[project]
name = "gdc-qag"
version = "0.1.0"
description = "a package to run query augmented generation on the genomic data commons"
authors = [
    {name = "aartiv",email = "aartiv@uchicago.edu"}
]
readme = "README.md"
requires-python = "^3.10"
dependencies = [
    "spacy (==3.7.5)",
    "en-core-sci-md @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_md-0.5.4.tar.gz#sha256=7c8fc52542dd1452ffce00b045c1298e2c185b7cf84793f8e0ec941987c09808",
    "en-ner-bc5cdr-md @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_ner_bc5cdr_md-0.5.4.tar.gz#sha256=ffc73130a710edf851206199720cb2c744a043e032f5da6ba4bb36863deca778",
    "huggingface-hub (>=0.33.2,<0.34.0)",
    "langchain (>=0.3.26,<0.4.0)",
    "langchain-core (>=0.3.68,<0.4.0)",
    "langchain-text-splitters (>=0.3.8,<0.4.0)",
    "langsmith (>=0.4.4,<0.5.0)",
    "matplotlib-inline (>=0.1.7,<0.2.0)",
    "numpy (==1.26.4)",
    "pandas (==2.2.3)",
    "requests (>=2.32.4,<3.0.0)",
    "torch (==2.5.1)",
    "tqdm (>=4.67.1,<5.0.0)",
    "transformers (==4.49.0)",
    "uvicorn (>=0.35.0,<0.36.0)",
    "uvloop (==0.21.0)",
    "vllm (==0.7.2)",
    "gradio (>=5.35.0,<6.0.0)",
    "tabulate (>=0.9.0,<0.10.0)",
    "guidance (>=0.2.4,<0.3.0)",
    "spaces (>=0.37.1,<0.38.0)",
    "matplotlib (>=3.10.3,<4.0.0)",
    "scipy (==1.13.1)",
    "seaborn (>=0.13.2,<0.14.0)",
    "statannotations (>=0.7.2,<0.8.0)",
    "mcp (>=1.12.0,<2.0.0)",
    "accelerate (>=1.9.0,<2.0.0)",
    "scikit-learn (>=1.7.1,<2.0.0)"
]
package-mode = false


[build-system]
requires = ["poetry-core>=2.0.0,<3.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.group.dev.dependencies]
pre-commit = "^4.2.0"