pyproject.toml

[build-system]
requires = ["setuptools >= 42, < 85", "versioningit >= 1,< 4", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "atomate2"
description = "atomate2 is a library of materials science workflows"
readme = "README.md"
keywords = ["automated", "dft", "high-throughput", "vasp", "workflow"]
license = "BSD-3-Clause-LBNL"
authors = [{ name = "Alex Ganose", email = "alexganose@gmail.com" }]
dynamic = ["version"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Information Technology",
    "Intended Audience :: Science/Research",
    "Intended Audience :: System Administrators",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Other/Nonlisted Topic",
    "Topic :: Scientific/Engineering",
]
requires-python = ">=3.11"
dependencies = [
    "PyYAML",
    "click",
    "custodian>=2024.4.18",
    "emmet-core>=0.86.1",
    "jobflow>=0.1.11",
    "monty>=2024.12.10",
    "numpy",
    "pydantic-settings>=2.0.3",
    "pydantic>=2.0.1",
    "pymatgen>=2024.11.13",
    "pymatgen-core>=2026.5.18",
    "pymongo<=4.18.2",
]

[project.optional-dependencies]
abinit = [
    "abipy>=0.9.3",
    "netCDF4<1.7.5", # TODO: latest NetCDF missing 3.12 support: https://github.com/Unidata/netcdf4-python/issues/1461
]
aims = ["pymatgen-io-aims>=0.0.5", "pymatgen>=2025.10.7"]
amset = ["amset>=0.4.15", "pydash"]
cclib = ["cclib>=1.8.1"]
mp = ["mp-api>=0.37.5"]
# phonopy 4.x changed force-constants/primitive-axis handling, breaking the
# phonon.save -> phonopy.load round-trip used by the Grüneisen workflow
# ("Force constants shape disagrees with crystal structure setting").
phonons = ["phonopy>=2.43,<5", "seekpath>=2.0.0"]
pheasy = ["hiphive==1.5", "numpy<=2.2", "pheasy @ git+https://gitlab.com/hpsahasrabuddhe/pheasy.git@support-disp-force-matrix-input"]
alamode = ["alm @ git+https://github.com/ttadano/ALM.git@develop#subdirectory=python"]
hiphive = ["hiphive==1.5", "trainstation>=1.0", "atomate2[phonons,alamode]"]
lobster = ["ijson>=3.2.2", "lobsterpy>=0.6.0"]
defects = [
    "dscribe>=1.2.0",
    "pymatgen-analysis-defects>=2024.5.11",
    "python-ulid>=2.7",
]

ase = ["ase>=3.26.0"]
ase-ext = ["tblite>=0.3.0; platform_system=='Linux'"]
forcefields-demo = ["chgnet>=0.3.8","atomate2[ase]"]

torchsim = [
    "torch-sim-atomistic[symmetry]==0.6.1; python_version >= '3.12'"
]

# TorchSim's optional model backends pin to minimum versions to avoid the backend
# from being absent. We also have to keep mace separate from the generic group
# to avoid conflicts with e3nn versions. Note that the groups are different
# from the ones used for the forcefields backend.

# ALWAYS REMEMBER to update `.github/workflows/testing.yml` to reflect the
# current set of torchsim dependency groups.
torchsim-mace = [
    "torch-sim-atomistic[mace,symmetry]==0.6.1; python_version >= '3.12'"
]
# mattersim can be added to torchsim-generic once they clean their dependencies
torchsim-generic = [
    "torch-sim-atomistic[fairchem,metatomic,nequip,orb,sevenn,symmetry]==0.6.1; python_version >= '3.12'"
]
jdftx = ["pymatgen==2026.9.24"]
approxneb = ["pymatgen-analysis-diffusion>=2024.7.15"]
openmm = [
    "mdanalysis>=2.8.0",
    "openmm-mdanalysis-reporter>=0.1.0",
    "openmm>=8.1.0",
]
fireworks = ["fireworks==2.1.4"]
strict-openff = [
    "mdanalysis==2.10.0",
    "monty==2026.7.16",
    "openmm-mdanalysis-reporter==0.1.0",
    "openmm==8.6.1",
    "pymatgen==2026.9.24", # EXERCISE CAUTION WHEN UPDATING - open ff is extremely sensitive to pymatgen version
]

# Forcefields have separate strict groupings because of conflicting dependencies.
# The labels below should not be taken as fixed in time.
# They are meant to be instructive as to why certain forcefields are grouped together.
# Ex: `strict-forcefields-torch-limited` might indicate that these require a lower version of `pytorch`
# Whereas `strict-forcefields-generic` might indicate that no dependency conflicts are known for the group

