pyproject.toml

[project]
name = 'scikit-image'
description = 'Image processing in Python'
requires-python = '>=3.12'
readme = 'README.md'
classifiers = [
    'Development Status :: 4 - Beta',
    'Environment :: Console',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: BSD License',
    'Programming Language :: C',
    'Programming Language :: Python',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3.12',
    'Programming Language :: Python :: 3.13',
    'Programming Language :: Python :: 3.14',
    'Programming Language :: Python :: 3.15',
    'Programming Language :: Python :: 3 :: Only',
    'Topic :: Software Development :: Libraries',
    'Topic :: Scientific/Engineering',
    'Operating System :: Microsoft :: Windows',
    'Operating System :: POSIX',
    'Operating System :: Unix',
    'Operating System :: MacOS',
]
dynamic = ['version']
dependencies = [
    'numpy>=2.2',
    'scipy>=1.15; sys_platform != "emscripten"',
    'scipy>=1.14; sys_platform == "emscripten"',
    'networkx>=3.4',
    'pillow>=10.1',
    'imageio>=2.33,!=2.35.0',
    'tifffile>=2025.1.10',
    'packaging>=24',
    'lazy-loader>=0.6',
]

[[project.maintainers]]
name = 'scikit-image developers'
email = 'skimage-core@discuss.scientific-python.org'

[project.license]
file = 'LICENSE.txt'

[project.optional-dependencies]
build = [
    # Also update [build-system] -> requires
    'meson-python>=0.16',
    'ninja>=1.11.1.3',
    'Cython>=3.2',
    'pythran>=0.16',
    'numpy>=2.2',
    # Developer UI
    'spin>=0.14',
    'build>=1.3',
]
data = ['pooch>=1.6.0']
developer = [
    'pre-commit',
    'ipython',
    'docstub==0.7.0rc0',
    'scikit-image[asv]',
]
asv = [
    'asv; sys_platform != "emscripten"',
]
docs = [
    'sphinx>=8.0',
    'sphinx-gallery[parallel]>=0.20',
    'numpydoc>=1.7',
    'sphinx-copybutton',
    'sphinx-togglebutton',
    'matplotlib>=3.10',
    'dask[array]>=2025.1.0',
    'pandas>=2.3',
    'seaborn>=0.13',
    'pooch>=1.6',
    'tifffile>=2025.1.10',
    'myst-parser',
    'intersphinx-registry>=0.2411.14',
    'ipywidgets',
    'ipykernel',  # needed until https://github.com/jupyter-widgets/ipywidgets/issues/3731 is resolved
    'plotly>=6.1.1',
    'kaleido>=1.0',
    'scikit-learn>=1.6',
    'sphinx_design>=0.5',
    'pydata-sphinx-theme>=0.17',
    'PyWavelets>=1.7',
    'pytest-doctestplus>=1.6.0',
]
optional = [
    'SimpleITK; sys_platform != "emscripten"',
    'scikit-learn>=1.6',
    'pyamg>=5.2; sys_platform != "emscripten" and python_version < "3.14"',  # not packaged for Pyodide yet
    'scikit-image[optional_free_threaded]'
]
optional_free_threaded = [
    'astropy>=6.1',
    'dask[array]>=2025.1.0',
    'matplotlib>=3.10; sys_platform != "emscripten"',  # the pyodide maintainers recommend not testing with matplotlib
    'pooch>=1.6.0; sys_platform != "emscripten"',  # requires stack switching with alternative pytest runner
    'PyWavelets>=1.7',
]

test = [
    'numpydoc>=1.7',
    'pooch>=1.6.0; sys_platform != "emscripten"',
    'pytest>=9',
    'pytest-cov>=2.11.0',
    'pytest-pretty',
    'pytest-localserver',
    'pytest-faulthandler',
    'pytest-doctestplus>=1.6.0',
]

[project.urls]
homepage = 'https://scikit-image.org'
documentation = 'https://scikit-image.org/docs/stable'
source = 'https://github.com/scikit-image/scikit-image'
download = 'https://pypi.org/project/scikit-image/#files'
tracker = 'https://github.com/scikit-image/scikit-image/issues'

[build-system]
build-backend = 'mesonpy'
requires = [
    'meson-python>=0.16',
    'Cython>=3.2',
    'pythran>=0.16',
    'lazy-loader>=0.6',
    'numpy>=2.0',
]

[tool.spin]
package = 'skimage'

[tool.spin.commands]
Build = [
    'spin.cmds.meson.build',
    'spin.cmds.pip.install',
    '.spin/cmds.py:test',
    '.spin/cmds.py:sdist',
]
Environments = [
    'spin.cmds.meson.run',
    '.spin/cmds.py:ipython',
    'spin.cmds.meson.python',
]
Documentation = ['.spin/cmds.py:docs']
Metrics = [
    '.spin/cmds.py:asv'
]

[tool.ruff.format]
quote-style = "preserve"

[tool.ruff.lint]
select = [
    'F',
    'E',
    'W',
    'UP',
    'NPY201',
]
ignore = [
    'E501',
    'E741',
    'E712',
    'E721',
    'UP038',  # non-pep604-isinstance -- https://github.com/astral-sh/ruff/issues/7871
]

[tool.ruff.lint.per-file-ignores]
"**/__init__.py" = [
    'E402',
    'F401',
    'F403',
    'F405',
]
"**/__init__.pyi" = [
    'E402',
    'F401',
    'F403',
    'F405',
]
"src/skimage/_shared/testing.py" = ['F401']
"doc/examples/**/*.py" = ['E402']

