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mkdocs.yml
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mkdocs.yml
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site_name: 'Pheno-Search Documentation'
site_description: 'Pheno-Search Documentation'
site_author: 'Manuel Rueda, PhD'
copyright: '© Copyright 2024, Manuel Rueda, CNAG'
repo_name: 'Pheno-Search'
repo_url: https://github.com/mrueda/pheno-search
edit_uri: edit/main/docs/
extra_css:
- css/theme_overrides.css
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css
extra_javascript:
- js/theme_overrides.js
- js/katex.js
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js
plugins:
- search
- macros
- mermaid2:
arguments:
startOnLoad: true
markdown_extensions:
- toc:
toc_depth: 2-3
permalink: true
- admonition
- attr_list
- footnotes
- md_in_html
- pymdownx.critic
- pymdownx.caret
- pymdownx.details
- pymdownx.keys
- pymdownx.mark
- pymdownx.tilde
- pymdownx.saneheaders
- pymdownx.magiclink:
hide_protocol: true
- pymdownx.tabbed:
alternate_style: true
- pymdownx.tasklist:
custom_checkbox: true
- tables
- mdx_gh_links:
user: CNAG-Biomedical-Informatics
repo: pheno-search
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets:
base_path: docs
url_download: true
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:mermaid2.fence_mermaid
- pymdownx.arithmatex:
generic: true
nav:
- Introduction:
- What is Pheno-Search?: what-is-pheno-search.md
- Which are the supported formats:
- BFF: bff.md
- PXF: pxf.md
- Other formats: other-formats.md
- 'Download & Installation': download-and-installation.md
- Help:
- 'Tutorial: JSON format': tutorial-json-format.md
- Google colab: https://colab.research.google.com/drive/1n3Etu4fnwuDWNveSMb1SzuN50O2a05Rg#scrollTo=8tbJ0f5-hJAB
- Usage: usage.md
- FAQs: faq.md
- About:
- About: about.md
- Citation: citation.md
theme:
name: material
#custom_dir: overrides
palette:
- media: '(prefers-color-scheme: dark)'
scheme: default
primary: blue grey
accent: amber
toggle:
icon: material/lightbulb
name: Switch to light mode
- media: '(prefers-color-scheme: light)'
scheme: slate
primary: blue grey
accent: amber
toggle:
icon: material/lightbulb-outline
name: Switch to dark mode
logo: img/iconhex.svg
favicon: img/favicon-2x.png
icon:
repo: fontawesome/brands/github-alt
features:
- content.code.select
- content.code.copy
- content.tabs.link
- search.highlight
- search.share
# - navigation.instant # otherwise blocks rendering of mermaid on page load
- navigation.tracking
- navigation.sections
- toc.integrate
# Options
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/mrueda