mkdocs.yml

site_name: Foundation Model for Cancer Imaging Biomarkers
theme: 
  font:
    code: Roboto Mono
  name: 'material'
  favicon: 'assets/favicon.svg'
  logo: 'assets/favicon.svg'
  features:
    - content.code.copy
    - content.code.select
    - header.autohide
    - content.tooltips
    - attr_list
    - footnotes
    - navigation.tabs
    - navigation.footer

  palette:
    - scheme: slate
      accent: blue
extra_css:
  - assets/extra.css


# 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:
          docstring_style: google
          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': 
    - 'Installation': 'getting-started/installation.md'
    - 'Cloud Quick Start': 'getting-started/cloud-quick-start.md'
    - 'Quick Start': 'getting-started/quick-start.md'
  - 'Replication Guide':
    - 'Data Download and Preprocessing': 'replication-guide/data.md'
    - 'Pre-training the FM': 'replication-guide/reproduce_fm.md'
    - 'Adapt the FM to downstream tasks': 'replication-guide/fm_adaptation.md'
    - 'Baselines for downstream tasks': 'replication-guide/baselines.md'
    - 'Extracting Features & Predictions': 'replication-guide/inference.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

repo_url: https://github.com/AIM-Harvard/foundation-cancer-image-biomarker
repo_name: AIM-Harvard/foundation-cancer-image-biomarker
copyright: <a href="https://aim.hms.harvard.edu">AIM &copy; 2023</a>
extra:
  generator: false