pyproject.toml

[build-system]
requires = [
    "Cython>=0.29.23",
    # pin NumPy version used in the build
    "oldest-supported-numpy",
    "setuptools>=65.0.0",
]
build-backend = "setuptools.build_meta"


[project]
name = "pymatgen"
authors = [
    { name = "Pymatgen Development Team", email = "ongsp@ucsd.edu" },
]
maintainers = [
    { name = "Shyue Ping Ong", email = "ongsp@ucsd.edu" },
    { name = "Matthew Horton", email = "m.k.horton@gmail.com" },
    { name = "Janosh Riebesell", email = "janosh.riebesell@gmail.com" },
]
description = """
Python Materials Genomics is a robust materials analysis code that defines core object representations for structures
and molecules with support for many electronic structure codes. It is currently the core analysis code powering the
Materials Project (https://materialsproject.org)."""
readme = "README.md"
requires-python = ">=3.9"
keywords = [
    "ABINIT",
    "analysis",
    "crystal",
    "diagrams",
    "electronic",
    "gaussian",
    "materials",
    "nwchem",
    "phase",
    "project",
    "qchem",
    "science",
    "structure",
    "VASP",
]
license = { text = "MIT" }
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Physics",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
    "matplotlib>=3.8",
    "monty>=2024.5.24",
    "networkx>=2.2",
    "numpy>=1.25.0,<2.0.0",
    "palettable>=3.1.1",
    "pandas>=2",
    "plotly>=4.5.0",
    "pybtex>=0.24.0",
    "requests>=2.32",
    "ruamel.yaml>=0.17.0",
    "scipy>=1.13.0",
    "spglib>=2.0.2",
    "sympy>=1.2",
    "tabulate>=0.9",
    "tqdm>=4.60",
    "uncertainties>=3.1.4",
    "joblib>=1",
]
version = "2024.6.10"

[project.urls]
Homepage = "https://pymatgen.org"
Documentation = "https://pymatgen.org"
Repository = "https://github.com/materialsproject/pymatgen"
Issues = "https://github.com/materialsproject/pymatgen/issues"
Pypi = "https://pypi.org/project/pymatgen"

[project.optional-dependencies]
ase = ["ase>=3.23.0"]
# don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"]
vis = ["vtk>=6.0.0"]
abinit = ["netcdf4>=1.6.5"]
mlp = ["matgl>=1.1.1", "chgnet>=0.3.8"]
electronic_structure = ["fdint>=2.0.2"]
dev = [
    "mypy>=1.10.0",
    "pre-commit>=3",
    "pytest-cov>=4",
    "pytest-split>=0.8",
    "pytest>8",
    "ruff>=0.4.8",
]
ci = [
    "pytest>=8",
    "pytest-cov>=4",
    "pytest-split>=0.8",
]
docs = [
    "sphinx",
    "sphinx_rtd_theme",
]
optional = [
    "ase>=3.23.0",
    # TODO restore BoltzTraP2 when install fixed, hopefully following merge of
    # https://gitlab.com/sousaw/BoltzTraP2/-/merge_requests/18
    # caused CI failure due to ModuleNotFoundError: No module named 'packaging'
    # "BoltzTraP2>=22.3.2; platform_system!='Windows'",
    "chemview>=0.6",
    "chgnet>=0.3.8",
    "f90nml>=1.1.2",
    "galore>=0.6.1",
    "h5py>=3.11.0",
    "jarvis-tools>=2020.7.14",
    "matgl>=1.1.1",
    "netCDF4>=1.6.5",
    "phonopy>=2.23",
    "seekpath>=2.0.1",
    # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
    "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
    # "hiphive>=0.6",
    # "openbabel>=3.1.1; platform_system=='Linux'",
]
numba = ["numba>=0.55"]

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

[tool.setuptools.package-data]
"pymatgen.analysis" = ["*.yaml", "*.json", "*.csv"]
"pymatgen.analysis.chemenv" = [
    "coordination_environments/coordination_geometries_files/*.json",
    "coordination_environments/coordination_geometries_files/*.txt",
    "coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json",
]
"pymatgen.analysis.structure_prediction" = ["*.yaml", "data/*.json"]
"pymatgen.analysis.diffraction" = ["*.json"]
"pymatgen.analysis.magnetism" = ["default_magmoms.yaml"]
"pymatgen.analysis.solar" = ["am1.5G.dat"]
"pymatgen.entries" = ["*.json.gz", "*.yaml", "data/*.json"]
"pymatgen.core" = ["*.json"]
"pymatgen" = ["py.typed"]
"pymatgen.io.vasp" = ["*.yaml", "*.json", "*.json.gz", "*.json.bz2"]
"pymatgen.io.feff" = ["*.yaml"]
"pymatgen.io.cp2k" = ["*.yaml"]
"pymatgen.io.lobster" = ["lobster_basis/*.yaml"]
"pymatgen.command_line" = ["*"]
"pymatgen.util" = ["structures/*.json", "*.json"]
"pymatgen.vis" = ["*.yaml"]
"pymatgen.io.lammps" = ["CoeffsDataType.yaml", "templates/*.template"]
"pymatgen.symmetry" = ["*.yaml", "*.json", "*.sqlite"]

