CoreMS/pyproject.toml at master · EMSL-Computing/CoreMS · GitHub

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[build-system]
requires = ["setuptools>=72", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "CoreMS"
version = "4.0.1"
description = "Mass Spectrometry Framework for Small Molecules Analysis"
readme = "README.md"
license = { text = "BSD" }
authors = [{ name = "Corilo, Yuri", email = "corilo@pnnl.gov" }]
requires-python = ">=3.10"
classifiers = [
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Development Status :: 4 - Beta",
]
dependencies = [
    "beautifulsoup4>=4.12.3",
    "chardet>=5.2.0",
    "h5py>=3.13.0",
    "IsoSpecPy>=2.2.2",
    "lmfit>=1.3.0",
    "lxml>=5.2.0",
    "matplotlib>=3.9.0",
    "ms-entropy>=1.2.2",
    "netCDF4>=1.7.0",
    "numpy>=2.1.0",
    "openpyxl>=3.1.2",
    "pandas>=2.2.2",
    "psycopg2-binary>=2.9.10",
    "pyswarm>=0.6",
    "pythonnet>=3.0.3",
    "pymzml>=2.5.11",
    "requests>=2.32.0",
    "ripser>=0.6.4",
    "s3path>=0.5.0",
    "scikit_learn>=1.5.0",
    "scipy>=1.14.0",
    "seaborn>=0.13.2",
    "setuptools>=72.0.0",
    "SQLAlchemy>=2.0.0",
    "packaging>=23.0",
    "toml>=0.10.2",
    "tqdm>=4.66.0",
]

[project.urls]
Homepage = "https://github.com/EMSL-Computing/CoreMS"
Repository = "https://github.com/EMSL-Computing/CoreMS"
Issues = "https://github.com/EMSL-Computing/CoreMS/issues"

[project.optional-dependencies]
dev = [
    "pylint",
    "pytest>=8.3.2",
    "pytest-cov>=5.0.0",
    "pytest-xdist>=3.6.1",
    "pyprof2calltree",
    "memory_profiler",
    "twine",
    "bump2version",
    "psutil>=5.6.6",
    "PyWavelets",
    "pdoc>=14.1.0",
]

[tool.setuptools.packages.find]
where = ["."]
exclude = ["tests*", "*.win_only"]

[tool.setuptools.package-data]
"*" = ["ext_lib/*", "ext_lib/dotnet/*", "disclaimer.txt"]

[tool.pytest.ini_options]
addopts = "-ra -v --cov=corems --cov-config=pytest.ini --cov-report html --cov-report term -p no:warnings"
norecursedirs = ["win_only"]
testpaths = ["tests"]

[tool.coverage.run]
branch = true
omit = [
    "corems/mass_spectra/input/win_only/BrukerCompassXtract.py",
    "corems/mass_spectra/input/win_only/ThermoMSFileReader.py",
    "corems/transient/input/MidasDatFile.py",
    "corems/encapsulation/constant.py",
    "corems/molecular_id/factory/molecularMongo.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
]