mkdocs.yml

# Project information
site_name: TF2.2_OSIPI-ASL-toolbox
site_url: https://osipi.github.io/TF2.2_OSIPI-ASL-toolbox/
site_author: OSIPI
site_description: >-
  OSIPI aims to develop resources and best practices for the analysis of perfusion imaging data and interoperability of the analysis results.

# Repository
repo_name: OSIPI/TF2.2_OSIPI-ASL-toolbox
repo_url: https://github.com/OSIPI/TF2.2_OSIPI-ASL-toolbox

# Copyright
copyright: Copyright © 2025 OSIPI

# Configuration
theme:
  name: material
  logo: assets/osipiImgs/OSIPI_logo.png
  favicon: assets/osipiImgs/OSIPI_logo_only_square.png

  features:
    - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tooltips
    - navigation.footer
    - navigation.indexes
    - navigation.tabs
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/link
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/toggle-switch
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: indigo
      toggle:
        icon: material/toggle-switch-off
        name: Switch to system preference
  font:
    text: Roboto
    code: Roboto Mono

plugins:
  - search:
      separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true

# Additional configuration
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/OSIPI
    - icon: fontawesome/brands/slack
      link: https://app.slack.com/client/TFGVCE9HS

extra_css:
    - assets/stylesheets/extra.css

# Extensions
markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
      emoji_index: !!python/name:material.extensions.emoji.twemoji
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink:
      normalize_issue_symbols: true
      repo_url_shorthand: true
      user: squidfunk
      repo: mkdocs-material
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      auto_append:
        - includes/mkdocs.md
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
      combine_header_slug: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

not_in_nav: |
  /tutorials/**/*.md

# Page tree
nav:
  - 'Home': 'index.md'
  - 'Motion Correction': 'motion_correction.md'
  - 'Brain Extraction': 'brain_extraction.md'
  - 'Segmentation': 'segmentation.md'
  - 'Co-registration': 'co_registration.md'
  - 'CBF Quantification': 'cbf_quantification.md'
  - 'Outlier Removal / Denoising': 'denoising.md'
  - 'Normalization': 'normalization.md'
  - 'Deep Learning Denoising': 'deep_learning.md'
  - 'ROI Creation': 'roi_creation.md'
  - 'Smoothing': 'smoothing.md'
  - 'Additional Functions': 'additional_tools.md'