synthlab/pyproject.toml at main · bschilder/synthlab · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "synthlab"
version = "0.1.0"
description = "Python tools for working with synthetic healthcare datasets (Synthea, UK Biobank Synthetic Dataset)"
readme = "README.md"
requires-python = ">=3.8"
license = {text = "MIT"}
authors = [
    {name = "Your Name", email = "your.email@example.com"},
]
keywords = ["synthea", "ukbiobank", "synthetic", "healthcare", "omop", "cdm", "patient", "data", "biobank"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]

dependencies = [
    "pooch>=1.6.0",
    "pandas>=1.5.0",
    "polars>=0.19.0",
    "requests>=2.28.0",
    "matplotlib>=3.5.0",
    "tiktoken>=0.6.0",
    "torch",
    "torchvision",
    "transformers>=4.50.0",
    "sentence-transformers",
    "python-dotenv",
    "litellm",
    "accelerate",
    "bitsandbytes",
    "biomcp-python",
    "biodb @ git+https://github.com/standardmodelbio/bioDB",
]

[project.optional-dependencies]
aws = [
    "boto3>=1.26.0",
]
viz = [
    # Notebook visualisation stack used by notebooks/olink_demo.ipynb.
    "matplotlib>=3.8",
    "seaborn>=0.13",
    "scikit-learn>=1.5",
    "umap-learn>=0.5",
]
genomics = [
    "numpy>=1.20.0",
]
imaging = [
    "pydicom>=2.4.0",
]
tracking = [
    "wandb>=0.16.0",
]
snomed = [
    "faiss-cpu>=1.7.0",
    "faiss-gpu>=1.7.0",
    "numpy>=1.20.0",
]
visualization = [
    "pyvis>=0.3.0",
    "networkx>=2.8.0",
]
meds = [
    # Medical Event Data Standard ETL (OMOP / MIMIC-IV → MEDS parquet).
    # https://github.com/Medical-Event-Data-Standard/meds_etl
    "meds_etl>=0.3",
    "meds>=0.4",
]
tests = [
    "pytest>=8.0",
    "pytest-cov>=5.0",
]
all = [
    "boto3>=1.26.0",
    "numpy>=1.20.0",
    "pydicom>=2.4.0",
    "wandb>=0.16.0",
    "tqdm>=4.60.0",
    "tiktoken>=0.6.0",
    "faiss-cpu>=1.7.0",
    "faiss-gpu>=1.7.0",
    "pyvis>=0.3.0",
    "networkx>=2.8.0",
    "meds_etl>=0.3",
    "meds>=0.4",
]

[project.urls]
Homepage = "https://github.com/yourusername/synthlab"
Documentation = "https://github.com/yourusername/synthlab#readme"
Repository = "https://github.com/yourusername/synthlab"
Issues = "https://github.com/yourusername/synthlab/issues"

[tool.setuptools.packages.find]
where = ["."]
include = ["synthlab*"]

[tool.setuptools.package-data]
synthlab = ["py.typed", "data/*.csv"]

[tool.black]
line-length = 100
target-version = ['py38', 'py39', 'py310', 'py311', 'py312']

[tool.isort]
profile = "black"
line_length = 100