tdfextractor/pyproject.toml at main · tacular-omics/tdfextractor · GitHub

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

[project]
name = "tdfextractor"
dynamic = ["version"]
description = "Extract MS2, MGF, and mzML files from Bruker timsTOF .d folders"
authors = [
    {name = "Patrick Garrett", email = "pgarrett@scripps.edu"},
]
dependencies = [
    "tdfpy>=5.0,<6",
    "serenipy>=0.4.0",
    "psims>=1.3.5",
    "numpy",
    "pandas",
    "tqdm",
    "numba>=0.65.0",
]
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Development Status :: 4 - Beta",
    "Operating System :: OS Independent",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Intended Audience :: Science/Research",
    "Typing :: Typed",
]
readme = "README.md"
requires-python = ">=3.12"
license = "MIT"
license-files = ["LICENSE"]
keywords = ["bruker", "timstof", "mass-spectrometry", "proteomics", "tdf", "ms2", "mgf", "mzml", "pasef"]

[project.urls]
Homepage = "https://github.com/tacular-omics/tdfextractor"
Documentation = "https://github.com/tacular-omics/tdfextractor#readme"
Repository = "https://github.com/tacular-omics/tdfextractor"
Issues = "https://github.com/tacular-omics/tdfextractor/issues"
Changelog = "https://github.com/tacular-omics/tdfextractor/blob/main/CHANGELOG.md"

[project.optional-dependencies]
# Optional compression backends for the mzML extractor. numpress-* compression
# modes need pynumpress; zstd needs pyzstd.
compression = [
    "pynumpress>=0.0.9",
    "pyzstd>=0.16",
]

[project.scripts]
mgf-extractor = "tdfextractor.mgf_extractor:main"
ms2-extractor = "tdfextractor.ms2_extractor:main"
mzml-extractor = "tdfextractor.mzml_extractor:main"
mgf-ex = "tdfextractor.mgf_extractor:main"
ms2-ex = "tdfextractor.ms2_extractor:main"
mzml-ex = "tdfextractor.mzml_extractor:main"

[tool.hatch.version]
path = "src/tdfextractor/__init__.py"

[tool.hatch.build.targets.wheel]
packages = ["src/tdfextractor"]

[tool.hatch.build.targets.sdist]
include = [
    "src/tdfextractor",
    "tests",
    "README.md",
    "LICENSE",
    "CHANGELOG.md",
]

[dependency-groups]
dev = [
    "pytest>=8.0",
    "pytest-cov>=6.0",
    "ty>=0.0.9",
    "ruff>=0.14.3",
    "pyupgrade>=3.21.0",
    # pynumpress ships only an sdist whose build crashes on Windows CPython
    # 3.13+; no test needs it, so skip it there.
    "pynumpress>=0.0.9; sys_platform != 'win32'",
    "pyzstd>=0.16",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "slow: end-to-end extractor tests that read .d folders. Run with `pytest -m \"not slow\"` to skip.",
]

[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ty.rules]
# psims does not ship a PEP 561 marker, so every `from psims.mzml.writer
# import ...` would otherwise fail the checker. Ignore resolution errors
# rather than vendoring stubs.
unresolved-import = "ignore"