mkdocs.yml

# General site information
site_name: CyVerse Learning Materials
site_description: Documentation for CyVerse Platforms and Education
site_author: CyVerse Science Team
site_url: https://learning.cyverse.org
copyright: Copyright © 2025 The Arizona Board of Regents
# Repository information
repo_name: CyVerse-learning-materials/learning-materials-home
repo_url: https://github.com/CyVerse-learning-materials/learning-materials-home
edit_uri: edit/main/docs

# Footer
copyright: 'Copyright © 2025 CyVerse'

# Navigation Page (merging both sets of navigation items)
nav:
  - 'Home':
    - index.md
    - 'What is CyVerse?': home/what_is_cyverse.md
    - 'Set Up an Account': home/account.md
    - 'Subscriptions': home/subscriptions.md
    - 'Powered by CyVerse': home/powered_by.md
    # - 'FAQ': home/faq.md # needs to be updated
    - 'Glossary': home/glossary.md
  - 'Data Management':
    - ds/index.md
    - 'Discovery Environment':
      - ds/de/index.md
      - 'Metadata': ds/de/metadata.md
      - 'DOI': ds/de/doi.md
      - 'Data Use': ds/de/check_data.md
      - 'Sharing with Teams': ds/de/teams.md
    - 'GoCommands':
      - ds/gocommands/index.md
      - 'Installation and Upgrade': ds/gocommands/installation.md
      - 'Configuration': ds/gocommands/configuration.md
      - 'Data Management': ds/gocommands/data_management.md
      - 'Data Transfer': ds/gocommands/data_transfer.md
      - 'Access Management': ds/gocommands/access_management.md
      - 'Metadata Management': ds/gocommands/metadata_management.md
      - 'SFTP Public-key Authentication Configuration': ds/gocommands/sftp_public_key_auth.md
      - 'Troubleshooting and Issue Report': ds/gocommands/issue_report.md
    - 'iCommands':
      - ds/icommands/index.md
      - 'Installation': ds/icommands/installation.md
      - 'Configuration': ds/icommands/configuration.md
      - 'Data Management': ds/icommands/data_management.md
      - 'Data Transfer': ds/icommands/data_transfer.md
      - 'Access Management': ds/icommands/access_management.md
      - 'Metadata Management': ds/icommands/metadata_management.md
      - 'Troubleshooting and Issue Report': ds/icommands/issue_report.md
    - 'SFTP':
      - ds/sftp/index.md
      - 'CLI tools': ds/sftp/cli.md
      - 'FileZilla': ds/sftp/filezilla.md
      - 'Cyberduck': ds/sftp/cyberduck.md
      - 'Directory Structure': ds/sftp/structure.md
      - 'Public-key Authentication Configuration': ds/sftp/public_key_auth.md
    - 'WebDav':
      - ds/webdav/index.md
      - 'Web Browsers': ds/webdav/browser.md
      - 'CLI tools': ds/webdav/cli.md
      - 'File Managers': ds/webdav/file_manager.md
      - 'Data Locations': ds/webdav/data_location.md
  - 'Discovery Environment':
    - de/index.md
    - 'Logging In': de/login.md
    - 'Using Apps': de/using_apps.md
    - 'Managing Analyses': de/managing_analyses.md
    - 'Interactive Analysis': de/vice/about.md
    - 'Integrate Apps and Tools': de/create_apps.md
    - 'Integrate Interactive Apps': de/vice/extend_apps.md
    - 'App Integration Tutorials':
      - 'HPC Apps': de/create_hpc_apps.md
    - 'Data Store in Interactive Apps': de/vice/csi.md   
    - 'Sharing Apps': de/vice/quick-app-launch.md
    - 'Sharing and Using Bags': de/bags.md
    - 'Sharing Data': ds/de/share.md
    - 'Adding Metadata': ds/de/metadata.md
    - 'Getting a DOI': ds/de/doi.md
    - 'Checking Data Usage': ds/de/check_data.md
    - 'Teams': ds/de/teams.md
    - 'Quick Starts':
      - 'RStudio': de/vice/quick-rstudio.md
      - 'JupyterLab': de/vice/quick-jupyter.md
      - 'Cloud Shell': de/vice/quick-cloudshell.md
      - 'Ollama': de/vice/quick-ollama.md
  - 'Cloud Native Services':
    - cloud/index.md
    - 'CACAO': cloud/cacao.md
    - 'DataWatch': cloud/datawatch.md
    - 'Harbor Container Registry': cloud/harbor.md
  - 'Artificial Intelligence':
    - ai/index.md
    - 'VERDE': ai/verde.md
    - 'MCP Servers': ai/mcp/index.md
  - 'Education':
    - edu/index.md
    - 'Workshops':
      - edu/workshops/index.md
      - 'Container Camp': edu/workshops/container_camp.md
      - 'Foundational Open Science Skills': edu/workshops/foss.md
    - 'Science Tutorials': edu/tutorials/index.md
    - 'DNA Subway': edu/tutorials/dna_subway_guide.md    
  - 'Developer Tools':
    - 'Developer Manuals': dev/manuals.md
  

# Theme settings
theme:
  name: material
  prev_next_buttons_location: bottom
  palette:
    - media: "(prefers-color-scheme)"
      toggle: 
        icon: material/brightness-auto
        name: Switch to light mode
    # Light mode settings
    - media: "(prefers-color-scheme: light)"
      primary: '#002E99'
      accent: 'orange'
      scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode settings
    - media: "(prefers-color-scheme: dark)"
      primary: '#002E99'
      accent: 'orange'
      scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to system preference
  font:
    text: Roboto
    code: 'Roboto Mono'
  favicon: 'assets/favicon.ico'
  logo: 'assets/android-chrome-512x512.png'
  features:
    - navigation.instant
    - navigation.tracking
    #- navigation.tabs
    - navigation.sections
    - navigation.path
    - navigation.prune
    #- navigation.tabs.sticky
    #- navigation.indexes
    - navigation.top
    - navigation.footer
    - toc.follow
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.tooltips
    - palette.toggle

# Analytics and social links
extra:
  social:
    - icon: fontawesome/brands/orcid
      link: https://orcid.org/
    - icon: fontawesome/brands/github
      link: https://github.com/cyverse-learning-materials/
    - icon: fontawesome/brands/twitter
      link: https://twitter.com/cyverseorg
    - icon: fontawesome/brands/linkedin
      link: https://www.linkedin.com/company/cyverse.org
    - icon: fontawesome/brands/docker
      link: https://harbor.cyverse.org/
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/c/CyverseOrgProject
  analytics:
    provider: google
    property: UA-72224033-6

# Extra CSS and JavaScript (added chatbot)
extra_css:
  - stylesheets/extra.css
  - chatbot_widget.css

extra_javascript:
  - chatbot_widget.js

# Markdown Extensions
markdown_extensions:
  - admonition
  - abbr
  - attr_list
  - def_list
  - footnotes
  - meta
  - md_in_html
  - toc:
      permalink: true
      title: On this page
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink:
      repo_url_shorthand: true
      user: squidfunk
      repo: mkdocs-material
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Plugins
plugins:
  - search
  - social
  - mkdocstrings
  - git-revision-date
  - mkdocs-jupyter:
      include_source: True
      ignore_h1_titles: True