svcv4-model/mkdocs.yml at main · clingen-data-model/svcv4-model · GitHub

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site_name: SVCv4 Classification Model
site_description: GA4GH GKS VA-Spec community profile for the ACMG/AMP/CAP/ClinGen SVCv4 Standards
site_url: https://clingen-data-model.github.io/svcv4-model/
repo_url: https://github.com/clingen-data-model/svcv4-model
repo_name: clingen-data-model/svcv4-model
edit_uri: edit/main/docs/
strict: true

theme:
  name: material
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - toc.follow
    - content.code.copy
    - content.action.edit
    - content.action.view
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/weather-sunny
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/weather-night
        name: Switch to light mode

extra_css:
  - assets/stylesheets/applicability.css

plugins:
  - search
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [src]
          options:
            show_source: false
            show_root_heading: true
            show_root_full_path: false
            show_signature_annotations: true
            separate_signature: true
            members_order: source
            heading_level: 2
            merge_init_into_class: true
            show_bases: true
            docstring_section_style: table

markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - pymdownx.details
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - tables
  - toc:
      permalink: true

nav:
  - Overview:
      - Home: index.md
      - SVCv4 Standards in brief: overview/svcv4-in-brief.md
      - How SVCv4 maps to the model: overview/alignment.md
      - What this project is — and isn't: overview/scope.md
  - Getting Started:
      - "Show your work: structured evidence": getting-started/show-your-work.md
      - The assertion framework: getting-started/assertion-framework.md
      - Evidence Lines & Evidence Items: getting-started/evidence-lines-and-items.md
      - Capture your first case: getting-started/first-case.md
  - Workflows:
      - Workflows overview: workflows/index.md
      - Human Observational Data (HOD):
          - workflows/hod/index.md
          - Clinical Observations (CLN):
              - workflows/hod/cln/index.md
              - Affected (CLN_AFF): workflows/hod/cln/cln-aff.md
              - De novo (CLN_DNV): workflows/hod/cln/cln-dnv.md
              - Alternative Cause (CLN_ALT): workflows/hod/cln/cln-alt.md
              - Unaffected (CLN_UAF): workflows/hod/cln/cln-uaf.md
          - Population (POP): workflows/hod/pop.md
          - Locus Specificity (LOC): workflows/hod/loc.md
      - Predictive & Functional Data (PFD):
          - workflows/pfd/index.md
      - Case model & applicability: workflows/case-model.md
  - Examples:
      - Examples overview: examples/index.md
  - Reference:
      - Model reference: reference/model.md
      - JSON Schemas: reference/schemas.md
      - Summary Table: reference/summary-table.md
      - VA-Spec community profile: reference/va-spec-profile.md
      - Glossary: reference/glossary.md
      - "Interop: GA4GH GKS": reference/gks-interop.md
      - "Interop: ClinGen CSpec": reference/cspec-interop.md
      - Contributing: reference/contributing.md
      - Credits & acknowledgements: reference/credits.md