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mkdocs.yml
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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-abba.md
- tips-qupath.md
- tips-brain-contours.md
- tips-preprocessing.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