build_preprint.yml

name: Build Professional Preprint

on:
  push:
    branches: [main]

env:
  # Opting into Node.js 24 as per GitHub's 2025 deprecation roadmap
  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true

jobs:
  build-paper:
    runs-on: ubuntu-latest
    name: Build Preprint PDF
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Install apt packages
        run: |
          sudo apt-get update
          sudo apt-get install -y pandoc texlive texlive-latex-extra texlive-fonts-recommended texlive-xetex texlive-fonts-extra zip python3-yaml

      - name: Extract Metadata and Build LaTeX Title
        run: |
          python3 - << 'PYEOF'
          import yaml
          import os

          # Ensure we are reading the correct path
          file_path = 'paper/paper.md'
          if not os.path.exists(file_path):
              file_path = 'paper.md'

          with open(file_path, 'r') as f:
              content = f.read()

          parts = content.split('---\n')
          fm = yaml.safe_load(parts[1])

          authors = fm.get('authors', [])
          affiliations = fm.get('affiliations', [])
          aff_map = {str(a['index']): a for a in affiliations}

          # 1. Generate Pandoc Metadata
          meta = {
              'title': fm.get('title', ''),
              'date': str(fm.get('date', '')),
              'colorlinks': True,
              'linkcolor': 'blue',
              'urlcolor': 'blue',
              'citecolor': 'blue',
              'geometry': 'a4paper, margin=2.5cm',
          }
          with open('/tmp/pandoc_meta.yaml', 'w') as f:
              yaml.dump(meta, f)

          # 2. Build LaTeX Title Block
          lines = [r'\begin{center}']
          lines.append(r'{\LARGE\bfseries ' + fm.get('title','').replace('&', r'\&') + r'}\\[1.2em]')

          auth_line = []
          for a in authors:
              name = a['name'].replace('&', r'\&')
              aff_indices = str(a.get('affiliation', '')).split(',')
              marker = ",".join([idx.strip() for idx in aff_indices])
              if a.get('corresponding'):
                  marker += r",*"
              auth_line.append(rf'{name}$^{{{marker}}}$')
          lines.append(r'\large ' + r', '.join(auth_line) + r'\\[0.8em]')

          for idx, aff in sorted(aff_map.items()):
              name = aff['name'].replace('&', r'\&')
              ror_id = aff.get('ror', '')
              ror_link = rf" \small (ROR: \href{{https://ror.org/{ror_id}}}{{{ror_id}}})" if ror_id else ""
              lines.append(rf'$^{{{idx}}}$\small {name}{ror_link}\\[0.2em]')

          corres = [a for a in authors if a.get('corresponding') and a.get('email')]
          if corres:
              email = corres[0]['email']
              lines.append(rf'\small $^*$Corresponding author: \href{{mailto:{email}}}{{{email}}}\\[0.2em]')
          
          lines.append(r'\small DOI: \href{https://doi.org/10.5281/zenodo.18377216}{10.5281/zenodo.18377216}\\[0.2em]')
          lines.append(r'\small ' + str(fm.get('date','')))
          lines.append(r'\end{center}')
          lines.append(r'\vspace{0.5em}\noindent\rule{\textwidth}{0.6pt}\vspace{1.5em}')

          with open('/tmp/title_block.tex', 'w') as f:
              f.write('\n'.join(lines))
          PYEOF

      - name: Create Professional Header
        run: |
          cat > /tmp/header.tex << 'EOF'
          \usepackage{hyperref}
          \usepackage{xurl}
          \usepackage{fontspec}
          \setmainfont{TeX Gyre Termes}
          \usepackage{unicode-math}
          \setmathfont{TeX Gyre Termes Math}
          \usepackage{fancyhdr}
          \usepackage{xcolor}

          \hypersetup{
            breaklinks=true,
            colorlinks=true,
            linkcolor=blue,
            urlcolor=blue,
            citecolor=blue,
            pdfauthor={Deshmukh and Mukherjee},
            pdftitle={PICA: High-Precision Automation}
          }
          
          \pagestyle{fancy}
          \fancyhf{}
          \fancyhead[L]{\small \textbf{\textcolor{gray}{PREPRINT -- NOT PEER REVIEWED}}}
          \fancyhead[R]{\small \textit{PICA: Python-based Instrument Control and Automation}}
          \fancyfoot[C]{\thepage}
          \renewcommand{\headrulewidth}{0.4pt}
          
          \renewcommand{\maketitle}{}
          EOF

      - name: Generate Publication-Ready PDF
        run: |
          TARGET_DIR="paper"
          if [ ! -d "$TARGET_DIR" ]; then TARGET_DIR="."; fi
          cd $TARGET_DIR

          awk '/^# AI usage disclosure/{skip=1} /^# / && !/^# AI usage disclosure/{skip=0} !skip' paper.md > paper_cleaned.md

          pandoc paper_cleaned.md -o paper.pdf \
            --standalone \
            --citeproc \
            --pdf-engine=xelatex \
            --metadata-file=/tmp/pandoc_meta.yaml \
            --include-in-header=/tmp/header.tex \
            --include-before-body=/tmp/title_block.tex \
            --variable=link-citations=true
          
          rm paper_cleaned.md

      - name: Upload Artifact
        uses: actions/upload-artifact@v6
        with:
          name: professional-preprint
          path: |
              paper/paper.pdf
              paper.pdf