mkdocs.yml

site_name: Example Project
site_url: https://fmi-faim.github.io//example-project
repo_url: https://github.com/fmi-faim/example-project
repo_name: example-project
copyright: Copyright © 2024, Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)
nav:
  - Home: index.md
  - Installation: installation.md
  - Data: data.md
  - Tutorial:
    - 'Step-by-Step': tutorial/run_processing_steps.md
    - 'Nextflow Workflow': tutorial/run_workflow.md
    - 'Working with the Template': tutorial/working_with_the_template.md
  - 'How-to Guides': how_to/guides.md
  - Explanation: explanation/explanations.md
  - References: references/references.md
  - Imprint: imprint.md
theme:
  name: material
  favicon: images/favicon.ico
  icon:
    repo:
      fontawesome/brands/github
  font:
    text: Source Sans Pro
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode

    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.footer
    - header.autohide
    - content.code.copy
    - content.tabs.link
  shortcuts:
    help: 191    # ?
    next: 78     # n
    previous: 80 # p
    search: 83   # s
plugins:
  - offline:
      enabled: !ENV [ OFFLINE, false ]  # noqa
  - git-revision-date-localized:
      enable_creation_date: true
  - git-committers:
     repository: fmi-faim/example-project
     branch: main
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [ source ]
          options:
            docstring_style: numpy
            docstring_section_style: spacy
            show_root_heading: false
            show_root_toc_entry: false
            show_root_full_path: false
            heading_level: 2
markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - md_in_html
  - markdown_include.include
  - def_list