pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel", "cython>=0.20"]
build-backend = "setuptools.build_meta"

[project]
name = "py3plex"
version = "2.0.1"
description = "A Multilayer network analysis python3 library"
readme = "README.md"
requires-python = ">=3.8"
license = {text = "MIT"}
authors = [
    {name = "Blaž Škrlj", email = "blaz.skrlj@ijs.si"}
]
keywords = [
    "network analysis",
    "multilayer networks",
    "heterogeneous networks",
    "graph visualization",
    "network science"
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Visualization",
]
dependencies = [
    "numpy>=1.19.0",  # Minimum for Python 3.8+
    "scipy>=1.5.0",  # Minimum for Python 3.8+
    "networkx>=2.5",  # Already reasonable
    "tqdm>=4.40.0",  # Modern version with better features
    "matplotlib>=3.3.0",  # Minimum for Python 3.8+
    "scikit-learn>=0.24.0",  # Minimum for Python 3.8+
    "bitarray>=2.0.0",  # Already modern
    "seaborn>=0.11.0",  # Modern version
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-timeout>=2.1",
    "pytest-cov>=4.0",
    "pytest-benchmark>=4.0,<5.0",  # 5.0+ requires Python >=3.9, but we support 3.8
    "pytest-rerunfailures>=12.0",  # Flaky test handling
    "black>=23.0",
    "ruff>=0.1.0",
    "mypy>=1.0",
    "types-six>=1.16.0",  # Type stubs for six library (mypy)
    "pre-commit>=3.0",
    "crosshair-tool>=0.0.60",  # Formal verification
    "icontract>=2.6.0",  # Design by contract
    "z3-solver>=4.12.0",  # SMT solver for CrossHair
    "hypothesis>=6.0",  # Property-based testing
]
# Testing dependencies (for property-based and integration tests)
tests = [
    "pytest>=7.0",
    "pytest-timeout>=2.1",
    "pytest-cov>=4.0",
    "pytest-rerunfailures>=12.0",  # Flaky test handling
    "hypothesis>=6.0",
    "hypothesis-networkx>=0.2.0",  # Hypothesis strategies for NetworkX graphs
    "networkx>=2.5",
    "numpy>=1.19.0",
    "scipy>=1.5.0",
    "python-louvain>=0.16",  # For community detection tests (optional, guarded)
]
# Optional: Infomap for advanced community detection
infomap = [
    "infomap>=2.0.0",
]
# Optional: Additional algorithms (Louvain, label propagation)
algos = [
    "python-louvain>=0.16",
    "cdlib>=0.3.0",
    "gensim>=4.0.0",
    "rdflib>=6.0.0",
]
# Optional: Advanced visualization
viz = [
    "plotly>=5.0.0",
    "python-igraph>=0.10.0",
]
# Optional: Config-driven workflows with YAML support
workflows = [
    "pyyaml>=5.1",
]
# Optional: Apache Arrow for high-performance serialization
arrow = [
    "pyarrow>=10.0.0",
]
# Optional: Cross-compatibility conversion layer
compat = [
    "networkx>=2.5",
    "scipy>=1.5.0",
    "pandas>=1.2.0",
    "pyarrow>=10.0.0",  # For parquet sidecar format
]
# Optional: igraph support for compat layer
igraph = [
    "python-igraph>=0.10.0",
]
# Optional: PyTorch Geometric support for compat layer
pyg = [
    "torch>=1.10.0",
    "torch-geometric>=2.0.0",
]
# Optional: DGL support for compat layer
dgl_compat = [
    "dgl>=0.9.0",
]
# Optional: MCP server for AI agent integration (requires Python >=3.10)
mcp = [
    "mcp>=0.9.0; python_version>='3.10'",
]
# Optional: Dependencies for running advanced examples
examples = [
    "sympy>=1.9",
]
# Convenience meta-extra for common optional features (without heavy ML backends)
optional = [
    "infomap>=2.0.0",
    "python-louvain>=0.16",
    "cdlib>=0.3.0",
    "gensim>=4.0.0",
    "rdflib>=6.0.0",
    "plotly>=5.0.0",
    "python-igraph>=0.10.0",
    "pyyaml>=5.1",
    "pyarrow>=10.0.0",
    "mcp>=0.9.0; python_version>='3.10'",
    "sympy>=1.9",
]

