Update lintr (#187) #1017
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| --- | |
| name: Roxygen 🅾 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| - ready_for_review | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| install-system-dependencies: | |
| description: Check for and install system dependencies | |
| required: false | |
| default: false | |
| type: boolean | |
| enable-staged-dependencies-check: | |
| description: Enable staged dependencies YAML check | |
| required: false | |
| default: false | |
| type: boolean | |
| auto-update: | |
| description: If man pages are not up-to-date, they will be automatically updated and committed back to the branch. | |
| required: false | |
| default: false | |
| type: boolean | |
| sd-direction: | |
| description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all' | |
| required: false | |
| type: string | |
| default: upstream | |
| package-subdirectory: | |
| description: Subdirectory in the repository, where the R package is located. | |
| required: false | |
| type: string | |
| default: "." | |
| secrets: | |
| REPO_GITHUB_TOKEN: | |
| description: | | |
| Github token with read access to repositories, required for staged.dependencies installation | |
| required: false | |
| concurrency: | |
| group: roxygen-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| roxygen: | |
| name: Manual pages check 🏁 | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip roxygen]') | |
| && github.event.pull_request.draft == false | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| steps: | |
| - name: Setup token 🔑 | |
| id: github-token | |
| run: | | |
| if [ "${{ 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: 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: ${{ inputs.sd-direction }} | |
| - name: Generate man pages 📄 | |
| run: | | |
| logfile <- "roxygen_${{ github.event.repository.name }}.log" | |
| con <- file(logfile) | |
| sink(con, append = TRUE, split = TRUE) | |
| sink(con, append = TRUE, type = "message") | |
| roxygen2::roxygenize('.') | |
| sink() | |
| sink(type = "message") | |
| logs <- readLines(logfile) | |
| error_marker <- grep("Error:", logs) | |
| warnings_marker <- grep("Warning message", logs) | |
| if (length(warnings_marker) > 0) { | |
| cat("⚠ One or more warnings were generated during the roxygen build:\n") | |
| cat(logs[warnings_marker[[1]]:length(logs)], sep = "\n") | |
| stop("Please 🙏 fix the warnings shown below this message 👇") | |
| } | |
| if (length(error_marker) > 0) { | |
| cat("☠ One or more errors were generated during the roxygen build:\n") | |
| cat(logs[error_marker[[1]]:length(logs)], sep = "\n") | |
| stop("Please 🙏 fix the errors shown below this message 👇") | |
| } | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| - name: Roxygen check 🅾 | |
| run: | | |
| AUTO_UPDATE=${{ inputs.auto-update }} | |
| if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]] | |
| then { | |
| ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')" | |
| echo "🙈 Manuals are not up-to-date with roxygen comments!" | |
| echo "🔀 The following differences were noted:" | |
| git diff man/* DESCRIPTION | |
| # Attempt to commit and push man-page updates | |
| if [ "${AUTO_UPDATE}" == "true" ] | |
| then { | |
| echo "Regenerating man pages via auto-update" | |
| git config --global user.name "github-actions" | |
| git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| git add man/* DESCRIPTION | |
| git commit -m "[skip actions] Roxygen Man Pages Auto Update" | |
| BRANCH_NAME="${{ steps.branch-name.outputs.head_ref_branch }}" | |
| git pull origin ${BRANCH_NAME} | |
| git push -v origin HEAD:${BRANCH_NAME} || \ | |
| echo "⚠️ Could not push to ${BRANCH_NAME} on $(git remote -v show -n origin | grep Push)" && \ | |
| AUTO_UPDATE=failed | |
| } | |
| fi | |
| # If auto-update is disabled or is unsuccessful, let 'em know to fix manually | |
| if [ "${AUTO_UPDATE}" != "true" ] | |
| then { | |
| echo -e "\n💻 Please rerun the following command on your workstation and push your changes" | |
| echo "--------------------------------------------------------------------" | |
| echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))" | |
| echo "--------------------------------------------------------------------" | |
| echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION" | |
| echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version" | |
| exit 1 | |
| } | |
| fi | |
| } else { | |
| echo "💚 Manuals are up-to-date with roxygen comments" | |
| } | |
| fi | |
| shell: bash | |
| working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} |