meta-hq/mkdocs.yml at main · phicks22/meta-hq · GitHub

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site_name: MetaHQ Documentation
site_description: Query systems for accessing the MetaHQ database.
site_author: Parker Hicks, Faisal Alquaddoomi
site_url: https://krishnanlab.github.io/meta-hq/

repo_name: krishnanlab/meta-hq
repo_url: https://github.com/krishnanlab/meta-hq
edit_uri: blob/main/docs/

extra_css:
  - stylesheets/extra.css

theme:
  name: material
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.top
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.code.annotate
  icon:
    repo: fontawesome/brands/github

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths: [packages/core/src, packages/cli/src]
          options:
            docstring_style: google
            show_source: false
            show_root_heading: false
            show_root_toc_entry: false
            show_root_full_path: false
            show_submodules: true
            members_order: source

markdown_extensions:
  - mkdocs-click
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - admonition
  - pymdownx.details
  - attr_list
  - md_in_html
  - tables
  - toc:
      permalink: true
      toc_depth: 4

nav:
  - Home: index.md
  - Getting Started:
      - Installation: getting-started/installation.md
      - Quick Start: getting-started/quickstart.md
  - User Guide:
      - Setup: user-guide/setup.md
      - Search: user-guide/search.md
      - Retrieve: user-guide/retrieve.md
      - Validate: user-guide/validate.md
      - Delete: user-guide/delete.md
  - Contribute:
    - Overview: contribute/index.md
    - Annotations: contribute/annotations.md
    - Code: contribute/code.md
  - Developer Guide:
      - Packages Overview: developer/index.md
      - Development Setup: developer/setup.md
      - Publish checklist: developer/checklist.md
      - Packages:
          - metahq-core:
              - Query:
                - Query: packages/core/api/query/query.md
                - LongAnnotations: packages/core/api/query/long_anno.md
                - ParsedEntry: packages/core/api/query/parsed.md
                - UnParsedEntry: packages/core/api/query/unparsed.md
              - Curations:
                - Annotations: packages/core/api/curations/annotations.md
                - Labels: packages/core/api/curations/labels.md
                - Ids: packages/core/api/curations/ids.md
                - Propagator: packages/core/api/curations/propagator.md
              - Export:
                - Annotations: packages/core/api/export/annotations.md
                - Labels: packages/core/api/export/labels.md
              - Search: packages/core/api/search.md
              - Utilities:
                - IO: packages/core/api/util/io.md
                - Exceptions: packages/core/api/util/exceptions.md
                - Helpers: packages/core/api/util/helpers.md
                - Progress: packages/core/api/util/progress.md
                - Supported: packages/core/api/util/supported.md
              - Logger: packages/core/api/logger.md
          - metahq-cli:
            - Commands:
              - Setup: packages/cli/commands/setup.md
              - Search: packages/cli/commands/search.md
              - Retrieve: packages/cli/commands/retrieve.md
              - Validate: packages/cli/commands/validate.md
              - Delete: packages/cli/commands/delete.md
            - Builder: packages/cli/api/builder.md
            - Retriever: packages/cli/api/retriever.md
            - Retrieval Configs:
              - QueryConfig: packages/cli/api/configs/query.md
              - CurationConfig: packages/cli/api/configs/curation.md
              - OutputConfig: packages/cli/api/configs/output.md
            - Setup:
              - Config: packages/cli/api/setup/config.md
              - Downloader: packages/cli/api/setup/download.md
  - About:
      - Cite Us: about/citation.md
      - Mission: about/mission.md
      - License: about/license.md

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/krishnanlab/meta-hq
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/metahq-cli/

extra_css:
  - stylesheets/extra.css

copyright: Copyright &copy; 2025 The Krishnan Lab