mkdocs.yml

site_name: PyEED Documentation
repo_url: https://github.com/PyEED/pyeed/
repo_name: PyEED/pyeed
site_url: https://pyeed.github.io/pyeed/
site_author: Max Häußler

nav:
  - Home: index.md
  - Usage: 
    - Basics:
      - Initial Setup: usage/initial_setup.ipynb
      - Query from Primary Database: usage/basics.ipynb
    - Tools:
      - Clustalo: usage/clustalo.ipynb
      - MMseqs: usage/mmseqs.ipynb
      - Blast: usage/blast.ipynb
    - Analysis:
      - Embeddings Analysis: usage/embeddings_analysis.ipynb
      - Network Analysis: usage/network_analysis.ipynb
      - Mutation Analysis: usage/mutation_analysis.ipynb
  - API Reference:
    - Pyeed: api/pyeed.md
    - DatabaseConnector: api/dbconnect.md
    - PrimaryDBAdapter: api/primarydbadapter.md
  - Setup:
    - Neo4j Database: setup/database.md

plugins:
  - search:
  - mkdocs-jupyter
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            docstring_style: google
            docstring_section_style: table
            docstring_options:
              ignore_init_summary: true
            merge_init_into_class: true
            show_source: false

theme:
  name: material
  logo: figs/pyeed.png
  features:
    - navigation.instant
    - navigation.instant.progress
    - navigation.instant.preview
    - navigation.indexes
    - navigation.footer
    - content.action.view
    - navigation.tabs
    - navigation.sections
    - toc.integrate
    - navigation.top
    - search.suggest
    - search.highlight
    - content.tabs.links
    - content.code.select
    - content.code.copy
    - content.code.annotation
  palette: 
    # Palette toggle for light mode
    - scheme: default
      toggle:
        icon: material/brightness-7 
        name: Switch to dark mode

    # Palette toggle for dark mode
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode


markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - admonition
  - pymdownx.keys
  - pymdownx.details
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - tables
  - attr_list
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - def_list
  - pymdownx.tasklist:
      custom_checkbox: true
  - md_in_html
  - pymdownx.tabbed:
      alternate_style: true