wai (Working with AI)

UCD-SERG lab notes on working responsibly and effectively with AI coding assistants: what they are, how to use them, and the policies lab members follow. The notes are published as a Quarto website at https://d-morrison.github.io/wai/.

The content was migrated out of the “Working with AI” chapter of the UCD-SERG Lab Manual, which had grown large enough to deserve a dedicated site. For the lab’s broader coding, reproducibility, and collaboration conventions, see the lab manual itself.

Technology in rapid evolution. As of early 2026, AI coding-assistant technology is changing extremely rapidly, and we are still figuring out how to use these tools well. Treat everything here as provisional — best practices and capabilities keep moving.

Contents

The site is organized into three main chapters:

• Policies for Using AI — responsibility for validation, disclosure, attribution, and using AI for journal articles
• Coding Agents — what language models, coding agents, and harnesses are; how to work with them; their benefits and hazards; and how to configure your environment
• Pull-Request Workflow with Agents — filing issues, claiming work, and driving a pull request to a clean, mergeable state

Supporting material lives under chapters/ai-tools/.

Reading the notes

The rendered site is the easiest way to read the notes: https://d-morrison.github.io/wai/. Each page is also available as RevealJS slides (-slides.html), a PDF handout (-handout.pdf), and a Word document (.docx).

Building locally

You need Quarto installed. This project uses Quarto’s llms-txt website option, which requires Quarto 1.9.36 or newer.

Clone the repository and its submodule (macros/):

git clone https://github.com/d-morrison/wai.git
cd wai
git submodule update --init --recursive

Preview with live reload while editing:

quarto preview

Render the complete site (output lands in _site/):

quarto render

Repository layout

.
├── index.qmd                # Site homepage
├── chapters/                # Chapter sources
│   ├── ai-use-policies.qmd
│   ├── coding-agents.qmd
│   ├── pr-workflow-with-agents.qmd
│   └── ai-tools/            # Supporting notes on specific tools/topics
├── references.qmd           # Standalone references page
├── references.bib           # BibTeX bibliography
├── _quarto.yml              # Quarto project configuration
├── _quarto-website.yml      # Website configuration (navbar, theme, URLs)
├── _extensions/             # Vendored Quarto extensions
├── macros/                  # Git submodule: shared shortcode/macro definitions
├── R/, man/, DESCRIPTION    # The project is also a small R package
├── styles.css               # Website styling
├── inst/WORDLIST            # Accepted spellings for the spell-check workflow
├── lychee.toml              # Link-checker configuration
└── .github/workflows/       # CI: publish, PR preview, spell/link/lint checks

See CLAUDE.md for a fuller description of the repository conventions and CI checks.

Contributing

Contributions are welcome — see CONTRIBUTING.md for the branch-and-PR workflow, and open an issue to discuss larger changes.

License

Released under the MIT License — see LICENSE.

Acknowledgments

Built from the UCD-SERG qwt (Quarto Website Template), whose structure is based on the UCD-SERG Lab Manual, adapted in turn from the Benjamin-Chung Lab Manual.