update _pkgdown.yml #24
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: Release R CMD check and build site | |
| on: | |
| push: | |
| branches: | |
| - RELEASE_3_19 | |
| workflow_dispatch: | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest | |
| BIOC_VERSION: RELEASE_3_19 | |
| jobs: | |
| checkRelease: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| bioc_version: [RELEASE_3_19] # Define versions as matrix variables | |
| container: bioconductor/bioconductor_docker:${{ matrix.bioc_version }} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ env.BIOC_VERSION }} | |
| - name: Query dependencies | |
| run: | | |
| BiocManager::install("remotes") | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ runner.os }}-r-${{ env.BIOC_VERSION }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ env.BIOC_VERSION }}- | |
| - name: Install Dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(c("rcmdcheck", "pkgdown", "covr"), ask = FALSE, update = TRUE) | |
| shell: Rscript {0} | |
| - name: System dependencies | |
| run: | | |
| pip install ghp-import | |
| - name: Check Package | |
| id: rcmdcheck | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| run: | | |
| PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()' | |
| - name: Install deploy dependencies | |
| run: | | |
| apt-get update | |
| apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages # The branch the action should deploy to. | |
| FOLDER: docs # The folder the action should deploy. | |