mkdocs.yml

site_name: noelTexturesPy - The Textures Pipeline for Focal Cortical Dysplasias
site_url: https://noel-mni.github.io/noelTexturesPy/
site_author: Ravnoor Gill
site_description: >-
  Write your documentation in Markdown and create a professional static site in
  minutes – searchable, customizable, for all devices

# Repository
repo_name: NOEL-MNI/noelTexturesPy
repo_url: https://github.com/NOEL-MNI/noelTexturesPy

# Copyright
copyright: Copyright © 2023 Neuroimaging of Epilepsy Laboratory

# Configuration
theme:
  name: material
  features:
    # - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    # - content.tabs.link
    - content.tooltips
    # - header.autohide
    # - navigation.expand
    - navigation.footer
    - navigation.indexes
    # - navigation.instant
    # - navigation.prune
    - navigation.sections
    - navigation.tabs
    # - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    # - toc.integrate
  palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  font:
    text: Fira Sans
    code: Fira Code
  favicon: assets/favicon.png
  icon:
    logo: logo

# Plugins
plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true
      
# Customization
extra:
  annotate:
    json: [.s2]
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/NOEL-MNI
    - icon: fontawesome/brands/docker
      link: https://hub.docker.com/repository/docker/noelmni/pynoel-gui-app

# 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:materialx.emoji.to_svg
      emoji_index: !!python/name:materialx.emoji.twemoji
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink:
      repo_url_shorthand: true
      user: squidfunk
      repo: mkdocs-material
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Page tree
nav:
  - Home: index.md
  - About: about.md
  - Getting started:
    - Installation:
      - Installation: install/index.md
      - Install Docker: install/docker.md
      - Install noelTexturesPy: install/noeltexturespy.md
  - Processing & Quality Check: processing-qc.md
  - MRI visualization:
    - Using register: visualize/register.md
    - Using ITK-SNAP: visualize/itk-snap.md
  - Examples: case-presentations.md