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 ; platform_system == "Windows"',
    'numpy>=1.25.0 ; platform_system != "Windows"',
    "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>=2.5.0",
    "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"]
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"]

[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.setuptools.packages.find]
where = ["src"]
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"]

[tool.pdm.dev-dependencies]
lint = [
    "mypy>=1.10.0",
    "ruff>=0.4.9",
    "pre-commit>=3.7.1",
]
test = [
    "pytest>=8.2.2",
    "pytest-cov>=5.0.0",
    "pytest-split>=0.9.0",
]

[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 = ["ALL"]
ignore = [
  # Rule families
  "ANN",  # flake8-annotations (not ready, require types for ALL args)
  "ARG",  # Check for unused function arguments
  "BLE",  # General catch of Exception
  "C90",  # Check for functions with a high McCabe complexity
  "COM",  # flake8-commas (conflict with line wrapper)
  "CPY",  # Missing copyright notice at top of file (need preview mode)
  "EM",   # Format nice error messages
  "ERA",  # Check for commented-out code
  "FIX",  # Check for FIXME, TODO and other developer notes
  "FURB", # refurb (need preview mode, too many preview errors)
  "G",    # validate logging format strings
  "INP",  # Ban PEP-420 implicit namespace packages
  "N",    # pep8-naming (many var/arg names are intended)
  "NPY",  # NumPy-specific rules (TODO: enable this)
  "PTH",  # Prefer pathlib over os.path
  "S",    # flake8-bandit (TODO: enable this)
  "SLF",  # Access "private" class members
  "T20",  # Check for print/pprint
  "TD",   # TODO tags related

  # Single rules
  "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
  "DTZ003",  # TODO: fix this (issue #3791)
  "FBT001",  # Boolean-typed positional argument in function definition
  "FBT002",  # Boolean default positional argument in function
  "PD901",   # pandas-df-variable-name
  "PERF203", # try-except-in-loop
  "PERF401", # manual-list-comprehension
  "PLR0911", # too many return statements
  "PLR0912", # too many branches
  "PLR0913", # too many arguments
  "PLR0915", # too many statements
  "PLR2004", # magic values in comparison
  "PLW2901", # Outer for loop variable overwritten by inner assignment target
  "PT013",   # pytest-incorrect-pytest-import
  "SIM105",  # Use contextlib.suppress() instead of try-except-pass
  "TRY003",  # Avoid specifying long messages outside the exception class
  "TRY300",  # Checks for return statements in try blocks
  "TRY301",  # Checks for raise statements within try blocks
]
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", "PLR0124"]
"src/pymatgen/analysis/*" = ["D"]
"src/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"]