changed x and m to number instead of numeric #25
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | ||
| name: Roxygen 🅾 | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| 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 | ||
| secrets: | ||
| 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_4.2.1_bioc_3.15:latest | ||
| steps: | ||
| - name: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v5 | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| fetch-depth: 0 | ||
| - name: Run Staged dependencies 🎦 | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| SD_REPO_PATH: ${{ github.event.repository.name }} | ||
| SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
| - name: Generate man pages 📄 | ||
| run: | | ||
| setwd("${{ github.event.repository.name }}") | ||
| logfile <- "roxygen_${{ github.event.repository.name }}.log" | ||
| con <- file(logfile) | ||
| sink(con, append = TRUE, split = TRUE) | ||
| sink(con, append = TRUE, type = "message") | ||
| roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace')) | ||
| 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} | ||
| - name: Roxygen check 🅾 | ||
| run: | | ||
| cd ${{ github.event.repository.name }} | ||
| git status -s | ||
| if [[ -n `git status -s | grep man` ]] | ||
| then { | ||
| ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')" | ||
| echo "🙈 Manuals are not up-to-date with roxygen comments!" | ||
| echo "🔀 The following differences were noted:" | ||
| git diff man/* | ||
| if [ "${{ inputs.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/* | ||
| git commit -m "[skip actions] ROxygen Man Pages Auto Update" | ||
| git pull origin ${GITHUB_HEAD_REF} | ||
| git push -v origin ${GITHUB_HEAD_REF} | ||
| } | ||
| else { | ||
| 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" | ||
| } | ||
| fi | ||
| exit 1 | ||
| } else { | ||
| echo "💚 Manuals are up-to-date with roxygen comments" | ||
| } | ||
| fi | ||
| shell: bash | ||
