Merge pull request #34 from antoniojbt/codex/propose-fixes-for-issues… #42
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| # See https://github.com/r-lib/actions/tree/master/examples#readme for | |
| # additional example workflows available for the R community. | |
| name: R-CMD-check | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| # Optional: build pkgdown on tag push | |
| tags: [ "v*" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| # run on OSes, skip windows-latest: | |
| os: [ ubuntu-latest, macos-latest] | |
| # add R versions: | |
| r-version: [ "4.3" ] | |
| steps: | |
| # 1) Checkout the repo: | |
| - uses: actions/checkout@v4 | |
| # 2) Set up R: | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| # 2.1) Cache installs: | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ runner.tool_cache }}/R | |
| key: ${{ runner.os }}-r-${{ matrix.r-version }} | |
| restore-keys: | | |
| ${{ runner.os }}-r- | |
| # 3) Set up Pandoc (needed for vignettes, pkgdown, etc.): | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| # ─── Explicitly install rcmdcheck + covr ─────────────────────────────────────── | |
| - name: Install CRAN/Bioc dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| # This will install whatever is in DESCRIPTION, plus: | |
| extra-packages: "rcmdcheck,covr" | |
| # ─────────────────────────────────────────────────────────────────────────────── | |
| # 4) Install bioconductor manager and Bioconductor dependencies: | |
| - name: Install Bioconductor packages | |
| run: | | |
| Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' | |
| # Install any Bioconductor packages listed in DESCRIPTION (Imports/Suggests). | |
| # Install specific Bioc packages outside DESCRIPTION: | |
| #Rscript -e 'BiocManager::install()' | |
| # 5) Install CRAN (and remotes-based) dependencies: | |
| #- uses: r-lib/actions/setup-r-dependencies@v2 | |
| # with: | |
| # By default, this reads DESCRIPTION and installs Imports, Depends, Suggests. | |
| # On Windows/macOS/Ubuntu, remotes::install_deps() will fetch CRAN + Bioconductor remotes as needed. | |
| # extra-packages: covr # needed later | |
| # Additional packages: | |
| # extra-packages: "covr,pkgdown,roxygen2" | |
| # 6) Run R CMD check (includes running tests): | |
| - name: Check package | |
| uses: r-lib/actions/check-r-package@v2 | |
| #with: | |
| # By default, runs on the current OS/R combo | |
| # Add conditions here for specific checks | |
| # e.g. disable on windows: if: matrix.os != 'windows-latest' | |
| # 7) Run coverage report on Linux/macOS (skip Windows as may fail): | |
| - name: Upload coverage to Codecov | |
| #if: runner.os != 'Windows' # covr often fails or is slower on Windows | |
| env: | |
| # For public repo, CODECOV_TOKEN is not strictly required. | |
| # For a private repo, add CODECOV_TOKEN to GitHub Secrets. | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| run: | | |
| Rscript -e 'covr::codecov()' | |
| # 8) Build and deploy pkgdown site (only on Linux, and only on push to master): | |
| # pkgdown-deploy: | |
| # needs: R-CMD-check | |
| # runs-on: ubuntu-latest | |
| # if: github.ref == 'refs/heads/master' && github.event_name == 'push' | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # | |
| # - name: Set up R | |
| # uses: r-lib/actions/setup-r@v2 | |
| # with: | |
| # r-version: "4.3" | |
| # | |
| # - uses: r-lib/actions/setup-r-dependencies@v2 | |
| # with: | |
| # # Ensure pkgdown itself (and its dependencies) are installed | |
| # extra-packages: pkgdown | |
| # | |
| # - name: Build pkgdown site | |
| # run: | | |
| # Rscript -e 'pkgdown::build_site()' | |
| # | |
| # - name: Deploy pkgdown to GitHub Pages | |
| # uses: r-lib/actions/pkgdown@v3 | |
| # with: | |
| # github_token: ${{ secrets.GITHUB_TOKEN }} |