pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "Auto3D"
version = "3.0.0"
description = "Generating Low-energy 3D Conformers from SMILES/SDF"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "Zhen Liu", email = "liu5@andrew.cmu.edu"},
    {name = "Tetiana Zubatiuk", email = "tetiana@zubatyuk.com"},
    {name = "Adrian Roitberg", email = "roitberg@ufl.edu"},
    {name = "Olexandr Isayev", email = "olexandr@olexandrisayev.com"},
]
maintainers = [
    {name = "Olexandr Isayev", email = "olexandr@olexandrisayev.com"},
]
keywords = [
    "chemistry",
    "molecular-dynamics",
    "conformer-generation",
    "neural-network-potentials",
    "cheminformatics",
    "drug-discovery",
]
requires-python = ">=3.10"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Typing :: Typed",
]
dependencies = [
    "tqdm>=4.60.0",
    "psutil>=5.8.0",
    "Send2Trash>=1.8.0",
    "pyyaml>=6.0",
    "numpy>=1.21.0",
    "pandas>=1.3.0",
    "rdkit>=2022.9.5",
    "torch>=2.0.0",
    "typer>=0.12.0",
    "rich>=13.0.0",
]

[project.optional-dependencies]
ani = [
    "torchani>=2.2",
]
ase = [
    "ase>=3.22.1",
]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "mypy>=1.0",
    "ruff>=0.1.0",
    "pre-commit>=3.0",
]
docs = [
    "sphinx>=7.0",
    "sphinx-rtd-theme>=1.3.0",
    "nbsphinx>=0.9.0",
    "myst-parser>=2.0",
]
all = [
    "Auto3D[ani,ase,dev,docs]",
]

[project.scripts]
auto3d = "Auto3D.auto3Dcli:cli"

[project.urls]
Homepage = "https://github.com/isayevlab/Auto3D_pkg"
Documentation = "https://auto3d.readthedocs.io"
Repository = "https://github.com/isayevlab/Auto3D_pkg"
"Bug Tracker" = "https://github.com/isayevlab/Auto3D_pkg/issues"
Changelog = "https://github.com/isayevlab/Auto3D_pkg/releases"

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

[tool.setuptools.package-data]
Auto3D = ["models/*.jpt", "models/*.pt"]

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "F",      # Pyflakes
    "I",      # isort
    "N",      # pep8-naming
    "UP",     # pyupgrade
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "SIM",    # flake8-simplify
]
ignore = [
    "E501",   # line too long (handled by formatter)
    "E402",   # module level import not at top (needed for sys.path manipulation)
    "E741",   # ambiguous variable name (scientific notation l, I, O)
    "N801",   # class name should use CapWords (legacy code compatibility)
    "N802",   # function name should be lowercase (legacy API compatibility)
    "N803",   # argument name should be lowercase (scientific computing conventions)
    "N806",   # variable name should be lowercase (scientific computing conventions)
    "N815",   # mixedCase variable (scientific notation like pKa)
    "N999",   # invalid module name (Auto3D is the package name)
    "SIM102", # nested if (sometimes clearer)
    "SIM103", # return condition directly (explicit is clearer)
    "SIM105", # contextlib.suppress (try-except-pass is clearer for optional imports)
    "SIM108", # ternary operator (less readable for complex conditions)
    "SIM110", # any/all (explicit loops can be clearer)
    "SIM115", # context manager for open (sometimes not applicable)
    "SIM118", # key in dict instead of dict.keys()
    "B007",   # unused loop variable (intentional in some cases)
    "B008",   # function call in default argument (torch.device is acceptable)
    "B028",   # stacklevel in warnings (not always needed)
    "B904",   # raise from in except (not always needed)
    "C403",   # set comprehension (list comprehension is often clearer)
    "C408",   # dict() call (more readable with keyword arguments)
    "C416",   # list comprehension (intentional in some cases)
    "C417",   # map usage (sometimes clearer than list comprehension)
    "F401",   # unused import (optional dependency checks)
    "F841",   # unused variable (sometimes needed for clarity)
    "UP031",  # format specifiers (% format is fine for simple cases)
]

[tool.ruff.lint.isort]
known-first-party = ["Auto3D"]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true
exclude = [
    "tests/",
    "docs/",
    "example/",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = "test_*.py"
python_classes = "Test*"
python_functions = "test_*"
addopts = "-v --tb=short -m 'not slow'"
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "gpu: marks tests requiring GPU",
    "openeye: marks tests requiring OpenEye license",
]
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::UserWarning",
]

[tool.coverage.run]
source = ["src/Auto3D"]
omit = [
    "*/tests/*",
    "*/__init__.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "raise NotImplementedError",
]