pyproject.toml

[build-system]
requires = [
    # pin NumPy version used in the build
    "numpy>=1.20.1",
    "setuptools>=43.0.0",
]
build-backend = "setuptools.build_meta"

[project]
name = "pymatgen-analysis-diffusion"
authors = [
    { name = "Materials Virtual Lab", email = "ongsp@ucsd.edu" },
]
maintainers = [
    { name = "Shyue Ping Ong", email = "ongsp@ucsd.edu" },
]
description = "Pymatgen add-on for diffusion analysis."
readme = "README.rst"
requires-python = ">=3.9"
keywords = [
    "ABINIT",
    "analysis",
    "crystal",
    "diagrams",
    "electronic",
    "gaussian",
    "materials",
    "nwchem",
    "phase",
    "project",
    "qchem",
    "science",
    "structure",
    "VASP",
    "diffusion", "molecular dynamics", "MD"
]
license = { text = "BSD" }
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Physics",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
    'numpy>=1.25.0,<2.0',
    "pymatgen>=2024.6.10",
    "joblib",
    "ase",
    "seaborn"
]
version = "2024.7.15"

[project.urls]
Homepage = "http://materialsvirtuallab.github.io/pymatgen-analysis-diffusion/"
Documentation = "http://materialsvirtuallab.github.io/pymatgen-analysis-diffusion/"
Repository = "https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion"
Issues = "https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/issues"
Pypi = "https://pypi.org/project/pymatgen-analysis-diffusion"

[project.optional-dependencies]
ci = [
    "pytest>=8",
    "pytest-cov>=4",
    "pytest-split>=0.8",
    "maggma"
]
docs = [
    "sphinx",
    "sphinx_rtd_theme",
]


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


[tool.ruff]
target-version = "py39"
line-length = 120
lint.select = [
    "ANN", # flake8-annotations
    "B", # flake8-bugbear
    "C4", # flake8-comprehensions
    "D", # pydocstyle
    "E", # pycodestyle error
    "EXE", # flake8-executable
    "F", # pyflakes
    "FA", # flake8-future-annotations
    "FLY", # flynt
    "I", # isort
    "ICN", # flake8-import-conventions
    "ISC", # flake8-implicit-str-concat
    "PD", # pandas-vet
    "PERF", # perflint
    "PIE", # flake8-pie
    "PL", # pylint
    "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", # tidy imports
    "TID", # flake8-tidy-imports
    "UP", # pyupgrade
    "W", # pycodestyle warning
    "YTT", # flake8-2020
]
lint.ignore = [
    "ANN003", # Missing type annotation for kwargs
    "ANN101", # Missing type annotation for self in method
    "ANN102", # Missing type annotation for cls in classmethod
    "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
    "E501",
    "PD901", # pandas-df-variable-name
    "PERF203", # try-except-in-loop
    "PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)
    "PLR", # pylint refactor
    "PLW2901", # Outer for loop variable overwritten by inner assignment target
    "PT009",
    "PT011",
    "PT013", # pytest-incorrect-pytest-import
    "PYI024", # collections-named-tuple (TODO should maybe fix these)
    "RUF012", # Disable checks for mutable class args. This is a non-problem.
    "SIM105", # Use contextlib.suppress(OSError) instead of try-except-pass
    "SIM115",
    "ISC001"
]
lint.pydocstyle.convention = "google"
lint.isort.required-imports = ["from __future__ import annotations"]
lint.isort.split-on-trailing-comma = false

[tool.ruff.lint.per-file-ignores]
"**/tests/**" = ["D"]
"tasks.py" = ["D"]


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

[tool.coverage.run]
branch = true


[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,hove,
fase,rute,reson,titels,ges,scalr,strat,struc,hda,nin,ons,pres,kno,loos,lamda,lew,fof,
tje,afe
"""
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"]