MetaboT/mkdocs.yml at main · HolobiomicsLab/MetaboT · GitHub

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# Project information
site_name: 🧪 MetaboT 🍵 Documentation
site_description: Documentation for MetaboT, an LLM-based multi-agent framework for interactive analysis of mass spectrometry metabolomics knowledge graphs
site_author: HolobiomicsLab
site_url: https://holobiomicslab.github.io/MetaboT
docs_dir: docs

# Repository
repo_name: HolobiomicsLab/MetaboT
repo_url: https://github.com/HolobiomicsLab/MetaboT
edit_uri: edit/main/docs/

# Copyright
copyright: Copyright &copy; 2025 Holobiomics Lab

# Configuration
theme:
  name: material
  custom_dir: overrides
  collapse_navigation: false
  language: en
  icon:
    logo: material/book
    repo: fontawesome/brands/github

  # Color schemes
  palette:
    # Light mode (CNRS Colors)
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: "#00284b"  # ✅ CNRS Blue
      accent: "#ffeb6e"   # ✅ CNRS Yellow
      toggle:
        icon: material/brightness-4
        name: Switch to dark mode

    # Dark mode (CNRS Colors)
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: "#1c2c3a"  # Lighter dark blue for better contrast
      accent: "#8296a5"   # Softer accent color for better readability
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  # Theme features
  features:
    # Navigation
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.indexes
    - navigation.sections
    - navigation.expand
    - navigation.top
    - navigation.footer
    - content.action.view
    - toc.integrate

    # Search
    - search.suggest
    - search.highlight
    - search.share

    # Content
    - content.code.copy
    - content.code.annotate
    - content.tabs.link
    - content.tooltips
    - content.admonitions
    - content.tabs
    - content.action.edit

    # Header
    - header.autohide


# Plugins
plugins:
  - search:
      lang: en
      separator: '[\s\-]+'

  # Python API documentation
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [app]
          options:
            show_source: true
            show_root_heading: true
            show_category_heading: true
            show_submodules: true
            docstring_style: google
            docstring_section_style: table
            show_signature: true
            show_signature_annotations: true
            separate_signature: true

# Extensions
markdown_extensions:
  # Python Markdown
  - abbr
  - admonition
  - codehilite
  - def_list
  - footnotes
  - meta
  - md_in_html
  - tables
  - toc:
      permalink: true
      toc_depth: 3

  # Python Markdown Extensions
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - attr_list
  - 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.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      check_paths: true
  - 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
  - footnotes

# Extra styling and scripts
extra_css:
  - assets/stylesheets/extra.css
extra_javascript:
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
  - assets/javascripts/navigation.js
  - assets/javascripts/parallax.js

# Navigation structure
nav:
  - Home: index.md
  - Getting Started:
    - Installation: getting-started/installation.md
    - Quick Start: getting-started/quickstart.md
  - User Guide:
    - Overview: user-guide/overview.md
    - Configuration: user-guide/configuration.md
  - API Reference:
    - Core: api-reference/core.md
    - Agents: api-reference/agents.md
    - Graph Management: api-reference/graph-management.md
  - Examples:
    - Basic Usage: examples/basic-usage.md
    - LangSmith Evaluation: examples/langsmith-evaluation.md

  - Contributing: contributing.md

# Additional settings
extra:
  # Social links
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/holobiomicslab
      name: HolobiomicsLab on GitHub
    - icon: fontawesome/brands/twitter
      link: https://twitter.com/HolobiomicLab
      name: HolobiomicsLab on Twitter
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/@holobiomicslab
      name: HolobiomicsLab on YouTube
    - icon: material/web
      link: https://holobiomicslab.eu
      name: HolobiomicsLab Website

  # Analytics
  analytics:
    provider: google
    property: !ENV GOOGLE_ANALYTICS_KEY