Add pkgdown to renv.lock #10
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| # Workflow for building and deploying pkgdown site | |
| # Uses renv for reproducible package versions | |
| # | |
| # Last updated: 2025-01-14 | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| name: pkgdown | |
| permissions: read-all | |
| jobs: | |
| pkgdown: | |
| runs-on: ubuntu-latest | |
| concurrency: | |
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| permissions: | |
| contents: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.5.2' | |
| use-public-rspm: true | |
| # Install system dependencies | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev \ | |
| libfontconfig1-dev \ | |
| libfreetype6-dev \ | |
| libpng-dev \ | |
| libtiff5-dev \ | |
| libjpeg-dev \ | |
| libharfbuzz-dev \ | |
| libfribidi-dev \ | |
| libgit2-dev \ | |
| libglpk-dev \ | |
| libgmp3-dev \ | |
| libhdf5-dev | |
| # Cache renv library | |
| - name: Cache renv packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('renv.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-renv- | |
| # Restore renv packages from lockfile | |
| - name: Restore renv packages | |
| run: | | |
| install.packages("renv") | |
| renv::restore() | |
| shell: Rscript {0} | |
| # Cache workshop data | |
| - name: Restore workshop data cache | |
| id: cache-data | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: data | |
| key: workshop-data-v3 | |
| - name: Download workshop data from Zenodo | |
| if: steps.cache-data.outputs.cache-hit != 'true' | |
| run: | | |
| echo "Cache miss - downloading from Zenodo..." | |
| mkdir -p data | |
| echo "Downloading heart-counts.Rds (~420MB)..." | |
| curl -L --retry 3 --max-time 1200 -o data/heart-counts.Rds "https://zenodo.org/records/18237749/files/heart-counts.Rds?download=1" | |
| echo "Downloading cellinfo_updated.Rds..." | |
| curl -L --retry 3 --max-time 60 -o data/cellinfo_updated.Rds "https://zenodo.org/records/18237749/files/cellinfo_updated.Rds?download=1" | |
| ls -lh data/ | |
| - name: Save workshop data cache | |
| if: steps.cache-data.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: data | |
| key: workshop-data-v3 | |
| - name: Verify data files | |
| run: | | |
| echo "Data files:" | |
| ls -lh data/ | |
| test -s data/heart-counts.Rds || exit 1 | |
| test -s data/cellinfo_updated.Rds || exit 1 | |
| # Print package versions for verification | |
| - name: Print package versions | |
| run: | | |
| cat("R version:", R.version.string, "\n\n") | |
| pkgs <- c("Seurat", "SeuratObject", "harmony", "scDblFinder", | |
| "edgeR", "limma", "speckle", "ggplot2", "pkgdown") | |
| for (pkg in pkgs) { | |
| cat(sprintf("%-20s %s\n", pkg, as.character(packageVersion(pkg)))) | |
| } | |
| shell: Rscript {0} | |
| # Build pkgdown site | |
| - name: Build site | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| # Deploy to GitHub Pages | |
| - name: Deploy to GitHub pages | |
| if: github.event_name != 'pull_request' | |
| uses: JamesIves/[email protected] | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs |