Another linting rule #96
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| tags: '*' | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| jobs: | |
| python: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.x" | |
| - run: pip install -r python/requirements.txt | |
| - run: pip install sphinx | |
| - run: pip install sphinx-rtd-theme | |
| - run: cd python/ && pytest --cov=motifcluster tests/ | |
| - run: cd python/ && pylint --rcfile=.pylintrc motifcluster | |
| - run: cd python/doc/ && make html | |
| - run: cd python/ && coverage xml | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./python/coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| R: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: "R/" | |
| extra-packages: | | |
| devtools | |
| - run: sudo apt-get update | |
| - uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: >- | |
| pandoc | |
| libcurl4-openssl-dev | |
| texlive-latex-base | |
| texlive-latex-extra | |
| texlive-fonts-extra | |
| ghostscript | |
| version: 1.0 | |
| - run: cd R/ && Rscript -e "library(devtools); document()" | |
| - run: cd R/ && Rscript -e "library(devtools); test()" | |
| - run: cd R/ && Rscript -e "library(lintr); lint_package(linters = with_defaults(object_name_linter=NULL,object_usage_linter=NULL,cyclocomp_linter=NULL,indentation_linter=NULL))" | |
| - run: cd R/ && Rscript -e "library(covr); cov = package_coverage(); to_cobertura(cov)" | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./R/cobertura.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| julia: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: julia-actions/setup-julia@v1 | |
| with: | |
| version: "1" | |
| arch: x64 | |
| - uses: julia-actions/cache@v1 | |
| - uses: julia-actions/julia-buildpkg@v1 | |
| - run: cd julia/MotifCluster.jl && julia --color=yes --depwarn=yes --inline=yes --project -e 'using Pkg; Pkg.test(coverage=true)' | |
| - uses: julia-actions/julia-processcoverage@v1 | |
| with: | |
| directories: julia/MotifCluster.jl/src | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| files: lcov.info | |
| fail_ci_if_error: true | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |