Manually Rebuild All Docs and Create a PR with Docs Changes #13
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| name: Manually Rebuild All Docs and Create a PR with Docs Changes | |
| on: | |
| workflow_dispatch: | |
| 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 | |
| - 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" >> "$GITHUB_ENV"' | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 | |
| working-directory: 'r' | |
| extra-packages: | | |
| bioc::BSgenome.Hsapiens.UCSC.hg38 | |
| github::GreenleafLab/motifmatchr | |
| github::GreenleafLab/chromVARmotifs | |
| needs: website | |
| - name: Install BPCells | |
| run: | | |
| Rscript -e 'install.packages("r", repos=NULL, type="source")' | |
| - name: Create git worktree with docs | |
| run: | | |
| git worktree add r/docs docs-html | |
| - name: Build documentation | |
| run: | | |
| Rscript -e 'pkgdown::build_site_github_pages("r")' | |
| - name: Configure Git | |
| run: | | |
| git config user.name 'github-actions[bot]' | |
| git config user.email 'github-actions[bot]@users.noreply.github.com' | |
| - name: Create new branch | |
| run: | | |
| git checkout -b update-docs-rebuild-$(git rev-parse --short=6 ${{ github.sha }}) | |
| git add . | |
| if git diff --cached --quiet; then echo "No changes to commit. Exiting."; exit 1; fi | |
| git commit -m "Rebuild documentation for commit $(git rev-parse --short=6 ${{ github.sha }})" | |
| working-directory: r/docs | |
| - name: Push changes to new branch | |
| run: git push origin update-docs-rebuild-$(git rev-parse --short=6 ${{ github.sha }}) | |
| - name: Create Pull Request # use message with last commit | |
| run: | | |
| gh pr create --title "Rebuild docs for commit: $(git log -n 1 --pretty=%s)" --body "$(git log -n 1 main)" --base docs-html --head update-docs-rebuild-$(git rev-parse --short=6 ${{ github.sha }}) | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} |