mkdocs.yml

site_name: pySingleCellNet
site_author: Patrick Cahan
copyright: Copyright © 2024 Cahan Lab
repo_url: https://github.com/CahanLab/PySingleCellNet

use_directory_urls: false

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/extra.js

theme:
  name: material
  font:
    text: Noto Sans
  palette:
    primary: light blue
  logo: img/logoGlow.png
  favicon: img/logo.png
  features:
    - content.footnote.tooltips
    - navigation.expand
    - toc.integrate
#    - navigation.tabs
#    - navigation.tabs.sticky
#    - navigation.sections

markdown_extensions:
  - md_in_html
  - footnotes
  - admonition
  - attr_list
  - tables
  - def_list
  - toc:
      title: On this page
  - pymdownx.blocks.caption
  - pymdownx.tasklist:
      custom_checkbox: false
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

plugins:
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            separate_signature: true
            docstring_section_style: list
            heading_level: 3
  - search
  - mkdocs-jupyter:
      execute: false
      include_source: True

nav:
#  - Home: index.md
  - Installation: install.md
  - Tutorials: 
    - 'Quickstart': notebooks/quickstart.ipynb
    - 'Explore': notebooks/categorize.ipynb
#    - 'train & classify': 'notebooks/Basics.ipynb'
#    - 'analyze _in vitro_ cells': 'notebooks/explore.ipynb'
#    - 'prepare training data': 'notebooks/how-to_prepare_reference_data.ipynb'
#    - 'Train a classifier': 'notebooks/train_classifier.ipynb'
#    - 'Enrichment analysis': 'notebooks/enrichment.ipynb'
  - Training data: training_data.md
  - References: refs.md
  - API:
    - 'Utility functions': 'utils.md'
    - 'Classifier functions': 'classifier.md'
    - 'Plotting functions': 'plotting.md'