tdfpy/mkdocs.yml at main · tacular-omics/tdfpy · GitHub

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site_name: tdfpy
site_description: Read Bruker timsTOF .d data in Python, with centroiding and noise filtering.
site_url: https://tacular-omics.github.io/tdfpy/
repo_url: https://github.com/tacular-omics/tdfpy
repo_name: tacular-omics/tdfpy
edit_uri: edit/main/docs/
copyright: Copyright &copy; the tdfpy authors. MIT licence.

theme:
  name: material
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.sections
    - navigation.top
    - navigation.footer
    - content.code.copy
    - search.highlight
    - search.suggest

validation:
  omitted_files: warn
  absolute_links: warn
  unrecognized_links: warn
  anchors: warn

nav:
  - Home: index.md
  - Getting started: getting-started.md
  - Guides:
    - Slicing .d folders: utilities.md
    - Spectrum batches and file checks: analysis.md
    - MCP interface: mcp.md
    - Maintenance: maintenance.md
    - Migrating to 5.0: migration.md
  - API reference:
    - Readers: api/readers.md
    - Frames: api/frames.md
    - Precursor: api/precursor.md
    - DIA windows: api/windows.md
    - PRM data elements: api/prm.md
    - Metadata: api/metadata.md
    - Lookups: api/lookup.md
    - Centroiding: api/centroiding.md
    - Pipeline: api/pipeline.md
    - Noise filters: api/noise.md
    - Region exclusion: api/regions.md
    - Visualization: api/viz.md
    - Low-level access: api/low-level.md
  - Changelog: https://github.com/tacular-omics/tdfpy/blob/main/CHANGELOG.md
  - Citation: citation.md

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            docstring_style: google
            show_source: true
            show_root_heading: true
            show_symbol_type_heading: true
            members_order: source
            inherited_members: true
            merge_init_into_class: true
            filters: ["!^_"]
            show_signature_annotations: true
            separate_signature: true
            annotations_path: source
            signature_crossrefs: true

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.superfences
  - md_in_html
  - toc:
      permalink: true