mkdocs.yml

site_name: Dorado Documentation
site_url: !ENV READTHEDOCS_CANONICAL_URL

# Adds the Github Link at top right
repo_url: https://github.com/nanoporetech/dorado/
repo_name: Dorado

nav:
  - index.md
  - Basecaller:
      - Introduction: basecaller/basecall_overview.md
      - Simplex: basecaller/simplex.md
      - Duplex: basecaller/duplex.md
      - Modifications: basecaller/mods.md
      - Barcoding:
          - Barcode Classification: barcoding/barcoding.md
          - Custom Barcodes: barcoding/custom_barcodes.md
          - Custom Primers: barcoding/custom_primers.md
          - Sample Sheet: barcoding/sample_sheet.md
      - Alignment: basecaller/alignment.md
      - Read Trimming: basecaller/read_trimming.md
      - Poly(A) Estimation: basecaller/polya_estimation.md
      - Details:
          - Read Splitting: basecaller/read_splitting.md
          - Moves Table: basecaller/move_table.md
          - Q-score: basecaller/qscore.md
          - SAM Specification: basecaller/sam_spec.md
  - Models:
      - Introduction: models/models.md
      - Selection Complex: models/complex.md
      - Downloading Models: models/downloader.md
      - Models List: models/list.md
  - Assembly:
      - Dorado Polish: assembly/polish.md
      - Dorado Correct: assembly/correct.md
  - Help:
      - Troubleshooting: troubleshooting/troubleshooting.md
      - FAQ: troubleshooting/faq.md

theme:
  name: material
  font: false
  custom_dir: docs/extra/overrides # Used to add readthedocs version selector
  features:
    - navigation.instant # Do not fully reload pages
    # - navigation.footer # Show pages at tabs at the top
    # - navigation.tabs.sticky # Show tab name when scrolling down
    # - navigation.tabs # Show pages at tabs at the top
    - navigation.sections # Show docs groups as sections instead of nesting as tree
    - navigation.top # Back to top button
    - navigation.indexes # Makes the index of a section a page

    - toc.integrate # Hide right-side toc pane

    - search.suggest
    - search.highlight
    - search.share

    - content.tabs.link
    - content.code.annotate
    - content.code.copy
  language: en
  logo: extra/assets/nanopore.logo.png
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      primary: custom
      accent: custom
      scheme: ont
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode

    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      primary: custom
      accent: custom
      scheme: ont
      # scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
      # primary: cyan
      # accent: blue

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      primary: custom
      accent: custom
      scheme: ont-dark
      # scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to system preference
      # primary: deep purple
      # accent: blue

plugins:
  - search
  - macros:
      verbose: false # Set to true to debug the `find` function

extra_javascript:
  - extra/javascript/readthedocs.js
extra_css:
  - extra/stylesheets/extra.css

extra:
  dorado:
    version: "0.9.1"
    code: https://github.com/nanoporetech/dorado/
  mm2_docs: https://github.com/lh3/minimap2
  github:
    repo: https://github.com/nanoporetech/dorado
    issues: https://github.com/nanoporetech/dorado/issues
  social:
    - icon: fontawesome/brands/github-alt
      link: https://github.com/nanoporetech/dorado
    - icon: fontawesome/brands/x-twitter
      link: https://x.com/nanopore
    - icon: fontawesome/brands/linkedin
      link: https://www.linkedin.com/company/oxford-nanopore-technologies
# Not collecting cookies via RTD
# 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.

markdown_extensions:
  - admonition # Add nice Note, Warning, Error areas
  # Code-block syntax highlighting
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
      extend_pygments_lang:
        - name: dorado
          lang: dorado
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.details
  - pymdownx.caret # Adds ^^insert-tag^^ and ^superscript^
  - pymdownx.mark # Adds ==mark-tag== for highlighting
  - pymdownx.tilde # Adds ~~strike-through~~ and ~subscript~
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          # format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - def_list
  - tables