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 = [
  "huggingface_hub>=0.23",
  "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 = [
  "pgmpy[torch]",
  "daft-pgm>=0.1.4",
  "xgboost>=2.0.3",
  "litellm>=1.61.15",
  "pygraphviz",
]
tests = [
  "xdoctest>=0.11.0",
  "pytest>=3.3.1",
  "pytest-cov",
  "pytest-split",
  "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 = [
  "pgmpy[optional,tests,docs]",
]

[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]
include-package-data = true

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

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

[tool.ruff]
line-length = 120
exclude = [".git", "examples/*", "docs/source/conf.py", "pgmpy/estimators/__init__.py",
	   "pgmpy/factors/discrete/__init__.py", "pgmpy/identification/__init__.py", "pgmpy/inference/__init__.py",
           "pgmpy/extern/*", "pgmpy/.github/*"]
target-version = "py314"
extend-include = ["*.ipynb"]

[tool.ruff.lint]
select = [
  "E",       # https://pypi.org/project/pycodestyle
  "W",       # https://pypi.org/project/pycodestyle
  "F",       # https://pypi.org/project/pyflakes
  "S",       # https://pypi.org/project/flake8-bandit
  "UP",      # https://docs.astral.sh/ruff/rules/#pyupgrade-up
  "YTT",     # https://pypi.org/project/flake8-2020/
  "I",       # isort
  "C4",      # https://pypi.org/project/flake8-comprehensions
  "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.
]

ignore = [
  "E203",  # Whitespace-before-punctuation.
  "E221",  # Multiple spaces before operator.
  "E222",  # Multiple spaces after operator.
  "E231",  # Missing whitespace after comma.
  "E241",  # Multiple spaces after comma.
  "E712",  # Comparison to True/False using == or !=.
  "E402",  # Module-import-not-at-top-of-file.
  "E731",  # Do not assign a lambda expression, use a def.
  "E741",  # Ambiguous variable name

  "S101",  # Use of `assert` detected.
  "S102",  # Use of excec
  "S105",  # Possible hardcoded password
  "S107",  # Possible hardcoded password
  "S110",  # try-except-pass detected.
  "S113",  # Probable use of httpx call without timeout
  "S202",  # Uses of `tarfile.extractall()`
  "S301",  # pickle and modules that wrap it can be unsafe
  "S307",  # Use of possibly insecure function
  "S310",  # Audit URL open for permitted schemes
  "S311",  # Standard pseudo-random generators not suitable for crypto.
  "S314",  # Using xml to parse untrusted data.
  "S318",  # Using xml minidom to parse untrusted data.
  "S602",  # sub process call with shell=True unsafe
  "S605",  # Starting a process with a shell, possible injection detected

  "C408",  # Unnecessary dict call - rewrite as a literal.
  "C409",  # Unnecessary `list` literal passed to `tuple()` (rewrite as a `tuple` literal)
  "C414",  # Unnecessary `list` call within `sorted()`
  "C416",  # Unnecessary list comprehension - rewrite as a generator
  "C417",  # Unnecessary `map` usage (rewrite using a generator expression)
  "C419",  # Unnecessary list comprehension, some are flagged yet are not

  "UP026", # Replace mock with unittest.mock (external mock has different behavior).
  "UP031", # Use format specifier instead of %
]