koza/mkdocs.yaml at main · monarch-initiative/koza · GitHub

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site_name: 'Koza Documentation'
site_url: 'https://koza.monarchinitiative.org/'

repo_name: 'monarch-initiative/koza'
repo_url: 'https://github.com/monarch-initiative/koza'


nav:
  - Welcome: 'index.md'
  - Ingests:
    - Configuring an Ingest: 'Ingests/index.md'
    - Koza Config: 'Ingests/koza_config.md'
    - Mapping: 'Ingests/mapping.md'
    - Transform Code: 'Ingests/transform.md'
    - Testing: 'Ingests/testing.md'
  - Graph Operations:
    - Overview: 'graph-operations/index.md'
    - Tutorials:
      - 'graph-operations/tutorials/index.md'
      - Build Your First Graph: 'graph-operations/tutorials/first-graph.md'
      - Complete Merge Workflow: 'graph-operations/tutorials/merge-pipeline.md'
    - How-to Guides:
      - 'graph-operations/how-to/index.md'
      - Join Files: 'graph-operations/how-to/join-files.md'
      - Split Graphs: 'graph-operations/how-to/split-graph.md'
      - Normalize IDs: 'graph-operations/how-to/normalize-ids.md'
      - Clean Graphs: 'graph-operations/how-to/clean-graph.md'
      - Closurize: 'graph-operations/how-to/closurize.md'
      - Incremental Updates: 'graph-operations/how-to/incremental-updates.md'
      - Generate Reports: 'graph-operations/how-to/generate-reports.md'
      - Export Formats: 'graph-operations/how-to/export-formats.md'
    - Reference:
      - 'graph-operations/reference/index.md'
      - CLI Reference: 'graph-operations/reference/cli.md'
      - Python API: 'graph-operations/reference/api.md'
      - Configuration: 'graph-operations/reference/configuration.md'
    - Explanation:
      - 'graph-operations/explanation/index.md'
      - Architecture: 'graph-operations/explanation/architecture.md'
      - Schema Handling: 'graph-operations/explanation/schema-handling.md'
      - Data Integrity: 'graph-operations/explanation/data-integrity.md'
      - Biolink Compliance: 'graph-operations/explanation/biolink-compliance.md'
  - CLI: 'Usage/CLI.md'
  - Module: 'Usage/Module.md'


theme:
    name: 'material'
    docs_dir: docs/
    logo: 'img/pupa.png'
    favicon:
        'images/favicon.ico'
    features:
        - content.code.copy
        - navigation.expand
        - navigation.instant
        - navigation.tracking
        - navigation.tabs
        - navigation.tabs.sticky
    palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-2
        name: Switch to dark mode
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to light mode
    font:
        text: 'Source Sans Pro'
        code: 'Source Sans Pro Mono'


plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          inventories:
          - https://docs.python.org/3/objects.inv
          - https://mkdocstrings.github.io/objects.inv
          - https://mkdocstrings.github.io/griffe/objects.inv
          options:
            docstring_style: google
            docstring_section_style: table
            docstring_options:
              ignore_init_summary: yes
            merge_init_into_class: yes
            show_signature: no
            # separate_signature: yes
            # show_source: no
            show_root_full_path: no
            show_root_toc_entry: False
            filters:
              - "!^_[^_]"
              # - "^_[^_]"


markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.emoji
  - pymdownx.keys
  - pymdownx.magiclink
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed
  - attr_list
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.tabbed:
      alternate_style: true


extra:
  social:
    - icon: 'fontawesome/solid/house'
      link: 'https://monarchinitiative.org'
    - icon: 'fontawesome/brands/github-alt'
      link: 'https://github.com/monarch-initiative/'

#copyright: 'Copyright &copy; 2020 - 2022 Glass (contact@glass-ships.com)'