We aim to develop AI-enabled solutions for agriculture and food systems

Scripts

Fetch publications (OpenAlex + Google Scholar)

Compares publications from OpenAlex and optionally Google Scholar with your existing _data/publications.yml and reports any that might be missing.

Setup

cd /path/to/plant-ai-biophysics-lab.github.io
pip install -r scripts/requirements.txt

Usage

OpenAlex only (no API key; uses OpenAlex public API):

python scripts/fetch_publications.py

OpenAlex + Google Scholar (Scholar is scraped via scholarly; you may hit rate limits or CAPTCHAs):

python scripts/fetch_publications.py --scholar

Report only (no file writes):

python scripts/fetch_publications.py --report
python scripts/fetch_publications.py --scholar --report

Config: _data/publications_config.yml

  • OpenAlex (used by default): authors[].openalex_id or orcid.
  • Google Scholar (optional): add one of these per author:
    • google_scholar_author_id: from the profile URL
      https://scholar.google.com/citations?user=**XXXX**&hl=en
    • name_for_scholar: search string (e.g. "Mason Earles UC Davis") if you don’t have the ID.

The script prints:

  • How many works were fetched from each source.
  • OpenAlex works not yet in publications.yml.
  • (With --scholar) Papers that appear in Google Scholar but not in OpenAlex, for you to add manually if needed.

Add any missing entries by editing _data/publications.yml (you can copy the format from existing entries and add optional podcast_url, github, etc.).

Look up URLs for papers with empty url

Use scripts/lookup_paper_urls.py to find URLs (DOI, arXiv, etc.) for publications that have url: "":

python scripts/lookup_paper_urls.py

This queries OpenAlex by title and prints suggested URLs. Run with --apply to write them into _data/publications.yml (a .yml.bak backup is created first). Papers not found in OpenAlex (e.g. very recent or niche) may need manual lookup on Google Scholar or the journal site.