[build-system]
requires = [
    "setuptools>=77",
    "setuptools-scm>=8",
    "packaging",
    # same as scikit-learn
    "Cython>=3.1.4",
    # building against numpy 2.x is compatible with numpy 1.x
    "numpy>=2.0.0",

    # scikit-learn requirements
    "scikit-learn~=1.9.0; python_version<='3.14'",
    "scikit-learn; python_version>'3.14'",
]
build-backend = "setuptools.build_meta"

[project]
name = "scikit-survival"
description = "Survival analysis built on top of scikit-learn"
readme = "README.rst"
authors = [
    {name = "Sebastian Pölsterl", email = "sebp@k-d-w.org"}
]
license = "GPL-3.0-or-later"
license-files = ["COPYING"]
requires-python = ">=3.11"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX",
    "Programming Language :: C++",
    "Programming Language :: Cython",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Software Development",
    "Topic :: Scientific/Engineering"
]
dependencies = [
    "clarabel",
    "ecos",
    "joblib",
    "narwhals >=2.0.1",
    "numexpr",
    "numpy >=2.0.0",
    "osqp >=1.0.2",
    "pandas >=2.2.0",
    "scipy >=1.13.0",
    "scikit-learn >=1.9.0,<1.10",
]
dynamic = ["version"]

[project.urls]
"Homepage" = "https://github.com/sebp/scikit-survival"
"Documentation" = "https://scikit-survival.readthedocs.io"
"Source Code" = "https://github.com/sebp/scikit-survival"
"Bug Tracker" = "https://github.com/sebp/scikit-survival/issues"
"Release Notes" = "https://scikit-survival.readthedocs.io/en/latest/release_notes.html"

[dependency-groups]
formatting = [
    "black[jupyter]",
    "ruff",
]

# This file purposely does not contain libraries that depend on C modules.
# See https://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
docs = [
    "ipython !=8.7.0",
    "matplotlib ~=3.10.0",
    "nbsphinx >=0.9.2",
    "docutils",
    "setuptools-scm",
    "sphinx ~=8.2.3",
    "pydata-sphinx-theme ~=0.18.0",
    "sphinxcontrib-spelling",
    "sphinx-design ~=0.7.0",
    "sphinx-copybutton ~=0.5.2",
]

test = [
    "coverage",
    "polars >=1.0.0",
    "pytest >=9",
]

test-nb = [
    "ipykernel",
    "ipython!=8.7.0",
    "matplotlib~=3.10.0",
    "nbformat",
    "nbval>=0.10.0",
    "seaborn~=0.13.2",
]

dev = [
    {include-group = "formatting"},
    {include-group = "test"},
    "build",
    "Cython >=3.0.10",
    "packaging",
    "pre-commit",
    "setuptools-scm >=8",
    "tomli",
    "tox",
]

[tool.setuptools]
include-package-data = false

[tool.setuptools.packages.find]
include = ["sksurv*"]
namespaces = false

[tool.setuptools.package-data]
"sksurv.datasets" = ["data/*.arff"]

[tool.black]
line-length = 120
extend-exclude = "sksurv/linear_model/src/eigen"
target-version = ["py311"]

