mkdocs.yml

site_name: cuisto
repo_url: https://github.com/TeamNCMC/cuisto
site_description: Quantify histological data
site_author: Guillaume Le Goc
copyright: Julien Bouvier lab -- NeuroPSI -- CNRS/University Paris-Saclay UMR 9197

theme:
  name: material
  custom_dir: docs/overrides
  palette:
  - scheme: default
    primary: indigo
    toggle:
      icon: material/brightness-7
      name: Switch to dark mode
  - scheme: slate
    primary: pink
    toggle:
      icon: material/brightness-4
      name: Switch to light mode
  features:
    - navigation.path
    - navigation.footer
    - navigation.top
    - content.code.copy
    - content.code.select
    - toc.follow

nav:
  - index.md
  - main-getting-started.md
  - Guides:
    - guide-install-abba.md
    - guide-create-pyramids.md
    - guide-qupath-objects.md
    - guide-register-abba.md
    - guide-prepare-qupath.md
    - guide-pipeline.md
  - Tips:
    - tips-formats.md
    - tips-qupath.md
    - tips-abba.md
    - tips-brain-contours.md
  - main-configuration-files.md
  - Examples:
    - main-using-notebooks.md
    - demo_notebooks/cells_distributions.ipynb
    - demo_notebooks/fibers_coverage.ipynb
    - demo_notebooks/density_map.ipynb
    - demo_notebooks/fibers_length_multi.ipynb
  - Package reference:
    - cuisto.config: api-config.md
    - cuisto.compute: api-compute.md
    - cuisto.process: api-process.md
    - cuisto.display: api-display.md
    - cuisto.utils: api-utils.md
    - cuisto.io: api-io.md
    - cuisto.seg: api-seg.md
  - Scripts reference:
    - segment_images: api-script-segment.md
    - qupath_script_runner: api-script-qupath-script-runner.md
  - main-getting-help.md
  - main-citing.md

plugins:
- autorefs
- search
- privacy
- offline
- mkdocs-jupyter:
    execute: False
    include_source: True
- mkdocstrings:
    default_handler: python
    handlers:
      python:
        import:
        - https://docs.python.org/3/objects.inv
        - https://numpy.org/doc/stable/objects.inv
        - https://docs.scipy.org/doc/scipy/reference/objects.inv
        - https://pandas.pydata.org/pandas-docs/stable/objects.inv
        - https://matplotlib.org/stable/objects.inv
        - https://seaborn.pydata.org/objects.inv
        options:
          docstring_style: numpy
          parameters_headings: true
          show_symbol_type_heading: true
          show_symbol_type_toc: true
          merge_init_into_class: true
    enable_inventory: false
- git-revision-date-localized:
    enable_creation_date: true

markdown_extensions:
  - attr_list
  - admonition
  - def_list
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.highlight
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.keys
  - pymdownx.arithmatex:
      generic: true
      inline_syntax: ['round']
      block_syntax: ['square', 'begin']
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  
  - toc:
      permalink: "#"

extra_javascript:
  - javascripts/katex.js
  - https://unpkg.com/katex@0/dist/katex.min.js
  - https://unpkg.com/katex@0/dist/contrib/auto-render.min.js

extra_css:
  - stylesheets/extra.css
  - https://unpkg.com/katex@0/dist/katex.min.css