pyNullstrap/pyproject.toml at main · PromptBio/pyNullstrap · GitHub

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[build-system]
requires = ["flit_core>=3.9"]
build-backend = "flit_core.buildapi"

[project]
name = "nullstrap"
dynamic = ["version"]
description = "Python implementation of Nullstrap — a versatile method for variable selection with false discovery rate control."
authors = [{name = "Wenbin Guo", email = "wbguo@ucla.edu"}]
keywords = ["variable selection", "false discovery rate", "statistics", "machine learning", "feature selection"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
readme = "README.md"
license = {text = "Apache-2.0"}
requires-python = ">=3.10"
dependencies = [
    "numpy>=1.24,<2.0",  # Constrained to NumPy 1.x for stability
    "scikit-learn>=1.7",  # Requires 1.7+ for LassoCV alphas int support
    "scipy>=1.10,<1.15",  # Compatible with NumPy 1.x
    "scikit-survival>=0.25; platform_system!='Windows'",  # 0.25+ supports sklearn 1.7
]

[project.optional-dependencies]
survival = ["scikit-survival>=0.25"]  # 0.25+ supports sklearn 1.7
test = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "pytest-xdist>=3.0",
    "pytest-timeout>=2.0"
]
dev = [
    "black>=23.0",
    "isort>=5.12",
    "flake8>=6.0",
    "mypy>=1.0",
    "pre-commit>=3.0"
]
docs = [
    "sphinx>=4.0.0",
    "sphinx-rtd-theme>=1.0.0",
    "myst-parser>=0.18.0",
    "linkify-it-py>=2.0.0",
    "sphinx-autodoc-typehints>=1.0"
]
all = [
    "nullstrap[survival,test,dev,docs]"
]

[project.urls]
Repository = "https://github.com/PromptBio/pyNullstrap"
Documentation = "https://github.com/PromptBio/pyNullstrap"
Issue Tracker = "https://github.com/PromptBio/pyNullstrap/issues"