spine/pyproject.toml at main · DeepLearnPhysics/spine · GitHub

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[build-system]
requires = ["setuptools>=65.0,<70.0", "wheel", "build>=0.8.0"]
build-backend = "setuptools.build_meta"

[project]
name = "spine"
dynamic = ["version"]
description = "SPINE: Scalable Particle Imaging with Neural Embeddings for 3D high energy physics data analysis"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "DeepLearnPhysics Collaboration", email = "drielsma@stanford.edu"}
]
maintainers = [
    {name = "Francois Drielsma", email = "drielsma@stanford.edu"}
]
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",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Physics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence"
]
keywords = ["machine learning", "physics", "neutrino", "sparse convolution", "graph neural network"]
requires-python = ">=3.10"

# Core dependencies (minimal functionality)
dependencies = [
    "numexpr>=2.8.0",
    "numpy>=1.19.0",
    "scipy>=1.7.0",
    "pandas>=1.3.0",
    "PyYAML>=5.4.0",
    "h5py>=3.1.0",
    "numba>=0.56.0",
    "psutil>=5.8.0",
    "tqdm>=4.60.0",
]

[project.urls]
Homepage = "https://github.com/DeepLearnPhysics/spine"
Repository = "https://github.com/DeepLearnPhysics/spine.git"
Documentation = "https://spine.readthedocs.io/"
"Bug Tracker" = "https://github.com/DeepLearnPhysics/spine/issues"

[project.optional-dependencies]
# Visualization dependencies
viz = [
    "matplotlib>=3.3.0",
    "particle>=1,<2",
    "plotly>=4.14.0",
    "seaborn>=0.11.0",
]

# Development and testing
dev = [
    "pytest>=6.0.0",
    "pytest-cov>=2.10.0",
    "black>=23.0.0",
    "flake8>=6.0.0",
    "isort>=5.12.0",
    "pre-commit>=3.0.0",
    "build>=0.8.0",
    "twine>=4.0.0",
    "wheel>=0.38.0",
    "sphinx>=4.0.0",
    "sphinx-rtd-theme>=1.0.0",
    "sphinx-copybutton>=0.5.0",
    "numpydoc>=1.4.0",
    "mypy>=1.0.0",
    "pylint>=3.0.0",
    # Include all pip-installable optional runtime features for development.
    "matplotlib>=3.3.0",
    "particle>=1,<2",
    "plotly>=4.14.0",
    "seaborn>=0.11.0",
]

[project.scripts]
spine = "spine.bin.cli:cli"
spine-cache = "spine.bin.cache:cli"
spine-config = "spine.bin.config:cli"
spine-filter = "spine.bin.filter:cli"
spine-report = "spine.bin.report:cli"

[tool.setuptools.dynamic]
version = {attr = "spine.version.__version__"}

[tool.setuptools.packages.find]
where = ["src"]
include = ["spine*"]
exclude = ["test*", "docs*"]

[tool.setuptools.package-data]
spine = ["config/*.cfg", "physics/data/csda/*.table", "*.yaml", "*.yml"]

# Black code formatting
[tool.black]
line-length = 88
target-version = ['py310', 'py311', 'py312', 'py313']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''

# isort import sorting (compatible with Black)
[tool.isort]
profile = "black"
line_length = 88
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
ensure_newline_before_comments = true

# Pytest configuration
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "-ra -q --strict-markers"
testpaths = ["test"]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "gpu: marks tests that require GPU",
    "integration: marks tests as integration tests",
    "model: marks tests that require the full model runtime",
]

# Coverage configuration
[tool.coverage.run]
source = ["src/spine"]
omit = [
    "*/test/*",
    "*/tests/*",
    "setup.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]