mkdocs.yml

# Project information
site_name: Cellulus
site_url: https://funkelab.github.io/cellulus
site_author: Manan Lalit
site_description: >-
  Documentation for Cellulus

# Repository
repo_name: funkelab/cellulus
repo_url: https://github.com/funkelab/cellulus

# Configuration
theme:
  name: material
  custom_dir: docs/overrides
  features:
    - content.code.annotate
    - content.code.copy
    - content.tooltips
    - navigation.footer
    - navigation.indexes
    - navigation.sections
    - navigation.tabs
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/link
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/toggle-switch
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: indigo
      toggle:
        icon: material/toggle-switch-off
        name: Switch to system preference
  icon:
    logo: logo

plugins:
  - mkdocs-jupyter:
      execute: True
      ignore: ["*/*/*/.ipynb_checkpoints/*.py"]
      include_source: True
  - search:
      separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - mkdocstrings

nav:
  - Home: index.md
  - Getting Started:
    - Installation: getting-started.md
  - Examples:
      - 2D:
        - 01: examples/2d/01-data.py
        - 02: examples/2d/02-train.py
        - 03: examples/2d/03-infer.py
      - 3D:
        - 01: examples/3d/01-data.py
        - 02: examples/3d/02-train.py
        - 03: examples/3d/03-infer.py
  - API Reference:
      - Configs:
          - DatasetConfig: api/dataset_config.md
          - ExperimentConfig: api/experiment_config.md
          - InferenceConfig: api/inference_config.md
          - ModelConfig: api/model_config.md
          - TrainConfig: api/train_config.md
      - Datasets:
          - ZarrDataset: api/zarr_dataset.md
          - DatasetMetaData: api/meta_data.md
      - OCELoss: api/oce_loss.md