scikit-image: Add version 0.26.0 - #2041
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…thon-freethreading enable group scikit-image v0.26.0's pyproject.toml sets [tool.cibuildwheel] enable="cpython-freethreading", but cibuildwheel 4.2.0 (the version this repo pins for riscv64 builds) no longer recognises that enable group -- it errors "Failed to parse enable group" before any build starts, on every interpreter, since [tool.cibuildwheel] is parsed as a whole. Free-threaded builds (cp314t) no longer need an opt-in. scikit-image's own next commit (2c3a869aebcc82c7802a9ec3d112df0878df2d4d, "Drop 3.13t builds from cibuildwheel configuration (#8127)") drops the same line with no replacement, confirming this is upstream's own bug. patches/scikit-image/0.26.0/ backports that line removal, and build-scikit-image.yml checks out python-wheels alongside the upstream tag and applies it before the cibuildwheel step.
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Upstream's default test-extras ("test", "optional") pulls in SimpleITK,
which has no riscv64 wheel and fails to build from source (CMake cannot
find PythonLibs on this platform). Upstream already excludes SimpleITK
on aarch64/win_arm64/musllinux via a "optional_free_threaded" test-extras
override; apply the same set for riscv64 (gotcha 336).
CIBW_TEST_EXTRAS is substituted directly into pip's requirement
string as <wheel>[<extras>]; pip requires a comma between extra
names, not a space. The space-separated value produced an invalid
requirement ("Expected comma between extra names") and failed
every matrix leg at the test-install step.
0.26.0's own test suite passes raw itertools.product() generators to @pytest.mark.parametrize(); pytest 9.1 deprecates that shape, and scikit-image's filterwarnings = ["error"] turns the deprecation into a hard collection error on every interpreter (cp312/cp313/cp314/cp314t all failed identically in run 35437213081). Not riscv64-specific: upstream fixed this on main post-0.26.0 by wrapping the calls in list(...) and bumping to pytest>=9, confirming 0.26.0 itself was never tested against pytest 9.1 (gotcha 339: pin to the project's own working ceiling instead of patching the test).
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With pytest<9.1 fixing the earlier collection-time error, all four
matrix legs (cp312/cp313/cp314/cp314t) still failed, now further in:
UNEXPECTED EXCEPTION: DeprecationWarning('Setting the shape on a NumPy
array has been deprecated in NumPy 2.5...') from
skimage/morphology/grayreconstruct.py:216, reached via the
h_maxima/h_minima/CircleModel/EllipseModel/ransac doctests.
reconstruction() assigns `rec_img.shape = ...` in place; NumPy 2.5
deprecation-warns on that, and scikit-image's own
filterwarnings=["error"] turns the warning fatal.
scikit-image 0.26.0's pyproject.toml requires numpy>=2.0 with no
upper bound, so cibuildwheel resolves the latest available release
(confirmed numpy==2.5.3 installed in run 35461367550) -- a version
that postdates 0.26.0 and triggers a deprecation the project was
never tested against. Same class of bug as the pytest<9.1 pin above
(gotcha 339, generalized by gotcha 355 to any unpinned test-venv
dependency): pin numpy below the version that introduced the new
deprecation, scoped to the test venv only, rather than patch
scikit-image's own library code.
Round 3 of the same unpinned-test-dependency bug class (gotcha 339/355): scikit-image 0.26.0's pyproject.toml requires pillow>=10.1 and scipy>=1.11.4 with no upper bound, so cibuildwheel resolves the latest available Pillow (12.3.0) and SciPy (1.18.1). - skimage/io/_plugins/pil_plugin.py calls the now-deprecated Image.getdata() (deprecated in Pillow 12.1.0 in favor of get_flattened_data()), reached via io.imread()/MultiImage and exercised by test_multi_image.py's test_len/test_slicing/ test_concatenate. - skimage/measure/fit.py and skimage/transform/_thin_plate_splines.py call scipy.spatial.minkowski_distance/distance_matrix, both deprecated as of SciPy 1.18.0 in favor of scipy.spatial.distance.minkowski/cdist, reached via the CircleModel and ThinPlateSplineTransform doctests. filterwarnings=["error"] in scikit-image's own pytest config turns both deprecations fatal. Pin the test venv below the version that introduced each deprecation, same as the existing pytest<9.1 and numpy<2.5 pins.
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Automatically generated by the nightly
check_versions.pyrun.scikit-image v0.25.2 -> v0.26.0
Every
- version:entry added todocs/packages/scikit-image.yamlis built by this PR's ownbuild-scikit-image.ymlrun; merging publishes the wheels.