mkdocs.yml

site_name: dynamight
site_url: https://github.com/schwabjohannes/dynamight
site_author: Johannes Schwab
site_description: >-
  Documentation for dynamight, a tool for estimating dynamics from cryo-EM images
  which *might* improve your map. The tools main application area is flexible proteins, which are compositionally homogeneous.
  The workflow consists of following four steps:
  *Estimating the deformations present in the dataset*
  *Exploring latent space to see if the results are useful*
  *Computing the inverse deformations per particle*
  *Reconstruct a map using the inverse deformations, which might be better*
# Repository
repo_name: schwabjohannes/dynamight
repo_url: https://github.com/schwabjohannes/dynamight

# Copyright
copyright: Copyright © 2022 - 2022 Johannes Schwab

theme:
  icon:
    logo: material/home-circle
  name: material
  palette:
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/toggle-switch
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: blue grey
      accent: blue grey
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to light mode
  features:
    - navigation.instant
    #- navigation.tabs
    #- navigation.top
    #- navigation.tracking
    - search.highlight
    - search.suggest
    # - toc.follow
    # - content.code.annotate
    - content.tabs.link

markdown_extensions:
  - admonition
  - tables
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - attr_list
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - md_in_html
  - pymdownx.arithmatex:
      generic: true


extra:
  analytics:
    feedback:
      title: Was this page helpful?
      ratings:
        - icon: material/emoticon-happy-outline
          name: This page was helpful
          data: 1
          note: >-
            Thanks for your feedback!
        - icon: material/emoticon-sad-outline
          name: This page could be improved
          data: 0
          note: >- 
            Thanks for your feedback! Help us improve this page by
            using our <a href="..." target="_blank" rel="noopener">feedback form</a>.
nav:
  - Introduction: index.md


plugins:
  - search


extra_css:
  - stylesheets/extra.css
  - gallery/stylesheets/extra.css