mkdocs.yml

site_name: Shiba
site_description: Shiba documentation
site_author: Naoto Kubota
site_url: https://naotokubota/shiba
copyright: © 2024 Naoto Kubota
repo_url: https://github.com/NaotoKubota/Shiba
repo_name: NaotoKubota/Shiba

theme:
  name: material
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  font:
    text: Roboto
  language: en
  features:
    - search.suggest
    - search.highlight
    - navigation.instant
    - navigation.instant.progress
    - navigation.instant.prefetch
    - navigation.tracking
    - navigation.footer
    - content.code.copy
    - content.code.select
    - content.code.annotate

markdown_extensions:
  - toc:
      permalink: true
  - admonition
  - codehilite
  - extra
  - pymdownx.highlight:
      linenums: true
      linenums_style: pymdownx.inline
  - pymdownx.inlinehilite
  - pymdownx.superfences
  - pymdownx.betterem:
      smart_enable: all
  - attr_list
  - md_in_html

extra:
  # consent:
  #   title: Cookie consent
  #   description: >-
  #     We use cookies to recognize your repeated visits and preferences, as well
  #     as to measure the effectiveness of our documentation and whether users
  #     find what they're searching for. With your consent, you're helping us to
  #     make our documentation better.
  social:
    - type: "github"
      icon: fontawesome/brands/github
      link: "https://github.com/NaotoKubota"
    - type: "docker"
      icon: fontawesome/brands/docker
      link: "https://hub.docker.com/u/naotokubota"
    - type: "twitter"
      icon: fontawesome/brands/x-twitter
      link: "https://twitter.com/naoto_kubota"

edit_uri: edit/main/docs/

nav:
- Home: index.md
- Installation: installation.md
- Quick start:
  - With bulk RNA-seq data: quickstart/diff_splicing_bulk.md
  - With single-cell RNA-seq data: quickstart/diff_splicing_sc.md
- Output:
  - Shiba/SnakeShiba: output/shiba.md
  - scShiba/SnakeScShiba: output/scshiba.md
- Usage:
  - Shiba: usage/shiba.md
  - scShiba: usage/scshiba.md
  - SnakeShiba: usage/snakeshiba.md
  - SnakeScShiba: usage/snakescshiba.md