pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "biodem"
version = "0.9.1"
description = "Dual-extraction method for phenotypic prediction and functional gene mining"
authors = [
    {name = "Chenhua Wu", email = "chanhuawu@outlook.com"},
    {name = "Yanlin Ren", email = "ryl1999@126.com"},
]
readme = "README.md"
requires-python = ">=3.10, <3.13"
license = {file = "LICENSE"}
keywords = ["bioinformatics", "agriculture", "deep learning", "machine learning", "pytorch"]
classifiers = [
    "Environment :: Console",
    "Natural Language :: English",
    "Development Status :: 4 - Beta",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Intended Audience :: Science/Research",
    "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",
    "Operating System :: Microsoft :: Windows :: Windows 10",
    "Operating System :: Microsoft :: Windows :: Windows 11",
    "Operating System :: POSIX :: Linux",
]
dependencies = [
    "torch>=2.1.0",
    "lightning>=2.4.0",
    "litdata>=0.2.29",
    "mosaicml-streaming>=0.8.0",
    "pyarrow>=17.0",
    "torchmetrics>=1.4.0",
    "tensorboard>=2.18.0",
    "numpy>=2.0",
    "polars>=1.9.0",
    "scikit-learn>=1.5.0",
    "scipy>=1.13.0",
    "optuna>=4.0",
    "optuna-dashboard>=0.16.0",
    "zstd>=1.5.5",
]

[project.urls]
Homepage = "https://github.com/cma2015/DEM"

[project.scripts]
dem-rm-ckpt = "biodem.cli_dem:cli_rm_ckpt"
dem-install-pregv = "biodem.cli_dem:cli_install_pregv"

[tool.hatch.build.targets.wheel.force-include]
"bin/linux/pregv" = "bin/linux/pregv"
"bin/windows/pregv.exe" = "bin/windows/pregv.exe"