mkdocs.yml

site_name: Climate Health
site_description: Climate Health Analysis Platform (CHAP) Documentation
site_url: https://dhis2-chap.github.io/chap-core/
repo_url: https://github.com/dhis2-chap/chap-core
repo_name: dhis2-chap/chap-core
use_directory_urls: false

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

plugins:
  - search
  - markdown-exec
  - panzoom:
      full_screen: true
      always_show_hint: true
  - mkdocstrings:
      handlers:
        python:
          options:
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            heading_level: 2

markdown_extensions:
  - md_in_html
  - admonition
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - toc:
      permalink: true

docs_dir: docs

exclude_docs: |
  CLAUDE.md
  kigali-workshop/kigali-workshop-material/tuesday-afternoon-backup.md

not_in_nav: |
  features_overview.md
  contributor/adding_cli_commands.md
  contributor/creating_custom_backtest_plots.md
  contributor/creating_custom_metrics.md
  contributor/creating_custom_threshold_strategies.md
  contributor/evaluation_walkthrough_exec.md
  external_models/surplus_after_refactoring.md
  feature_tutorials/index.md
  feature_tutorials/extended_predictor.md
  kigali-workshop/index.md

nav:
  - Getting Started: index.md
  - DHIS2 Implementers:
      - Overview: modeling-app/index.md
      - Installation:
          - Installation overview: modeling-app/installation.md
          - Recommendation for server deployment: modeling-app/running-chap-on-server.md
          - First-time Setup: modeling-app/fresh-installation.md
          - Updating to a New Version: modeling-app/upgrading-installation.md
          - Enabling Optional Model Services: modeling-app/enabling-optional-model-services.md
          - Running Your Own Model: modeling-app/running-your-own-model.md
      - Managing models: modeling-app/managing-model-templates.md
      - Troubleshooting:
          - Viewing Logs: modeling-app/troubleshooting/logs.md
          - Accessing the Database: modeling-app/troubleshooting/database-access.md
  - For Newcomers:
      - For newcomers: external_models/newcomer.md
      - Learning Modelling: external_models/learn_modelling.md
  - Model Developers:
      - Overview: external_models/index.md
      - Getting Started:
          - For Experienced Modellers: external_models/experienced_modeller.md

      - Installing Chap Core:
          - Prepare for installation: external_models/prepare-for-installation.md
          - Install Chap Core: chap-cli/chap-core-cli-setup.md
          - Run a model through chap: chap-cli/minimalist-example.md
      - Make your model Chap compatible:
          - Prepare your data:
              - Chap data format: external_models/prepare_data/index.md
              - "Option 1: Own data": external_models/prepare_data/own-data.md
              - "Option 2: DHIS2 data": external_models/prepare_data/dhis2-data.md
              - "Option 3: Example data": external_models/prepare_data/example-data.md
              - Validate your data: external_models/prepare_data/validate-data.md
          - Create your train and predict functions: external_models/train_and_predict.md
          - Connect your model to the Chap standard: external_models/describe_model.md
          - Defining the MLproject environment for your model: external_models/defining-virtual-environment.md
          - Additional Configuration: external_models/additional_configuration.md
          - Model Metadata: external_models/model_metadata.md
          - Generated Features: external_models/generated_features.md
      - Evaluate models with Chap:
          - Evaluation Workflow: chap-cli/evaluation-workflow.md
          - Evaluating Models: external_models/running_models_in_chap.md
      - Integration:
          - Chapkit: external_models/chapkit.md
          - Data Formats: external_models/data_formats.md
          - DHIS2 Connection: external_models/chap-dhis2-connection.md
          - Supporting Functionality: external_models/supporting_functionality.md
          - Evaluation Examples: external_models/chap_evaluate_examples.md
          - Side by Side Comparison: external_models/side_by_side_comparison.md
          - Model Explainability: external_models/model_explainability.md
      - CLI:
          - Overview: chap-cli/index.md

          - eval Reference: chap-cli/eval-reference.md
          - report Reference: chap-cli/report-reference.md
          - explain-lime Reference: chap-cli/explain-lime-reference.md

