qmt/_quarto.yml at main · Morrison-Lab/qmt · GitHub

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project:
  type: manuscript
  output-dir: _manuscript
  render:
    - "*.qmd"
    - "notebooks/*.qmd"
    - "!README.md"

manuscript:
  article: index.qmd
  meca-bundle: true
  notebooks:
    - notebook: notebooks/supplementary-analysis.qmd
      title: "Supplementary Analysis"

# GitHub repo — update this when using the template in a new repo.
# Drives the "Edit this page" / "View source" links and the GitHub icon
# in the title banner (injected by _repo-links.lua).
repo-url: https://github.com/d-morrison/qmt
repo-actions: [edit, source]


bibliography: references.bib

editor_options:
  chunk_output_type: console

editor:
  markdown:
    wrap: 72

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

callouty-theorem:
  thm:
    override-title: false
    callout:
      type: lem
      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:
    override-title: true
    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: false
    callout:
      type: remark
      appearance: minimal

custom-callout:
  lem:
    color: "#1565C0"
  cor:
    color: "#00838F"
  prp:
    color: "#827717"
  cnj:
    color: "#558B2F"
  def:
    color: "#1B5E20"
  exm:
    color: "#6A1B9A"
  exr:
    color: "#FFA500"
  proof:
    color: "#37474F"
  solution:
    color: "#4E342E"
  remark:
    color: "#AD1457"

filters:
  - div-anchors
  - equation-anchors
  - code-language-labels

format:
  html:
    filters:
      - _repo-links.lua
      - 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: true
    code-tools: true
    code-link: true
    code-summary: "Show R code"
    highlight-style: pygments
    lightbox: true
    link-external-icon: true
    embed-resources: false
    fig-cap-location: top
    html-math-method: mathjax
    number-sections: false
    df-print: paged
  pdf:
    filters:
      - sun123zxy/callouty-theorem
      - coatless-quarto/custom-callout
    include-in-header:
      text: |
        \usepackage{needspace}
        \usepackage{etoolbox}
        \AtBeginEnvironment{longtable}{\Needspace{8\baselineskip}}
    number-sections: false
  docx:
    number-sections: false
    df-print: tibble
    prefer-html: true
  jats: default

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

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