# ALWAYS REMEMBER to update `.github/workflows/testing.yml` to reflect the current set of
# forcefield dependency groups.
strict-forcefields-generic = [
    "calorine==4.0; python_version >= '3.12'",
    "calorine==3.1; python_version < '3.12'",
    "chgnet==0.4.2",
    "quippy-ase==0.10.3",
    "sevenn==0.13.0",
    "deepmd-kit==3.2.0",
    "tensorflow-cpu==2.21.0; sys_platform == 'linux'",
    "tensorflow==2.21.0; sys_platform == 'darwin' or sys_platform == 'win32'",
#     "mattersim>=1.2.3", # need to be activated again
    "wandb==0.30.0", # required for mattersim
    "upet==0.2.5",
]
strict-forcefields-torch-limited = [
    "matgl==4.0.3",
    "nequip==0.19.1", # requires numpy<2 because of matscipy
]

strict-forcefields-e3nn-limited = [
    "mace-torch==0.3.16",
    "torch-dftd==0.5.3",
]
strict-forcefields-numpy-limited = [
    "nequip-allegro==0.8.3",
]

strict = [
    "atomate2[cclib, phonons, lobster, openmm, mp, defects, ase, ase-ext]",
    "numpy<3.0",
    "numba>=0.60.0", # needed to get numpy >2,<3 installed
    "pymatgen==2026.9.24",
    "pymatgen-core==2026.9.23",
]

[project.scripts]
atm = "atomate2.cli:cli"

[project.urls]
homepage = "https://materialsproject.github.io/atomate2/"
repository = "https://github.com/materialsproject/atomate2"
documentation = "https://materialsproject.github.io/atomate2/"
changelog = "https://github.com/materialsproject/atomate2/blob/main/CHANGELOG.md"

[dependency-groups]
dev = ["pre-commit>=4.5.1"]
tests = [
    "fireworks==2.1.4",
    "nbmake==1.5.5",
    "pytest-cov==7.1.0",
    "pytest-mock==3.15.1",
    "pytest-split==0.11.0",
    "pytest-xdist==3.8.0",
    "pytest==9.1.1",
]
docs = [
    "fireworks==2.1.4",
    "autodoc_pydantic==2.2.0",
    "furo==2025.12.19",
    "ipython==9.17.1",
    "jsonschema[format]",
    "myst_parser==5.1.0",
    "numpydoc==1.11.0",
    "sphinx-copybutton==0.5.2",
    "sphinx==9.0.4",
    "sphinx_design==0.7.0",
    "jupyterlab==4.6.4",
]

[tool.setuptools.package-data]
atomate2 = ["py.typed"]
"atomate2.vasp.sets" = ["*.yaml"]
"atomate2.cp2k.sets" = ["*.yaml"]
"atomate2.cp2k.schemas.calc_types" = ["*.yaml"]
"atomate2.jdftx.sets" = ["*.yaml"]

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

[tool.mypy]
ignore_missing_imports = true
no_strict_optional = true

[tool.pytest.ini_options]
addopts = "-p no:warnings --import-mode=importlib --cov-config=pyproject.toml"
filterwarnings = [
    "ignore:.*POTCAR.*:UserWarning",
    "ignore:.*input structure.*:UserWarning",
    "ignore:.*is not gzipped.*:UserWarning",
    "ignore:.*magmom.*:UserWarning",
    "ignore::DeprecationWarning",
]

[tool.coverage.run]
include = ["src/*"]
parallel = true
branch = true

[tool.coverage.paths]
source = ["src/"]

[tool.coverage.report]
skip_covered = true
show_missing = true
exclude_lines = [
    '^\s*@overload( |$)',
    '^\s*assert False(,|$)',
    'if typing.TYPE_CHECKING:',
    'if TYPE_CHECKING:',
]

[tool.ruff]
target-version = "py310"
output-format = "concise"

[tool.ruff.lint]
select = ["ALL"]
ignore = [
    "ANN002",  # Missing type annotation for *arg
    "ANN003",  # Missing type annotation for **kwargs
    "ANN401",  # typing.Any disallowed
    "ARG002",  # unused method argument
    "C408",    # Unnecessary (dict/list/tuple) call - remove call
    "C901",    # function too complex
    "COM812",  # trailing comma missing
    "CPY001",  # copyright notice at top of file
    "EM",      # exception message must not use f-string literal
    "ERA001",  # found commented out code
    "FBT001",
    "FBT002",
    "FIX002",
    "G004",    # logging uses f-string
    "ISC001",
    "PD011",   # pandas-use-of-dot-values
    "PERF203", # try-except-in-loop
    "PLC0415", # imports not at top level are OK
    "PLR0911", # too many returns
    "PLR0912", # too many branches
    "PLR0913", # too many arguments
    "PLR0915", # too many local statements
    "PLR0917", # too many positional arguments
    "PLR2004",
    "PT006",   # pytest-parametrize-names-wrong-type
    "PT013",   # pytest-incorrect-pytest-import
    "PTH",     # prefer Pathlib to os.path
    "RUF013",  # implicit-optional
    "S324",    # use of insecure hash function
    "S507",    # paramiko auto trust
    "S603",    # use of insecure subprocess
    "TD",      # todos
    "TRY003",  # long message outside exception class
]
pydocstyle.convention = "numpy"
isort.known-first-party = ["atomate2"]
isort.split-on-trailing-comma = false

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

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"**/tests/*" = ["ANN", "ARG001", "D", "INP001", "PLR2004", "S101"]
# flake8-type-checking (TCH): things inside TYPE_CHECKING aren't available
#     at runtime and so can't be used by pydantic models
# flake8-future-annotations (FA): pipe operator for type unions only work in pydantic models in python 3.10+
"**/schemas/*" = ["FA", "TCH", "UP007"]
"**/schemas.py" = ["FA", "TCH", "UP007"]
"**/settings.py" = ["FA", "TCH", "UP007"]
"docs/*" = ["INP001"]