mkdocs.yml

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

site_name: Open Science Collective
site_url: https://docs.osc.earth
site_author: Open Science Collective
site_description: >-
  Documentation for the Open Science Collective (OSC) and its projects,
  including the Open Science Assistant (OSA).

repo_name: OpenScience-Collective
repo_url: https://github.com/OpenScience-Collective

copyright: Copyright © 2026 Open Science Collective

theme:
  name: material
  custom_dir: overrides
  favicon: assets/logo.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:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: deep purple
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: deep purple
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  font:
    text: Inter
    code: JetBrains Mono

plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true
  - section-index
  # API Reference Generation
  # --------------------------
  # These plugins auto-generate API documentation from OSA source code.
  # They are disabled by default because they require OSA dependencies.
  #
  # To enable:
  # 1. Install OSA dependencies: cd osa && uv sync
  # 2. Uncomment the plugins below
  # 3. Run: uv run mkdocs build
  #
  # - mkdocstrings:
  #     default_handler: python
  #     handlers:
  #       python:
  #         paths:
  #           - osa/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:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
  - 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:
  homepage: https://osc.earth
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/OpenScience-Collective
    - icon: fontawesome/brands/discord
      link: https://discord.gg/5dWJCUmUww

extra_javascript:
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

nav:
  - Home: index.md
  - Collective:
      - collective/index.md
      - About: collective/about.md
      - Mission: collective/mission.md
      - Contributing: collective/contributing.md
  - OSA:
      - osa/index.md
      - Getting Started: osa/getting-started.md
      - Architecture:
          - Overview: osa/architecture.md
          - Details: osa/architecture-details.md
      - Community Registry:
          - osa/registry/index.md
          - Adding a Community: osa/registry/quick-start.md
          - Local Testing: osa/registry/local-testing.md
          - Schema Reference: osa/registry/schema-reference.md
          - Extensions: osa/registry/extensions.md
      - CLI Reference: osa/cli-reference.md
      - API Reference: osa/api-reference.md
      - Database Mirrors: osa/mirrors.md
      - Knowledge Sync: osa/knowledge-sync.md
      - Sync Status: osa/status.md
      - Deployment:
          - Widget: osa/deployment/widget.md
      - Troubleshooting: osa/troubleshooting.md
      - Tools:
          - osa/tools/index.md
          - HED Tools: osa/tools/hed.md
          - BIDS Tools: osa/tools/bids.md
          - EEGLAB Tools: osa/tools/eeglab.md
          - MNE-Python Tools: osa/tools/mne.md
          - NEMAR Tools: osa/tools/nemar.md
      - Presentations:
          - osa/presentations/index.md
          - UC Open 2026: osa/presentations/uc-open-2026.md
          - OSA Platform Overview: osa/presentations/osa-platform.md
      - Development: osa/development.md
      - Version Management: osa/version-management.md