OptiMHC/pyproject.toml at main · 5h4ng/OptiMHC · GitHub

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

[project]
name = "optimhc"
version = "0.1.0"
description = "A high-performance rescoring pipeline for immunopeptidomics data to significantly enhance peptide identification performance"
authors = [
  { name="Zixiang Shang", email="steven5h4ng@gmail.com" }
]
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.10,<3.13"
dependencies = [
    "deeplc==3.1.1",
    "koinapy>=0.0.10",
    "lxml==5.3.0",
    "matplotlib==3.9.2",
    "mhctools @ git+https://github.com/openvax/mhctools.git@868ed09b4dfcab18aed563727d65bca3408476ea",
    "setuptools<82,>=61", # mhctools uses pkg_resources at runtime
    "mhcflurry==2.1.4",
    "mokapot==0.10.0",
    "networkx==3.2.1",
    "numpy==1.26.4",
    "pandas==2.2.3",
    "pyteomics==4.7.5",
    "PyYAML==6.0.2",
    "scikit_learn==1.5.2",
    "scipy==1.13.1",
    "seaborn==0.13.2",
    "tqdm==4.67.0",
    "xgboost==1.7.6",
    "numba>=0.64.0",
]

[dependency-groups]
dev = [
    "pytest>=8.4.0",
    "pre-commit>=4.3.0",
    "ruff",
]

[project.scripts]
optimhc = "optimhc.__main__:cli"

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

[tool.setuptools.packages.find]
where = ["."]
include = ["optimhc*"]

[tool.setuptools.package-data]
optimhc = ["PWMs*"]

[tool.ruff]
exclude = ["docs", "examples"]
line-length = 99
target-version = "py311"

[tool.ruff.lint]
select = ["E", "F", "I"]
ignore = ["E501"]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["S101"]