mkdocs.yml

site_name: SNPick
site_description: Fast, memory-efficient extraction of variable sites from FASTA alignments
site_url: https://pathogenomics-lab.github.io/snpick/
site_author: Paula Ruiz-Rodriguez
repo_url: https://github.com/PathoGenOmics-Lab/snpick
repo_name: PathoGenOmics-Lab/snpick
edit_uri: edit/main/docs/
copyright: Copyright © Paula Ruiz-Rodriguez & Mireia Coscolla, I²SysBio (UV-CSIC)

theme:
  name: material
  custom_dir: overrides
  # Baked PNGs, not the SVGs: the wordmark is set in the "Sixtyfour Convergence"
  # pixel font, which a visitor's browser will not have, so an <img> of the SVG
  # would fall back to a plain face. The PNGs carry the pixel shapes as raster.
  # The logo partial in overrides/ swaps a light and a dark PNG by scheme.
  logo: assets/logo.png
  favicon: assets/logo.png
  language: en
  # Three states: the site follows the reader's system setting until they choose
  # otherwise, and their choice is remembered. Primary is white on light and
  # black on dark so the header is a neutral ground; the accent is teal, and the
  # stylesheet pins the exact link colour that clears contrast in each scheme.
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: white
      accent: teal
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: teal
      toggle:
        icon: material/brightness-auto
        name: Follow the system setting
  font:
    text: IBM Plex Sans
    code: IBM Plex Mono
  features:
    - announce.dismiss
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.instant.progress
    # The nav is grouped into a handful of sections shown open in the sidebar,
    # the way get_MNV lays its out; tabs are deliberately left off so the whole
    # map stays visible on a site this small.
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - navigation.footer
    - navigation.tracking
    - navigation.path
    - toc.follow
    - search.suggest
    - search.highlight
    - search.share
    - content.code.copy
    - content.code.annotate
    - content.code.select
    - content.tabs.link
    - content.tooltips
    - content.action.edit
    - content.action.view
  icon:
    repo: fontawesome/brands/github
    edit: material/pencil
    view: material/eye

nav:
  - Home: index.md
  - Get started:
      - Installation: installation.md
      - Usage: usage.md
      - Tutorial: tutorials/tutorial.ipynb
  - Reference:
      - Output formats: output.md
      - Benchmarks: benchmarks.md
      - Architecture: architecture.md
  - Project:
      - Contributing: contributing.md
      - Changelog: changelog.md
      - Tags: tags.md

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
      title: On this page
  - pymdownx.betterem
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      base_path: [".", "docs"]
      auto_append: ["includes/abbreviations.md"]
      check_paths: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

plugins:
  - search
  - tags
  - mkdocs-jupyter:
      execute: false
      include_source: true
      ignore_h1_titles: true
  - glightbox:
      touchNavigation: true
      loop: false
      effect: zoom
      draggable: true
  - git-revision-date-localized:
      type: timeago
      enable_creation_date: true
      enable_git_follow: false
      fallback_to_build_date: true
  - social:
      # Social cards need Cairo/Pango; generate them only in CI (where the libs
      # are installed), so local builds don't require the native dependencies.
      enabled: !ENV [CI, false]
      cards_layout_options:
        background_color: "#004d40"
  - minify:
      minify_html: true

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/PathoGenOmics-Lab
      name: PathoGenOmics-Lab on GitHub
    - icon: fontawesome/brands/python
      link: https://anaconda.org/bioconda/snpick
      name: SNPick on Bioconda

extra_css:
  - stylesheets/extra.css

# The abbreviations glossary is auto-appended via snippets, not a standalone page.
exclude_docs: |
  includes/