AGENTS.md — Documentation Repository

This is Brian Yandell’s (byandell) personal documentation site, published at byandell.github.io/Documentation and versioned at GitHub.

Purpose

A consolidated reference for digital tools and workflows spanning R, Python, GitHub, environmental data science, Shiny apps, AI, and Quarto. The site is rendered as GitHub Pages using the just-the-docs theme configured in _config.yml and _quarto.yml.

Repository Structure

Path	Contents
`R/`	R language notes and tutorials
`python/`	Python language notes and tutorials
`github/`	Git and GitHub references
`envsys/`	Environmental systems / earth data science
`AI/`	Notes on AI tools and concepts
`prompts/`	AI prompt examples and walkthroughs
`quarto/`	Quarto slides and references
`datasci/`	Data science topics
`images/`	Images used across pages
`AI_prompts.md`	Detailed AI prompt examples (actively edited)
`ShinyApps.md`	Notes on Shiny app development
`README.md`	Top-level site index / landing page

Key Files

README.md — Main site index; keep in sync with _quarto.yml nav.
AI_prompts.md — Living document of AI prompt examples; update when new prompts are added.
prompts/ — Individual saved prompt files (e.g., powerpoint.md, workflow.md, file_versions.md).

Conventions

All prose documents are Markdown (.md) or Quarto (.qmd).
Quarto slides are rendered to HTML in quarto/.
Do not overwrite versioned files (e.g., *_v1.R) when committing version histories — follow the multi-version commit workflow in prompts/file_versions.md.
Respect .gitignore when updating README.md or adding new files.
When creating or updating README.md files for sub-folders, keep summaries concise and high-level, with links to relevant files.

byandell-sysgen — Systems genetics code
byandell-envsys — Environmental systems code
AttieLab-Systems-Genetics — Collaborative lab repos
byandell/geyser — Shiny app examples (R and Python)

Code Preferences

R: use tidyverse; document functions with roxygen2; build packages with devtools.
Python: use pandas, scikit-learn; document with docstrings and type hints.
Reports/Slides: prefer Quarto (.qmd) over R Markdown (.Rmd).
Shiny: use bslib for UI layout and theming.