version bump 1.32.2 #10
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| name: PR CMD check & build site | |
| on: | |
| pull_request: | |
| push: | |
| paths: | |
| - 'DESCRIPTION' | |
| - '**.yml' | |
| branches: | |
| - devel | |
| - RELEASE_3_21 | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CRAN: https://p3m.dev/cran/__linux__/noble/latest | |
| BIOC_RELEASE: RELEASE_3_21 | |
| jobs: | |
| set-matrix: | |
| runs-on: ubuntu-24.04 | |
| outputs: | |
| matrix: ${{ steps.set.outputs.matrix }} | |
| dockerfile_exists: ${{ steps.dockerfile.outputs.exists }} | |
| steps: | |
| - name: Set Matrix Bioconductor Version | |
| id: set | |
| run: | | |
| MATRIX="{\"include\":[{\"bioc_version\":\"$GITHUB_REF_NAME\"}]}" | |
| echo "matrix=$MATRIX" >> $GITHUB_OUTPUT | |
| - name: Check for Dockerfile | |
| id: dockerfile | |
| run: | | |
| echo "exists=$( [ -f ./inst/docker/pkg/Dockerfile ] && echo true || echo false )" >> $GITHUB_OUTPUT | |
| check: | |
| needs: set-matrix | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: ${{ fromJson(needs.set-matrix.outputs.matrix) }} | |
| container: bioconductor/bioconductor_docker:${{ matrix.bioc_version }} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ matrix.bioc_version }} | |
| - name: Query dependencies | |
| run: | | |
| BiocManager::install(c("covr", "BiocCheck")) | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ runner.os }}-r-${{ matrix.bioc_version }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.bioc_version }}- | |
| - name: Install GPG | |
| if: ${{ github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }} | |
| run: sudo apt-get update && sudo apt-get install -y gpg | |
| - name: Install Dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(c("rcmdcheck", "BiocCheck"), ask = FALSE, update = TRUE) | |
| shell: Rscript {0} | |
| - name: Check Package | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: ${{ success() && github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }} | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| type = "all", | |
| install_path = file.path( | |
| normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), | |
| "package" | |
| ) | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - name: Upload test results to Codecov | |
| if: ${{ success() && github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
| file: ./cobertura.xml | |
| plugin: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Run BiocCheck | |
| id: bioccheck | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| if: ${{ github.ref == format('refs/heads/{0}', env.BIOC_RELEASE) && github.event_name != 'pull_request' }} | |
| run: | | |
| PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()' | |
| - name: Upload pkgdown artifact | |
| if: github.ref == format('refs/heads/{0}', env.BIOC_RELEASE) | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: docs | |
| dock: | |
| needs: | |
| - check | |
| - set-matrix | |
| runs-on: ubuntu-24.04 | |
| if: ${{ github.ref == 'refs/heads/devel' && needs.set-matrix.outputs.dockerfile_exists == 'true' }} | |
| steps: | |
| - name: Checkout Repository | |
| if: ${{ success() && github.event_name != 'pull_request' }} | |
| uses: actions/checkout@v4 | |
| - name: Register repo name | |
| if: ${{ github.event_name != 'pull_request' }} | |
| id: reg_repo_name | |
| run: | | |
| echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV | |
| - name: Login to Docker Hub | |
| if: ${{ github.event_name != 'pull_request' }} | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and Push Docker | |
| if: ${{ success() && github.event_name != 'pull_request' }} | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./inst/docker/pkg/Dockerfile | |
| push: true | |
| tags: > | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, | |
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel | |
| deploy: | |
| needs: check | |
| permissions: | |
| contents: write | |
| pages: write | |
| id-token: write | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| if: ${{ github.ref == format('refs/heads/{0}', env.BIOC_RELEASE) && github.event_name != 'pull_request' }} | |
| id: deployment | |
| uses: actions/deploy-pages@v4 | |