mkdocs.yml

# Project information
site_name: RBrowser Documentation
site_url: https://www.rbrowser.org
site_author: Lei Zheng
site_description: RBrowser Documentation
docs_dir: docs
site_dir: site
# Repository
repo_name: typekey/rbrowser-doc
repo_url: https://github.com/typekey/rbrowser-doc
edit_uri: tree/main/docs

# Copyright
copyright: Copyright &copy; 2025 RBrowser. Developed by <a href="https://ziptop.top/" target="_blank" rel="noopener">Lei Zheng</a>.<br>The website content is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA 4.0</a>

# Configuration
theme:
  name: material
  custom_dir: overrides
  language: en
  features:
    # - announce.dismiss
    - content.action.edit
    # - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tabs.link
    - content.tooltips
    # - header.autohide
    - navigation.expand
    - navigation.indexes
    # - navigation.instant
    # - navigation.prune
    # - navigation.sections
    # - navigation.tabs
    # - navigation.tabs.sticky
    - navigation.top
    - navigation.footer
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    # - toc.integrate
  palette:
    - scheme: default
      primary: white
      accent: teal
      toggle:
        icon: material/theme-light-dark
        name: Dark mode
    - scheme: slate
      primary: black
      accent: teal
      toggle:
        icon: material/theme-light-dark
        name: Light mode
  font:
    text: Roboto
    code: Roboto Mono
  favicon: assets/images/favicon.png
  logo: assets/images/logo.png
  icon:
    logo: logo
    repo: fontawesome/brands/github
    edit: fontawesome/regular/pen-to-square

  social:
    - icon: fontawesome/brands/github
      link: https://github.com/typekey

  generator: false
  status:
    new: Recently Added

# Plugins
plugins:
  - search
  - glightbox:
      touchNavigation: true
      loop: false
      effect: zoom
      slide_effect: none
      width: 100%
      height: auto
      zoomable: true
      draggable: false
      auto_caption: false
      caption_position: bottom

# Extensions
markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - 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
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.keys
  # - pymdownx.magiclink:
  #     repo_url_shorthand: true
  #     user: squidfunk
  #     repo: mkdocs-material
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

extra_javascript:
  - javascripts/mathjax.js
  - https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-chtml.min.js
  # - javascripts/katex.js
  # - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
  # - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js

extra_css:
  - stylesheets/extra.css
  # - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css

# Page tree
nav:
  - Overview:
      - 1_before_starting/index.md
  - Quick Start:
      # [icon: material/book-open-outline]
      - 2_quick_start/index.md
      - 1.1 User interface: 2_quick_start/1_user_interface.md
      - 1.2 RBrowser Main Viewer: 2_quick_start/2_main_viewer.md
      - 1.3 Channel and Track: 2_quick_start/3_channel_and_track.md
      - 1.4 Coordinate System: 2_quick_start/4_coordinate.md
      - 1.5 Selection Region: 2_quick_start/5_region.md
      - 1.6 RBrowser GPT: 2_quick_start/6_rbrowser_gpt.md
      - 1.7 RBrowser Renderer: 2_quick_start/7_config_grammar.md
  - DataHub:
      - 4_datahub/index.md
      - 2.1 DataHub Overview: 4_datahub/1_datahub_overview.md
      - 2.2 DataHub API: 4_datahub/2_datahub_api.md
  - Plugins:
      - 3_plugins/index.md
      - 3.1 Plugin Overview: 3_plugins/1_plugin_overview.md
      - 3.2 RNA Modification: 3_plugins/2_rna_modification_atlas.md
      - 3.3 RNA Interaction: 3_plugins/3_rna_interaction.md
      - 3.4 RNA Sequence: 3_plugins/4_rna_sequence.md
      - 3.5 RNA 2D Structure: 3_plugins/5_rna_2d_structure.md
      - 3.6 RNA 3D Structure: 3_plugins/6_rna_3d_structure.md
      - 3.7 RNA and Chromatin: 3_plugins/7_rna_chromtin.md
      - 3.8 Localization: 3_plugins/8_localization.md
      - 3.9 ASO Design: 3_plugins/9_aso_design.md
      - 3.10 Plugin Config: 3_plugins/0_plugin_config.md

  - Error Ref:
      - 0_error_message_reference/index.md

  - Contact:
      - 5_contact/index.md