chemeleon2/pyproject.toml at main · learncat163/chemeleon2 · GitHub

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

[project]
name = "chemeleon2"
version = "0.1.0"
description = "Generative AI framework for crystalline materials"
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "ase>=3.26.0",
    "average-minimum-distance>=1.6.0",
    "fire>=0.7.1",
    "h5py>=3.14.0",
    "huggingface_hub>=0.20.0",
    "hydra-colorlog==1.2.0",
    "hydra-core==1.3.2",
    "hydra-optuna-sweeper==1.2.0",
    "lightning>=2.5.4",
    "mp-api>=0.45.8",
    "pydantic>=2.11.7",
    "pymatgen>=2025.6.14",
    "pyyaml>=6.0",
    "timm>=1.0.19",
    "torch>=2.6.0",
    "torch-ema>=0.3",
    "torch-geometric>=2.6.1",
    "torchmetrics>=1.8.1",
    "tqdm>=4.67.1",
    "wandb>=0.21.3",
]

[project.optional-dependencies]
training = [
    "mace-torch>=0.3.0",  # Energy calculations for e_above_hull in RL rewards
    "smact>=3.2.0",       # Composition validity checks in RL rewards
]
dev = [
    "jupyterlab>=4.4.6",  # Jupyter development environment
    "nglview>=3.1.4",     # 3D structure visualization
    "pre-commit>=4.0.0",  # Pre-commit hooks framework
    "pytest>=7.0",        # Testing framework
    "pyright==1.1.406",   # Type checking
    "rich>=14.1.0",       # Terminal output formatting
    "ruff==0.13.3",       # Linting and formatting
]

[tool.setuptools.packages.find]
where = ["."]
include = ["src*", "custom_reward*"]

[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
pythonpath = ["src"]
markers = [
    "smoke: Quick smoke tests for basic functionality",
    "baseline: Baseline tests to validate code before/after formatting",
    "unit: Unit tests for individual components",
    "integration: Integration tests for component interactions",
    "slow: Tests that take significant time to run",
]
addopts = ["-ra", "-q", "--strict-markers"]
filterwarnings = [
    "ignore::UserWarning:torch.nn.modules.transformer",
    "ignore::UserWarning:lightning.pytorch.utilities.parsing",
]

[tool.ruff]
# Python version target
target-version = "py311"
# Black-compatible line length
line-length = 88

[tool.ruff.lint]
# Rule sets to enable:
select = [
    "F",    # F: Pyflakes errors (undefined names, unused imports)
    "E",    # E: PEP 8 style errors (indentation, whitespace)
    "W",    # W: PEP 8 style warnings (deprecated features)
    "I",    # I: isort import sorting
    "N",    # N: PEP 8 naming conventions
    "D",    # D: Docstrings (pydocstyle)
    "UP",   # UP: pyupgrade (modernize Python syntax)
    "ANN",  # ANN: Type annotations (flake8-annotations)
    "S",    # S: Security checks (flake8-bandit)
    "B",    # B: Bugbear (design issues, anti-patterns)
    "C90",  # C90: McCabe complexity checker
]

# Rules to ignore for existing codebase (retroactive linting)
ignore = [
    "ANN001",  # Missing type annotation for function argument
    "ANN002",  # Missing type annotation for *args
    "ANN003",  # Missing type annotation for **kwargs
    "ANN201",  # Missing return type annotation for public function
    "ANN202",  # Missing return type annotation for private function
    "ANN204",  # Missing return type annotation for __init__
    "ANN205",  # Missing return type annotation for static method
    "B028",    # No explicit `stacklevel` keyword argument found
    "D102",    # Missing docstring in public method
    "D103",    # Missing docstring in public function
    "D105",    # Missing docstring in magic method
    "D107",    # Missing docstring in __init__
    "D200",    # One-line docstring should fit on one line
    "D205",    # Missing blank line after summary
    "D417",    # Missing argument description in docstring
    "E501",    # Line too long (existing code has long lines)
    "N802",    # Function name should be lowercase
    "N806",    # Variable in function should be lowercase
    "N812",    # Lowercase imported as non-lowercase
    "S101",    # Use of assert detected (common in ML code for shape checks)
    "S301",    # Pickle usage (needed for model checkpoints)
    "B007",    # Unused loop control variable
    "B008",    # Function call in default argument
    "C901",    # Function is too complex
    "UP008",   # Use super() without arguments
]

[tool.ruff.lint.pydocstyle]
# Docstring style convention
convention = "google"

[tool.ruff.lint.mccabe]
# Maximum cyclomatic complexity threshold
max-complexity = 10

[tool.pyright]
# Type checking mode - basic provides essential type checking without being overly strict
typeCheckingMode = "basic"
# Python version target - must match project requirements
pythonVersion = "3.11"
# Virtual environment configuration
venvPath = "."
venv = ".venv"
exclude = [
    "./src/utils/ema_callback.py",
    "./src/vae_module/vae_module.py",
    "./src/ldm_module/ldm_module.py",
    "./src/rl_module/rl_module.py",
    "./src/vae_module/predictor_module.py",
]