mkdocs.yml

site_name: 'Beacon v2 CBI Tools Documentation'
site_description: 'Beacon v2 CBI Tools Documentation'
site_author: 'Manuel Rueda, PhD'
copyright: '© Copyright 2023-2026, Manuel Rueda, CNAG'
repo_name: 'beacon2-cbi-tools'
repo_url: https://github.com/mrueda/beacon2-cbi-tools
edit_uri: edit/main/docs/

extra_css: [css/theme_overrides.css]
extra_javascript: [js/theme_overrides.js]

plugins:
  - search
  - macros
  - include-markdown
  - mermaid2:
      arguments:
        startOnLoad: true

markdown_extensions:
    - toc:
        toc_depth: 2-3
        permalink: true
    - admonition
    - attr_list
    - footnotes
    - md_in_html
    - pymdownx.critic
    - pymdownx.caret
    - pymdownx.details
    - pymdownx.keys
    - pymdownx.mark
    - pymdownx.tilde
    - pymdownx.saneheaders
    - pymdownx.magiclink:
        hide_protocol: true
    - pymdownx.tabbed:
        alternate_style: true
    - pymdownx.tasklist:
        custom_checkbox: true
    - tables
    - mdx_gh_links:
        user: CNAG-Biomedical-Informatics
        repo: beacon2-cbi-tools
    - pymdownx.emoji:
        emoji_index: !!python/name:material.extensions.emoji.twemoji
        emoji_generator: !!python/name:material.extensions.emoji.to_svg
    - pymdownx.highlight:
        anchor_linenums: true
        line_spans: __span
        pygments_lang_class: true
    - pymdownx.inlinehilite
    - pymdownx.snippets:
        base_path: ["docs", "non-containerized", "docker", "apptainer", "examples", "bin"]
        url_download: true
    - pymdownx.superfences:
        custom_fences:
            - name: mermaid
              class: mermaid
              format: !!python/name:mermaid2.fence_mermaid

nav:
  - "🏠 Introduction": index.md
  - "⬇️  Download & Installation":
      - "🐳 Containerized": 
        - Docker: download-and-installation/docker-based.md
        - Apptainer: download-and-installation/apptainer-based.md
      - "🛠️ Non-containerized": download-and-installation/non-containerized.md
  - "🚀 Quick Start": quick-start.md
  - "🧪 Examples": 
      - "🧬 GRCh37 / hg19": https://github.com/CNAG-Biomedical-Informatics/beacon2-cbi-tools/tree/main/testdata/README.md
      - "🧬 GRCh38 / hg38": examples/hg38.md
  - "📚 Tutorial": data-beaconization.md
  - "📊 CINECA cohort": https://github.com/CNAG-Biomedical-Informatics/beacon2-cbi-tools/tree/main/CINECA_synthetic_cohort_EUROPE_UK1
  - "🛠️  Utilities": utilities.md
  - "🆘 Help": 
      - "❓ FAQ": help/faq.md
  - "ℹ️ About":
      - "📄 About": about/about.md
      - "📖 Citation": about/citation.md
      - "⚠️  Disclaimer": about/disclaimer.md

theme:
  name: material
  #custom_dir: overrides
  palette:
  - media: '(prefers-color-scheme: dark)'
    scheme: default
    primary: blue grey
    accent: amber
    toggle:
      icon: material/lightbulb
      name: Switch to light mode
  - media: '(prefers-color-scheme: light)'
    scheme: slate
    primary: blue grey
    accent: amber
    toggle:
      icon: material/lightbulb-outline
      name: Switch to dark mode
  logo: img/logo.png
  icon:
      repo: fontawesome/brands/github-alt 
  features:
        - content.code.select
        - content.code.copy
        - content.tabs.link
        - search.highlight
        - search.share
        # - navigation.instant # otherwise blocks rendering of mermaid on page load
        #- navigation.tabs
        - navigation.tracking
        - navigation.sections
        - toc.integrate

# Options
extra:
  social:
    - icon: fontawesome/brands/github 
      link: https://github.com/mrueda

# https://pypi.org/project/mkdocs-with-pdf/ for more PDF configuration ...