Upgrade to SuperLinter v5 (#186) #338
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| --- | |
| name: Pkgdown Docs 📚 | |
| on: | |
| push: | |
| tags: | |
| - "v*" | |
| branches: | |
| - main | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| - ready_for_review | |
| branches: | |
| - main | |
| paths: | |
| - inst/templates/** | |
| - _pkgdown.yaml | |
| - DESCRIPTION | |
| - "**.md" | |
| - "**.Rmd" | |
| - man/** | |
| - LICENSE.* | |
| - NAMESPACE | |
| workflow_dispatch: | |
| workflow_call: | |
| secrets: | |
| REPO_GITHUB_TOKEN: | |
| description: | | |
| Github token with read access to repositories, required for staged.dependencies installation | |
| required: false | |
| inputs: | |
| install-system-dependencies: | |
| description: Check for and install system dependencies | |
| required: false | |
| default: false | |
| type: boolean | |
| fail-pkgdown-on-warnings: | |
| description: Fail the pkgdown workflow if warnings are generated while generating docs | |
| required: false | |
| default: false | |
| type: boolean | |
| enable-staged-dependencies-check: | |
| description: Enable staged dependencies YAML check | |
| required: false | |
| default: false | |
| type: boolean | |
| additional-env-vars: | |
| description: | | |
| Extra environment variables, as a 'key=value' pair, with each pair on a new line. | |
| Example usage: | |
| additional-env-vars: | | |
| ABC=123 | |
| XYZ=456 | |
| required: false | |
| default: "" | |
| type: string | |
| refs-order: | |
| description: | | |
| The order in which refs should appear in the drop-down list. Versions not in the vector | |
| will appear below refs listed here. | |
| If docs have never been generated for the ref, the ref will not appear in the | |
| drop-down. Similarly, if docs have been generated for the ref, but the ref is not | |
| listed in the vector, it will not appear in the drop-down. | |
| required: false | |
| default: c("devel", "pre-release", "main", "latest-tag") | |
| type: string | |
| default-landing-page: | |
| description: | |
| The default branch or tag on gh-pages that corresponds to the landing page. | |
| For instance, if your root index page on gh-pages is built using the 'main' | |
| branch, then the root page of the website will correspond to this page. | |
| If 'latest-tag' is selected, then the latest version will become the default. | |
| required: false | |
| default: main | |
| type: string | |
| sd-direction: | |
| description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all' | |
| required: false | |
| type: string | |
| default: upstream | |
| # If you provide latest-tag-alt-name and/or release-candidate-alt-name inputs | |
| # to this workflow in some repo, you should also provide these inputs in | |
| # R CMD check and Coverage workflows in order to make the unit test report | |
| # and coverage report available in pkgdown documentation for the alt-names. | |
| # Additionally, branches-or-tags-to-list input should be overridden with | |
| # the additional alt-name inputs. | |
| latest-tag-alt-name: | |
| description: An alternate name for the 'latest-tag' documentation item | |
| required: false | |
| type: string | |
| default: '' | |
| release-candidate-alt-name: | |
| description: An alternate name for the 'release-candidate' documentation item | |
| required: false | |
| type: string | |
| default: '' | |
| branches-or-tags-to-list: | |
| description: | |
| Which branches or tags should be listed under the | |
| 'Versions' dropdown menu on the landing page? | |
| This input should be a regular expression in R. | |
| required: false | |
| type: string | |
| default: >- | |
| ^main$|^devel$|^pre-release$|^latest-tag$|^release-candidate$|^develop$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)(-rc[0-9]+)$ | |
| package-subdirectory: | |
| description: Subdirectory in the repository, where the R package is located. | |
| required: false | |
| type: string | |
| default: "." | |
| concurrency: | |
| group: docs-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| docs: | |
| name: Generate 🐣 | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip docs]') | |
| && github.event.pull_request.draft == false | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| # Only one job can publish to gh-pages branch concurrently. | |
| concurrency: | |
| group: ghpages | |
| steps: | |
| - name: Setup token 🔑 | |
| id: github-token | |
| run: | | |
| if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then | |
| echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | |
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "Using REPO_GITHUB_TOKEN." | |
| echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Get branch names 🌿 | |
| id: branch-name | |
| uses: tj-actions/branch-names@v6 | |
| - name: Get current branch or tag 🏷️ | |
| id: current-branch-or-tag | |
| run: | | |
| if [ "${{ steps.branch-name.outputs.is_tag }}" == "true" ]; then | |
| echo "Current tag: ${{ steps.branch-name.outputs.tag }}" | |
| echo "ref-name=${{ steps.branch-name.outputs.tag }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "Current branch: ${{ steps.branch-name.outputs.current_branch }}" | |
| echo "ref-name=${{ steps.branch-name.outputs.current_branch }}" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Checkout repo (PR) 🛎 | |
| uses: actions/checkout@v3 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| path: ${{ github.event.repository.name }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| path: ${{ github.event.repository.name }} | |
