ms-mint/mkdocs.yml at main · LewisResearchGroup/ms-mint · GitHub

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site_name: MS-MINT Documentation
site_description: Documentation for MS-MINT, a mass spectrometry data analysis toolkit
site_author: Lewis Research Group
site_url: https://lewisresearchgroup.github.io/ms-mint/
repo_url: https://github.com/LewisResearchGroup/ms-mint
repo_name: LewisResearchGroup/ms-mint

theme:
  name: material
  favicon: assets/favicon.png
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: deep purple
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: deep purple
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.sections
    - navigation.expand
    - navigation.indexes
    - navigation.top
    - toc.integrate
    - search.suggest
    - search.highlight
    - content.tabs.link
    - content.code.copy
    - content.code.annotate

markdown_extensions:
  - admonition
  - attr_list
  - def_list
  - footnotes
  - meta
  - md_in_html
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/LewisResearchGroup/ms-mint
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/ms-mint/
  copyright: Copyright &copy; 2022-2025 Lewis Research Group
  consent:
    title: Cookie consent
    description: >-
      We use cookies to recognize your repeated visits and preferences, as well
      as to measure the effectiveness of our documentation and whether users
      find what they're searching for. With your consent, you're helping us to
      make our documentation better.
    actions:
      - accept
      - reject
      - manage
    cookies:
      analytics:
        name: Google Analytics
        checked: true
  analytics:
    provider: google
    property: G-9RJ7Z0BG5W

extra_css:
  - stylesheets/extra.css

plugins:
  - search
  - autorefs:
      resolve_closest: true
  - mkdocstrings:
      handlers:
        python:
          rendering:
            show_root_heading: true
            show_root_full_path: true
            show_submodules: true
            members_order: source
          paths: [./src]

nav:
  - Home: index.md
  - Getting Started:
    - Installation: installation.md
    - Quickstart: quickstart.md
  - User Guide:
    - user_guide/index.md
    - File Formats: user_guide/file_formats.md
    - Target Lists: user_guide/target_lists.md
    - Visualization: user_guide/visualization.md
    - GUI: user_guide/gui.md
  - API Reference:
    - api_reference/index.md
    - Core Classes: api_reference/core.md
    - I/O: api_reference/io.md
    - Processing: api_reference/processing.md
    - Targets: api_reference/targets.md
    - Visualization: api_reference/visualization.md
    - Tools: api_reference/tools.md
  - Troubleshooting: troubleshooting.md