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mkdocs.yml
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mkdocs.yml
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# Project information
site_name: synphage
site_url: https://vestalisvirginis.github.io/synphage/
site_author: Virginie Grosboillot
site_description: >-
Documentation of synphage, a pipeline to create phage genome synteny graphics from genbank files
# Repository
repo_url: https://github.com/vestalisvirginis/synphage
repo_name: vestalisvirginis/synphage
# Page tree
nav:
- Home: index.md
- Getting Started: short_guide.md
- User Guide:
- Installation: installation.md
- Navigating synphage pipeline: pipeline.md
- Configurations: configurations.md
- Output data: output.md
- Step-by-step example:
- Bacteriophage genomes: phages.md
- Plasmid sequences: plasmids.md
# Configuration
theme:
name: material
features:
- navigation.tabs
- navigation.sections
- navigation.expand
- navigation.path
- navigation.indexes
- navigation.footer
- navigation.tracking
- toc.follow
- navigation.top
- search.suggest
- search.highlight
- search.share
- content.code.annotate
- content.code.copy
- content.tooltips
- content.tabs.link
palette:
# Palette toggle for light mode
- scheme: default
primary: teal
accent: cyan
toggle:
icon: material/brightness-5
name: Switch to dark mode
# Palette toggle for dark mode
- scheme: slate
primary: teal
accent: cyan
toggle:
icon: material/brightness-2
name: Switch to light mode
# icon:
# logo: material/marker-check
markdown_extensions:
- tables
- admonition
- md_in_html
- pymdownx.details # coloured box
# - codehilite
# - pymdownx.highlight
- pymdownx.superfences: # grey background zone behind code and tables
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
# - pymdownx.keys
- pymdownx.snippets:
base_path: ["docs/snippets"]
- pymdownx.tabbed: # in-content tabs
alternate_style: true
- def_list
- attr_list
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.keys:
plugins:
- search
# - autorefs
# - mkdocstrings:
# handlers:
# python:
# options:
# docstring_style: google
extra_css:
- stylesheets/extra.css
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/vestalisvirginis/synphage
- icon: fontawesome/brands/docker
link: https://hub.docker.com/r/vestalisvirginis/synphage