| - name: Restore SD cache 💰 | |
| uses: actions/cache@v3 | |
| with: | |
| key: sd-${{ runner.os }}-${{ github.event.repository.name }} | |
| path: ~/.staged.dependencies | |
| - name: Run Staged dependencies 🎦 | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| env: | |
| GITHUB_PAT: ${{ steps.github-token.outputs.token }} | |
| with: | |
| path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| enable-check: ${{ inputs.enable-staged-dependencies-check }} | |
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | |
| direction: ${{ inputs.sd-direction }} | |
| - name: Install R package 🚧 | |
| run: | | |
| if (file.exists("renv.lock")) renv::restore() | |
| install.packages(".", repos=NULL, type="source") | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| - name: Build docs 🏗 | |
| if: > | |
| github.event_name == 'pull_request' || startsWith(github.ref, 'refs/tags/v') | |
| || github.event_name == 'push' | |
| run: | | |
| repo="${{ github.event.repository.name }}" | |
| if [ "${{ inputs.additional-env-vars }}" != "" ] | |
| then { | |
| echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env | |
| export $(tr '\n' ' ' < /tmp/dotenv.env) | |
| } | |
| fi | |
| Rscript - <<EOF 2>&1 | tee pkgdown_${repo}.log | |
| if (file.exists("renv.lock")) renv::restore() | |
| pkgdown::build_site(devel = TRUE) | |
| EOF | |
| if [ "${{ inputs.fail-pkgdown-on-warnings }}" == "true" ]; then { | |
| grep "Warning message" pkgdown_${repo}.log > pkgdown_warnings_${repo}.log | |
| if [[ $(wc -l <pkgdown_warnings_${repo}.log) -gt 0 ]]; then { | |
| echo "----------------------------------------" | |
| echo "⚠ One or more warnings were generated during the pkgdown build." | |
| echo "Please 🙏 fix the warnings shown above 👆" | |
| exit 1 | |
| } | |
| fi | |
| } | |
| fi | |
| shell: bash | |
| working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| - name: Checkout gh-pages 🛎 | |
| if: startsWith(github.ref, 'refs/tags/v') || github.event_name == 'push' | |
| uses: actions/checkout@v3 | |
| with: | |
| path: "gh-pages" | |
| fetch-depth: 0 | |
| ref: "gh-pages" | |
| - name: Upload docs to gh-pages 📙 | |
| if: startsWith(github.ref, 'refs/tags/v') || github.event_name == 'push' | |
| run: | | |
| GH_PAGES_DIR="gh-pages/${{ steps.current-branch-or-tag.outputs.ref-name }}" | |
| mkdir -p $GH_PAGES_DIR | |
| ls -l $GH_PAGES_DIR | |
| # Remove contents except coverage-report and unit-test-report directories. | |
| find $GH_PAGES_DIR -mindepth 1 -maxdepth 1 \ | |
| ! -name coverage-report ! -name unit-test-report -exec rm -rf {} + | |
| ls -l $GH_PAGES_DIR | |
| # Copy generated pkgdown documentation to gh-pages branch. | |
| cp -a ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/docs/. $GH_PAGES_DIR | |
| ls -l $GH_PAGES_DIR | |
| cd gh-pages | |
| git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| git config --global user.name "github-actions[bot]" | |
| git config pull.rebase false | |
| git status | |
| git pull origin gh-pages || true | |
| git add -f . | |
| git commit -m "Update pkgdown documentation ${{ github.sha }}" || true | |
| git push origin gh-pages | |
| shell: bash | |
| - name: Create documentation artifact 📂 | |
| if: github.event_name == 'pull_request' || startsWith(github.ref, 'refs/tags/v') | |
| run: | | |
| pushd ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/docs/ | |
| zip -r9 $OLDPWD/pkgdown.zip * | |
| popd | |
| shell: bash | |
| - name: Upload docs for review ⬆ | |
| if: github.event_name == 'pull_request' || startsWith(github.ref, 'refs/tags/v') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pkgdown.zip | |
| path: pkgdown.zip | |
| multi-version-docs: | |
| name: Multi-version docs 📑 | |
| needs: docs | |
| runs-on: ubuntu-latest | |
| # Only one job can publish to gh-pages branch concurrently. | |
| concurrency: | |
| group: ghpages | |
| if: > | |
| (github.event_name == 'push' || github.event_name == 'workflow_dispatch') | |
| && !contains(github.event.commits[0].message, '[skip docs]') | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: ${{ github.event.repository.name }} | |
| ref: "gh-pages" | |
| - name: Create and publish docs ↗️ | |
| uses: insightsengineering/r-pkgdown-multiversion@v2 | |
| with: | |
| path: ${{ github.event.repository.name }} | |
| default-landing-page: ${{ inputs.default-landing-page }} | |
| refs-order: ${{ inputs.refs-order }} | |
| latest-tag-alt-name: ${{ inputs.latest-tag-alt-name }} | |
| release-candidate-alt-name: ${{ inputs.release-candidate-alt-name }} | |
| branches-or-tags-to-list: ${{ inputs.branches-or-tags-to-list }} | |
| upload-release-assets: | |
| name: Upload documentation assets 🔼 | |
| needs: docs | |
| runs-on: ubuntu-latest | |
| if: > | |
| startsWith(github.ref, 'refs/tags/v') | |
| && !contains(github.event.commits[0].message, '[skip docs]') | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| - name: Download artifact ⏬ | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: pkgdown.zip | |
| - name: Check if release exists | |
| id: check-if-release-exists | |
| uses: insightsengineering/release-existence-action@v1 | |
| - name: Upload binaries to release ⤴ | |
| if: >- | |
| steps.check-if-release-exists.outputs.release-exists == 'true' | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: pkgdown.zip | |
| asset_name: pkgdown.zip | |
| tag: ${{ github.ref }} | |
| overwrite: true |