pyproject.toml

[project]
name = "torch-sim-atomistic"
version = "0.5.2"
description = "A pytorch toolkit for calculating material properties using MLIPs"
authors = [
    { name = "TorchSim Maintainers", email = "torchsimatomistic@gmail.com" },
    { name = "Abhijeet Gangan", email = "abhijeetgangan@g.ucla.edu" },
    { name = "Janosh Riebesell", email = "janosh.riebesell@gmail.com" },
    { name = "Orion Cohen", email = "orioncohen@berkeley.edu" },
]
readme = "README.md"
license = { file = "LICENSE" }
keywords = [
    "chemistry",
    "interatomic-potentials",
    "machine-learning",
    "materials-science",
]
classifiers = [
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Physics",
]
requires-python = ">=3.12"
dependencies = [
    "h5py>=3.15.1",
    "numpy>=1.26,<3; python_version < '3.13'",
    "numpy>=2.3.2,<3; python_version >= '3.13'",
    "nvalchemi-toolkit-ops[torch]>=0.3.0",
    "tables>=3.11.1",
    "torch>=2",
    "tqdm>=4.67",
]

[project.optional-dependencies]
test = [
    "torch-sim-atomistic[io,symmetry,vesin]",
    "physical-validation>=1.0.5",
    "platformdirs>=4.0.0",
    "psutil>=7.0.0",
    "pytest-cov>=6",
    "pytest>=8",
    "spglib>=2.6",
]
vesin = ["vesin[torch]>=0.5.3"]
io = ["ase>=3.26", "phonopy>=2.37.0", "pymatgen>=2026.3.23"]
symmetry = ["moyopy>=0.7.8"]
mace = ["mace-torch>=0.3.15"]
mattersim = ["mattersim>=1.2.2"]
metatomic = ["metatomic-torchsim>=0.1.1", "metatomic-ase>=0.1.0", "upet>=0.2.0"]
orb = ["orb-models>=0.6.2"]
sevenn = ["sevenn[torchsim]>=0.12.1"]
nequip = ["nequip>=0.17.1"]
nequix = ["nequix[torch-sim]>=0.4.5"]
fairchem = ["fairchem-core>=2.19.0", "scipy<1.17.0"]
docs = [
    "autodoc_pydantic==2.2.0",
    "furo==2024.8.6",
    "ipykernel==6.30.1",
    "ipython==8.34.0",
    "jsonschema[format]",
    "jupyter-core==5.8.1",
    "jupyterlab==4.3.4",
    "jupytext==1.16.7",
    "myst_parser==4.0.0",
    "nbsphinx>=0.9.7",
    "numpydoc==1.8.0",
    "sphinx-copybutton==0.5.2",
    "sphinx==8.1.3",
    "sphinx_design==0.6.1",
]

[project.urls]
Repo = "https://github.com/torchsim/torch-sim"

[build-system]
requires = ["uv_build>=0.7.12"]
build-backend = "uv_build"

[tool.uv.build-backend]
module-name = "torch_sim"
module-root = ""

[tool.ruff]
target-version = "py312"
line-length = 90
output-format = "concise"

[tool.ruff.lint]
select = ["ALL"]
ignore = [
    "ANN002",  # Checks that *args arguments have type annotations.
    "ANN003",  # Checks that **kwargs arguments have type annotations.
    "ANN401",  # Allow use of type Any for function argument {name}
    "C408",    # Unnecessary {obj_type} call (rewrite as a literal)
    "COM812",  # missing-trailing-comma
    "D205",    # 1 blank line required between summary line and description
    "EM101",   # Exception must not use a string literal, assign to variable first
    "EM102",   # Exception must not use an f-string literal, assign to variable first
    "ERA001",  # Found commented-out code
    "FIX002",  # Line contains TODO, consider resolving the issue
    "G004",    # Logging statement uses f-string -> TODO refactor for performance
    "N803",    # Variable name should be lowercase
    "N806",    # Uppercase letters in variable names
    "PLC0415", # import should be at the top-level of a file
    "PLR0912", # too many branches
    "PLR0913", # too many function arguments
    "PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
    "PLW2901", # Outer for loop variable overwritten by inner assignment target
    "PTH",     # flake8-use-pathlib
    "RUF002",  # Greek letters are discouraged
    "S301",    # pickle and modules that wrap it can be unsafe, possible security issue
    "S311",    # Standard pseudo-random generators are not suitable for cryptographic purposes
    "SIM105",  # Use contextlib.suppress instead of try-except-pass
    "TD",      # flake8-todos
    "TRY003",  # Avoid specifying long messages outside the exception class
]
pydocstyle.convention = "google"
isort.split-on-trailing-comma = false
isort.lines-after-imports = 2
pep8-naming.ignore-names = ["get_kT", "kT"]

