mkdocs.yml

site_name: image2image
site_url: https://github.com/vandeplaslab/image2image-docs
site_author: Lukasz Migas
site_description: >-
  Suite of tools for image registration and visualisation.
  
# Repository
repo_name: vandeplaslab/image2image-docs
repo_url: https://github.com/vandeplaslab/image2image-docs

# Copyright
copyright: Copyright © 2023 - present Van de Plas lab
extra_css:
  - assets/css/extra.css

theme:
  name: material
  logo: assets/icon.svg
  favicon: assets/icon.svg
  palette:
    - scheme: default
      primary: grey
      accent: green
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - scheme: slate
      primary: amber
      accent: yellow
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.top
    - navigation.tabs
    - navigation.expand
    - search.highlight
    - search.suggest
    - toc.integrate
    - toc.follow

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - changelog
  - attr_list
  - md_in_html
  - pymdownx.keys
  - tables
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - def_list
  - pymdownx.tasklist:
      custom_checkbox: true

plugins:
  - search
  - autorefs
  - minify:
      minify_html: true
  - glightbox
  - offline

nav:
  - Home: index.md
  - Viewer apps: 
    - Viewer app: apps/viewer.md
    - Sync app (not available yet): apps/na.md
    - Volume app (not available yet): apps/na.md
  - Registration apps: 
    - Register app: apps/register.md
    - Elastix app: apps/elastix.md
    - Valis app: apps/valis.md
  - Utility apps: 
    - Crop app: apps/crop.md
    - Convert app: apps/convert.md
    - Merge app: apps/merge.md
    - Fusion app: apps/fusion.md
  - Dialogs:
    - Dataset selection: dialogs/dataset-selection.md
    - Channel selection: dialogs/channel-selection.md
    - Transformation selection: dialogs/transformation-selection.md
    - Export masks: dialogs/export-masks.md
    - Fiducials table: dialogs/fiducials-table.md
    - Generate fiducials: dialogs/generate-fiducials.md
    - Initial transformation: dialogs/initial-transform.md
    - Mask maker: dialogs/mask-maker.md
  - Requests/Bug reports: request.md
  - Planned features: planned.md
  - Changelog: changelog.md