roxygen.yaml

---
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 }}