  #- Modeling App:
  #  - '!import https://github.com/dhis2-chap/chap-frontend?branch=main&docs_dir=apps/modeling-app/docs'
  - Contributors:
      - Overview: contributor/index.md
      - Contributors:
          - Getting Started: contributor/getting_started.md
          - Setup: contributor/chap-contributor-setup.md
          - Local DHIS2 Installation: contributor/local-dhis2-installation.md
          - Windows Setup: contributor/windows_contributors.md
          - Code Overview: contributor/code_overview.md
          - Architecture Diagrams: contributor/architecture_diagrams.md
          - Architecture Model (C4): contributor/architecture_model.md
          - Modeling Internals: contributor/modeling_internals.md
          - CLI vs REST API: contributor/cli_vs_rest_api.md
          - REST API and Database: contributor/rest_api_and_database.md
          - MLproject Configuration: contributor/mlproject_configuration.md
          - Vocabulary: contributor/vocabulary.md
          - Testing: contributor/testing.md
          - Database Migrations: contributor/database_migrations.md
          - Documentation: contributor/writing_building_documentation.md
          - Development Tools: contributor/development_tools.md
          - Evaluation Pipeline: contributor/evaluation_pipeline.md
          - Evaluation Walkthrough: contributor/evaluation_walkthrough.md
          - Evaluation Abstraction: contributor/evaluation_abstraction.md
          - Preference Learning: contributor/preference_learning.md
          - Creating Feature Generators: contributor/creating_feature_generators.md
      - Web API:
          - Overview: webapi/index.md
          - Developer Guide: webapi/developer.md
          - Docker Compose: webapi/docker-compose-doc.md
          - API Authentication: webapi/api-authentication.md
          - Service Registration: webapi/service-registration.md
      - API Reference: api/index.md
      - Changelog: changelog.md
  - Modeling Webinar Series:
      - "Overview": kigali-workshop/kigali-webinar-series/index.md
      - "Session 1": kigali-workshop/kigali-webinar-series/session-1/index.md
      - "Session 2":
          - kigali-workshop/kigali-webinar-series/session-2/index.md
          - kigali-workshop/kigali-webinar-series/session-2/terminal.md
          - kigali-workshop/kigali-webinar-series/session-2/git-github.md
          - kigali-workshop/kigali-webinar-series/session-2/virtual-environments.md
          - kigali-workshop/kigali-webinar-series/session-2/homework.md
      - "Session 3":
          - kigali-workshop/kigali-webinar-series/session-3/index.md
          - kigali-workshop/kigali-webinar-series/session-3/install-chap.md
          - kigali-workshop/kigali-webinar-series/session-3/fork-example.md
          - kigali-workshop/kigali-webinar-series/session-3/homework.md
      - "Session 4": kigali-workshop/kigali-webinar-series/session-4/index.md
      - "Session 5": kigali-workshop/kigali-webinar-series/session-5/index.md
      - "Session 6": kigali-workshop/kigali-webinar-series/session-6/index.md
  - DAC2026:
      - Overview: dac2026/index.md
      - Make your model configurable: dac2026/configurable-model.md
  - Kigali Workshop Material:
      - Overview: kigali-workshop/kigali-workshop-material/index.md
      - Pre-session 11 Feb: kigali-workshop/kigali-workshop-material/11_feb_presession.md
      - Monday Morning 23 Feb: kigali-workshop/kigali-workshop-material/monday-morning.md
      - Monday Afternoon 23 Feb: kigali-workshop/kigali-workshop-material/monday-afternoon.md
      - Tuesday Morning 24 Feb: kigali-workshop/kigali-workshop-material/tuesday-morning.md
      - Tuesday Afternoon 24 Feb: kigali-workshop/kigali-workshop-material/tuesday-afternoon.md
      - Progressive Effects Walkthrough: kigali-workshop/kigali-workshop-material/progressive_effects_walkthrough.md
      - Multi-Region Strategies Walkthrough: kigali-workshop/kigali-workshop-material/multi_region_walkthrough.md
      - Location Specificity Overview: kigali-workshop/kigali-workshop-material/location_specificity_overview.md
      - Interaction Effects: kigali-workshop/kigali-workshop-material/interaction_effects.md
      - Wednesday Morning 25 Feb: kigali-workshop/kigali-workshop-material/wednesday-morning.md
      - Wednesday Afternoon 25 Feb: kigali-workshop/kigali-workshop-material/wednesday-afternoon.md
      - Thursday Morning 26 Feb: kigali-workshop/kigali-workshop-material/thursday-morning.md
      - Thursday Afternoon 26 Feb: kigali-workshop/kigali-workshop-material/thursday-afternoon.md
      - Friday Morning 27 Feb: kigali-workshop/kigali-workshop-material/friday-morning.md
      - Friday Afternoon 27 Feb: kigali-workshop/kigali-workshop-material/friday-afternoon.md