pUniFind/pyproject.toml at main · pFindStudio/pUniFind · GitHub

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

[project]
name = "pUniFind"
version = "1.0.0"
description = "pUniFind: A unified deep learning framework for de novo peptide sequencing and database search rescoring"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "pUniFind Team"}
]
keywords = ["proteomics", "mass-spectrometry", "deep-learning", "peptide-sequencing", "de-novo"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.8,<3.12"
dependencies = [
    # NumPy must be <2.0 for pandas 1.5.3 compatibility
    "numpy>=1.21.0,<2.0.0",
    "pandas==1.5.3",
    "pyarrow==12.0.1",
    # Scientific computing
    "scipy>=1.7.0,<1.12.0",
    "scikit-learn>=1.0.0,<1.4.0",
    # MS/proteomics
    "spectrum_utils>=0.4.0",
    "pyteomics>=4.5",
    # Deep learning utilities
    "tqdm",
    "einops",
    "opt_einsum",
    "tensorboard",
]

[project.optional-dependencies]
# =============================================================================
# PyTorch Installation (choose ONE based on your hardware):
#
#   CPU only:     pip install -e ".[cpu]"
#   CUDA 11.8:    pip install -e ".[cu118]"
#   CUDA 12.1:    pip install -e ".[cu121]"
#
# Or install PyTorch separately first, then: pip install -e .
# =============================================================================
cu118 = [
    "torch==2.1.0",
]
cu121 = [
    "torch==2.1.0",
]
cpu = [
    "torch==2.1.0",
]
dev = [
    "pytest",
    "black",
    "flake8",
]

[project.scripts]
pUniFind = "punifind.cli:main"

[project.urls]
Homepage = "https://github.com/pUniFind/pUniFind"
Documentation = "https://github.com/pUniFind/pUniFind"
Repository = "https://github.com/pUniFind/pUniFind"

[tool.setuptools.packages.find]
where = ["."]
include = ["punifind*", "PepMS*", "compat*", "scripts*", "consts*"]

[tool.setuptools.package-data]
"consts" = ["*.pkl", "*.json", "*.py"]
"PepMS.data" = ["*.json"]
"*" = ["*.pkl", "*.json"]

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