mkdocs.yml

site_name: Long-read sequence analysis
nav:
    - Home: index.md
    - Precourse preparations: precourse.md
    - Course schedule: course_schedule.md
    - Course material:
      - Introduction: course_material/introduction.md
      - Server login: course_material/server_login.md
      - QC and alignment: course_material/qc_alignment.md
      - Applications: course_material/applications.md
      - Group work: 
        - Introduction: course_material/group_work/group_work.md
        - Project 1: course_material/group_work/project1.md
        - Project 2: course_material/group_work/project2.md
        - Project 3: course_material/group_work/project3.md

theme:
  name: material
  logo: assets/images/SIB_logo.svg
  favicon: assets/images/SIB_logo.svg
  custom_dir: overrides

# Repository
repo_name: sib-swiss/NGS-longreads-training
repo_url: https://github.com/sib-swiss/NGS-longreads-training

markdown_extensions:
  - abbr
  - def_list
  - footnotes
  - tables
  - admonition
  - codehilite:
      guess_lang: false
  - sane_lists
  - smarty
  - toc
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true 
  - attr_list
  - pymdownx.tabbed
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
      options:
        custom_icons:
          - overrides/.icons
  - pymdownx.arithmatex:
      generic: true

extra_css:
  - stylesheets/extra.css

extra:
  version:
    provider: mike
  analytics:
    provider: matomo
    base_url: https://matomo.sib.swiss/
    site_id: 220

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