Clarify threading works at reference genome level #14
Workflow file for this run
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| name: Build with CMake and Test | |
| run-name: Build FastANI with CMake and Test by ${{github.actor}} | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| # Allows to run this workflow from the Actions tab (w.o. trigger) | |
| workflow_dispatch: | |
| env: | |
| # CMake build type (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: Debug | |
| jobs: | |
| Build-Test: | |
| permissions: write-all | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| lfs: true | |
| - name: Install zlib, gsl, cppcheck and lcov | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install zlib1g-dev libgsl-dev cppcheck lcov | |
| # Static Analysis with cppcheck | |
| - name: cppcheck | |
| run: cppcheck --enable=all --inconclusive --force --std=c++20 -iext/ -I src/ --output-file=cppcheck_report.txt . | |
| - name: Upload CPPCheck Report as artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: CPPCheck-Report | |
| path: ${{github.workspace}}/cppcheck_report.txt | |
| # Building | |
| - name: Configure CMake | |
| # https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type | |
| run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DBUILD_TESTING=ON | |
| - name: Build | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} | |
| # Testing | |
| - name: Test | |
| working-directory: ${{github.workspace}}/build | |
| # https://cmake.org/cmake/help/latest/manual/ctest.1.html | |
| run: ctest -C ${{env.BUILD_TYPE}} | |
| # Run code coverage | |
| - name: Run lcov to generate coverage | |
| working-directory: ${{github.workspace}}/build | |
| run: make lcov2 | |
| # Uploading to Codecov | |
| - name: Upload coverage reports to codecov.io | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| directory: ${{github.workspace}}/build | |
| files: ${{github.workspace}}/build/coverage.info | |
| fail_ci_if_error: true | |
| verbose: true | |
| # Uploading to Github Action as artifact | |
| - name: Upload Coverage Summary as artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Coverage-Summary | |
| path: ${{github.workspace}}/build/coverage_list.txt | |
| retention-days: 5 |