keiserlab.org

Website for the Keiser Lab, an AI/ML research lab at UCSF (2014-2025) led by Michael Keiser.

development

We use Docker for Jekyll serving only. VS Code, Claude Code, and other dev tools run on the host (not in the devcontainer).

• start Jekyll: $ docker compose up (or docker compose up -d for background)
  • get interactive terminal: $ docker compose exec -it keiserlab bash
• dev website serves at http://localhost:4000
• edit files, run python scripts, and use git on the host

ruby environment via bundler

• bundle manages the container's ruby environment (for Jekyll)
• check for dependency updates:
  1. bundler: $ bundle update --bundler
  2. all other gems: $ bundle update

python environment via uv

• uv manages python on the host (not in the container)
• run python scripts like uv run myscript.py or uvx --with <pkg> python3 -c "..."
• check for dependency updates: $ uv lock --upgrade
  • if updated, include uv.lock in the git commit

claude code

• run Claude Code CLI on the host: claude
• set ANTHROPIC_API_KEY in your environment to authenticate

alternative: devcontainer workflow

• a vscode devcontainer is available if you prefer running everything inside the container
• the devcontainer auto-installs the Claude Code extension
• or install the CLI directly: curl -fsSL https://claude.ai/install.sh | bash
• set GH_TOKEN on the host so it's available inside the container:

  export GH_TOKEN=$(gh auth token)

• add this to ~/.zshenv (not ~/.zshrc) so it's available during vscode devcontainer auto-rebuilds

linting

./scripts/lint.sh                             # all linters (internal links only)
uvx ruff check utils/                         # python
uvx yamllint -d relaxed _config.yml _data/    # yaml
npx @biomejs/biome check .                    # scss, json
bundle exec htmlproofer ./_site               # built html + internal links

check external links (DOIs, Zenodo, GitHub, etc. — slow, network-flaky):

docker compose exec keiserlab bundle exec htmlproofer ./_site \
  --allow-hash-href --no-enforce-https \
  --ignore-urls '/tags/,/tbproxy/' \
  --typhoeus '{"followlocation": true, "timeout": 30}'

rebuilds

• force container rebuild with $ docker-compose build --no-cache

jekyll theme

• we're using the Minimal Mistakes jekyll theme
• theme setup and use: setup guide