pyproject.toml

[project]
name = "pgmpy"
version = "1.0.0"
description = "Python Library for Causal and Probabilistic Modeling using Bayesian Networks"
readme = "README.md"
license = { file = "LICENSE" }
authors = [
  { name = "Ankur Ankan", email = "ankurankan@gmail.com" }
]
requires-python = ">=3.10,<3.15"
classifiers = [
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Intended Audience :: Education",
  "Intended Audience :: Science/Research",
  "Operating System :: Unix",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: MacOS",
  "Topic :: Scientific/Engineering",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
  "Topic :: Scientific/Engineering :: Bio-Informatics"
]

dependencies = [
  "networkx>=3.0",
  "numpy>=2.0",
  "scipy>=1.10",
  "scikit-learn>=1.2",
  "pandas>=1.5",
  "statsmodels>=0.14.5",
  "tqdm>=4.64",
  "pyparsing>=3.0",
  "joblib>=1.2",
  "opt_einsum>=3.3",
  "scikit-base>=0.12.4",
]

[project.optional-dependencies]
torch = [
  "torch>=2.5",
  "pyro-ppl>=1.9.1",
]
optional = [
  "daft-pgm>=0.1.4",
  "xgboost>=2.0.3",
  "litellm==1.61.15",
  "pyparsing>=3.0",
  "pygraphviz",
  "torch>=2.5",
  "pyro-ppl>=1.9.1",
]
tests = [
  "xdoctest>=0.11.0",
  "pytest>=3.3.1",
  "pytest-cov",
  "pytest-xdist",
  "coverage>=4.3.4",
  "mock",
  "black",
  "pre-commit",
  "jsonschema",
]
docs = [
  "sphinx>=5.0",
  "nbsphinx",
  "numpydoc",
  "sphinx_rtd_theme",
  "sphinx-copybutton",
  "sphinx-design",
  "sphinxext-opengraph",
  "sphinx_sitemap",
]
all = [
  "networkx>=3.0",
  "numpy>=2.0",
  "scipy>=1.10",
  "scikit-learn>=1.2",
  "pandas>=1.5",
  "torch>=2.5",
  "statsmodels>=0.13",
  "tqdm>=4.64",
  "joblib>=1.2",
  "opt_einsum>=3.3",
  "pyro-ppl>=1.9.1",
  "daft-pgm>=0.1.4",
  "xgboost>=2.0.3",
  "litellm==1.61.15",
  "pyparsing>=3.0",
  "requests>=2.0",
]

[project.urls]
Documentation = "https://www.pgmpy.org"
Download = "https://pypi.org/project/pgmpy/#files"
Homepage = "https://www.pgmpy.org"
Repository = "https://github.com/pgmpy/pgmpy"

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

[tool.setuptools.packages.find]
exclude = ["tests"]

[tool.setuptools.package-data]
pgmpy = [
  "utils/example_models/*.bif.gz",
  "utils/example_models/*.json",
  "utils/example_models/*.txt"
]
[tool.setuptools]
include-package-data = true

[tool.pytest.ini_options]
addopts = "-p no:doctest"
norecursedirs = [".git", "ignore", "build", "__pycache__"]
filterwarnings = ["default"]

[tool.isort]
skip = [
  "pgmpy/identification/__init__.py",
  "pgmpy/datasets/__init__.py",
]

[tool.ruff]
line-length = 120
exclude = [".git", "examples/*"]
target-version = "py311"
extend-include = ["*.ipynb"]

[tool.ruff.lint]
select = [
  # https://pypi.org/project/pycodestyle
  "D",
  "E",
  "W",
  # https://pypi.org/project/pyflakes
  "F",
  # https://pypi.org/project/flake8-bandit
  "S",
  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
  "UP",
  "I002",    # Missing required imports
  "UP008",   # Super calls with redundant arguments passed.
  "G010",    # Deprecated log warn.
  "PLR1722", # Use sys.exit() instead of exit() and quit().
  "PT014",   # pytest-duplicate-parametrize-test-cases.
  "PT006",   # Checks for the type of parameter names passed to pytest.mark.parametrize.
  "PT007",   # Checks for the type of parameter values passed to pytest.mark.parametrize.
  "PT018",   # Checks for assertions that combine multiple independent condition
  "RUF001", # Checks for non unicode string literals
  "RUF002", # Checks for non unicode string literals
  "RUF003", # Checks for non unicode string literals
]

extend-select = [
  "I", # isort
  "C4", # https://pypi.org/project/flake8-comprehensions
]
ignore=[
  "E203", # Whitespace-before-punctuation.
  "E402", # Module-import-not-at-top-of-file.
  "E731", # Do not assign a lambda expression, use a def.
  "RET504", # Unnecessary variable assignment before `return` statement.
  "S101", # Use of `assert` detected.
  "RUF100", # https://docs.astral.sh/ruff/rules/unused-noqa/
  "C408", # Unnecessary dict call - rewrite as a literal.
  "UP031", # Use format specifier instead of %
  "S102", # Use of excec
  "C414", # Unnecessary `list` call within `sorted()`
  "S301", # pickle and modules that wrap it can be unsafe
  "C416", # Unnecessary list comprehension - rewrite as a generator
  "S310", # Audit URL open for permitted schemes
  "S202", # Uses of `tarfile.extractall()`
  "S307", # Use of possibly insecure function
  "C417", # Unnecessary `map` usage (rewrite using a generator expression)
  "S605", # Starting a process with a shell, possible injection detected
  "E741", # Ambiguous variable name
  "S107", # Possible hardcoded password
  "S105", # Possible hardcoded password
  "PT018", # Checks for assertions that combine multiple independent condition
  "S602", # sub process call with shell=True unsafe
  "C419", # Unnecessary list comprehension, some are flagged yet are not
  "C409", # Unnecessary `list` literal passed to `tuple()` (rewrite as a `tuple` literal)
  "S113", # Probable use of httpx call without timeout
]
allowed-confusables=["σ"]