macrolactone-toolkit/mkdocs.yml

site_name: Macrolactone Fragmenter
site_description: A comprehensive tool for analyzing and fragmenting macrolactone (12-20 membered ring) side chains
site_author: Macro Split Team
site_url: https://yourusername.github.io/macro_split/

# Repository
repo_name: yourusername/macro_split
repo_url: https://github.com/yourusername/macro_split
edit_uri: edit/main/docs/

# Copyright
copyright: Copyright © 2025 Macro Split Team

# Configuration
theme:
  name: material
  language: zh
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.expand
    - navigation.indexes
    - navigation.top
    - search.suggest
    - search.highlight
    - search.share
    - toc.follow
    - content.code.copy
    - content.code.annotate
  
  icon:
    repo: fontawesome/brands/github
    edit: material/pencil
    view: material/eye

# Extensions
markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - toc:
      permalink: true
      toc_depth: 3
  - 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.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

# Plugins
plugins:
  - search:
      lang:
        - zh
        - en
  - mkdocstrings:
      enabled: true
      default_handler: python
      handlers:
        python:
          options:
            docstring_style: google
            docstring_section_style: table
            show_root_heading: true
            show_root_toc_entry: true
            show_source: true
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            members_order: source
            heading_level: 2
            show_if_no_docstring: false

# Extra CSS and JavaScript
extra_css:
  - stylesheets/extra.css

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

# Page tree
nav:
  - 首页:
    - index.md
    - 快速开始: getting-started.md
    - 安装指南: installation.md

  - 用户指南:
    - user-guide/index.md
    - MacrolactoneFragmenter 使用: user-guide/fragmenter-usage.md
    - 环编号系统: user-guide/ring-numbering.md
    - 可视化功能: user-guide/visualization.md
    - 批量处理: user-guide/batch-processing.md
    - 数据导出: user-guide/data-export.md

  - 教程与示例:
    - tutorials/index.md
    - 基础教程: tutorials/basic-tutorial.md
    - 环数识别教程: tutorials/using-macro-lactone-analyzer.md
    - 高级用法: tutorials/advanced-usage.md
    - 使用案例: tutorials/use-cases.md

  - API 参考:
    - api/index.md
    - MacroLactoneAnalyzer: api/macro-lactone-analyzer.md
    - MacrolactoneFragmenter: api/macrolactone-fragmenter.md
    - Fragment 数据类: api/fragment-dataclass.md
    - 环编号模块: api/ring-numbering.md
    - 可视化模块: api/ring-visualization.md
    - 工具函数: api/utilities.md

  - 开发者指南:
    - development/index.md
    - 贡献指南: development/contributing.md
    - 项目结构: development/project-structure.md
    - 测试: development/testing.md

  - 项目文档:
    - project-docs/AGENTS.md
    - 实现总结: project-docs/IMPLEMENTATION_SUMMARY.md
    - 清理总结: project-docs/CLEANUP_SUMMARY.md
    - 文档指南: project-docs/DOCUMENTATION_GUIDE.md
    - 快速命令: project-docs/QUICK_COMMANDS.md

  - 关于:
    - about/index.md
    - 更新日志: about/changelog.md
    - 许可证: about/license.md

# Extra
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/yourusername/macro_split
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/macrolactone-fragmenter/
  
  version:
    provider: mike
    default: latest
  
  analytics:
    feedback:
      title: Was this page helpful?
      ratings:
        - icon: material/emoticon-happy-outline
          name: This page was helpful
          data: 1
          note: >-
            Thanks for your feedback!
        - icon: material/emoticon-sad-outline
          name: This page could be improved
          data: 0
          note: >- 
            Thanks for your feedback! Help us improve this page by
            creating an issue.