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mkdocs.yml
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mkdocs.yml
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site_name: napari-ndev
site_url: https://TimMonko.github.io/napari-ndev/
site_description: Napari widgets to process microscopy images
repo_name: timmonko/napari-ndev
repo_url: https://github.com/timmonko/napari-ndev
copyright: Copyright © 2023-2024 Tim Monko
theme:
name: material
favicon: resources/images/neuralDev-icon.svg
logo: resources/images/neuralDev-icon.svg
icon:
repo: fontawesome/brands/github
palette:
# Palette toggle for light mode
- scheme: default
toggle:
icon: material/brightness-7
name: Switch to dark mode
# Palette toggle for dark mode
- scheme: slate
primary: teal
accent: light-green
toggle:
icon: material/brightness-4
name: Switch to light mode
features:
- content.code.annotate
- navigation.sections
- navigation.indexes
- toc.follow
- search.suggest
- search.share
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/timmonko/napari-ndev
name: napari-ndev on GitHub
- icon: fontawesome/brands/python
link: https://pypi.org/project/napari-ndev
name: napari-ndev on PyPI
nav:
- Overview: index.md
- Installation: installation.md
- Beginner Setup: beginner_setup.md
- Further Widget Info: widget_further_info.md
- Poster: BINA_poster.md
- I2K Workshop:
- 1) Tutorial Setup: tutorial/00_setup.md
- 2) Example Pipeline: tutorial/01_example_pipeline.md
- 3) Easy Machine Learning: tutorial/02_easy_ML.md
- 4) Build Your Own Pipeline: tutorial/03_build_pipeline.md
- Examples:
- Image Utilities: examples/utilities/image_utilities.ipynb
- Workflow:
- napari workflow: examples/workflow/workflow_napari-assistant.ipynb
- workflow widget: examples/workflow/workflow_widget.ipynb
- script workflow: examples/workflow/workflow_scripting.ipynb
- Measure Widget: examples/measure/measure_widget.ipynb
- API:
- Widgets:
- api/widgets/image_utilities.md
- api/widgets/workflow_widget.md
- api/widgets/apoc_widget.md
- api/widgets/custom_apoc_feature_set.md
- api/widgets/measure_widget.md
- api/widgets/napari_reader.md
- Image Overview: api/image_overview.md
- PlateMapper: api/plate_mapper.md
- Measure: api/measure.md
- Morphology: api/morphology.md
- Helpers: api/helpers.md
- nImage: api/nimage.md
watch:
- src
markdown_extensions:
- tables
- admonition
- attr_list
- pymdownx.details
- pymdownx.highlight
- pymdownx.extra
- pymdownx.superfences
- attr_list
- md_in_html
- pymdownx.tabbed:
alternate_style: true
- toc:
permalink: "#"
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
plugins:
- search
- table-reader
- autorefs
- literate-nav
- spellcheck:
backends:
- codespell:
dictionaries: [clear, rare]
- mkdocstrings:
handlers:
python:
import:
- https://docs.python.org/3/objects.inv
- https://psygnal.readthedocs.io/en/latest/objects.inv
- https://pint.readthedocs.io/en/stable/objects.inv
- https://napari.org/stable/objects.inv
options:
docstring_style: numpy # required
heading_level: 2
separate_signature: true
line_length: 80
parameter_headings: true
show_source: true
show_symbol_type_heading: true
show_symbol_type_toc: true
show_signature_annotations: false # unsure here, adds type annotations to the function signature, but this is redundant with the parameters section
annotations_path: brief
show_root_heading: true # adds name of module to top of page
show_root_full_path: true # adds full path to root of module
show_root_toc_entry: true
show_bases: true
docstring_section_style: list
- mkdocs-jupyter:
include_source: true
include: ["*.ipynb"]
remove_tag_config:
remove_input_tags: ["hide"]
- mkdocs-pdf