mkdocs.yml

site_name: "SOPs template (cookiecutter)"
site_description: Templates and bootstrapping documentation for standard operating procedures (SOPs)
site_author: The NiPreps developers
site_url: https://www.nipreps.org/sops-cookiecutter/
google_analytics: ['UA-170131052-1', 'www.nipreps.org']

# Copyright
copyright: Copyright © 2023

nav:
    - Home: index.md
    - Change History: changes.md
    - Recruitment, Scheduling, and Screening:
      - Introduction: recruitment-scheduling-screening/index.md
      - Example 1: recruitment-scheduling-screening/example1.md
      - Example 2: recruitment-scheduling-screening/example2.md
    - Data collection: data-collection.md
    - Data storage: data-storage.md
    - After the session: post-session.md
    - Quality Assessment and Control: qa-qc.md
    - Preprocessing: preprocessing.md
    - Release of data: release.md
theme:
  name: material
  features:
    - tabs
    - content.code.copy
    - content.code.annotate
  icon:
    admonition:
      thanks: octicons/code-of-conduct-16
      quote: octicons/comment-16

plugins:
  - search
  - macros:
      include_dir: includes
      include_yaml:
        # - secrets: 'secrets/settings.yml'
        - settings: 'study-settings.yml'
      on_undefined: lax

markdown_extensions:
  - admonition
  - attr_list
  - footnotes
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - pymdownx.tabbed
  - pymdownx.tasklist:
      custom_checkbox: true
      clickable_checkbox: true
  - markdown_include.include:
      base_path: docs

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - js/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js