache_size: 525M | |
| - name: Install CMake | |
| uses: seqan/actions/setup-cmake@main | |
| with: | |
| cmake: 3.21.7 | |
| - name: Install gcovr | |
| env: | |
| CC: ${{ matrix.compiler }} | |
| run: | | |
| sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100 | |
| pip install gcovr==6.0 | |
| - name: Configure tests | |
| run: | | |
| mkdir build | |
| cd build | |
| cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \ | |
| -DHIBF_NATIVE_BUILD=OFF | |
| make -j2 gtest_main | |
| - name: Build tests | |
| run: | | |
| ccache -z | |
| cd build | |
| make -k -j2 | |
| ccache -sv | |
| - name: Run tests | |
| run: | | |
| cd build | |
| ctest . -j2 --output-on-failure | |
| - name: Generate coverage report | |
| run: | | |
| gcovr --gcov-executable ${{ github.workspace }}/raptor/.github/workflows/scripts/gcov.sh \ | |
| --root ${{ github.workspace }}/raptor/test/coverage \ | |
| ${{ github.workspace }}/build \ | |
| --filter ${{ github.workspace }}/raptor/include \ | |
| --filter ${{ github.workspace }}/raptor/src \ | |
| --exclude-lines-by-pattern '^\s*$' \ | |
| --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 report | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ${{ github.workspace }}/build/coverage_report.xml | |
| root_dir: ${{ github.workspace }}/raptor | |
| fail_ci_if_error: false |