mkdocs.yml

site_name: Vision Foundation Models for Computed Tomography

theme: 
  font:
    icon:
      repo: fontawesome/brands/github
    font:
      code: Roboto Mono  
  name: 'material'
  features:
    - content.code.copy
    - content.code.select
    - header.autohide
    - content.tooltips
    - attr_list
    - footnotes
    - navigation.tabs
    - navigation.footer
    - content.code.annotate    
  icon:
    annotation: material/star-four-points-circle

  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      toggle:
        icon: fontawesome/solid/circle-half-stroke
        name: Switch to light mode

    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default 
      toggle:
        icon: fontawesome/solid/lightbulb
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: fontawesome/solid/moon
        name: Switch to system preference


# Plugins
# Auto API reference generation: https://mkdocstrings.github.io/recipes/#automatic-code-reference-pages
plugins:
  - search
  - autorefs
  # - gen-files:
  #     scripts:
  #     - scripts/generate_api_reference_pages.py
  - literate-nav:
      nav_file: SUMMARY.md
  - section-index
  # - mkdocstrings:
  #     handlers:
  #       python:
  #         options:
  #           # Removed the default filter that excludes private members (that is, members whose names start with a single underscore).
  #           filters: null     
  #           show_source: true 
                
nav:
  - 'index.md'
  - 'Getting Started': 'getting-started/using_ctfm.md'
  - 'Replication Guide':
    - 'Installation': 'replication-guide/installation.md'
    - 'Data Download and Preprocessing': 'replication-guide/data.md'
    - 'Pre-training the FM': 'replication-guide/pretraining.md'
    - 'Adapt the FM to downstream tasks': 'replication-guide/downstream.md'
    - 'Baselines for downstream tasks': 'replication-guide/baselines.md'
    - 'Reproduce Analysis': 'replication-guide/analysis.md'
    # - 'Training baselines': 'replication-guide/reproduce_baselines.md'
  # - 'Tutorials': https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/tree/master/tutorials
  # - 'API Reference': 'reference/'

markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - attr_list
  - md_in_html
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg  

repo_url: https://github.com/project-lighter/CT-FM
repo_name: project-lighter/CT-FM
copyright: <a href="https://aim.hms.harvard.edu">AIM &copy; 2023</a>
extra:
  generator: false


extra_javascript:
  - assets/sh-annotation.js  

extra_css:
  - assets/extra.css