content: [build-system]
  requires = ["setuptools>=61.0", "wheel"]
  build-backend = "setuptools.build_meta"
  
  [project]
  name = "lambda3-dual-sync-model"
  version = "0.1.0"
  description = "Lambda³ Theory implementation for dual synchronization Bayesian modeling with structure tensor analysis"
  readme = "README.md"
  requires-python = ">=3.9"
  license = {text = "MIT"}
  authors = [
      {name = "Masamichi iizumi", email = "m.iizumi@miosync.email"},
  ]
  keywords = ["lambda3", "bayesian", "synchronization", "structure-tensor", "time-series"]
  classifiers = [
      "Development Status :: 3 - Alpha",
      "Intended Audience :: Science/Research",
      "License :: OSI Approved :: MIT License",
      "Operating System :: OS Independent",
      "Programming Language :: Python :: 3",
      "Programming Language :: Python :: 3.9",
      "Programming Language :: Python :: 3.10",
      "Programming Language :: Python :: 3.11",
      "Programming Language :: Python :: 3.12",
      "Topic :: Scientific/Engineering :: Mathematics",
      "Topic :: Scientific/Engineering :: Physics",
      "Topic :: Scientific/Engineering :: Artificial Intelligence",
  ]
  
  dependencies = [
      "pymc>=5.0.0",
      "numpy>=1.21.0",
      "scipy>=1.7.0",
      "arviz>=0.15.0",
      "matplotlib>=3.5.0",
      "seaborn>=0.11.0",
      "scikit-learn>=1.0.0",
      "networkx>=2.6.0",
      "pandas>=1.3.0",
      "aesara>=2.8.0",
      "pytensor>=2.8.0",
  ]
  
  [project.optional-dependencies]
  dev = [
      "pytest>=7.0.0",
      "pytest-cov>=4.0.0",
      "black>=22.0.0",
      "isort>=5.10.0",
      "flake8>=5.0.0",
      "mypy>=0.991",
      "pre-commit>=2.20.0",
  ]
  docs = [
      "sphinx>=5.0.0",
      "sphinx-rtd-theme>=1.0.0",
      "myst-parser>=0.18.0",
      "sphinx-autodoc-typehints>=1.19.0",
  ]
  jupyter = [
      "jupyter>=1.0.0",
      "ipykernel>=6.0.0",
      "ipywidgets>=8.0.0",
      "plotly>=5.0.0",
  ]
  performance = [
      "numba>=0.56.0",
      "jax>=0.3.0",
      "jaxlib>=0.3.0",
  ]
  
  [project.urls]
  Homepage = "https://github.com/iizumi/lambda3-dual-sync-model"
  Documentation = "https://lambda3-dual-sync-model.readthedocs.io/"
  Repository = "https://github.com/iizumi/lambda3-dual-sync-model.git"
  Issues = "https://github.com/iizumi/lambda3-dual-sync-model/issues"
  
  [project.scripts]
  lambda3-analyze = "lambda3_dual_sync.cli:main"
  
  [tool.setuptools.packages.find]
  where = ["src"]
  include = ["lambda3_dual_sync*"]
  exclude = ["tests*"]
  
  [tool.setuptools.package-dir]
  "" = "src"
  
  [tool.pytest.ini_options]
  testpaths = ["tests"]
  python_files = ["test_*.py"]
  python_classes = ["Test*"]
  python_functions = ["test_*"]
  addopts = [
      "--strict-markers",
      "--strict-config",
      "--cov=lambda3_dual_sync",
      "--cov-report=term-missing",
      "--cov-report=html",
      "--cov-report=xml",
  ]
  markers = [
      "slow: marks tests as slow (deselect with '-m \"not slow\"')",
      "integration: marks tests as integration tests",
      "unit: marks tests as unit tests",
      "lambda3: marks tests specific to Lambda³ theory",
  ]
  
  [tool.black]
  line-length = 88
  target-version = ['py39']
  include = '\.pyi?$'
  extend-exclude = '''
  /(
    # directories
    \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | build
    | dist
  )/
  '''
  
  [tool.isort]
  profile = "black"
  multi_line_output = 3
  line_length = 88
  known_first_party = ["lambda3_dual_sync"]
  known_third_party = ["pymc", "numpy", "scipy", "arviz", "matplotlib", "seaborn", "sklearn", "networkx", "pandas"]
  
  [tool.mypy]
  python_version = "3.9"
  warn_return_any = true
  warn_unused_configs = true
  disallow_untyped_defs = true
  disallow_incomplete_defs = true
  check_untyped_defs = true
  disallow_untyped_decorators = true
  no_implicit_optional = true
  warn_redundant_casts = true
  warn_unused_ignores = true
  warn_no_return = true
  warn_unreachable = true
  strict_equality = true
  show_error_codes = true
  
  [[tool.mypy.overrides]]
  module = [
      "pymc.*",
      "arviz.*",
      "seaborn.*",
      "networkx.*",
      "sklearn.*",
      "aesara.*",
      "pytensor.*",
  ]
  ignore_missing_imports = true
  
  [tool.coverage.run]
  source = ["src"]
  omit = [
      "*/tests/*",
      "*/test_*",
      "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",
  ]
  
  [tool.ruff]
  target-version = "py39"
  line-length = 88
  select = [
      "E",  # pycodestyle errors
      "W",  # pycodestyle warnings
      "F",  # pyflakes
      "I",  # isort
      "B",  # flake8-bugbear
      "C4", # flake8-comprehensions
      "UP", # pyupgrade
  ]
  ignore = [
      "E501",  # line too long, handled by black
      "B008",  # do not perform function calls in argument defaults
      "C901",  # too complex
  ]
  
  [tool.ruff.per-file-ignores]
  "__init__.py" = ["F401"]
  "tests/*" = ["E501"]
  
  [tool.bandit]
  exclude_dirs = ["tests"]
  skips = ["B101", "B601"]
  