[tool.pytest]
minversion = "9.0"
addopts = ["--strict-markers"]
doctest_optionflags = ["NORMALIZE_WHITESPACE", "ELLIPSIS"]
norecursedirs = [".*", "*.egg", "build", "dist", "venv", "{arch}", "eigen"]
testpaths = ["tests"]
filterwarnings = [
    # Treat all warnings as errors other than the ignored ones
    "error",
    "ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning",
    # deprecated since Pandas 2.2.0
    "ignore:\\nPyarrow will become a required dependency of pandas in the next major release of pandas.*:DeprecationWarning",
    # deprecated since Python 3.12
    "ignore:datetime\\.datetime\\.utcfromtimestamp\\(\\) is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
    "ignore:ast\\.Num is deprecated and will be removed in Python 3\\.14.*:DeprecationWarning",
    "ignore:Attribute n is deprecated and will be removed in Python 3\\.14.*:DeprecationWarning",
    # deprecated since scipy 1.16.0, scheduled for removal in 1.18
    "ignore:scipy\\.optimize. The `disp` and `iprint` options of the L-BFGS-B solver are deprecated.*:DeprecationWarning",
    # deprecated since pandas 3.0.0
    "ignore:The copy keyword is deprecated and will be removed in a future version.*:DeprecationWarning",
    # pandas 4 deprecates the implicit ``str``-via-``object`` inclusion in
    # ``DataFrame.select_dtypes``. Listing ``"str"`` explicitly would resolve
    # the deprecation but is rejected by pandas <= 3.x with ``TypeError``,
    # so the cross-version-safe call still emits the warning on pandas 4.
    "ignore:For backward compatibility, 'str' dtypes are included by select_dtypes.*",
    # deprecated since polars 1.40.1
    "ignore: the default behavior of `how='horizontal'` for `concat` is deprecated and will require equal heights in the next breaking release.*:DeprecationWarning",
    # deprecated since polars 1.43, to be removed in 2.0
    "ignore:`cat.get_categories\\(\\)` is deprecated.*:DeprecationWarning",
]

[tool.coverage.run]
branch = true
plugins = ["Cython.Coverage"]
relative_files = true
source = ["sksurv"]

[tool.coverage.report]
exclude_lines = [
    # Have to re-enable the standard pragma
    "pragma: no cover",

    # Don't complain about missing debug-only code:
    "def __repr__",
    "if self\\.debug",

    # Don't complain if tests don't hit defensive assertion code:
    "raise AssertionError",
    "raise NotImplementedError",

    # Don't complain if non-runnable code isn't run:
    "if 0:",
    "if __name__ == .__main__.:",
]
ignore_errors = true

omit = [
    "tests/*",
    "*/setup.py",
    "*/_version.py",
]

[tool.ruff]
extend-exclude = [
    "doc/conf.py",
    "sksurv/linear_model/src/eigen",
]
# Group violations by containing file.
output-format = "grouped"
line-length = 120
target-version = "py311"

[tool.ruff.lint]
ignore = ["A005", "C408"]
select = [
    # pycodestyle
    "E",
    "W",
    # mccabe
    "C90",
    # pyflakes
    "F",
    # isort
    "I",
    # flake8-builtins
    "A",
    # flake8-comprehensions
    "C4",
    # flake8-pytest-style
    "PT",
]

[tool.ruff.lint.flake8-pytest-style]
fixture-parentheses = true
mark-parentheses = true
parametrize-names-type = "csv"

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

[tool.ruff.lint.isort]
force-sort-within-sections = true
known-first-party = ["sksurv"]

[tool.numpydoc_validation]
checks = [
    "all",   # report on all checks, except the below
    "ES01",  # no extended summary
    "EX01",  # no examples section
    "SA01",  # no See Also section
]
exclude = [
    # Exclude all private functions and classes (those beginning with _):
    '\._',
    '.+_$',
]
exclude_files = [
    '(^|.*/)_[^/]*\.py$',
    '(^|.*/)tests/.*',
    '(^|.*/)sksurv/linear_model/src/eigen/.*',
]

[tool.setuptools_scm]

[tool.tox]
requires = ["tox>=4.40"]
env_list = [
    "lint",
    "docs",
]

[tool.tox.env.lint]
description = "Run linters"
skip_install = true
deps = [
    "numpydoc",
    "sphinx-lint",
]
commands = [
    ["sphinx-lint", "doc", "-i", "doc{/}api{/}generated"],
    ["numpydoc", "lint", { replace = "glob", pattern = "sksurv/**/*.py", extend = true }],
]

[tool.tox.env.docs]
description = "Build documentation"
dependency_groups = [
    "docs",
]
change_dir = "doc"
commands = [
    ["sphinx-build", "-j", "1", "-d", "_build{/}doctrees", "-E", "-W", "-b", "html", ".", "_build{/}html"]
]

[tool.tox.env.spelling]
description = "Spellcheck documentation"
dependency_groups = [
    "docs",
]
change_dir = "doc"
commands = [
    ["sphinx-build", "-j", "auto", "-d", "_build{/}doctrees", "-E", "-W", "-b", "spelling", ".", "_build{/}spelling"]
]