pyproject.toml

# Minimum requirements for the build system to execute.
[build-system]
requires = [
    "setuptools>=61.0",
    "setuptools_scm[toml]>=6.2",
]
build-backend = "setuptools.build_meta"

[project]
name = "Auto-FOX"
dynamic = [
    "version",
    "readme",
]
description = "A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters."
license = { file = "LICENSE" }
authors = [
    { name = "Bas van Beek", email = "b.f.van.beek@vu.nl" },
]
keywords = [
    "quantum-mechanics",
    "molecular-mechanics",
    "science",
    "chemistry",
    "forcefield-parameterization",
    "forcefield",
    "python",
    "python-3",
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
    "Natural Language :: English",
    "Operating System :: Unix",
    "Operating System :: MacOS",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Software Development :: Libraries ",
    "Typing :: Typed",
]
requires-python = ">=3.8"
dependencies = [
    "Nano-Utils>=2.3.2",
    "pyyaml>=5.1.2",
    "numpy>=1.18.5",
    "scipy>=1.3.2",
    "pandas>=1.4.0,<2.0.0",
    "schema>=0.7.1,!=0.7.5",
    "AssertionLib>=2.3",
    "noodles>=0.3.3",
    "h5py>=2.10",
    "qmflows>=0.12.0",
    "plams>=1.5.1",
    "packaging>=17.1",
]

[project.scripts]
init_armc = "FOX.entry_points:main_armc"
armc2yaml = "FOX.entry_points:main_armc2yaml"
"FOX.recipes.xyz_to_gro" = "FOX.recipes._xyz_to_gro:main"

[project.urls]
Homepage = "https://github.com/nlesc-nano/Auto-FOX"
"Bug Tracker" = "https://github.com/nlesc-nano/auto-FOX/issues"
Documentation = "https://auto-fox.readthedocs.io/en/latest/"

[project.optional-dependencies]
docs = [
    "sphinx>=2.4,<7",
    "sphinx_rtd_theme>=0.3.0",
    "matplotlib>=3.0",
    "rdkit",
]
lint = [
    "flake8",
    "pydocstyle[toml]>=6.1",
    "Flake8-pyproject>=1.2.2",
]
test = [
    "Auto-FOX[test-no-optional]",
    "ase>=3.21.1",
    "nlesc-CAT>=0.10.0",
    "ipython>=5.0.0",
]
test-no-optional = [
    "pytest>=6.0.0",
    "pytest-cov",
    "numpy>=1.18.5,<1.25",
    "assertionlib>=3.1.0",
]

[tool.setuptools]
license-files = ["LICENSE*.txt"]

[tool.setuptools.packages.find]
include = ["FOX*"]

[tool.setuptools.package-data]
FOX = [
    "data/*.xyz",
    "data/*.yaml",
    "data/*.csv",
    "properties/*.pyi",
    "recipes/*.pyi",
    "py.typed",
    "*.pyi",
]

[tool.setuptools.dynamic]
readme = { file = ["README.rst"], content-type = "text/x-rst" }

[tool.setuptools_scm]
write_to = "FOX/_version.py"

[tool.mypy]
plugins = "numpy.typing.mypy_plugin"
show_error_codes = true

[[tool.mypy.overrides]]
module = [
    "scm.*",
    "noodles.*",
    "rdkit.*",
    "pandas.*",
    "matplotlib.*",
    "scipy.*",
    "schema.*",
    "h5py.*",
]
ignore_missing_imports = true

[tool.pydocstyle]
convention = "numpy"
add_ignore = ["D401", "D103", "D102", "D105"]
ignore_decorators = "set_docstring"

[tool.flake8]
ignore = ["E226", "E704", "E731", "W503", "W504", "E721"]
exclude = [
    "FOX/examples/ ALL",
    "FOX/properties/*.pyi ALL",
    "src/qmflows/_version.py ALL",
]
max-line-length = 100

[tool.pytest.ini_options]
testpaths = "FOX tests"
addopts = "--tb=short --cov=FOX --cov-report xml --cov-report term --cov-report html --pdbcls=IPython.terminal.debugger:TerminalPdb"
filterwarnings = [
    "ignore::pandas.errors.PerformanceWarning",
    "ignore:numpy\\.ufunc size changed, may indicate binary incompatibility\\. Expected [0-9]+ from C header, got [0-9]+ from PyObject:RuntimeWarning",
    "ignore::DeprecationWarning:numpy.distutils.*",
    "ignore:elementwise comparison failed:FutureWarning:pandas",
    "error::qmflows.warnings_qmflows.QMFlows_Warning",
    "ignore:Generic keyword '_pytestfixturefunction' not implemented for package \\w:qmflows.warnings_qmflows.Key_Warning",
    "ignore:`(product|cumproduct)` is deprecated as of NumPy 1\\.25\\.0, and will be removed in NumPy 2\\.0:DeprecationWarning:h5py",
    "ignore:`(product|cumproduct)` is deprecated as of NumPy 1\\.25\\.0, and will be removed in NumPy 2\\.0:DeprecationWarning:pandas",
    "ignore:`(product|cumproduct)` is deprecated as of NumPy 1\\.25\\.0, and will be removed in NumPy 2\\.0:DeprecationWarning:FOX.io.hdf5_utils",
    "ignore:`np\\.find_common_type is deprecated:DeprecationWarning:pandas.*",
]

[tool.coverage.run]
branch = true
source = ["FOX"]
omit = ["FOX/examples"]