pyproject.toml

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

[tool.setuptools]
include-package-data = true

[project]
name = "FinaleToolkit"
authors = [
    { name = "James Li", email = "lijw21@wfu.edu" },
    { name = "Ravi Bandaru", email = "ravi.bandaru@northwestern.edu" },
    { name = "Yaping Liu", email = "yaping@northwestern.edu" },
]
description = "FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data."
readme = "README.md"
requires-python = ">=3.9"
license = {file = "LICENSE"}
keywords = ["bioinformatics", "cell free DNA", "computational biology",
"genomics", "epigenomics"]
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: MacOS",
    "Operating System :: POSIX :: Linux",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "numpy",
    "pysam",
    "pybigwig",
    "py2bit",
    "tqdm",
    "numba",
    "scipy",
    "pandas",
    "statsmodels",
    "loess",
    "matplotlib",
]
dynamic = ["version"]

[tool.setuptools.dynamic]
version = {attr = "finaletoolkit.__version__"}

[project.scripts]
finaletoolkit = "finaletoolkit.cli.main_cli:main_cli"

[project.urls]
Homepage = "https://epifluidlab.github.io/FinaleToolkit/"
Repository = "https://github.com/epifluidlab/finaletoolkit"
Issues = "https://github.com/epifluidlab/FinaleToolkit/issues"
Changelog = "https://github.com/epifluidlab/FinaleToolkit/blob/main/CHANGELOG.md"
Wiki = "https://github.com/epifluidlab/FinaleToolkit/wiki"
"Lab Website" = "https://epifluidlab.github.io/"

[dependency-groups]
test = ["pytest", "pytest-cov"]
docs = ["sphinx", "sphinx-argparse", "pydata-sphinx-theme"]