man-pages.yml

on:
  workflow_dispatch:
  workflow_call:
    inputs:
      r-version:
        description: 'The version of R to use'
        default: '4.1'
        required: false
        type: string
  push:
    branches:
      - main
      - devel
      - pre-release
  pull_request:
    branches:
      - main
      - devel
      - pre-release

name: Man Pages

concurrency:
  group: roxygen-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  get_r_version:
    name: Get R version
    runs-on: ubuntu-latest
    if: >
      !contains(github.event.commits[0].message, '[skip lint]')
    outputs:
      r-version: ${{ steps.normalizer.outputs.R_VERSION }}
    steps:
      - name: Normalize inputs
        id: normalizer
        run: |
          R_VERSION="${{ inputs.r-version }}"
          if [ "$R_VERSION" == "" ]
          then {
            R_VERSION="4.1"
          }
          fi
          echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
        shell: bash
  lint:
    name: Roxygen
    runs-on: ubuntu-latest
    container:
      image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest"
    if: >
      !contains(github.event.commits[0].message, '[skip lint]')
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    needs: get_r_version
    steps:
      ##################### BEGIN boilerplate steps #####################
      - name: Get branch names
        id: branch-name
        uses: tj-actions/branch-names@v5.4

      - name: Checkout repo (PR) 🛎
        uses: actions/checkout@v3
        if: github.event_name == 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
          repository: ${{ github.event.pull_request.head.repo.full_name }}

      - name: Checkout repository
        uses: actions/checkout@v3
        if: github.event_name != 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}

      - name: Normalize inputs
        id: normalizer
        run: |
          R_VERSION="${{ inputs.r-version }}"
          if [ "$R_VERSION" == "" ]
          then {
            R_VERSION="4.1"
          }
          fi
          echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
        shell: bash

      - name: Restore cache
        uses: actions/cache@v3
        with:
          path: |
            ~/.staged.dependencies
          key: staged-deps

      - name: Run Staged dependencies
        uses: insightsengineering/staged-dependencies-action@v1
        with:
          run-system-dependencies: false
          renv-restore: false
          enable-check: false
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      ##################### END boilerplate steps #####################

      - name: Generate man pages
        run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
        shell: Rscript {0}

      - name: Set-up safe dir
        run: git config --global --add safe.directory "${GITHUB_WORKSPACE}"
        shell: bash

      - name: Roxygen check
        if: "!startsWith(github.event.comment.body, '/roxygenize')"
        run: |
          git status -s
          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
            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
          } else {
            echo "💚 Manuals are up-to-date with roxygen comments"
          }
          fi
        shell: bash