mkdocs.yml

# Project information
site_name: Practical Haplotype Graph
site_description: Pangenome system for plant breeding and genetics
site_author: Buckler Lab
site_url: https://phg.maizegenetics.net

# Repository configuration
repo_name: PHGv2
repo_url: https://github.com/maize-genetics/phg_v2

# Theme configuration
theme:
  icon:
    repo: fontawesome/brands/github
  name: material
  custom_dir: docs/index_override
  logo: img/product/phg_logo_white.svg
  favicon: img/product/favicon.png
  palette:
      scheme: default
      primary: green
      accent: green
  features:
    - content.code.select
    - content.code.copy
    - content.code.annotate
    - navigation.tabs
    - navigation.top
    - navigation.sections
    - navigation.indexes
    - navigation.expand
    - search.highlight
  language: en
  font:
    text: Roboto
    code: Roboto Mono

# Copyright
copyright: Copyright &copy; 2023 - 2024  <a href="https://www.maizegenetics.net "><b>Buckler Lab</b></a>

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/maize-genetics
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/c/BucklerLab

# Markdown extensions
markdown_extensions:
  - attr_list
  - md_in_html
  - toc:
      permalink: true
  - tables
  - admonition
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

# Extra 
extra_javascript:
  - javascript/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

extra_css:
  - stylesheets/extra.css

# Navigation
nav:
  - Home: 
      - index.md
  - Getting Started:
      - Installation: installation.md
      - Building and loading: build_and_load.md
      - Imputation: imputation.md
      - Resequencing: resequencing.md
      - Exporting data: export_data.md
  - Reference:
      - Convenience commands: convenience_commands.md
      - hVCF region handling: hvcf_region_handling.md
      - hVCF specifications: hvcf_specifications.md
      - Ktor specifications: ktor_specifications.md
      - QC metrics: qc_metrics.md
      - SLURM usage: slurm_usage.md
      - Terminology: terminology.md
      - Variant caller comparisons: variant_comparisons.md
  - Community:
      - References: citations.md
      - Contributing: CONTRIBUTING.md
      - Code of Conduct: CODE_OF_CONDUCT.md