[tool.ruff.lint.per-file-ignores]
"**/tests/*" = ["ANN001", "ANN201", "ANN202", "D", "INP001", "S101", "T201"]
"examples/**/*" = ["ANN001", "ANN201", "ANN202", "B018", "T201"]
"examples/tutorials/**/*" = ["ALL"]
"docs/tutorials/*.ipynb" = ["ANN001", "ANN201", "B905", "BLE001", "E501", "F841", "N816", "PLR1714", "RUF001", "T201"]

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

[tool.codespell]
check-filenames = true
ignore-words-list = ["convertor"]  # codespell:ignore convertor
skip = "docs/tutorials/integrator_tests_analysis.ipynb"

[tool.pytest.ini_options]
addopts = ["-p no:warnings", "-m not physical_validation"]
testpaths = ["tests"]
markers = [
    "physical_validation: long-running physical validation tests (run with: pytest -m physical_validation)",
]

[tool.uv]
# make these dependencies mutually exclusive since they use incompatible e3nn versions
# see https://docs.astral.sh/uv/concepts/projects/config/#conflicting-dependencies for more details
conflicts = [
    [
        { extra = "fairchem" },
        { extra = "mace" },
    ],
    [
        { extra = "fairchem" },
        { extra = "mace" },
    ],
    [
        { extra = "mace" },
        { extra = "mattersim" },
    ],
    [
        { extra = "mace" },
        { extra = "nequip" },
    ],
    [
        { extra = "mace" },
        { extra = "nequix" },
    ],
    [
        { extra = "mace" },
        { extra = "sevenn" },
    ],
]

[dependency-groups]
dev = ["prek>=0.3.4", "ty>=0.0.19"]

[tool.ty.rules]
unused-ignore-comment = "warn"

[[tool.ty.overrides]]
include = [
    "tests/models/**/*.py",
    "torch_sim/constraints.py",
    "torch_sim/io.py",
    "torch_sim/models/**/*.py",
    "torch_sim/neighbors/alchemiops.py",
    "torch_sim/neighbors/vesin.py",
    "torch_sim/state.py",
    "torch_sim/symmetrize.py",
    "torch_sim/trajectory.py",
    "torch_sim/typing.py",
    "torch_sim/workflows/**/*.py",
]

[tool.ty.overrides.rules]
unresolved-import = "ignore"

[[tool.ty.overrides]]
include = [
    "torch_sim/models/dispersion.py",
    "torch_sim/neighbors/vesin.py",
]
[tool.ty.overrides.rules]
invalid-argument-type = "ignore"
invalid-assignment = "ignore"

[[tool.ty.overrides]]
include = ["tests/**/*.py"]

[tool.ty.overrides.rules]
invalid-argument-type = "ignore"
invalid-assignment = "ignore"
no-matching-overload = "ignore"
unresolved-attribute = "ignore"
unresolved-import = "ignore"

[[tool.ty.overrides]]
include = ["docs/**/*.py", "docs/**/*.ipynb", "examples/**/*.py"]
[tool.ty.overrides.rules]
invalid-argument-type = "ignore"
not-iterable = "ignore"
not-subscriptable = "ignore"
unresolved-attribute = "ignore"
unresolved-import = "ignore"


[[tool.ty.overrides]]
include = ["torch_sim/neighbors/alchemiops.py"]
[tool.ty.overrides.rules]
call-non-callable = "ignore"