mesoscopy/mkdocs.yml at main · DuguidLab/mesoscopy · GitHub

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site_name: Mesoscopy
site_url: https://docs.mesoscopy.org/
repo_url: https://github.com/DuguidLab/mesoscopy
repo_name: DuguidLab/mesoscopy

theme:
  name: material
  favicon: assets/favicon.png
  # custom_dir: docs/overrides
  font:
    text: Montserrat
  logo: assets/mesoscopy-logo.png
  icon:
    repo: fontawesome/brands/github
  features:
    - navigation.instant
    - navigation.instant.progress
    - navigation.tracking
    - navigation.sections
    - navigation.path
    # - navigation.indexes
    # - toc.integrate
    - navigation.top
    - navigation.tabs
    - toc.follow
    - content.code.copy
    - content.code.annotate
    - navigation.footer
  palette:
    - media: "(prefers-color-scheme: light)"
      primary: deep purple
      accent: teal
      toggle:
        icon: material/eye
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: deep purple
      accent: teal
      toggle:
        icon: material/eye-outline
        name: Switch to light mode

extra_css:
  - stylesheets/extra.css
  # - stylesheets/dark-hc.css
  # - stylesheets/dark-mc.css
  # - stylesheets/dark.css
  # - stylesheets/light-hc.css
  # - stylesheets/light-mc.css
  # - stylesheets/light.css

plugins:
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [src]
          options:
            show_source: true
            docstring_style: google
            docstring_section_style: list
            members_order: source
  - search
  # - material-plausible

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - mkdocs-click

extra:
  homepage: https://mesoscopy.org
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/orgs/DuguidLab
    - icon: material/web
      link: https://www.duguidlab.com
  # analytics:
  #   provider: plausible
  #   domain: docs.mesoscopy.org

copyright: Copyright &copy; 2024 Constantinos Eleftheriou

nav:
  - Getting started:
    - Installation: index.md
    - Typical workflow: typical-workflow.md
    - Where to go from here: where-to-go.md
    - Contributing: contributing.md
    - Troubleshooting: troubleshooting.md
  - How-to:
    - Overview: how-to/index.md
    - Preprocessing: how-to/preprocessing.md
    - Registration to the ABA: how-to/registration.md
    - Quality control: how-to/qa.md
    - Resting-state recordings: how-to/resting-state-analysis.md
    - Imaging with behaviour: how-to/imaging-with-behaviour-analysis.md
    - Converting video files to HDF5: how-to/convert-video-to-h5.md
    - Using mesoscopy as a library: how-to/using-mesoscopy-as-a-library.md
  - Design principles:
    - Overview: design-principles/index.md
    - Data structure: design-principles/data-structure.md
    - Haemodynamic correction: design-principles/haemodynamics.md
    - Channel separation in mixed recordings: design-principles/channel-separation.md
    - Landmark registration & the Allen Brain Atlas: design-principles/registration.md
  - Reference:
    - Overview: reference/index.md
    - Mesoscopy CLI: reference/cli-mesoscopy.md
    - Mesoscopy API:
      - mesoscopy: reference/api-mesoscopy.md
      - mesoscopy.io: reference/api-mesoscopy-io.md
      - mesoscopy.plots: reference/api-mesoscopy-plots.md
      - mesoscopy.convert: reference/api-mesoscopy-convert.md
      - mesoscopy.preprocess: reference/api-mesoscopy-preprocess.md
      - mesoscopy.register: reference/api-mesoscopy-register.md
      - mesoscopy.process: reference/api-mesoscopy-process.md
      - mesoscopy.postprocess: reference/api-mesoscopy-postprocess.md
      - mesoscopy.resources: reference/api-mesoscopy-resources.md