mkdocs.yml

site_name: tbp-parser
site_author: Sage Wright
site_description: A TBProfiler output parser
site_url: https://theiagen.github.io/tbp-parser/

repo_url: https://github.com/theiagen/tbp-parser

theme: 
  name: material
  logo: assets/Theiagen-Logo-White.png
  favicon: assets/Theiagen-Symbol-Standard-01.png
  custom_dir: docs/overrides
  features:
    - content.code.annotate
    - content.code.copy
    - content.tabs.link
    - content.tooltips
    - navigation.instant
    - navigation.path
    - navigation.tabs
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.suggest
    - toc.follow
    - toc.integrate
  language: en
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: light 
      toggle:
        icon: material/weather-night
        name: Switch to Dark Mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      accent: indigo
      primary: black
      toggle:
        icon: material/white-balance-sunny
        name: Switch to Light Mode

nav:
  - Home: index.md
  - Getting Started: usage.md
  - Inputs: 
      - inputs/inputs.md
      - TheiaProk Inputs on Terra: inputs/theiaprok.md
  - Outputs:
      - outputs/index.md
      - Laboratorian report: outputs/laboratorian.md
      - LIMS report: outputs/lims.md
      - Looker report: outputs/looker.md
      - Coverage report: outputs/coverage.md
      - TheiaProk Outputs on Terra: outputs/theiaprok.md
  - Versioning: 
     - versioning/index.md
     - Brief Description of Versions: versioning/brief.md
     - Exhaustive List of Versions: versioning/exhaustive.md
  - Algorithm:
      - algorithm/index.md
      - Technical Code Breakdown: algorithm/technical.md
      - Interpretation Document: algorithm/interpretation.md

markdown_extensions: 
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.caret
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tasklist:
      custom_checkbox: true
  - toc:
      permalink: true

plugins:
  - git-revision-date-localized:
      enable_creation_date: true
      type: iso_date
  - search
  - glightbox
  - mike

extra_javascript:
  - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
  - javascripts/tablesort.js

extra_css:
  - stylesheets/extra.css        

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/theiagen
    - icon: fontawesome/brands/twitter
      link: https://twitter.com/theiagen
    - icon: fontawesome/brands/linkedin
      link: https://www.linkedin.com/company/theiagen
  version:
    provider: mike
    default: latest
    alias: true

copyright: |
  &copy; 2023-2024 <a href="https://www.theiagen.com" target="_blank" rel="noopener">Theiagen Genomics</a>