TrialMatchAI/pyproject.toml at main · cbib/TrialMatchAI · GitHub

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[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "TrialMatchAI"
version = "0.1.0"
description = "AI-driven clinical trial matching pipeline."
readme = "README.md"
requires-python = ">=3.10,<3.12"
license = {file = "LICENSE"}
dependencies = [
  # Core ML / NLP
  "torch==2.7.1",
  "torchvision==0.22.1",
  "torchaudio==2.7.1",
  "transformers==4.55.0",
  "accelerate==1.8.1",
  "tokenizers==0.21.1",
  "safetensors==0.5.3",
  "sentence-transformers==2.7.0",
  "sentencepiece==0.2.0",
  "datasets==2.19.0",
  "faiss-cpu==1.9.0.post1",
  "peft==0.15.2",
  "einops==0.8.0",
  "tiktoken==0.8.0",
  "bitsandbytes==0.46.1",
  "vllm==0.10.1.1",
  # Classical stack & utilities
  "numpy==1.26.4",
  "scipy==1.15.1",
  "scikit-learn==1.6.1",
  "pandas==2.2.3",
  "tqdm==4.67.1",
  "regex==2024.11.6",
  "orjson==3.10.14",
  "PyYAML==6.0.2",
  "python-dotenv==1.0.1",
  "rich==13.9.4",
  # spaCy / medspaCy (for your medical text work)
  "spacy==3.7.5",
  "medspacy==1.3.1",
  "medspacy_quickumls==3.2",
  "PyRuSH==1.0.9",
  "PyFastNER==1.0.10",
  "pysbd==0.3.4",
  "quicksectx==0.4.0",
  "gliner==0.2.16",
  # App / infra
  "SQLAlchemy==2.0.37",
  "pydantic==2.11.7",
  "pydantic-settings==2.7.1",
  # Optional APIs
  "openai==1.99.1",
  "httpx==0.28.1",
  "langchain==0.3.18",
  "langchain-core==0.3.35",
  "langchain-community==0.3.17",
  "langchain-openai==0.3.5",
  "langsmith==0.2.11",
  "huggingface_hub==0.34.4",
]

[project.scripts]
trialmatchai-healthcheck = "Matcher.cli.healthcheck:main"

[dependency-groups]
dev = [
  "pytest>=7.4",
  "ruff>=0.6.0",
]

[tool.setuptools]
package-dir = {"" = "source"}
include-package-data = true

[tool.setuptools.packages.find]
where = ["source"]

[tool.uv]
index-url = "https://pypi.org/simple"

[[tool.uv.index]]
name = "pytorch-cuda"
url = "https://download.pytorch.org/whl/cu128"
explicit = true

[tool.uv.sources]
torch = { index = "pytorch-cuda" }
torchvision = { index = "pytorch-cuda" }
torchaudio = { index = "pytorch-cuda" }