fix R version #28
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| name: biocbook | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| - RELEASE_** | |
| jobs: | |
| build-push: | |
| runs-on: ubuntu-latest | |
| name: Build and push Docker [${{ github.ref_name }}] | |
| permissions: | |
| contents: write | |
| packages: write | |
| steps: | |
| - name: 🧾 Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| persist-credentials: false | |
| - name: 📝 Get book info | |
| id: info | |
| run: | | |
| echo pkgversion=$(grep -m1 -E '^Version: +' DESCRIPTION | sed -E 's/.*: +//') >> "${GITHUB_ENV}" | |
| - name: 🔐 Log in to the Container registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: 🏷 Get metadata for Docker | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ghcr.io/${{ github.repository_owner }}/${{ github.workflow }} | |
| tags: | | |
| type=raw,value=${{ env.pkgversion}},enable=true | |
| type=raw,value=${{ github.ref_name }},enable=true | |
| - name: 👷 Build and push multi-arch Docker image | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: . | |
| platforms: linux/amd64 | |
| file: Dockerfile | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| outputs: type=image,annotation-index.org.opencontainers.image.description=${{ github.workflow }} | |
| build-args: | | |
| BIOC_VERSION=${{ github.ref_name }} | |
| render-deploy: | |
| needs: build-push | |
| runs-on: ubuntu-latest | |
| name: Render and publish book [${{ github.ref_name }}] | |
| container: ghcr.io/${{ github.repository_owner }}/${{ github.workflow }}:${{ github.ref_name }} | |
| permissions: | |
| contents: write | |
| packages: read | |
| steps: | |
| - name: 🧾 Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| persist-credentials: false | |
| - name: 📦 List installed packages | |
| run: | | |
| pkgs <- installed.packages()[,"Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: 📚 Install rsync | |
| run: | | |
| apt-get update && apt-get install -y rsync | |
| - name: 🔧 Install quarto dependencies | |
| run: | | |
| quarto install tinytex | |
| quarto check | |
| # - name: 🔧 Install python dependencies | |
| # uses: py-actions/py-dependency-install@v4 | |
| # with: | |
| # path: "inst/assets/requirements.txt" | |
| - name: 🖌 Render book from versioned container | |
| run: | | |
| quarto render | |
| - name: 🏷 Get gh-branch directory to deploy to | |
| run: | | |
| echo folder=$(echo ${{ github.ref_name }} | sed 's,RELEASE_,,' | tr '_' '.') >> "${GITHUB_ENV}" | |
| - name: 🚀 Deploy book to Github Pages on versioned branch | |
| uses: JamesIves/github-pages-deploy-action@v4.4.3 | |
| with: | |
| folder: docs/ | |
| target-folder: docs/${{ env.folder }}/ | |
| branch: gh-pages | |
| clean: false |