pyvcell/mkdocs.yml at main · virtualcell/pyvcell · GitHub

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site_name: pyvcell
repo_url: https://github.com/virtualcell/pyvcell
site_url: https://virtualcell.github.io/pyvcell
site_description: Python interface for Virtual Cell modeling and simulation
site_author: Jim Schaff
edit_uri: edit/main/docs/
repo_name: virtualcell/pyvcell
copyright: Maintained by <a href="https://vcell.org">Virtual Cell Project</a>.

nav:
  - Home: index.md
  - Getting Started:
      - Installation: getting-started/installation.md
      - Quick Start: getting-started/quickstart.md
  - Guides:
      - Building a Model: guides/building-a-model.md
      - Working with SBML: guides/sbml-models.md
      - Complex Geometries: guides/complex-geometries.md
      - Parameter Exploration: guides/parameter-exploration.md
      - Remote Simulations: guides/remote-simulations.md
      - Field Data Workflows: guides/field-data.md
      - Visualization & Analysis: guides/visualization.md
      - "Tutorial: Building a Model": guides/notebooks/building-a-model.ipynb
      - "Tutorial: Complex Geometries": guides/notebooks/complex-geometries.ipynb
      - "Tutorial: Remote Simulations": guides/notebooks/remote-simulations.ipynb
      - "Tutorial: Visualization": guides/notebooks/visualization.ipynb
  - API Reference:
      - Models: reference/models.md
      - I/O Functions: reference/io.md
      - Simulation & Results: reference/simulation.md

plugins:
  - search
  - mkdocs-jupyter:
      execute: false
  - mkdocstrings:
      handlers:
        python:
          setup_commands:
            - import sys
            - sys.path.append('../')
          options:
            show_source: false
            show_signature_annotations: true
            members_order: source

theme:
  name: material
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - content.code.copy
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: white
      accent: deep orange
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: deep orange
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  icon:
    repo: fontawesome/brands/github

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/virtualcell/pyvcell
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/pyvcell

markdown_extensions:
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - admonition
  - pymdownx.details