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 = "4.1.0"
description = "Mass Spectrometry Framework for Small Molecules Analysis"
readme = "README.md"
license = { text = "BSD" }
authors = [{ name = "Corilo, Yuri", email = "corilo@pnnl.gov" }]
requires-python = ">=3.11"
classifiers = [
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "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",
    # Cap below 3.0 until CoreMS is validated on pandas 3 (Python>=3.11 only)
    # and remaining CoW / default-str-dtype call sites are fully migrated.
    "pandas>=2.2.2,<3",
    "pyarrow>=14.0.0",
    "psycopg[binary]>=3.2",
    "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>=2.1",
    "packaging>=23.0",
    "tomlkit>=0.13.3",
    "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"
Documentation = "https://emsl-computing.github.io/CoreMS/corems.html"

[project.optional-dependencies]
dev = [
    "ruff>=0.8",
    "pylint>=3.0",  # pyreverse for just uml / just docu
    "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",
]
# Optional: molecular network graph layout/plotting + interactive HTML
# (MolecularNetwork.plot_network, clustering, plot_interactive_network)
networking = [
    "networkx>=3.0",
    "ipysigma>=0.24",
]

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

[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__",
]

# ---------------------------------------------------------------------------
# Ruff (release / maintainer format+fix via `just lint`; see RELEASE.md)
# `just lint` rewrites files. Do not run it except during release prep
# unless you intend to commit the diff. Default rule set only.
# ---------------------------------------------------------------------------
[tool.ruff]
target-version = "py311"
line-length = 88
src = ["corems"]
extend-exclude = [
    "corems/mass_spectra/input/win_only",
]

[tool.ruff.lint]
# Pin ruff defaults so a newer ruff does not enable extra families at release.
select = ["E4", "E7", "E9", "F"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"