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mkdocs.yml
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site_name: BioChatter
theme:
name: material
font:
text: Lato
code: Roboto Mono
palette:
# Palette toggle for dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: blue grey
accent: indigo
toggle:
icon: material/brightness-4
name: Switch to light mode
# Palette toggle for light mode
- media: "(prefers-color-scheme: light)"
scheme: default
primary: indigo
accent: blue
toggle:
icon: material/brightness-7
name: Switch to dark mode
features:
- content.code.copy
- content.action.edit
- search.suggest
- search.highlight
- navigation.instant
- navigation.tabs
- toc.integrate
icon:
repo: fontawesome/brands/github
plugins:
- search
- mkdocstrings:
default_handler: python
handlers:
python:
options:
heading_level: 3
- table-reader
- social
- redirects:
redirect_maps:
"vignette-custom-bclight-simple.md": "vignettes/custom-bclight-simple.md"
"vignette-custom-bclight-advanced.md": "vignettes/custom-bclight-advanced.md"
"vignette-kg.md": "vignettes/kg.md"
"vignette-rag.md": "vignettes/rag.md"
"benchmarking.md": "features/benchmark.md"
"chat.md": "features/chat.md"
"rag.md": "features/rag.md"
"reflexion-agent.md": "features/reflexion-agent.md"
"open-llm.md": "features/open-llm.md"
"wasm.md": "features/wasm.md"
"podcast.md": "features/podcast.md"
"llm_connect-reference.md": "api-docs/llm_connect.md"
"vectorstore-reference.md": "api-docs/vectorstore.md"
"kg-reference.md": "api-docs/kg.md"
"api-reference.md": "api-docs/api-calling.md"
"reflexion-reference.md": "api-docs/reflexion.md"
"podcast-reference.md": "api-docs/podcast.md"
"benchmark.md": "benchmark/overview.md"
"benchmark-results.md": "benchmark/results.md"
"benchmark-developer.md": "benchmark/developer.md"
site_url: https://biochatter.org/
nav:
- Home: index.md
- Features:
- Home: features/index.md
- Basic Usage - Chat: features/chat.md
- Retrieval-Augmented Generation: features/rag.md
- API Calling: features/api.md
- Reflexion via LangGraph: features/reflexion-agent.md
- Open-source and Local LLMs: features/open-llm.md
- LLM in your Browser - WebAssembly: features/wasm.md
- The Living Benchmark: features/benchmark.md
- Podcast my Paper: features/podcast.md
- Benchmark:
- Overview: benchmark/overview.md
- All Results: benchmark/results.md
- Developer Guide: benchmark/developer.md
- Vignettes:
- Home: vignettes/index.md
- Knowledge Graph RAG: vignettes/kg.md
- Retrieval-Augmented Generation (RAG): vignettes/rag.md
- Customising BioChatter Light - Simple: vignettes/custom-bclight-simple.md
- Customising BioChatter Light - Advanced: vignettes/custom-bclight-advanced.md
- Customising BioChatter Light and Next - Cancer Genetics Use Case: vignettes/custom-decider-use-case.md
- API Reference:
- Home: api-docs/index.md
- LLM Connectivity: api-docs/llm_connect.md
- Vectorstore Agent: api-docs/vectorstore.md
- Knowledge Graph Agent: api-docs/kg.md
- "API Calling: Base Classes": api-docs/api-calling-base.md
- "API Calling: Web APIs": api-docs/api-calling-web.md
- "API Calling: Python APIs": api-docs/api-calling-python.md
- Reflexion Agent: api-docs/reflexion.md
- Podcast: api-docs/podcast.md
repo_url: https://github.com/biocypher/biochatter
repo_name: biocypher/biochatter
edit_uri: edit/main/docs/
markdown_extensions:
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences
- pymdownx.tabbed:
alternate_style: true
slugify: !!python/object/apply:pymdownx.slugs.slugify
kwds:
case: lower
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- attr_list
- md_in_html
- admonition
- pymdownx.details
- toc:
toc_depth: 3
extra_javascript:
- https://unpkg.com/[email protected]/dist/tablesort.min.js
- scripts/tablesort.js
hooks:
- docs/scripts/hooks.py