digest.yml

name: Daily Paper Digest

on:
  schedule:
    # Run daily at 11:50 PM EST (4:50 AM UTC next day)
    - cron: '50 4 * * *'
  workflow_dispatch:
    # Allow manual trigger from GitHub Actions UI
    inputs:
      days:
        description: 'Number of days to fetch papers'
        required: false
        default: '2'
      arxiv_days:
        description: 'Number of days to fetch from arXiv (has API delay)'
        required: false
        default: '3'
      num_results:
        description: 'Number of recommendations'
        required: false
        default: '100'

jobs:
  digest:
    runs-on: ubuntu-latest
    env:
      PAPERFIND_DATA_DIR: ${{ github.workspace }}/.paperfind
      # API keys
      OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
      ZOTERO_API_KEY: ${{ secrets.ZOTERO_API_KEY }}
      ZOTERO_USER_ID: ${{ secrets.ZOTERO_USER_ID }}
      # ZOTERO_LIBRARY_TYPE: group  # Uncomment for group libraries (default: user)
      CROSSREF_EMAIL: ${{ secrets.CROSSREF_EMAIL }}
      # Email settings (SMTP_HOST and SMTP_PORT use Gmail defaults)
      SMTP_HOST: smtp.gmail.com
      SMTP_PORT: "587"
      SMTP_USER: ${{ secrets.SMTP_USER }}
      SMTP_PASSWORD: ${{ secrets.SMTP_PASSWORD }}
      EMAIL_FROM: ${{ secrets.EMAIL_FROM }}
      EMAIL_TO: ${{ secrets.EMAIL_TO }}
      # Optional: custom categories (uncomment to override defaults)
      # ARXIV_CATEGORIES: ${{ secrets.ARXIV_CATEGORIES }}
      # BIORXIV_CATEGORIES: ${{ secrets.BIORXIV_CATEGORIES }}
      # LLM reranking preferences (for --rerank flag)
      LLM_RERANK_PREFERENCES: ${{ secrets.LLM_RERANK_PREFERENCES }}
      # Default keywords for recommendations (semicolon-separated)
      PAPERFIND_KEYWORDS: ${{ secrets.PAPERFIND_KEYWORDS }}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'
          cache: 'pip'

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .

      - name: Cache Paperfind data
        uses: actions/cache@v4
        with:
          path: ${{ env.PAPERFIND_DATA_DIR }}
          key: ${{ runner.os }}-paperfind-data

      - name: Sync Zotero library
        run: |
          paperfind sync

      - name: Embed Zotero library
        run: |
          paperfind embed

      - name: Fetch papers
        run: |
          paperfind fetch \
            --days ${{ github.event.inputs.days || '2' }} \
            --arxiv-days ${{ github.event.inputs.arxiv_days || '3' }} \
            --source biorxiv medrxiv arxiv chemrxiv crossref

      - name: Run digest
        run: |
          paperfind digest \
            --skip-fetch \
            -k ${{ github.event.inputs.num_results || '100' }}
            # Keywords are read from PAPERFIND_KEYWORDS env var (set via secret)
            # --rerank  # Uncomment to enable LLM reranking (requires LLM_RERANK_PREFERENCES secret)

      - name: Prune old papers
        run: |
          paperfind prune --older-than 30