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
      - CLI: cli.md
      - Licence: distribution.md
  - Tutorials:
      - tutorials/index.md
      - ClinicalFlow Tutorial:
          - Introduction: tutorials/clinicalflow/index.md
          - Setup: tutorials/clinicalflow/setup.md
          - FHIR Basics: tutorials/clinicalflow/fhir-basics.md
          - Build Pipeline: tutorials/clinicalflow/pipeline.md
          - Create Gateway: tutorials/clinicalflow/gateway.md
          - Test with Sandbox: tutorials/clinicalflow/testing.md
          - Next Steps: tutorials/clinicalflow/next-steps.md
  - Cookbook:
      - cookbook/index.md
      - Setup FHIR Sandbox: cookbook/setup_fhir_sandboxes.md
      - Multi-Source Data Integration: cookbook/multi_ehr_aggregation.md
      - Automated Clinical Coding: cookbook/clinical_coding.md
      - Discharge Summarizer: cookbook/discharge_summarizer.md
      - ML Model Deployment: cookbook/ml_model_deployment.md
      - Format Conversion: cookbook/format_conversion.md
  - Docs:
      - Welcome: reference/index.md
      - Configuration: reference/config.md
      - Gateway:
        - Overview: reference/gateway/gateway.md
        - HealthChainAPI: reference/gateway/api.md
        - FHIR Gateway: reference/gateway/fhir_gateway.md
        - Events: reference/gateway/events.md
        - Protocols:
          - CDS Hooks: reference/gateway/cdshooks.md
          - SOAP/CDA: reference/gateway/soap_cda.md
      - I/O:
        - Containers:
          - Overview: reference/io/containers/containers.md
          - Document: reference/io/containers/document.md
          - Dataset: reference/io/containers/dataset.md
        - Adapters:
          - Overview: reference/io/adapters/adapters.md
          - CDA Adapter: reference/io/adapters/cdaadapter.md
          - CDS FHIR Adapter: reference/io/adapters/cdsfhiradapter.md
        - Mappers:
          - Overview: reference/io/mappers/mappers.md
          - FHIR Feature Mapper: reference/io/mappers/fhir_feature.md
      - Pipeline:
        - Overview: reference/pipeline/pipeline.md
        - Components:
          - Overview: reference/pipeline/components/components.md
          - CdsCardCreator: reference/pipeline/components/cdscardcreator.md
          - FHIRProblemListExtractor: reference/pipeline/components/fhirproblemextractor.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
      - Interoperability:
        - Overview: reference/interop/interop.md
        - Engine: reference/interop/engine.md
        - Configuration: reference/interop/configuration.md
        - Templates: reference/interop/templates.md
        - Mappings: reference/interop/mappings.md
        - Parsers: reference/interop/parsers.md
        - Generators: reference/interop/generators.md
        - Working with xmltodict: reference/interop/xmltodict.md
        - In Development: reference/interop/experimental.md
      - Utilities:
        - FHIR Helpers: reference/utilities/fhir_helpers.md
        - Sandbox: reference/utilities/sandbox.md
        - Data Generator: reference/utilities/data_generator.md
  - API Reference:
      - api/index.md
      - api/pipeline.md
      - api/component.md
      - api/containers.md
      - api/adapters.md
      - api/cds_hooks.md
      - api/sandbox.md
      - api/interop.md
      - api/fhir_helpers.md
  - Community:
      - community/index.md

copyright: dotimplement
theme:
  name: material
  custom_dir: docs/overrides/
  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.tabs.sticky
    - navigation.sections
    - navigation.footer
    - navigation.instant
    - header.autohide
    - announce.dismiss
    - search.suggest
    - search.highlight
  palette:
    - scheme: default
      primary: white
      accent: blue
      toggle:
        icon: material/white-balance-sunny
        name: Switch to dark mode
    - scheme: slate
      primary: custom
      accent: blue
      toggle:
        icon: material/weather-night
        name: Switch to light mode
# 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.details
  - 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
  - stylesheets/welcome.css

extra_javascript:
  - javascripts/cookbook-filter.js

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