# Biomni release and versions aligned with the v0.0.8 reproducible environment.
biomni==0.0.8

# LLM / graph stack used by Biomni 0.0.8.
langchain==0.3.27
langchain-core==0.3.72
langchain-openai==0.3.28
langchain-anthropic==0.3.18
langchain-community==0.3.27
langchain-ollama==0.3.6
langchain-text-splitters==0.3.9
langgraph==0.3.18
langgraph-checkpoint==2.1.1
langgraph-prebuilt==0.1.8
langgraph-sdk==0.1.74
langsmith==0.4.10
ollama==0.5.1
openai==1.98.0
pydantic==2.11.7
python-dotenv==1.2.2

# Core scientific/runtime packages from Biomni's v0.0.8 environment.yml/fixed_env.yml.
pandas==2.3.1
numpy==2.1.0
scipy==1.15.0
scikit-learn==1.7.1
matplotlib==3.10.5
seaborn==0.13.2
statsmodels==0.14.5
networkx==3.5
beautifulsoup4==4.13.4
lxml==6.0.0
PyYAML==6.0.2
requests==2.33.1
# Required by biomni.tool.database (Bio.Blast / Bio.Seq). Biomni's own
# v0.0.8 bio_env.yml includes Biopython, while the PyPI core metadata does not.
biopython==1.88
tqdm==4.67.1
transformers==4.54.1
sentencepiece==0.2.0
# Biomni 0.0.8's historical full environment also pinned ToolUniverse 0.2.0,
# FastMCP 2.11.0 and MCP 1.12.3. They are intentionally NOT installed in
# this default image: the UI does not call A1.add_mcp()/ToolUniverse, and the
# historical FastMCP 2.x line now has known security issues whose complete
# fix requires FastMCP 3.x. Reintroduce MCP/ToolUniverse only together with a
# compatibility-tested Biomni upgrade. Gradio supplies its own FastAPI/Uvicorn.
jupyter==1.1.1
notebook==7.4.4
ipykernel==6.30.0

# PDF export used by Biomni 0.0.8.
PyPDF2==3.0.1
reportlab==4.4.3
markdown==3.8.2
weasyprint==66.0

# Biomni 0.0.8's bundled UI targets Gradio 5.x.
gradio==5.39.0
gradio-client==1.11.0