[tool.ruff.lint.pydocstyle]
convention = 'numpy'

[tool.pytest.ini_options]
# pythonpath requires pytest >= 7.0; --strict-config (in addopts) would error
# on startup with older versions anyway.
minversion = "7.0"
# Add the repo root to sys.path so pytest can import from the ``tests/``
# directory without requiring ``__init__.py`` files in every subdirectory.
# It does not affect ``src/``; packages there are found via the installed
# wheel or the meson build directory (set up by spin).
pythonpath = ["."]
addopts = [
    "-ra",
    "--strict-config",
    "--strict-markers",
    "--showlocals",
    # Necessary for doctest collection with editable installations and
    # non-unique test module names (skimage/skimage2 duplicates those)
    "--import-mode=importlib",
    # See comment on `testpaths`
    "--pyargs",
]

# For out-of-tree installations, selecting `src/` as a test path fails.
# Pytest doesn't expect the doctest's sources and installation to be
# different. Instead, we use `--pyargs` in the `addopts` field so that pytest
# can find docstests by importing.
testpaths = [
    "skimage",
    "_skimage2",  # Exclude `skimage2` and its raised `ExperimentalAPIWarning`
    "./tests/",
]

log_cli_level = "INFO"
xfail_strict = true
filterwarnings = [
    "error",
    "ignore::skimage.util.PendingSkimage2Change",
    "ignore:.*use `imageio` or other I/O packages directly.*:FutureWarning",
    # Passing win_size with gaussian_weights=True is deprecated
    "ignore:.*win_size.*gaussian_weights.*:FutureWarning",
    # warn by pyamg in ruge_stuben_solver
    "ignore:Implicit conversion of A to CSR:scipy.sparse.SparseEfficiencyWarning",
    # Pyodide warning coming via threadpoolctl, remove when
    # https://github.com/joblib/threadpoolctl/pull/201 is released
    "ignore:.*JsProxy\\.as_object_map.*:RuntimeWarning",
    # Warning caused by matplotlib 3.7.0 because it uses deprecated API of pyparsing 3.3.1
    "ignore:.*(parseString|resetCache|enablePackrat|oneOf).*:DeprecationWarning:matplotlib",
    # tifffile (v2025.12.20) uses deprecated NumPy API
    "ignore:Setting the shape on a NumPy array:DeprecationWarning:tifffile",
    # SimpleITK (< 3.0) uses deprecated NumPy API; fixed in SimpleITK 3.0
    # TODO: remove once SimpleITK >= 3.0 is required
    "ignore:Setting the shape on a NumPy array:DeprecationWarning:SimpleITK",
    # pytest warning when running under PYTHONOPTIMIZE=2 (assertions are stripped)
    "ignore:assertions not in test modules or plugins:pytest.PytestConfigWarning",
]
norecursedirs = ["io/_plugins"]

[tool.changelist]
ignored_user_logins = [
    "web-flow",
    "pre-commit-ci[bot]"
]


[tool.docstub]
ignore_files = [
    # deprecated, to be removed before v0.27
    "io/_plugins",
    "io/manage_plugins.py",
]

[tool.docstub.type_prefixes]
warnings = "warnings"
matplotlib = "matplotlib"
scipy = "scipy"
dask = "dask"

[tool.docstub.type_nicknames]
dtype-like = "np.typing.DTypeLike"

[tool.docstub.types]
Path = "pathlib.Path"

[tool.cibuildwheel]
test-command = "pytest --doctest-plus"
test-extras = ["test", "optional"]
test-sources = ["tests", "pyproject.toml"]
environment = {PIP_PREFER_BINARY=1}
environment-pass = ["SKIMAGE_LINK_FLAGS", "PIP_EXTRA_INDEX_URL", "COLUMNS"]
build-verbosity = 0

[tool.cibuildwheel.config-settings]
# Could be overwritten using CIBW_CONFIG_SETTINGS environment variable

[[tool.cibuildwheel.overrides]]
select = "cp3??t-*"
test-environment = {PYTHON_GIL=0}
test-extras = ["test", "optional_free_threaded"]

[[tool.cibuildwheel.overrides]]
select = "*-m*linux_aarch64"
test-extras = ["test", "optional_free_threaded"]

[[tool.cibuildwheel.overrides]]
select = "*-win_arm64"
test-extras = ["test", "optional_free_threaded"]

[[tool.cibuildwheel.overrides]]
select = "*-musllinux*"
test-extras = ["test", "optional_free_threaded"]
# SimpleITK does not support musllinux yet

[[tool.cibuildwheel.overrides]]
select = "cp315*"
# scikit-learn, matplotlib, PyWavelets, and astropy have no cp315 wheels yet,
# so the `optional` and `optional_free_threaded` extras cannot be installed.
# Drop this override once they publish for 3.15.
test-extras = ["test"]

[tool.cibuildwheel.linux]
environment = {PIP_PREFER_BINARY=1, SKIMAGE_LINK_FLAGS="-Wl,--strip-debug"}

[tool.cibuildwheel.windows]
archs = ["auto"]
# cibuildwheel 4.0 made delvewheel the default repair command on Windows. Five
# of our extension modules import msvcp140.dll, so the default would start
# bundling it; disabling repair keeps wheel contents as they have always been.
# Revisit as its own change, not as a side effect of a cibuildwheel bump.
repair-wheel-command = ""

[tool.cibuildwheel.macos]
test-command = "pytest"
before-all = [
    "bash {project}/tools/build_libomp.sh",
]

[tool.cibuildwheel.pyodide]
test-command = "pytest"
test-extras = ["test", "optional_free_threaded"]