mkdocs copy.yml

# Project information
site_name: My page
site_url: "" # This should be nothing cause we build the webpage from local
site_author: Jose Alejandro Romero Herrera
site_description: >-
  This course is an introduction for how to approach bulk RNAseq data, starting from the sequencing reads. 
  It will provide an overview of the fundamentals of RNAseq analysis, including read preprocessing, data normalization, data exploration with PCAs and heatmaps, performing differential expression analysis and annotation of the differentially expressed genes. 
  Participants will also learn how to evaluate confounding and batch effects in the data. 
  The course will further touch upon laboratory protocols, library preparation, and experimental design of RNA sequencing experiments, especially about how they influence downstream bioinformatic analysis.   

# Repository
repo_name: hds-sandbox/bulk_RNAseq_course
repo_url: https://github.com/hds-sandbox/bulk_RNAseq_course

# Configuration
theme:

  # Use the Material for MkDocs theme
  # url: https://squidfunk.github.io/mkdocs-material/

  name: material
  
  # Necessary for search to work properly
  include_search_page: false
  search_index_only: true

  # Default values, taken from mkdocs_theme.yml
  language: en
  features:
    - content.code.annotate
    # - content.tabs.link
    - content.tooltips
    # - header.autohide
    # - navigation.expand
    - navigation.indexes
    # - navigation.instant
    # - navigation.prune
    - navigation.sections
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    # - toc.integrate

  palette:
    # Sandbox colours - "brightness" and "slate" - are defined in stylesheets/extra.css 
    # Palette toggle for light mode
    - scheme: brightness
      toggle:
        icon: material/brightness-7 
        name: Switch to dark mode

    # Palette toggle for dark mode
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  font:
    text: Roboto
    code: Roboto Mono

  favicon: img/favicon.png
  logo: img/logo.png

# Changes to website colours and image parameters
extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

plugins:
  - search

  # minify HTML of a page before it is written to disk
  - minify:
      minify_html: true

# Analytics and social media
extra:
  analytics:
    provider: google
    property: !ENV GOOGLE_ANALYTICS_KEY
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/hds-sandbox
    - icon: fontawesome/brands/twitter
      link: https://twitter.com/ucph_heads
  homepage: http://hds-sandbox.github.io/ 
  
# Extensions

markdown_extensions:
  - abbr # abbreviations   
  - admonition  
  - attr_list # Add HTML/CSS to Markdown elements  
  - def_list # Definition lists  
  - footnotes  
  - md_in_html  
  - toc: # Table of contents  
      permalink: true # Adds anchor link, can customise symbol with emoji  

  - tables  

  # Python extensions - can see descriptions  
  # at https://facelessuser.github.io/pymdown-extensions/  

  - pymdownx.arithmatex: # LaTeX  
      generic: true  
  - pymdownx.betterem: # improves emphasis (bold/italic) handling  
      smart_enable: all   
  - pymdownx.critic # useful for marking .md file without changes to html  
  - pymdownx.caret # improved functionality for caret symbol  
  - pymdownx.details # collapsable elements that hide content  
  - pymdownx.emoji: 
      emoji_generator: !!python/name:materialx.emoji.to_svg  
      emoji_index: !!python/name:materialx.emoji.twemoji  
  - pymdownx.highlight: # code highlighting  
      anchor_linenums: true  
  - pymdownx.inlinehilite # inline code highlight  
  - pymdownx.keys # to make entering and styling keyboard key presses easier  
  - pymdownx.mark # highlight/mark text  
  - pymdownx.smartsymbols # special characters (e.g. arrows, tm, fractions)  
  - pymdownx.superfences # arbitrary nesting of code and content blocks inside each other
  - pymdownx.tabbed: # add tabs to .md file
      alternate_style: true
  - pymdownx.tasklist: # checkbox task list  
      custom_checkbox: true
  - pymdownx.tilde # delete and subscript

# Extra configs
use_directory_urls: false
docs_dir: develop
site_dir: docs

# Page tree
nav:
  - index.md