pyproject.toml

[build-system]
requires = ["hatchling", "hatch-vcs", "numpy"]
build-backend = "hatchling.build"

[project]
name = "pyphi"
dynamic = ["version"]
description = "A package for integrated information theory"
readme = "README.md"
license = { text = "GNU General Public License v3 or later (GPLv3+)" }
authors = [{ name = "William GP Mayner", email = "wmayner@gmail.com" }]
keywords = [
    "neuroscience",
    "causality",
    "causal-modeling",
    "causation",
    "integrated-information-theory",
    "iit",
    "integrated-information",
    "modeling",
]
requires-python = ">=3.12"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Natural Language :: English",
    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering",
]
dependencies = [
    "Graphillion>=1.5",
    "joblib>=0.8.0",
    "more_itertools>=8.13.0",
    "numpy",
    "ordered-set>=4.0.2",
    "pandas>=2.0.0",
    "psutil>=2.1.1",
    "pyyaml>=3.13",
    "scipy>=0.13.3",
    "tblib>=1.3.2",
    "toolz>=0.9.0",
    "tqdm>=4.20.0",
]

[project.optional-dependencies]
# Note: Single-machine parallelization uses stdlib ProcessPoolExecutor - no extra deps needed.
# The 'cluster' extra will be available in v2.0 for Dask-based cluster support.
# cluster = ["dask[distributed]>=2024.1.0", "dask-jobqueue>=0.8.0"]
visualize = ["matplotlib", "networkx>=2.6.2", "plotly>=5.8.2", "seaborn"]
graphs = ["igraph>=0.9.10", "networkx>=2.6.2"]
caching = ["redis>=2.10.5"]
emd = ["pyemd>=0.3.0"]

[dependency-groups]
dev = [
    "asv",
    "build",
    "coverage",
    "hypothesis",
    "pre-commit",
    "pytest-cov",
    "pyright>=1.1.407",
    "pytest<8.0.0",
    "pytest-lazy-fixture",
    "ruff",
    "sphinx",
    "sphinx-rtd-theme",
    "towncrier>=24.8.0",
    "twine",
    "watchdog",
]

[project.urls]
documentation = "https://pyphi.readthedocs.io"
bugs = "https://github.com/wmayner/pyphi/issues"
homepage = "http://integratedinformationtheory.org/"
discussion = "https://groups.google.com/forum/#!forum/pyphi-users"

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.targets.sdist]
include = [
    "README.md",
    "INSTALLATION.rst",
    "CACHING.rst",
    "LICENSE.md",
    "CHANGELOG.md",
    "pyphi_config.yml",
    "redis.conf",
    "pyphi/data/**",
]

[tool.hatch.build.targets.wheel]
packages = ["pyphi"]
include = ["pyphi/data/**"]

[tool.ruff]
line-length = 89
target-version = "py312"
exclude = [
    "__pycache__",
    "__pyphi_cache__",
    ".cache",
    ".git",
    ".coverage",
    "build",
    "dist",
    "docs",
    "htmlcov",
    "benchmarks",
]

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "B",    # flake8-bugbear
    "C4",   # flake8-comprehensions
    "C90",  # mccabe complexity
    "UP",   # pyupgrade
    "T20",  # flake8-print
    "TID",  # flake8-tidy-imports
    "SIM",  # flake8-simplify
    "RET",  # flake8-return
    "ARG",  # flake8-unused-arguments
    "PTH",  # flake8-use-pathlib
    "ERA",  # eradicate (commented-out code)
    "PL",   # pylint
    "PERF", # perflint (performance anti-patterns)
    "RUF",  # Ruff-specific rules
]
ignore = [
    # Relax some rules for scientific computing
    "PLR0913", # Too many arguments - common in scientific functions
    "PLR0912", # Too many branches - common in complex algorithms
    "PLR0915", # Too many statements - common in scientific code
    "PLR2004", # Magic value comparisons - common with thresholds
    "PLW1641", # Missing __hash__ - not needed for all Orderable classes
    "RET504",  # Unnecessary variable assignment before return
    "SIM108",  # Use ternary operator - sometimes less readable
    "PTH123",  # open() instead of Path.open() - open() is fine
    "ERA001",  # Commented-out code - allow for scientific exploration
    "PLC0415", # Import outside top-level - needed for optional dependencies
]

[tool.ruff.lint.mccabe]
max-complexity = 88

[tool.ruff.lint.isort]
known-first-party = ["pyphi"]
force-single-line = true

[tool.ruff.lint.pylint]
# Increased limits for scientific computing
max-args = 10
max-branches = 20
max-statements = 100

