rusty-dot/mkdocs.yml at main · Adamtaranto/rusty-dot · GitHub

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site_name: rusty-dot
site_description: Fast dot plot comparisons of DNA sequences using an FM-Index
site_url: https://adamtaranto.github.io/rusty-dot/
repo_url: https://github.com/Adamtaranto/rusty-dot
repo_name: Adamtaranto/rusty-dot

theme:
  name: material
  palette:
    - scheme: default
      primary: teal
      accent: teal
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: teal
      accent: teal
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.top
    - search.suggest
    - search.highlight
    - content.code.copy

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          options:
            docstring_style: numpy
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            show_category_heading: true
            members_order: source
  - mkdocs-jupyter:
      execute: false
      include_source: true

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - attr_list
  - md_in_html
  - tables
  - toc:
      permalink: true

nav:
  - Home: index.md
  - Installation: installation.md
  - Development Guide: development.md
  - Tutorials:
      - Quick Start: tutorials/quickstart.ipynb
      - Dotplot Visualization: tutorials/dotplot_tutorial.ipynb
      - PAF Workflow: tutorials/paf_workflow.ipynb
      - All-vs-All Between Two Indices: tutorials/all_vs_all_two_indices.ipynb
      - Minimap2 PAF Visualization: tutorials/minimap2_paf_tutorial.ipynb
  - API Reference:
      - Overview: api/index.md
      - SequenceIndex: api/sequence_index.md
      - DotPlotter: api/dotplot.md
      - CrossIndex: api/cross_index.md
      - PAF I/O: api/paf_io.md
      - Low-Level Functions: api/functions.md