mkdocs.yml

site_name: scTM
site_description: The documentation for the scTM software library.
site_url: https://jinmiaochenlab.github.io/scTM/
repo_url: https://github.com/JinmiaoChenLab/scTM
repo_name: scTM

edit_uri: ""

nav:
  - 🏡 Home: index.md
  - Getting started:
      - 🛠️ Installation: installation.md
  - 🎓 Tutorials:
    - STAMP simulation example: notebooks/stamp/Simulation.ipynb
    - STAMP breast cancer and cell/phenotype inference with GSEA: notebooks/stamp/example1.ipynb
    - STAMP joint mouse brain Visium: notebooks/stamp/example2.ipynb
    - STAMP lung cancer SMI with DISCO: notebooks/stamp/example3.ipynb
    - STAMP Multi Technolgy Mouse olfactory bulb: notebooks/stamp/example4.ipynb
    - STAMP Multi Sample DLPFC: notebooks/stamp/example6.ipynb
    - STAMP Time series Mouse embryo: notebooks/stamp/example5.ipynb
  # - 💡 Background:
  #   - Intro to Topquic Models: examples/intro_to_topicmodel.py
  - 📕 Reference: api/

theme:
  name: material
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.sections
    - navigation.top # Show a back to top button
    - content.code.copy
    - search.suggest # Show search suggestions
    - search.highlight # Highlight search results in results
    - content.code.annotate # Allow individual lines of code to be annotated
  icon:
    repo: fontawesome/brands/github
  logo: _static/favicon.ico
  favicon: _static/favicon.ico

markdown_extensions:
  - admonition
  - pymdownx.details # Enhance admonitions with collapse/expand
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.superfences
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.tabbed

plugins:
  - search
  - gen-files:
      scripts:
        - docs/gen_ref_pages.py
  - literate-nav:
      nav_file: SUMMARY.md
  - mkdocs-jupyter:
      execute: false
      allow_errors: false
  #   # binder: true
  #   # binder_service_name: "gh"
  # #     binder_branch: "main"
  - mkdocstrings:
      watch:
        - sctm
      default_handler: python
      handlers:
        python:
          rendering:
            # show_root_heading: true
            # show_root_full_path: true
            # show_if_no_docstring: true
            # show_signature_annotations: true
            show_source: false
            members_order: source # order methods according to their order of definition in the source code, not alphabetical order
            heading_level: 4
          options:
            inherited_members: true # Allow looking up inherited methods
            docstring_style: "google"