mkdocs_en.yml

site_name: "C-Phasing"
site_url: https://wangyibin.github.io/CPhasing
repo_url: https://github.com/wangyibin/CPhasing
docs_dir: "docs/en"
edit_uri: edit/main/docs/
site_dir: "site/"
copyright: Copyright © 2022-2026 Tanger-lab, All rights reserved.
theme:
  name: material
  language: en
  custom_dir: docs/overrides/
  highlight: monokai
  favicon: https://raw.githubusercontent.com/wangyibin/CPhasing/main/docs/logo/logo.png
  logo: https://raw.githubusercontent.com/wangyibin/CPhasing/main/docs/logo/logo.png
  # font:
    # text: Red Hat Text
    # code: JetBrains Mono
    

  # palette:
  #   - media: "(prefers-color-scheme)"
  #     toggle:
  #       icon: material/brightness-auto
  #       name: Switch to light mode

  #   - media: "(prefers-color-scheme: light)"
  #     scheme: default
  #     primary: prefix-light
  #     accent: prefix-light
  #     toggle:
  #       icon: material/brightness-7
  #       name: Switch to dark mode

  #   - media: "(prefers-color-scheme: dark)"
  #     scheme: slate
  #     primary: prefix
  #     accent: prefix
  #     toggle:
  #       icon: material/brightness-4
  #       name: Switch to system preference
  # icon:
  #   edit: material/pencil
  #   view: material/eye
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: lucide/sun-moon
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: lucide/sun
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: orange
      toggle:
        icon: lucide/moon-star
        name: Switch to system preference
  icon:
    tag:
      default: lucide/hash


  features:
    - content.tabs.link
    - content.code.copy
    - content.code.select
    - content.code.annotate
    - content.action.view
    - content.action.source
    - content.code.annotate
    - content.tooltips 
    - navigation.instant
    - navigation.instant.progress
    - navigation.tracking
    - navigation.sections
    - navigation.prune
    - navigation.top
    - navigation.indexes
    - navigation.footer
    - navigation.tabs
    - navigation.version
    - toc.follow
    - search.share
    - search.highlight
    - search.suggest
    
markdown_extensions:
  - admonition
  - attr_list
  - tables
  - def_list
  - footnotes
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.critic
  - pymdownx.caret
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.inlinehilite
  - pymdownx.snippets:
      base_path: ./
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.tabbed:
      alternate_style: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - toc:
      toc_depth: 3
      permalink: true
  - mdx_truly_sane_lists
  - md_in_html

extra_css:
  - stylesheets/style.css
  # - https://unpkg.com/@algolia/sitesearch@latest/dist/search.min.css

extra_javascript:
  - javascript/extra.js
  # - https://unpkg.com/@algolia/sitesearch@latest/dist/search.min.js

extra:
  homepage: https://wangyibin.github.io/CPhasing
  analytics:
    provider: google
    property: G-CXCGTKN4NV
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/wangyibin
  version:
    provider: mike
  alternate:
    - name: English
      link: /CPhasing/
      lang: en
    - name: 简体中文
      link: /CPhasing/zh/
      lang: zh


plugins:
  - search
    # provider: algolia
    # algolia:
    #   app_id: 7I79MLDJV5
    #   api_key: bcdf8edc298cf3794b14bc7d5d788fe5
    #   index_name: wangyibin_github_io_7i79mldjv5_pages
  # - ultralytics:
  #     add_desc: False
  #     add_image: True
  #     add_authors: True
  #     add_json_ld: True
  #     add_share_buttons: True
  #     add_css: False



nav:
  - Home: index.md
  - Installation: installation.md
  - Get Started: basic_usage.md
  - Tutorials: 
    - Pore-C&HiFi-C:
      - tutorials/porec/porec_monoploid.md
      - tutorials/porec/porec_decaploid.md
      - tutorials/porec/porec_sugarcane.md
    - Hi-C:
      - tutorials/hic/hic_monoploid.md
      - tutorials/hic/hic_decaploid.md
      - tutorials/hic/hic_sugarcane.md

  - CLI: 
    - CLI/mapper.md
    - CLI/methalign.md
    - CLI/hic_mapper.md
    - CLI/prepartition.md
    - CLI/alleles.md
    - CLI/collapse.md
    - CLI/rename.md
    - CLI/plot.md
  
  - Citation: citation.md
  - Misc:
    - FAQ: faq.md
    - Changelog: CHANGES.md