project:
  type: website
  output-dir: www/
  render:
    - index.qmd
    - version.qmd
    - MS/SM.qmd
    - MS/MS.qmd
    - MS/RN.qmd
    - MS/CL.qmd
    - MS/HL.qmd
    - MS/RP.qmd
    - MS/index.qmd
    - TC/index.qmd
    - SD/
    - MS/RN.qmd
    - MS/AC.qmd
    - RP/
    - AC/
    - about.qmd

lang: en
date: last-modified
# bibliography: [BB/Ref.bib, BB/localRef.bib]
prefer-html: true
crossref:
  fig-title: Fig. # (default is "Figure")
  tbl-title: Table # (default is "Table")
  eq-title: Eq. # (default is "Equation")
  title-delim: ":" # (default is ":")
  fig-prefix: Fig. # (default is "Figure")
  tbl-prefix: Table # (default is "Table")
  eq-prefix: Eq.
  ref-hyperlink: true # (default is true)
  custom:
    - kind: float
      key: sfg
      reference-prefix: "Supplementary Fig."
      space-before-numbering: true
      caption-prefix: "Supplementary Fig."
      latex-env: sfg
      latex-list-of-file-extension: lost
      latex-list-of-description: Supplementary Figure
    - kind: float
      key: stb
      reference-prefix: "Supplementary Table"
      space-before-numbering: true
      caption-prefix: "Supplementary Table"
      latex-env: stb
      latex-list-of-file-extension: lost
      latex-list-of-description: Supplementary Table
    - kind: float
      key: seq
      reference-prefix: "Supplementary Eq."
      space-before-numbering: true
      caption-prefix: "Supplementary Eq."
      latex-env: seq
      latex-list-of-file-extension: lost
      latex-list-of-description: Supplementary Equation
    - kind: float
      key: rfg
      reference-prefix: "Fig. R"
      space-before-numbering: false
      caption-prefix: "Fig. R"
      latex-env: rfg
      latex-list-of-file-extension: lost
      latex-list-of-description: Revision Figure
    - kind: float
      key: rtb
      reference-prefix: "Table R"
      space-before-numbering: false
      caption-prefix: "Table R"
      latex-env: rtb
      latex-list-of-file-extension: lost
      latex-list-of-description: Revision Table
    - kind: float
      key: req
      reference-prefix: "Eq R"
      space-before-numbering: false
      caption-prefix: "Eq R"
      latex-env: req
      latex-list-of-file-extension: lost
      latex-list-of-description: Revision Equation
    - kind: float
      key: efg
      reference-prefix: "Extended Data Fig."
      space-before-numbering: true
      caption-prefix: "Extended Data Fig."
      latex-env: efg
      latex-list-of-file-extension: lost
      latex-list-of-description: Extended Data Figure
    - kind: float
      key: etb
      reference-prefix: "Extended Data Table"
      space-before-numbering: true
      caption-prefix: "Extended Data Table"
      latex-env: etb
      latex-list-of-file-extension: lost
      latex-list-of-description: Extended Data Table
website:
  title: "{{< var reponame >}}: {{< var branch >}}"
  reader-mode: true
  site-url: https://drc.drwater.net/{{< var projtype >}}/{{< var reponame >}}/{{< var branch >}}
  repo-url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}
  repo-actions: [edit, source, issue]
  page-navigation: true
  page-footer: "Copyright 2025, [Dr. Water](https://drwater.net)"
  navbar:
    logo: "./_extensions/drwater/dwinst/drwater-white0.svg"
    background: "#3D6E3B"
    search: true
    right:
      - icon: house
        text: "Home"
        file: index.qmd
      - text: "Main files"
        menu:
          - text: "Manuscript"
            file: MS/MS.qmd
          - text: "Supplementary Materials"
            file: MS/SM.qmd
          - text: "Revision Notes"
            file: MS/RN.qmd
          - text: "Cover Letter"
            file: MS/CL.qmd
          - text: "Highlights"
            file: MS/HL.qmd
      - text: "Slides"
        file: SD/index.qmd
      - text: "Links"
        menu:
          - text: "Version"
            href: version.qmd
          - text: "DRC"
            href: "https://drc.drwater.net/"
          - text: "Dr. Water"
            href: "https://drwater.net/"
      - text: "Others"
        menu:
          - text: "Reports"
            file: RP/index.qmd
          - text: "Author Credits"
            file: MS/AC.qmd
          - text: "Accomplishment"
            file: AC/index.qmd
          - text: "Trackchanges"
            file: TC/index.qmd
          # - text: "MS with raw bibkey"
          #   file: MS/MS_nobib.docx
      - text: "About"
        file: about.qmd
      - icon: git
        menu:
          - text: Codes
            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
          - text: Issue
            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues

  comments:
    hypothesis:
      theme: clean
      openSidebar: false

execute:
  freeze: false # re-render only when source changes
  cache: false
  echo: false

format:
  dwhm-html: default