mkdocs.yml

site_name: Metagenomics @ 2024 PIG-PARADIGM annual meeting
repo_url: https://github.com/ngs-docs/2024-pig-paradigm-workshop
copyright: Copyright © 2023-2024 Titus Brown and Anneliek ter Horst

nav:
  - Introduction:
    - index.md
  - Tutorials:
    - single-metagenomes-taxonomy.md
    - comparing-metagenomes.md
    - amr.md

markdown_extensions:
  - toc:
      permalink: true
  - def_list
  - attr_list
  - admonition
  - md_in_html
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true

plugins:
  - search
  - git-revision-date-localized:
      enable_creation_date: true

extra_css:
  - stylesheets/extra.css
extra_javascript:
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
#  - javascripts/mathjax.js

theme:
  name: material
  features:
    - content.code.annotate
    #- navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.indexes
    - navigation.top
    - navigation.footer
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
  logo: assets/ucdavis_logo_gold.png
  icon:
    repo: fontawesome/brands/github
  palette: 

    # Palette toggle for light mode
    - scheme: ucdavis
      toggle:
        icon: material/brightness-7 
        name: Switch to dark mode

    # Palette toggle for dark mode
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode