_quarto.yml

project:
  type: website
  output-dir: _site
  render:
    - index.qmd                                     # home
    # orientation drop down
    - "01_orientation/start-here.qmd"               # start-here prerequisites
    - "01_orientation/workflow-roadmap.qmd"         # workflow roadmap
    # guides drop down; has its own landing page
    - guides.qmd                                    # guides landing page
    - "02_guides/*.qmd"
    - "02_guides/02_projects-and-reproducibility/*.qmd"         # projects and reproducibility guide
    # reference pages
    - "resources.qmd"                               # resources listing
    # other pages
    - CONTRIBUTING.qmd                              # contribution guide
    - "about.qmd"                                   # about page           

website:
  title: Golden Lab Data Science Handbook
  description: Reproducible, collaborative, HPC-native data science guidance for students and researchers.
  page-navigation: true
  reader-mode: true
  open-graph: true
  search:
    location: navbar
    type: textbox
  navbar:
    pinned: true
    background: light
    foreground: dark
    right:
      - href: "01_orientation/start-here.qmd"
        text: Start Here
      - href: "01_orientation/workflow-roadmap.qmd"
        text: Workflow
      # - href: resources.qmd
      #   text: Resources
      # - href: about.qmd
      #   text: About
  announcement: 
    icon: exclamation-square
    dismissable: true
    content: "**Alert**  - ☀️ FASRC Will Be Down for Summer Maintenance **June 15th - 18th, 2026** ☀️ Please plan accordingly and reach out to FASRC support if you have any questions or concerns."
    type: warning
    position: below-navbar
  sidebar:
    style: floating
    collapse-level: 1
    contents:
      - href: index.qmd
        text: Home
      - section: Orientation
        contents:
          - href: "01_orientation/start-here.qmd"
            text: Start Here
          - href: "01_orientation/workflow-roadmap.qmd"
            text: Workflow Roadmap
      - section: Guides
        href: "guides.qmd"
        contents:
          - href: "02_guides/01_hpc-infrastructure.qmd"
            text: HPC and Infrastructure
          - href: "02_guides/02_projects-and-reproducibility.qmd"
            text: Projects and Reproducibility
          - href: "02_guides/03_data-access-and-management.qmd"
            text: Data Access and Management
          - href: "02_guides/04_collaboration-and-support.qmd"
            text: Collaboration and Support
          - href: "02_guides/05_environments-and-package-management.qmd"
            text: Environments and Package Management
      - href: resources.qmd
        text: Reference Library
      - href: CONTRIBUTING.qmd
        text: Contribution Guide
      - href: about.qmd
        text: About This Site
  page-footer:
    left: Golden Lab data workflows handbook
    right: Built with [Quarto](https://quarto.org)
  comments:
    giscus:
      repo: "GoldenPlanetaryHealthLab/GoldenPlanetaryHealthLab.github.io"
      repo-id: "R_kgDOR4BFuw"
      category: "General"
      category-id: "DIC_kwDOR4BFu84C6zHg"
      mapping: "pathname"
      theme: "preferred_color_scheme"
      reactions-enabled: true
      input-position: "top"

format:
  html:
    title-block-banner: true
    date-format: "MMMM D, YYYY"
    smooth-scroll: true
    code-copy: true
    link-external-newwindow: true
    link-external-icon: true
    toc: true
    toc-depth: 3
    theme:
      light:
        - journal
        - css/custom.scss
    css:
      - css/custom_style.css
    include-in-header: _includes/read-time-head.html
    include-after-body: _includes/read-time.html