biotope/mkdocs.yml at main · biocypher/biotope · GitHub

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site_name: Biotope
site_description: Build typed Python knowledge graphs from reviewed Croissant metadata, with provenance for every exported node and edge.
site_author: BioCypher Team
site_url: https://biocypher.github.io/biotope/

markdown_extensions:
  - admonition
  - attr_list
  - toc:
      permalink: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true

theme:
  features:
    - content.code.annotate
    - content.code.copy
    - navigation.indexes
    - navigation.instant
    - navigation.tracking
    - navigation.top
  name: material
  palette:
    - scheme: default
      primary: blue grey
      accent: light blue
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: blue grey
      accent: light blue
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

nav:
  - Home: index.md
  - Installation: installation.md
  - Tutorial: tutorial.md
  - Agent setup: plugin.md
  - Commands:
      - Overview: commands.md
      - Report formats: commands_sidenotes.md
  - Extraction: extraction.md
  - Typed graph projects:
      - Authoring: mapping.md
      - Technical notes: mapping_sidenotes.md
  - Architecture: architecture.md
  - Annotation policies:
      - Configuration: cluster-compliance.md
      - Administration examples: cluster-compliance_sidenotes.md
  - Migration to 0.10: migration.md
  - Development ideas: ideas.md
  - Roadmap: roadmap.md

validation:
  links:
    anchors: warn

plugins:
  - search

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/biocypher
      name: BioCypher Team

extra_css:
  - stylesheets/extra.css

copyright: Copyright &copy; 2025–2026 BioCypher Team

repo_url: https://github.com/biocypher/biotope
repo_name: biocypher/biotope
edit_uri: edit/main/docs

watch:
  - biotope