requirements.txt

# Core dependencies
langchain-openai
langchain_anthropic
langchain-core
langgraph
langchain-mcp-adapters
python-dotenv
jinja2

# Console display
rich

# Data processing
pyyaml
pandas

# MCP server support
fastmcp
starlette
nest_asyncio
mcp
gradio

# AlphaGenome package
alphagenome==0.2.0


contourpy==1.3.3
    # via matplotlib
cycler==0.12.1
    # via matplotlib
fonttools==4.59.2
    # via matplotlib
kiwisolver==1.4.9
    # via matplotlib
matplotlib==3.10.6
    # via plotnine
mizani==0.14.2
    # via plotnine
    # via
    #   contourpy
    #   matplotlib
    #   mizani
    #   pandas
    #   patsy
    #   plotnine
    #   scipy
    #   statsmodels
packaging==25.0
    # via
    #   matplotlib
    #   statsmodels
pandas==2.3.2
    # via
    #   mizani
    #   plotnine
    #   statsmodels
patsy==1.0.1
    # via statsmodels
pillow==11.3.0
    # via matplotlib
plotnine==0.15.0
    # via -r requirements.in
pyparsing==3.2.3
    # via matplotlib
python-dateutil==2.9.0.post0
    # via
    #   matplotlib
    #   pandas
pytz==2025.2
    # via pandas
scipy==1.16.1
    # via
    #   mizani
    #   plotnine
    #   statsmodels
six==1.17.0
    # via python-dateutil
statsmodels==0.14.5
    # via plotnine
tqdm==4.67.1
    # via -r requirements.in
tzdata==2025.2
    # via pandas

# Core dependencies for AlphaGenome functionality
absl-py
anndata
grpcio>=1.67.1
immutabledict
intervaltree
jaxtyping
matplotlib
ml_dtypes
numpy
pandas
protobuf>=5.28.3
pyarrow
scipy
seaborn
tqdm
typeguard
typing_extensions
zstandard

# Visualization dependencies
plotnine

# Build dependencies
hatchling
grpcio-tools<=1.67.1
importlib-resources