mkdocs.yml

site_name: MiADE
site_description: A set of tools for extracting formattable data from clinical notes stored in electronic health record systems.

# Repository
repo_name: uclh-criu/miade
repo_url: https://github.com/uclh-criu/miade

# Configuration for the theme
theme:
  name: material
  logo: assets/miade-logo-small.png
  favicon: assets/miade-logo-small.png
  palette:
    primary: teal
    accent: red
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.instant
    - navigation.sections
    - navigation.expand
    - navigation.path
    - navigation.indexes
    - toc.integrate 
    - content.code.copy
    - content.code.select

# Extensions
markdown_extensions:
  - admonition
  - toc:
      permalink: true
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true

# Pages
nav:
  - Home: index.md
  - User Guide:
    - Quickstart: user-guide/quickstart.md
    - Configurations: user-guide/configurations.md
    - Cookbook: user-guide/cookbook.md
  - API Reference:
    - Pipeline Components:
      - NoteProcessor: api-reference/noteprocessor.md
      - Annotator: api-reference/annotator.md
      - ProblemsAnnotator: api-reference/problemsannotator.md
      - MedsAllergiesAnnotator: api-reference/medsallergiesannotator.md
      - DosageExtractor: api-reference/dosageextractor.md
    - Objects:
      - Note: api-reference/note.md
      - Concept: api-reference/concept.md
      - Dosage: api-reference/dosage.md
      - MetaAnnotations: api-reference/metaannotations.md
  - About:
    - Overview: about/overview.md
    - Team: about/team.md
  - Community: contributing.md

plugins:
  - search
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          rendering:
            show_source: true