cloudscope/mkdocs.yml at main · mapmanager/cloudscope · GitHub

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site_name: CloudScope
site_description: Desktop and browser image loading, visualization, and analysis for acquisition-backed microscopy files.
site_url: https://mapmanager.github.io/cloudscope/
repo_url: https://github.com/mapmanager/cloudscope
repo_name: mapmanager/cloudscope

theme:
  name: material
  custom_dir: docs/assets/overrides
  logo: assets/cloudscope.png
  favicon: assets/cloudscope.png
  features:
    - navigation.indexes
    - navigation.top
    - toc.follow
    - content.code.copy
    - content.tabs.link
    - search.highlight
    - search.suggest
  palette:
    - scheme: default
      primary: blue
      accent: blue
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - scheme: slate
      primary: blue
      accent: blue
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode

extra_css:
  - assets/stylesheets/extra.css

hooks:
  - docs/hooks.py

plugins:
  - search
  - section-index
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            docstring_style: google
            show_source: true
            show_signature_annotations: true
            separate_signature: true
            members_order: source
            filters: ["!^_"]
  - mkdocs-jupyter:
      include_source: true
      execute: false

markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.snippets:
      base_path: !relative $docs_dir
  - pymdownx.highlight
  - pymdownx.inlinehilite
  - toc:
      permalink: true

exclude_docs: |
  hooks.py
  schemas/*.md

nav:
  - Home: index.md
  - End User:
      - users/index.md
      - Install the desktop app: users/install.md
      - Using the GUI: users/gui.md
      - Pool plots: users/pool-plots.md
      - "GUI: Experiment metadata": users/gui-experiment-metadata.md
      - "GUI: Image header": users/gui-image-header.md
      - "GUI: App config": users/gui-app-config.md
      - Saved file formats: users/saved-files.md
      - Recipes:
          - users/recipes/index.md
          - Velocity analysis: users/recipes/velocity-analysis.md
          - Diameter analysis: users/recipes/diameter-analysis.md
          - Sum intensity analysis: users/recipes/sum-intensity-analysis.md
          - Analyses from velocity:
              - users/recipes/analyses-from-velocity/index.md
              - Velocity event analysis: users/recipes/analyses-from-velocity/velocity-event-analysis.md
              - Heart rate analysis: users/recipes/analyses-from-velocity/heart-rate-analysis.md
  - Data Scientist:
      - scientists/index.md
      - Velocity Analysis: scientists/velocity-analysis.md
      - Diameter Analysis: scientists/diameter-analysis.md
      - Sum Intensity Analysis: scientists/sum-intensity-analysis.md
      - AcqImage Metadata: scientists/acqimage-metadata.md
      - Notebooks:
          - scientists/notebooks.md
          - Load and Plot Image: notebooks/load-and-plot-image.ipynb
          - Velocity Analysis Notebook: notebooks/velocity-analysis.ipynb
          - Diameter Analysis Notebook: notebooks/diameter-analysis.ipynb
          - Sum Intensity Analysis Notebook: notebooks/sum-intensity-analysis.ipynb
          - Kymograph Reference Images: notebooks/kymograph-reference-image.ipynb
          - Heart Rate Analysis Notebook: notebooks/heart-rate-analysis.ipynb
          - Heart Rate Batch Analysis Notebook: notebooks/heart-rate-batch-analysis.ipynb
      - Reproducibility: scientists/reproducibility.md
  - Developer:
      - developers/index.md
      - Architecture: developers/architecture.md
      - Release and Deployment: developers/release-and-deployment.md
      - MkDocs style guide: developers/mkdocs-style.md
      - Contributing: developers/contributing.md
  - API:
      - api/index.md
      - AcqImage: api/acq-image.md
      - AcqImageList: api/acq-image-list.md
      - Analysis Core: api/analysis-core.md
      - Velocity Analysis: api/velocity-analysis.md
      - Diameter Analysis: api/diameter-analysis.md
      - Sum Intensity Analysis: api/sum-intensity-analysis.md
      - Batch Analysis: api/batch-analysis.md