mkdocs.yml

site_name: cell2cell
site_description: "Python package to infer cell-cell interactions and communication from gene expression of interacting proteins."

theme:
    name: readthedocs
    highlightjs: true
repo_url: https://github.com/earmingol/cell2cell
plugins:
  - search
  - mkdocs-jupyter:
      execute: false
      include: ["*.ipynb"]
      include_source: True
      #ignore_h1_titles: True
  - mkdocstrings:
      watch:
        - cell2cell
      default_handler: python
      handlers:
        python:
          options:
            docstring_style: sphinx

markdown_extensions:
  - def_list
  - attr_list
  - admonition
  - codehilite
  - pymdownx.tasklist:
      custom_checkbox: true
  - md_in_html
  - pymdownx.superfences
  - pymdownx.betterem
  - pymdownx.caret
  - pymdownx.mark
  - pymdownx.tilde
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true

nav:
  - "Home": index.md
  - "API Documentation": documentation.md
  - "cell2cell Tutorials":
      - tutorials/Toy-Example-BulkPipeline.ipynb
      - tutorials/Toy-Example-SingleCellPipeline.ipynb
  - "Tensor-cell2cell Tutorials":
    - tutorials/ASD/01-Tensor-Factorization-ASD.ipynb
    - tutorials/ASD/02-Factor-Specific-ASD.ipynb
    - tutorials/ASD/03-GSEA-ASD.ipynb
    - tutorials/Tensor-cell2cell-Spatial.ipynb
    - tutorials/GPU-Example.ipynb