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| name: Build Docs and Create a PR with Docs Changes | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| jobs: | ||
| build_docs: | ||
| name: Build and Deploy Documentation | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 # to ensure other branches are available for build | ||
| - name: Install system dependencies | ||
| run: sudo apt-get install -y libhdf5-dev git-restore-mtime | ||
| - name: Set r compilation options | ||
| run: bash -c 'echo -e "MAKEFLAGS=--jobs=3\nCXXFLAGS += -O1 -UNDEBUG" > "$GITHUB_WORKSPACE/Makevars.user" && echo "R_MAKEVARS_USER=$GITHUB_WORKSPACE/Makevars.user" >> "$GITHUB_ENV"' | ||
| - name: Setup R | ||
| uses: r-lib/actions/setup-r@v2 | ||
| - name: Install R dependencies | ||
| uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| cache-version: 1 | ||
| working-directory: 'r' | ||
| extra-packages: | | ||
| any::pkgdown | ||
| any::devtools | ||
| any::uwot | ||
| any::irlba | ||
| any::RcppHNSW | ||
| any::igraph | ||
| any::BiocManager | ||
| bioc::BSgenome.Hsapiens.UCSC.hg38 | ||
| github::GreenleafLab/motifmatchr | ||
| github::GreenleafLab/chromVARmotifs | ||
| - name: Install BPCells | ||
| run: | | ||
| Rscript -e 'install.packages("r", repos=NULL, type="source")' | ||
| - name: Create git worktree with docs and fix git commit times | ||
| run: | | ||
| git worktree add r/docs docs-html | ||
| - name: restore timestamps | ||
| uses: chetan/git-restore-mtime-action@v2 | ||
| - name: Build documentation | ||
| run: | | ||
| Rscript .github/workflows/deploy-reference.R FALSE | ||
| - name: Configure Git | ||
| run: | | ||
| git config --global user.name "GitHub Action" | ||
| git config --global user.email "action@github.com" | ||
| - name: Create new branch | ||
| run: | | ||
| git checkout -b update-docs-$(git rev-parse --short=6 ${{ github.sha }}) | ||
| git add . | ||
| git commit -m "Update documentation for commit $(git rev-parse --short=6 ${{ github.sha }})" | ||
| working-directory: r/docs | ||
| - name: Push changes to new branch | ||
| run: git push origin update-docs-$(git rev-parse --short=6 ${{ github.sha }}) | ||
| - name: Create Pull Request # use message with last commit | ||
| run: | | ||
| gh pr create --title "Update docs for commit: $(git log -n 1 --pretty=%B)" --body "$(git log -n 1 main)" --base docs-html --head update-docs-$(git rev-parse --short=6 ${{ github.sha }}) | ||
| env: | ||
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
