pearsonlab.github.io

Lab webpage

Notes

In order to render publications into page:

1. Download citations from Google Scholar in .bib format.
2. Place in _publications/publications.bib
3. . process_refs

Everything else should just work.

Contributing

Local preview

The site is built by Jekyll. To preview changes locally:

bundle install
bundle exec jekyll serve --livereload

Then open http://localhost:4000.

Pre-commit hooks

The repo uses pre-commit to compress images and catch other small issues before they land. One-time setup:

pip install pre-commit
pre-commit install

# image tooling (one of these per platform):
sudo apt install jpegoptim && cargo install oxipng   # Ubuntu/Debian
brew install jpegoptim oxipng                        # macOS
npm install -g svgo

After that, every git commit will automatically:

• Compress staged JPEGs to quality 85 with jpegoptim
• Losslessly optimize staged PNGs with oxipng
• Minify staged SVGs with svgo
• Block any image still over 1 MB after compression, and warn on images between 500 KB and 1 MB (see "Image size policy" below)
• Verify internal image references in HTML/Markdown actually resolve to a file in the repo (catches typos and orphaned references; external URLs are covered by lychee in the site-health CI workflow)
• Strip trailing whitespace, fix mixed line endings, ensure files end with a final newline
• Validate YAML and JSON files (_data/, _config.yml, etc.)
• Block accidental merge-conflict markers and committed private keys
• Lint Markdown posts with markdownlint --fix (auto-fixes most formatting issues; see .markdownlint.json for the disabled rules)
• Style-check YAML files with yamllint (config: .yamllint)

If a hook modifies a file, the commit is aborted; re-stage the modified file and commit again. To run the hooks manually across just your changes vs. master:

pre-commit run --from-ref origin/master --to-ref HEAD

(Avoid --all-files — it will pick up the legacy ~26 MB of unoptimized images and fail. A separate one-shot backfill phase will normalize those.)

The same hooks run in CI on every PR — scoped to the PR's changed files. If you skip the local install, CI will tell you what would have changed.

Per-page SEO and social previews

The site uses jekyll-seo-tag to emit OpenGraph and Twitter card meta tags. Defaults come from _config.yml (site title, description, lab logo as fallback image). Pages can override any of these via front matter:

---
title: "Pearson Lab Research"
description: "We study ..."
image: /images/research/cover.png
---

A sitemap.xml is generated automatically at build time by jekyll-sitemap.

Site health

A separate CI workflow (.github/workflows/site-health.yml) builds the site and runs:

• lychee to check for broken links (config: lychee.toml)
• html5validator to check rendered HTML (config: .html5validator.yaml)

This runs on PRs that touch site content, on push to master, and once a week on Mondays. The weekly schedule catches link rot from external hosts before someone notices on the live site.

Image size policy

To keep the repo lean, images are subject to:

• Hard cap: 1 MB per file (post-compression). Commits with larger images are blocked.
• Soft warning: 500 KB. Commits succeed but print a warning.

Most properly-sized lab-member photos at q=85 land in 100–300 KB. If a figure genuinely needs to exceed 1 MB (e.g., a high-resolution research figure where detail matters), add its repo-relative path to .image-size-overrides and commit that change with a brief justification in the commit message.