mkdocs.yml

# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json

site_name: Annotation Garden Documentation
site_url: https://docs.annotation.garden
site_author: Annotation Garden Initiative
site_description: >-
  Documentation for the Annotation Garden Initiative (AGI) - an open infrastructure
  for collaborative annotation of neuroscience stimuli.

repo_name: Annotation-Garden
repo_url: https://github.com/Annotation-Garden

copyright: Copyright © 2024-2025 Annotation Garden Initiative

theme:
  name: material
  custom_dir: overrides
  favicon: assets/favicon.png
  logo: assets/logo.png
  icon:
    repo: fontawesome/brands/github

  features:
    - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tabs.link
    - navigation.footer
    - navigation.indexes
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.sections
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow

  palette:
    # Light mode - using AGI colors
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  font:
    text: Inter
    code: JetBrains Mono

extra_css:
  - stylesheets/extra.css

plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true
  - section-index
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths:
            - hedit
            - image-annotation/src
          options:
            docstring_style: google
            show_source: true
            show_bases: true
            show_root_heading: true
            members_order: source
  - gen-files:
      scripts:
        - scripts/gen_ref_pages.py
  - literate-nav:
      nav_file: SUMMARY.md

markdown_extensions:
  # Python Markdown extensions
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true

  # PyMdown extensions
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink
  - 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

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/Annotation-Garden
    - icon: material/web
      link: https://annotation.garden

  # Version provider for mike
  version:
    provider: mike

nav:
  - Home: index.md
  - Getting Started:
    - getting-started/index.md
    - Installation: getting-started/installation.md
    - Quick Start: getting-started/quickstart.md
  - Projects:
    - projects/index.md
    - HEDit:
      - projects/hedit/index.md
      - CLI Reference: projects/hedit/cli-reference.md
      - API Reference: projects/hedit/api-reference.md
      - Python API: projects/hedit/python-api.md
      - Telemetry: projects/hedit/telemetry.md
      - Presentations:
        - projects/hedit/presentations/index.md
        - Annotate Those Steps: projects/hedit/presentations/annotate-those-steps.md
    - Image Annotation:
      - projects/image-annotation/index.md
      - API Reference: projects/image-annotation/api-reference.md
  - Standards:
    - standards/index.md
    - HED Guidelines: standards/hed-guidelines.md
    - BIDS Integration: standards/bids-integration.md
    - Annotation Format: standards/annotation-format.md
  - Contributing:
    - contributing/index.md
    - Development Setup: contributing/development-setup.md
    - Code Style: contributing/code-style.md