mkdocs.yml

docs_dir: docs/
repo_name: 'CyVerse-learning-materials/learning-materials-home'
repo_url: 'https://github.com/CyVerse-learning-materials/learning-materials-home'

site_name: 'CyVerse Learning Home'
site_description: 'Documentation for CyVerse Platforms and Education'
site_author: 'CyVerse Science Team'
site_url: 'https://learning.cyverse.org'

edit_uri: edit/main/docs

# Copyright
copyright: 'Copyright © 2022 CyVerse'

# Navigation Page

nav:
  - 'Home':
    - index.md
    - 'What is CyVerse?': what_is_cyverse.md
    - 'Self-Guided Tour': mooc.md
    - 'Set Up an Account': account.md
    - 'Getting Help': getting_help.md
  - 'Manage Your Data':
    - ds/index.md
    - 'Moving Data':
      - ds/move_data/index.md
      - 'Data Management with Discovery Environment': de/manage_data.md
      - 'Transferring Data with Cyberduck': ds/cyberduck.md
      - 'Transferring Data with iCommands and Command Line': ds/icommands.md
      - 'Transferring Data with GoCommands and Command Line': ds/gocommands.md
      - 'HTTP Access with WebDAV': ds/webdav.md
      - 'Transferring Data with SFTP': ds/sftp.md
    - 'Adding Metadata': ds/metadata.md
    - 'Sharing Data': ds/share.md
    - 'Getting a DOI': ds/doi.md
    - 'Checking Data Storage': ds/check_data.md
  - 'Run Analyses':
    - de/index.md
    - 'Logging In': de/login.md
      ##- 'Managing Data through the DE': de/manage_data.md
    - 'Using Apps': de/using_apps.md
    - 'Managing Analyses': de/managing_analyses.md
    - 'Interactive Analysis': vice/about.md
      #- 'Interactive Apps': vice/apps.md
      #- 'Search': de/search.md
    - 'Sharing and Using Bags': de/bags.md
  - 'Quick Starts':
    - 'RStudio in 6 steps': vice/quick-rstudio.md
    - 'JupyterLab in 6 steps': vice/quick-jupyter.md
    - 'Cloud Shell in 6 steps': vice/quick-cloudshell.md
    - 'Distributing Data in 6 steps': ds/quick-data-share.md
      #- 'Cloud Virtual Machines': atmo/quick-atmo.md
  - 'Cloud Services':
    - cloud/index.md
      #- 'Atmosphere': atmo/atmo.md
      #- 'Jetstream': atmo/js.md
      #- 'Continuous Analyses': atmo/cacao.md
  - 'Analyze Images':
    - bisque/index.md
  - 'For the Classroom':
    #- 'Self-Guided Course': mooc.md
    - 'Teach using CyVerse': vice/teaching.md
    - 'DNA Subway': dna_subway_guide.md
  - 'Develop':
    - 'Integrate Apps and Tools': de/create_apps.md
    - 'Interactive Apps': vice/extend_apps.md
    - 'Powered by CyVerse': powered_by.md
    - 'Developer Manuals': manuals.md
  - 'Science Tutorials':
    - tutorials/index.md
      #- 'Bioinformatics': bioinformatics_tutorials.md
      #- 'Geoinformatics': geoinformatics_tutorials.md
      #- 'Other Topics': other_tutorials.md
  - 'CyVerse Workshops':
    - workshops/index.md
    - 'Container Camp': workshops/container_camp.md
    - 'Foundational Open Science Skills': workshops/foss.md
  - 'Reference':
    - 'Glossary': glossary.md
    - 'FAQ': faq.md

# JavaScript for Intercom Widget
extra_javascript:
  - javascripts/intercom-learning.js

# Set theme to `readthedocs`
# must also set Action to use `@nomaterial` branch instead of `@master` for material
theme:
  name: material
# setting features for the navigation tab
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.indexes
    - navigation.top
    - toc.integrate
    - toc.follow
  # Default values, taken from mkdocs_theme.yml
  language: en
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode

    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: youtube 
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to system preference
  font:
    text: Roboto
    code: Regular
  favicon: assets/favicon.png
  icon:
    logo: material/rocket

# Options
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: G-6WMK2Y07YW

# Extensions
markdown_extensions:
  - admonition
  - abbr
  - attr_list
  - def_list
  - footnotes
  - meta
  - md_in_html
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.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.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

extra_css:
  - stylesheets/extra.css
 
plugins:
    - search
    - mkdocstrings
    - git-revision-date
    - mkdocs-jupyter:
          include_source: True
          ignore_h1_titles: True