mkdocs.yml

site_name: HealthChain 💫 🏥
site_description: Simplify prototyping and testing NLP applications in a healthcare context.
site_author: Jennifer Jiang-Kells

# Repository
repo_name: dotimplement/healthchain
repo_url: https://github.com/dotimplement/healthchain

nav:
  - Home: index.md
  - Getting Started:
      - Installation: installation.md
      - Quickstart: quickstart.md
      - Licence: distribution.md
  - Cookbook:
      - cookbook/index.md
      - CDS Sandbox: cookbook/cds_sandbox.md
      - NoteReader Sandbox: cookbook/notereader_sandbox.md
  - Docs:
      - Welcome: reference/index.md
      - Pipeline:
        - Overview: reference/pipeline/pipeline.md
        - Data Container: reference/pipeline/data_container.md
        - Components:
          - Overview: reference/pipeline/components/components.md
          - CdsCardCreator: reference/pipeline/components/cdscardcreator.md
        - Connectors:
          - Overview: reference/pipeline/connectors/connectors.md
          - CDA Connector: reference/pipeline/connectors/cdaconnector.md
          - CDS FHIR Connector: reference/pipeline/connectors/cdsfhirconnector.md
        - Prebuilt Pipelines:
          - Medical Coding: reference/pipeline/prebuilt_pipelines/medicalcoding.md
          - Summarization: reference/pipeline/prebuilt_pipelines/summarization.md
      - Integrations:
        - Overview: reference/pipeline/integrations/integrations.md
      - Sandbox:
        - Overview: reference/sandbox/sandbox.md
        - Client: reference/sandbox/client.md
        - Service: reference/sandbox/service.md
        - Use Cases:
          - Overview: reference/sandbox/use_cases/use_cases.md
          - Clinical Decision Support: reference/sandbox/use_cases/cds.md
          - Clinical Documentation: reference/sandbox/use_cases/clindoc.md
      - Utilities:
        - Data Generator: reference/utilities/data_generator.md
        - CDA Parser: reference/utilities/cda_parser.md
  - API Reference:
      - api/index.md
      - api/pipeline.md
      - api/component.md
      - api/containers.md
      - api/connectors.md
      - api/use_cases.md
      - api/cds_hooks.md
      - api/service.md
      - api/clients.md
      - api/cda_parser.md
      - api/data_generators.md
      - api/data_models.md

  - Community:
      - community/index.md
      - Contribution Guide: community/contribution_guide.md
      - Resources: community/resources.md

copyright: dotimplement
theme:
  name: material
  favicon: assets/images/healthchain_logo.png
  logo: assets/images/healthchain_logo.png
  icon:
    repo: fontawesome/brands/github
  features:
    - content.code.copy
    - navigation.expand
    - navigation.tabs
    - navigation.sections
    - header.autohide
    - announce.dismiss
  palette:
    primary: white
    accent: blue
# font:
#     text: Roboto


# Additional configuration
extra:
  analytics:
    provider: google
    property: !ENV GOOGLE_ANALYTICS_TAG


# Extensions
markdown_extensions:
  - admonition
  - tables
  - def_list
  - attr_list
  - md_in_html
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
      noclasses: True
      pygments_style: material
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

extra_css:
  - stylesheets/extra.css

plugins:
  - blog
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          options:
            show_submodules: true
            heading_level: 2
            docstring_section_style: spacy
  - search
  # - section-index
  # - social:
  #     cards_layout_options:
  #       color: #173a58