mlmm_toolkit/pyproject.toml at main · t-0hmura/mlmm_toolkit · GitHub

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[build-system]
requires = ["setuptools", "wheel", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "mlmm-toolkit"
description = "mlmm - ML/MM toolkit for enzyme reaction analysis"
readme = "README.md"
authors = [{name = "Takuto Ohmura", email = "ohmura.takuto@gmail.com"}]
license = {file = "LICENSE"}
dynamic = ["version"]
requires-python = ">=3.11"
keywords = [
    "computational-chemistry",
    "enzyme",
    "QM/MM",
    "ML/MM",
    "UMA",
    "transition-state",
    "reaction-mechanism",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Chemistry",
]
dependencies = [
    # mlmm core dependencies
    "fairchem-core",
    "torch>=2.6.0",
    "torch_geometric",
    "torch_scatter",
    "numpy>=1.24",
    "biopython>=1.80,<2.0",
    "ase>=3.25.0",
    "ParmEd",
    "pyyaml>=6.0,<7.0",
    "click>=8.1,<9.0",
    "plotly>=6.1.1",
    "kaleido",

    # pysisyphus dependencies (bundled)
    "autograd",
    "dask",
    "distributed",
    "h5py",
    "fabric",
    "jinja2",
    "joblib",
    "matplotlib",
    "natsort",
    "psutil",
    "rmsd",
    "scipy",
    "sympy",
    "scikit-learn",
    "pyparsing",

    # thermoanalysis dependencies (bundled)
    "pandas",
    "tabulate",
]

[project.optional-dependencies]
orb = ["orb-models"]
aimnet = ["aimnet>=0.1.0"]
pdbfixer = ["pdbfixer"]
dft = [
    "pyscf>=2.8.0",
    "gpu4pyscf-cuda12x>=1.5.2; platform_machine == 'x86_64'",
    "cupy-cuda12x==13.4.1; platform_machine == 'x86_64'",
    "cutensor-cu12==2.2.0; platform_machine == 'x86_64'",
    "basis-set-exchange>=0.11",
]
dev = ["pytest", "pytest-cov", "pytest-timeout"]
docs = [
    "sphinx>=7.0",
    "myst-parser>=2.0",
    "furo>=2024.0",
    "sphinx-copybutton>=0.5",
]

[project.urls]
Homepage = "https://github.com/t-0hmura/mlmm_toolkit"
Repository = "https://github.com/t-0hmura/mlmm_toolkit"
Documentation = "https://github.com/t-0hmura/mlmm_toolkit/tree/main/docs"
"Bug Tracker" = "https://github.com/t-0hmura/mlmm_toolkit/issues"

[project.scripts]
mlmm = "mlmm.cli:cli"

[tool.pytest.ini_options]
testpaths = ["tests", "hessian_ff/tests"]
addopts = "-v --tb=short --timeout=120"
markers = [
    "slow: marks tests as slow",
]

[tool.setuptools.packages.find]
where = ["."]
include = ["mlmm*", "pysisyphus*", "thermoanalysis*", "hessian_ff*"]

[tool.setuptools.package-data]
mlmm = ["py.typed"]
pysisyphus = ["wavefunction/ints/*.npy"]
hessian_ff = ["native/*.cpp", "native/Makefile"]

[tool.setuptools_scm]
version_file = "mlmm/_version.py"
version_scheme = "guess-next-dev"
local_scheme = "no-local-version"