[project.scripts]
pmg = "pymatgen.cli.pmg:main"
feff_plot_cross_section = "pymatgen.cli.feff_plot_cross_section:main"
feff_plot_dos = "pymatgen.cli.feff_plot_dos:main"
get_environment = "pymatgen.cli.get_environment:main"

[tool.versioningit.vcs]
method = "git"
default-tag = "0.0.1"

[tool.cibuildwheel.linux]
archs = ["auto64"]
skip = ["*musllinux*"]
before-all = "ln -s /usr/lib64/libgfortran.so.5 /usr/lib64/libgfortran.so.3"

[tool.cibuildwheel.macos]
repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} --ignore-missing-dependencies"

[tool.ruff]
target-version = "py39"
line-length = 120

[tool.ruff.lint]
select = [
    "B", # flake8-bugbear
    "C4", # flake8-comprehensions
    "D", # pydocstyle
    "E", # pycodestyle error
    "EXE", # flake8-executable
    "F", # pyflakes
    "FA", # flake8-future-annotations
    "FBT003", # boolean-positional-value-in-call
    "FLY", # flynt
    "I", # isort
    "ICN", # flake8-import-conventions
    "ISC", # flake8-implicit-str-concat
    "NPY201", # numpy 2.0
    "PD", # pandas-vet
    "PERF", # perflint
    "PIE", # flake8-pie
    "PL", # pylint
    "PLR0402",
    "PLR1714",
    "PLR5501",
    "PT", # flake8-pytest-style
    "PYI", # flakes8-pyi
    "Q", # flake8-quotes
    "RET", # flake8-return
    "RSE", # flake8-raise
    "RUF", # Ruff-specific rules
    "SIM", # flake8-simplify
    "SLOT", # flake8-slots
    "TCH", # flake8-type-checking
    "TID", # flake8-tidy-imports
    "UP", # pyupgrade
    "W", # pycodestyle warning
    "YTT", # flake8-2020
]
ignore = [
    "B023", # Function definition does not bind loop variable
    "B028", # No explicit stacklevel keyword argument found
    "B904", # Within an except clause, raise exceptions with ...
    "C408", # unnecessary-collection-call
    "D105", # Missing docstring in magic method
    "D205", # 1 blank line required between summary line and description
    "D212", # Multi-line docstring summary should start at the first line
    "PD901", # pandas-df-variable-name
    "PERF203", # try-except-in-loop
    "PERF401", # manual-list-comprehension
    "PLR", # pylint refactor
    "PLW2901", # Outer for loop variable overwritten by inner assignment target
    "PT013", # pytest-incorrect-pytest-import
    "PTH", # prefer pathlib to os.path
    "SIM105", # Use contextlib.suppress() instead of try-except-pass
]
pydocstyle.convention = "google"
isort.required-imports = ["from __future__ import annotations"]
isort.split-on-trailing-comma = false

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"tests/**" = ["ANN201", "D", "S101"]
"tasks.py" = ["D"]
"pymatgen/analysis/*" = ["D"]
"pymatgen/vis/*" = ["D"]
"pymatgen/io/*" = ["D"]
"dev_scripts/*" = ["D"]

[tool.pytest.ini_options]
addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mode=importlib"

[tool.coverage.run]
parallel = true
omit = [
    "pymatgen/cli/feff_plot_cross_section.py",
    "pymatgen/cli/feff_plot_dos.py",
    "pymatgen/cli/pmg_config.py",
    "pymatgen/cli/pmg_plot.py",
    "pymatgen/cli/pmg_potcar.py",
    "pymatgen/cli/pmg_query.py",
    "pymatgen/dao.py",
]

[tool.coverage.report]
exclude_also = [
    "@deprecated",
    "@np.deprecate",
    "def __repr__",
    "except ImportError:",
    "if 0:",
    "if TYPE_CHECKING:",
    "if __name__ == .__main__.:",
    "if self.debug:",
    "if settings.DEBUG",
    "if typing.TYPE_CHECKING:",
    "pragma: no cover",
    "raise AssertionError",
    "raise NotImplementedError",
    "show_plot",
]

[tool.mypy]
ignore_missing_imports = true
namespace_packages = true
explicit_package_bases = true
no_implicit_optional = false
disable_error_code = "annotation-unchecked"

[[tool.mypy.overrides]]
module = ["requests.*", "tabulate.*"]
ignore_missing_imports = true

[tool.codespell]
ignore-words-list = """
titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo,nax,coo,
coul,ser,leary,thre,fase,rute,reson,titels,ges,scalr,strat,
struc,hda,nin,ons,pres,kno,loos,lamda,lew,atomate,nempty
"""
skip = "pymatgen/analysis/aflow_prototypes.json"
check-filenames = true

[tool.pyright]
typeCheckingMode = "off"
reportPossiblyUnboundVariable = true
reportUnboundVariable = true
reportMissingImports = false
reportMissingModuleSource = false
reportInvalidTypeForm = false
exclude = ["**/tests"]