mkdocs.yml

site_name: MetaLens Documentation
site_description: Documentation for MetaLens - Super-Resolved Spatial Metabolomics
repo_url: https://github.com/LRpz/metalens
docs_dir: docs
theme:
  name: material
  features:
    - navigation.sections
    - navigation.top
    - search.highlight
    - navigation.indexes
    - toc.follow
    - toc.integrate
  palette:
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
  font:
    text: Roboto
    code: Roboto Mono
  icon:
    repo: fontawesome/brands/github

nav:
  - Overview: index.md
  - Installation:
      - Prerequisites: '#11-prerequisites'
      - Step-by-Step Installation: '#12-step-by-step-installation'
  - Using MetaLens:
      - On Example Data: '#21-on-example-data'
      - On New Data: '#22-on-new-data'
      - Required Data Format: '#221-required-data-format'
      - Preprocessing Pipeline: '#222-preprocessing-pipeline'
      - Training: '#223-training'
      - Inference: '#224-inference'
  - Complete Pipeline Example: '#23-complete-pipeline-example'
  - Directory Structure: '#24-expected-directory-structure'

markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      use_pygments: false
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences:
      preserve_tabs: true
      css_class: 'highlight'
  - admonition
  - pymdownx.details
  - attr_list
  - md_in_html
  - def_list
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg

extra_css:
  - stylesheets/extra.css