_quarto.yml

project: 
  type: website

website: 
  page-navigation: true
  title: "NOAA quarto simple" 
  site-url: "https://nefsc.github.io/NEFSC_PAB_lab_manual/" 
  repo-url: "https://github.com/NEFSC/NEFSC_PAB_lab_manual"
  repo-actions: [edit, source, issue]
  favicon: favicon.ico
  
  page-footer:
    right: "This page is built with [Quarto](https://quarto.org/)."
    left: "© CC-1.0"
  
  sidebar:
    background: "#D9E3E4"
    logo: "https://upload.wikimedia.org/wikipedia/commons/7/79/NOAA_logo.svg"
    favicon: images/favicon.ico
    pinned: true
    align: center
    tools: 
      - icon: globe
        href: https://www.fisheries.noaa.gov/new-england-mid-atlantic/endangered-species-conservation/passive-acoustic-research-northeast
        text: "NEFSC Passive Acoustic Branch"
      - icon: github
        href: https://github.com/NEFSC/NEFSC_PAB_lab_manual
        text: "NEFSC Lab Manual Repo"

    style: "docked"
    search: true
    collapse-level: 1
    contents:
      - section: index.qmd
        text: Home
        contents: 
          - href: content/Home/Shared-values.qmd
            text: Shared values
          - href: content/Home/Collaborators.2.qmd
            text: Collaborators
      - section: content/LabManagement/LabManagement.qmd # this is the example that shows how to get a landing page
        contents: 
          - href: content/LabManagement/Team_member_bios.qmd
            text: Team Member Bios
          - href: content/LabManagement/PAB-alumn.qmd
            text: PAB Alumni
          - href: content/LabManagement/Safety.qmd
            text: Lab Safety
          - href: content/LabManagement/Onboarding.qmd
            text: Onboarding/Offboarding
          - href: content/LabManagement/RDC-info.qmd
            text: Remote Desktop Computer Information
          - href: content/LabManagement/PA_server_structure.qmd
            text: PassiveAcoustics Server Structure
          - href: content/LabManagement/Resources.2.qmd
            text: Resources
          - href: content/LabManagement/Media.qmd
            text: Media
      - section: content/DataManagement/DataManagement.qmd
        text: Data Management
        contents:
          - href: content/DataManagement/PA_soundfiles.qmd
            text: PassiveAcoustics Soundfiles
          - href: content/DataManagement/Data-repositories.qmd
            text: Data Repositories
          - href: content/DataManagement/QAQC.qmd
            text: QA/QC
      - href: content/Hardware/Hardware.2.qmd
        text: Hardware
      - href: content/Software/Software.qmd
        text: Software
      - section: content/Analysis/Analysis.qmd
        text: Analysis
        contents:
          - section: Sound Source list
            contents:
              - href: content/Analysis/Species_list/Myst_list.qmd
                text: Baleen
              - href: content/Analysis/Species_list/Odont_list.qmd
                text: Odontocetes
              - href: content/Analysis/Species_list/Pinniped.qmd
                text: Pinnipeds
              - href: content/Analysis/Species_list/Fish.qmd
                text: Fish & Invertebrates
              - href: content/Analysis/Species_list/Env-Anthro.qmd
                text: Environmental and Anthropogenic sounds
             # - href: content/Analysis/Species_list/Undefined.qmd
             #   text: Undefined sounds
          - section: Analysis protocols
            contents:
              - href: content/Analysis/Protocols/Mysticete_protocols.qmd
                text: Baleen 
              - href: content/Analysis/Protocols/Odont_protocols.qmd
                text: Odontocetes
              - href: content/Analysis/Protocols/Pinniped.2.qmd
                text: Pinnipeds
              - href: content/Analysis/Protocols/fish_protocols.qmd
                text: Fish 
              - href: content/Analysis/Protocols/Anthro_protocols.qmd
                text: Anthropogenic 
           #   - href: content/Analysis/Protocols/AMP_protocols.qmd
           #    text: Australia Marine Park 
      - href: content/FieldMethods/FieldMethods.qmd
        text: Field Methods
      - href: content/Reporting/Reporting.qmd
        text: Reporting
      - href: content/Publications/PublicationsPresentations.qmd
        text: Publications
        
format:
  html:
    link-external-icon: false
    link-external-newwindow: true
    theme:
      light: [cosmo, theme.scss] 
      dark: [cosmo, theme-dark.scss]
    code-copy: true
    code-overflow: wrap
    toc: true


filters:
  - include-files.lua
  - quarto