fusion_oncology/pyproject.toml at main · mytechnotalent/fusion_oncology · GitHub

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[build-system]
requires = ["setuptools>=68.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "fusion-oncology"
version = "0.1.0"
description = "Multi-modal cancer genomics analysis fusing XGBoost feature importance with DNABERT sequence embeddings"
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.10"
authors = [{ name = "Fusion Oncology Contributors" }]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]
dependencies = [
    "biopython>=1.83",
    "matplotlib>=3.8",
    "numpy>=1.26",
    "pandas>=2.1",
    "requests>=2.31",
    "scikit-learn>=1.4",
    "scipy>=1.12",
    "seaborn>=0.13",
    "torch>=2.1",
    "transformers>=4.41",
    "xgboost>=2.0",
    "click>=8.1",
    "rich>=12.4",
    "lifelines>=0.28",
    "pyarrow>=14.0",
    "optuna>=3.6",
    "shap>=0.46",
]

[project.optional-dependencies]
dev = [
    "pytest>=9.0.2",
    "pytest-cov>=7.0.0",
    "ruff>=0.2",
    "mypy>=1.8",
    "pre-commit>=4.5.1",
    "black>=26.1.0",
    "nbqa>=1.7",
]

[project.scripts]
fusion-oncology = "fusion_oncology.cli:main"

[project.urls]
Repository = "https://github.com/fusion-oncology/fusion-oncology"
Documentation = "https://github.com/fusion-oncology/fusion-oncology/tree/main/docs"

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

[tool.black]
line-length = 100
target-version = ["py310"]

[tool.ruff]
target-version = "py310"
line-length = 100
src = ["src", "tests"]

[tool.ruff.lint]
select = ["E", "F", "I", "N", "W", "UP", "B", "SIM", "ANN"]
ignore = ["ANN401"]

[tool.pytest.ini_options]
testpaths = ["tests"]
timeout = 120
timeout_method = "thread"
markers = [
    "slow: marks tests that download data or run models (deselect with '-m \"not slow\"')",
    "integration: marks integration tests requiring network access",
]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true

[tool.coverage.run]
source = ["src/fusion_oncology"]
omit = ["tests/*"]