_quarto-website.yml

project:
  type: website
  output-dir: _site
  render:
    - "*.qmd"
    - "chapters/*.qmd"
    - "!README.md"
    - "!appendix-document-metadata.qmd"
    - "!references.qmd"
    # The `macros` git submodule provides macro definitions for include/
    # shortcode use, not standalone site pages. Don't render its .qmd files
    # directly: macros-table.qmd uses DT::datatable() (an HTML widget) that
    # errors when the project also renders to PDF.
    - "!macros/"
    # chapters/ai-tools/*.qmd are {{< include >}} fragments transcluded by
    # chapters/*.qmd, not standalone pages. Their `@sec-ai-*` crossrefs are
    # only defined on the including page, so rendering them standalone also
    # produces broken crossref warnings.
    - "!chapters/ai-tools/"

website:
  title: "Working with AI"
  site-url: https://Morrison-Lab.github.io/wai/
  description: "UCD-SERG lab notes on working with AI coding assistants: policies, coding agents, and PR workflow"
  # https://quarto.org/docs/websites/website-llms.html — use `llms-txt:`, not `llms:` (schema error)
  llms-txt: true
  page-footer:
    center: "Built with [Quarto](https://quarto.org/)"
  back-to-top-navigation: true
  page-navigation: true
  reader-mode: true
  repo-url: https://github.com/Morrison-Lab/wai
  repo-actions: [edit, issue, source]
  navbar:
    left:
      - text: "Home"
        href: index.qmd
      - text: "Chapters"
        menu:
          - text: "Policies for Using AI"
            href: chapters/ai-use-policies.qmd
          - text: "Coding Agents"
            href: chapters/coding-agents.qmd
          - text: "Orchestrating Teams of Agents"
            href: chapters/agent-orchestration.qmd
          - text: "AI for Math and Statistics"
            href: chapters/ai-for-math.qmd
          - text: "Grok Bot and Alternatives"
            href: chapters/grok-bot-and-alternatives.qmd
          - text: "Data Dictionaries for Humans and Agents"
            href: chapters/data-dict.qmd
          - text: "Benchbook: A Personal Wiki Under Contract"
            href: chapters/benchbook.qmd
          - text: "Make: Visual Automation and AI Agents"
            href: chapters/make.qmd
          - text: "Pull-Request Workflow with Agents"
            href: chapters/pr-workflow-with-agents.qmd
    right:
      - icon: github
        href: https://github.com/Morrison-Lab/wai
        aria-label: GitHub

callouty-theorem:
  thm:
    override-title: false # do not have the filter set
                          # or override a callout title
    callout: # parameters of the wrapping callout
             # see Quarto callout docs for details
      type: lem  # same color as lem (royal blue); color set in custom-callout block below
      appearance: minimal
  lem:
    override-title: false
    callout:
      type: lem
      appearance: minimal
  cor:
    override-title: false
    callout:
      type: cor
      appearance: minimal
  prp:
    override-title: false
    callout:
      type: prp
      appearance: minimal
  cnj:
    override-title: false
    callout:
      type: cnj
      appearance: minimal
  def:
    override-title: false
    callout:
      type: def
      appearance: minimal
  exm:
    override-title: false
    callout:
      type: exm
      appearance: minimal
  exr:
    override-title: false
    callout:
      type: exr
      appearance: minimal
  proof: # also support wrapping proof-like environments
    override-title: true # override the callout title with
                         # the proof-type label,
                         # appending the element name when provided
    callout:
      type: proof
      appearance: default
      collapse: true
      icon: true
  solution:
    override-title: true
    callout:
      type: solution
      appearance: default
      collapse: true
      icon: false
  remark:
    override-title: true
    callout:
      type: remark
      appearance: default
      collapse: false
      icon: true

# Color palette for theorem/proof environments.
# The coatless-quarto/custom-callout extension reads this block and injects
# CSS (HTML) and LaTeX \definecolor (PDF) so each type gets a unique color.
# Rules: no reds; thm shares lem's royal blue.
custom-callout:
  lem:
    color: "#1565C0"  # royal blue (also used for thm)
  cor:
    color: "#00838F"  # dark cyan
  prp:
    color: "#827717"  # dark olive
  cnj:
    color: "#558B2F"  # grass green
  def:
    color: "#1B5E20"  # forest green (very distinct from theorem types)
  exm:
    color: "#6A1B9A"  # deep purple
  exr:
    color: "#FFA500"  # orange
  proof:
    color: "#37474F"  # blue-grey slate
  solution:
    color: "#4E342E"  # dark cocoa
  remark:
    color: "#AD1457"  # dark magenta

format:
  html:
    filters:
      - sun123zxy/callouty-theorem
      - coatless-quarto/custom-callout
    theme:
      light: cosmo
      dark: darkly
    css: styles.css
    toc: true
    anchor-sections: true
    toc-location: right
    toc-depth: 3
    code-fold: false
    code-tools: true
    code-link: true
    highlight-style: pygments
    lightbox: true
    link-external-icon: true
    embed-resources: false
    fig-cap-location: top
    html-math-method: mathjax
    number-sections: true
    number-depth: 3
    df-print: paged
  docx:
    number-sections: true
    number-depth: 3
    df-print: tibble
    prefer-html: true
  revealjs:
    output-file: "{stem}-slides.html"
    theme: [simple, styles-reveal.scss]
    include-in-header: qwt-reveal-toggle.html
    slide-number: true
    chalkboard: false
    preview-links: auto
    controls: true
    transition: slide
    background-transition: fade
    lightbox: true
    fig-cap-location: top
    html-math-method: mathjax
    smaller: true
    number-sections: true
    progress: true
    incremental: false
    df-print: paged
    number-depth: 2
    shift-heading-level-by: 0
    slide-level: 2
    scrollable: true
    echo: true
    margin: 0.0
    code-fold: true
    code-link: true
    code-summary: "[R code]"
    auto-stretch: true
    fig-height: 5
    fig-width: 7

date: last-modified
date-format: "[Last modified:] YYYY-MM-DD HH:mm:ss (z)"

execute:
  warning: false
  message: false
  cache: false
  freeze: auto

knitr:
  opts_chunk:
    collapse: true
    comment: "#>"