[tool.ruff.lint.per-file-ignores]
# Allow certain rules in test files
"test/**/*.py" = [
    "ARG001",  # Unused function arguments (fixtures)
    "PLR0913", # Too many arguments (test parametrization)
    "PLR2004", # Magic values (test data)
    "S101",    # Use of assert (standard in pytest)
    "T201",    # Print statements (debugging)
    "T203",    # Pretty print statements (debugging)
]
# Allow print statements in main init (welcome message) and profiling scripts
"pyphi/__init__.py" = ["T201"]
"profiling/**/*.py" = ["T201"]
# Allow print and magic values in examples
"docs/examples/**/*.py" = ["T201", "PLR2004"]
# Allow explicit re-exports in __init__ files (PEP 484 style)
"pyphi/**/__init__.py" = ["PLC0414"]
# Allow sentinel object() in cache_utils (standard pattern from functools)
"pyphi/cache/cache_utils.py" = ["B008"]
# Allow unused arguments in config callbacks and deferred imports
"pyphi/conf.py" = ["ARG001"]
"pyphi/deferred/*.py" = ["ARG002"]
# Allow unused kwargs in network generator (interface requirement)
"pyphi/network_generator/unit_functions.py" = ["ARG001"]
"pyphi/network_generator/ising.py" = ["ARG001"]
"pyphi/network_generator/weights.py" = ["ARG001"]
# Allow unused arguments in specific files (interface/callback requirements)
"pyphi/dynamics.py" = ["ARG001"]
"pyphi/jsonify.py" = ["ARG002"]
"pyphi/macro.py" = ["ARG002"]
"pyphi/metrics/distribution.py" = ["ARG001"]
"pyphi/models/mechanism.py" = ["ARG001"]
"pyphi/models/subsystem.py" = ["ARG002"]
"pyphi/parallel/__init__.py" = ["ARG001", "PLW0603"]
"pyphi/parallel/chunking.py" = ["PLR0911"]  # Many return statements in estimate_work_size
"pyphi/relations.py" = ["ARG001", "ARG002"]
"pyphi/subsystem.py" = ["ARG002"]
"pyphi/visualize/phi_structure/__init__.py" = ["ARG001"]

[tool.pytest.ini_options]
testpaths = ["pyphi", "test"]
addopts = [
    "--maxfail=0",
    "--log-level=INFO",
    "--strict-markers",
    "--durations=5",
    "--color=yes",
    "--tb=auto",
    "--doctest-glob=*.rst",
    "--doctest-modules",
    "--ignore=./profiling",
    "--ignore=./benchmarks",
    "-vv",
]
norecursedirs = ["docs/_*"]
markers = [
    "emd: marks tests that require the pyemd package (deselect with '-m \"not emd\"')",
    "outdated: marks tests as outdated (deselect with '-m \"not outdated\"')",
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "veryslow: marks tests as very slow (deselect with '-m \"not veryslow\"')",
]
filterwarnings = [
    "error",
    "ignore::ImportWarning",
    "ignore:The distutils package is deprecated:DeprecationWarning",
    "ignore:distutils Version classes are deprecated:DeprecationWarning",
    "ignore::FutureWarning",
    "ignore::UserWarning",
    "ignore::DeprecationWarning",
]

[tool.coverage.run]
branch = true
source = ["pyphi"]

[tool.coverage.report]
exclude_lines = [
    "coverage: disable",
    "pragma: no cover",
    "def __repr__",
    "def __str__",
    "def __ne__",
    "if self\\.DEBUG",
    "if DEBUG",
    "def print_",
    "def dprint",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
]
ignore_errors = true

[tool.coverage.html]
directory = "htmlcov"

[tool.pyright]
include = ["pyphi"]
exclude = ["**/__pycache__", "test", "docs", "benchmarks", "profiling"]
pythonVersion = "3.12"
typeCheckingMode = "standard"                                           # Start at standard, not basic
reportMissingImports = false
reportMissingTypeStubs = false
reportUnknownMemberType = false                                         # Disable for gradual migration
reportUnknownArgumentType = false
reportUnknownVariableType = false
reportGeneralTypeIssues = true
reportOptionalMemberAccess = true
reportOptionalSubscript = true

[tool.uv.sources]
# Build graphillion from source to avoid macOS libgomp dependency issues
# The PyPI wheel has hardcoded paths to Homebrew GCC's libgomp library
graphillion = { git = "https://github.com/takemaru/graphillion" }

[tool.towncrier]
directory = "changelog.d"
filename = "CHANGELOG.md"
title_format = "{version}"
underlines = ["-", "", ""]

# Fragment types matching PyPhi's existing CHANGELOG categories
[[tool.towncrier.type]]
directory = "feature"
name = "API additions"
showcontent = true

[[tool.towncrier.type]]
directory = "change"
name = "API changes"
showcontent = true

[[tool.towncrier.type]]
directory = "config"
name = "Config"
showcontent = true

[[tool.towncrier.type]]
directory = "optimization"
name = "Optimizations"
showcontent = true

[[tool.towncrier.type]]
directory = "fix"
name = "Fixes"
showcontent = true

[[tool.towncrier.type]]
directory = "doc"
name = "Documentation"
showcontent = true

[[tool.towncrier.type]]
directory = "refactor"
name = "Refactor"
showcontent = true

[[tool.towncrier.type]]
directory = "misc"
name = "Misc"
showcontent = false