manubot.yaml

name: Manubot
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  workflow_dispatch:
    inputs:
      BUILD_PDF:
        type: boolean
        description: generate PDF output
        default: true
      BUILD_DOCX:
        type: boolean
        description: generate DOCX output
        default: false
      BUILD_LATEX:
        type: boolean
        description: generate LaTeX output
        default: false
      SPELLCHECK:
        type: boolean
        description: Check spelling
        default: true
      MANUBOT_USE_DOCKER:
        type: boolean
        description: Use Docker to generate PDF
        default: true

concurrency:
  # only one run per branch at a time
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  manubot:
    name: Manubot
    runs-on: ubuntu-latest
    permissions:
      contents: write
      pull-requests: write
    env:
      BUILD_DOCX: true
      GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
      # Set SPELLCHECK to true/false for whether to check spelling in this action.
      # For workflow dispatch jobs, this SPELLCHECK setting will be overridden by the user input.
      SPELLCHECK: true
    defaults:
      run:
        shell: bash --login {0}
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4
        with:
          # fetch entire commit history to support get_rootstock_commit
          fetch-depth: 0
      - name: Set Environment Variables (Workflow Dispatch)
        if: github.event_name == 'workflow_dispatch'
        run: |
          echo "BUILD_PDF=${{ github.event.inputs.BUILD_PDF }}" >> $GITHUB_ENV
          echo "BUILD_DOCX=${{ github.event.inputs.BUILD_DOCX }}" >> $GITHUB_ENV
          echo "BUILD_LATEX=${{ github.event.inputs.BUILD_LATEX }}" >> $GITHUB_ENV
          echo "SPELLCHECK=${{ github.event.inputs.SPELLCHECK }}" >> $GITHUB_ENV
          echo "MANUBOT_USE_DOCKER=${{ github.event.inputs.MANUBOT_USE_DOCKER }}" >> $GITHUB_ENV
      - name: Set Environment Variables
        run: |
          TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
          echo "TRIGGERING_SHA: $TRIGGERING_SHA"
          DEFAULT_BRANCH=${{ github.event.repository.default_branch }}
          echo "DEFAULT_BRANCH=${DEFAULT_BRANCH}" >> $GITHUB_ENV
          echo "DEFAULT_BRANCH_REF=refs/heads/$DEFAULT_BRANCH" >> $GITHUB_ENV
          echo "DEFAULT_BRANCH=$DEFAULT_BRANCH"
      - name: Cache
        uses: actions/cache@v4
        with:
          path: ci/cache
          key: ci-cache-${{ github.ref }}
          restore-keys: |
            ci-cache-${{ env.DEFAULT_BRANCH_REF }}
      - name: Install Environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: manubot
          environment-file: build/environment.yml
          auto-activate-base: false
          miniforge-variant: Mambaforge
          miniforge-version: "latest"
          use-mamba: true
      - name: Install Spellcheck
        if: env.SPELLCHECK == 'true'
        run: bash ci/install-spellcheck.sh
      - name: Build Manuscript
        run: bash build/build.sh
      - name: Upload Artifacts
        uses: actions/upload-artifact@v4
        id: artifact-upload-step
        with:
          name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }}
          path: output
      - name: Deploy Manuscript
        if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name != 'pull_request' && !github.event.repository.fork
        env:
          MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}
          CI_BUILD_WEB_URL: https://github.com/${{ github.repository }}/commit/${{ github.sha }}/checks
          CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
        run: bash ci/deploy.sh
      - name: Count spelling errors
        run: |
          # count the number of spelling errors using the spelling-error-locations.txt file
          # this file does not include preamble or author list spelling errors
          if [ -s output/spelling-error-locations.txt ]; then
            echo "SPELLING_ERRORS=$(wc -l < output/spelling-error-locations.txt)" >> $GITHUB_ENV
          else
            echo "SPELLING_ERRORS=0" >> $GITHUB_ENV
          fi
      - name: Post artifact comment to PR
        if: github.event_name == 'pull_request'
        uses: peter-evans/create-or-update-comment@v4
        with:
          issue-number: ${{ github.event.pull_request.number }}
          body: |
            **Click the link below to download the manuscript build as a ZIP file.**
            This build is associated with commit ${{ env.TRIGGERING_SHA_7 }}.

            [Manuscript build](${{ steps.artifact-upload-step.outputs.artifact-url }})

            **There were ${{ env.SPELLING_ERRORS }} spelling errors.**
            Check the build link above for details.

      - name: Fail for spelling errors in manual builds
        if: github.event_name == 'workflow_dispatch' && env.SPELLCHECK == 'true'
        run: |
          if [ $SPELLING_ERRORS ]; then
            echo "Spelling errors (some may be in the author list):"
            cat output/spelling-errors.txt
            exit 1
          fi