mkdocs.yml

site_name: UnCoVar Documention
site_url: https://ikim-essen.github.io/uncovar/
site_description: SARS-CoV-2 Variant Calling and Lineage Assignment.
site_author: Institute for Artificial Intelligence in Medicine, Medical Faculty of the University of Duisburg Essen and the University Hospital Essen

repo_url: https://github.com/IKIM-Essen/uncovar/
repo_name: ""

nav:
  - Overview: index.md
  - Installation: installation.md
  - The Report: user-guide.md
  - Advanced Configuration: configuration.md
  - Tools: tools.md
  - License: license.md

theme:
  name: material
  custom_dir: docs/.overrides
  logo: assets/UnCoVar_virus_white_no_shadow.png
  palette:
    - media: "(prefers-color-scheme: light)" # light theme
      scheme: default
      primary: teal
      accent: teal
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)" #   dark theme
      scheme: slate
      primary: teal
      accent: green
      toggle:
        icon: material/toggle-switch
        name: Switch to light mode
  icon:
    repo: fontawesome/brands/github
    logo: fontawesome/solid/virus
  favicon: assets/UnCoVar_favicon.png
  features:
    - navigation.instant
    # - navigation.tabs
    - navigation.indexes
    - navigation.tracking
    - navigation.expand
    - navigation.sections
    - navigation.top
    - toc.integrate
    - header.autohide

extra:
  version: 1.0
  provider: mike
  analytics:
    provider: google
    property: G-9R7WBBNN2S
  generator: false

plugins:
  - search

extra_css:
  - css/extra.css

markdown_extensions:
  # permalinks: https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/?h=perma#table-of-contents
  - toc:
      permalink: True
  # buttons: https://squidfunk.github.io/mkdocs-material/reference/buttons/
  - attr_list
  # codeblocks: https://squidfunk.github.io/mkdocs-material/reference/code-blocks/
  # pymdownx.highlight
  # pymdownx.inlinehilite
  # pymdownx.superfences
  # pymdownx.snippets
  # call-outs: https://squidfunk.github.io/mkdocs-material/reference/admonitions/
  - admonition
  # pymdownx.details
  # lists: https://squidfunk.github.io/mkdocs-material/reference/lists/
  - def_list
  # pymdownx.tasklist:
  #   custom_checkbox: true
  # tables: https://squidfunk.github.io/mkdocs-material/reference/tables/
  - tables
  - pymdownx.arithmatex:
      generic: true

extra_javascript:
  - javascripts/katex.js
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js

extra_css:
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css