[project.urls]
Homepage = "https://github.com/SkBlaz/py3plex"
Documentation = "https://skblaz.github.io/py3plex/"
Repository = "https://github.com/SkBlaz/py3plex"
"Bug Tracker" = "https://github.com/SkBlaz/py3plex/issues"

[project.scripts]
py3plex = "py3plex.cli:main"
py3plex-mcp = "py3plex_mcp.server:main"

[tool.setuptools]
zip-safe = false
include-package-data = true

[tool.setuptools.packages.find]
where = ["."]
include = ["py3plex*", "py3plex_mcp*"]
exclude = ["tests*", "docs*", "examples*"]

[tool.setuptools.exclude-package-data]
"*" = ["*.pyc", "*.pyo", "__pycache__/*"]

[tool.isort]
profile = "black"
line_length = 88
skip_gitignore = true
extend_skip = ["py3plex/algorithms/statistics/powerlaw.py"]

[tool.black]
line-length = 88
target-version = ['py38', 'py39', 'py310', 'py311', 'py312']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
  | examples
  # files
  | py3plex/algorithms/statistics/powerlaw\.py
)/
'''

[tool.ruff]
line-length = 88
target-version = "py38"
extend-exclude = [
    "examples",
    "build",
    "dist",
    ".eggs",
    "py3plex/algorithms/statistics/powerlaw.py",
]

[tool.ruff.lint]
select = [
    "E",  # pycodestyle errors
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    # "I",  # isort (disabled - using standalone isort instead)
    "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 (we have legacy code)
    "W191",  # indentation contains tabs (legacy code)
    "F821",  # undefined name (pre-existing bugs in unused code paths)
    "F811",  # redefined-while-unused (generated code in infomap bindings)
    "E741",  # ambiguous-variable-name (subjective, legacy code)
    "B904",  # raise-without-from-inside-except (Python 2 compatibility)
    "E721",  # type-comparison (legacy pattern, works correctly)
    "B007",  # unused-loop-control-variable (false positives in some cases)
    "E402",  # module-import-not-at-top-of-file (required for some conditional imports)
    "UP031", # printf-string-formatting (legacy code, %formatting still valid Python)
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]  # Allow unused imports in __init__.py

[tool.mypy]
python_version = "3.10"  # Keep aligned with type-coverage workflow runtime
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true
disallow_untyped_defs = false  # Set to true when type hints are complete
strict_optional = false
warn_redundant_casts = true
warn_unused_ignores = true
check_untyped_defs = false  # Set to true when type hints are complete
exclude = [
    'build/',
    'dist/',
    '.eggs/',
    # Auto-generated SWIG bindings (many type errors, not maintainable)
    'py3plex/algorithms/infomap/infomap\.py$',
    'py3plex/algorithms/community_detection/infomap/infomap\.py$',
    # Pre-existing syntax errors in powerlaw.py
    'py3plex/algorithms/statistics/powerlaw\.py$',
]

[tool.pytest.ini_options]
testpaths = ["tests", "py3plex"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "-q",
    "--tb=short",
    "--strict-markers",
    "--doctest-modules",
    "--doctest-continue-on-failure",
]
markers = [
    "property: property-based tests using Hypothesis",
    "slow: potentially slow tests",
    "integration: integration tests that require multiple components",
    "unit: fast unit tests",
    "metamorphic: metamorphic tests that verify invariants under transformations",
    "fast: fast unit tests that run quickly",
    "fuzz: fuzzing tests for discovering edge cases",
    "cli: CLI command tests",
    "verification: verification and correctness tests",
    "flaky: tests that may fail intermittently (handled by pytest-rerunfailures)",
]
timeout = 300
doctest_optionflags = [
    "NORMALIZE_WHITESPACE",
    "ELLIPSIS",
    "IGNORE_EXCEPTION_DETAIL",
]
norecursedirs = [
    ".git",
    ".hg",
    ".tox",
    ".venv",
    "dist",
    "build",
    ".hypothesis",
    "py3plex/algorithms/community_detection/infomap",
]

[tool.coverage.run]
source = ["py3plex"]
omit = [
    "*/tests/*",
    "*/examples/*",
    "*/build/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "if verbose:",
    "@abstractmethod",
]

[tool.hypothesis]
max_examples = 100
deadline = 500

[tool.mutmut]
paths_to_mutate = "py3plex/utils.py"
tests_dir = "tests/"
runner = "PYTHONPATH=/home/runner/work/py3plex/py3plex python -m pytest -x tests/test_utils.py tests/property/test_utils_properties.py"