TIRmite/mkdocs.yml at main · Adamtaranto/TIRmite · GitHub

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site_name: TIRmite
site_description: Map profile HMMs of transposon termini to genomic sequences for annotation of cryptic transposon variants.
site_author: Adam Taranto
site_url: https://adamtaranto.github.io/TIRmite

repo_name: adamtaranto/TIRmite
repo_url: https://github.com/Adamtaranto/TIRmite
edit_uri: edit/main/docs/

theme:
  name: material
  logo: tirmite_hexlogo.jpg
  favicon: tirmite_hexlogo.jpg
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: teal
      accent: cyan
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: teal
      accent: cyan
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.top
    - navigation.expand
    - search.highlight
    - search.share
    - content.code.copy
    - content.action.edit

plugins:
  - search

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - attr_list
  - md_in_html
  - toc:
      permalink: true

extra_javascript:
  - https://unpkg.com/mermaid@10/dist/mermaid.min.js

nav:
  - Home: index.md
  - Tutorials:
      - Building HMMs for Transposon Termini: tutorials/building-hmms.md
      - Using tirmite search: tutorials/tirmite-search.md
      - Using tirmite pair: tutorials/tirmite-pair.md
      - Reconstructing and Validating Target Sites: tutorials/tirmite-validate.md

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/Adamtaranto/TIRmite