pyproject.toml

[project]
name = "hazardous"
description = "Predictive Competing Risks and Survival Analysis."
authors = [
    { name = "Olivier Grisel", email = "olivier.grisel@ensta.org" },
    { name = "Vincent Maladière", email = "vincent.maladiere@inria.fr" }
]
readme = "README.md"
requires-python = ">=3.9"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dependencies = [
    "numpy",
    "scikit-learn",
    "tqdm",
    # TODO: implement KM and make this a soft dependency for the
    # doc and tests.
    "lifelines",
    # lifelines.KaplanMeierFitter imports lifelines.datasets which has an
    # undeclared runtime dependency on setuptools.
    "setuptools",
    "pycox",
    "scikit-survival",
    "rpy2", # TODO: install R and install comprsk
]
dynamic = ["version"]

[project.optional-dependencies]
dev = [
    "pre-commit",
    "nox",
]
test = [
    "pytest",
    "pytest-cov",
    "pandas",
]
oldest_deps = [
    "numpy==1.22",
    "scikit-learn==1.1.3",
    "pandas==1.5.1",
]
doc = [
    "sphinx",
    "pydata-sphinx-theme",
    "sphinx-gallery",
    "matplotlib",
    "pillow",  # to scrape images from the examples
    "numpydoc",
    "seaborn",
]

[project.urls]
"Homepage" = "https://github.com/soda-inria/hazardous"
"Bug Tracker" = "https://github.com/soda-inria/hazardous/issues"

[build-system]
build-backend = "flit_core.buildapi"
requires = ["flit_core"]

[tool.black]
line-length = 88
target_version = ['py38', 'py39', 'py310', 'py311']
preview = true
exclude = '''
/(
    \.eggs         # exclude a few common directories in the
  | \.git          # root of the project
  | \.mypy_cache
  | \.vscode
  | build
  | dist
)/
'''

[tool.ruff]
# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
select = ["E", "F"]
ignore = []

# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
unfixable = []

# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
    "doc",
]

# Same as Black.
line-length = 88

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

target-version = "py39"

[tool.ruff.mccabe]
max-complexity = 10

[tool.ruff.per-file-ignores]
# It's fine not to put the import at the top of the file in the examples
"examples/*" = ["E402"]