full_dia/pyproject.toml at main · xomicsdatascience/full_dia · GitHub

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

[project]
name = "full_dia"
dynamic = ["version"]
description = "Generate a missingness-free protein quantification matrix from multiple diaPASEF runs through deep learning-based scoring."
readme = "README.md"
requires-python = ">=3.10.0"
license = "Apache-2.0"

authors = [
  { name = "Jian Song", email = "jian.song.2025@outlook.com" }
]

dependencies = [
  "psutil>=7.1,<7.2",
  "h5py>=3.15,<3.16",
  "matplotlib",
  "networkx>=3.5,<3.6",
  "numba>=0.63",
  "numpy<2.0.0",
  "pandas>=2.3",
  "pyzstd>=0.19",
  "scikit-learn>=1.8",
  "scipy>=1.16",
  "statsmodels>=0.14",
  "pyarrow>=22.0",
  "pyyaml>=6.0"
]

[project.optional-dependencies]
cuda11 = ["cupy-cuda11x==13.3"]
cuda12 = ["cupy-cuda12x==13.3"]

dev = [
  "pytest>=6",
  "flake8",
  "black"
]
docs = [
  "sphinx",
  "sphinx-rtd-theme"
]

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

[tool.setuptools.package-data]
"full_dia" = [
    "cfg/default.yaml",
    "pretrained/deepcenter_ys_fast.pt",
    "pretrained/deepbig_ys_fast.pt"
]
"full_dia.alphatims" = ["ext/*"]

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

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

[project.scripts]
full_dia = "full_dia.main:main"

[tool.ruff.lint]
exclude = [
    "full_dia/alphatims/**",
    "ipynb/**"
]
select = [
    "E",    # pycodestyle
    "F",    # pyflakes
    "UP",   # pyupgrade
    "B",    # flake8-bugbear
    "SIM",  # flake8-simplify
    "I",    # isort
]
ignore = [
    "E501",  # line too long (docstrings often exceed)
    "B028",  # warnings.warn stacklevel
    "B905",  # zip(strict=True) conflicts with Numba
    "UP032", # f-string or .format both ok
]
fixable = [
    "I",
    "UP"
]