[rpms/python-scikit-image] f45: Fix tests affected by deprecations in numpy and pytest

[rpms/python-scikit-image] f45: Fix tests affected by deprecations in numpy and pytest

[Sergio Pascual]

A new commit has been pushed.

Repo   : rpms/python-scikit-image
Branch : f45
Commit : e52acf82a08878d44647c0242fecc08112df8489
Author : Sergio Pascual <sergiopr@fedoraproject.org>
Date   : 2026-09-09T10:12:29+02:00
Stats  : +124/-3 in 3 file(s)
URL    : https://src.fedoraproject.org/rpms/python-scikit-image/c/e52acf82a08878d44647c0242fecc08112df8489?branch=f45

Log:
Fix tests affected by deprecations in numpy and pytest

---
diff --git a/fix-numpy25.patch b/fix-numpy25.patch
new file mode 100644
index 0000000..ea7ff4c
--- /dev/null
+++ b/fix-numpy25.patch
@@ -0,0 +1,12 @@
+diff -ur a/src/skimage/util/_map_array.py b/src/skimage/util/_map_array.py
+--- a/src/skimage/util/_map_array.py	2026-09-08 17:02:21.631914152 +0200
++++ b/src/skimage/util/_map_array.py	2026-09-08 17:05:40.745653059 +0200
+@@ -58,7 +58,7 @@
+         )
+     try:
+         out_view = out.view()
+-        out_view.shape = (-1,)  # no-copy reshape/ravel
++        out_view = np.reshape(out_view, (-1,), copy=False)
+     except AttributeError:  # if out strides are not compatible with 0-copy
+         raise ValueError(
+             'If out array is provided, it should be either contiguous '

diff --git a/pytest-param-iterators.patch b/pytest-param-iterators.patch
new file mode 100644
index 0000000..86737d0
--- /dev/null
+++ b/pytest-param-iterators.patch
@@ -0,0 +1,92 @@
+diff -ur a/tests/skimage/registration/test_phase_cross_correlation.py b/tests/skimage/registration/test_phase_cross_correlation.py
+--- a/tests/skimage/registration/test_phase_cross_correlation.py	2026-09-08 16:40:21.634314419 +0200
++++ b/tests/skimage/registration/test_phase_cross_correlation.py	2026-09-08 16:41:13.473682833 +0200
+@@ -179,7 +179,7 @@
+ 
+ @pytest.mark.parametrize(
+     ('shift0', 'shift1'),
+-    itertools.product((100, -100, 350, -350), (100, -100, 350, -350)),
++    list(itertools.product((100, -100, 350, -350), (100, -100, 350, -350))),
+ )
+ def test_disambiguate_2d(shift0, shift1):
+     image = eagle()[500:, 900:]  # use a highly textured part of image
+diff -ur a/tests/skimage/restoration/test_denoise.py b/tests/skimage/restoration/test_denoise.py
+--- a/tests/skimage/restoration/test_denoise.py	2026-09-08 16:40:21.640932650 +0200
++++ b/tests/skimage/restoration/test_denoise.py	2026-09-08 16:41:40.389870589 +0200
+@@ -855,7 +855,7 @@
+ @xfail_without_pywt
+ @pytest.mark.parametrize(
+     'rescale_sigma, method, ndim',
+-    itertools.product([True, False], ['VisuShrink', 'BayesShrink'], range(1, 5)),
++    list(itertools.product([True, False], ['VisuShrink', 'BayesShrink'], range(1, 5))),
+ )
+ def test_wavelet_denoising_nd(rescale_sigma, method, ndim):
+     rstate = np.random.default_rng(1234)
+diff -ur a/tests/skimage/transform/test_geometric.py b/tests/skimage/transform/test_geometric.py
+--- a/tests/skimage/transform/test_geometric.py	2026-09-08 16:40:21.641938210 +0200
++++ b/tests/skimage/transform/test_geometric.py	2026-09-08 16:44:50.929260134 +0200
+@@ -324,7 +324,7 @@
+ 
+ @pytest.mark.parametrize(
+     'pts, params',
+-    product(
++    list(product(
+         (SRC, DST),
+         (
+             dict(scale=(4, 5), shear=(1.4, 1.8), rotation=0.4, translation=(10, 12)),
+@@ -332,7 +332,7 @@
+                 scale=(-0.5, 3), shear=(-0.3, -0.1), rotation=1.4, translation=(-4, 3)
+             ),
+         ),
+-    ),
++    ))
+ )
+ def test_affine_params(pts, params):
+     # Test AffineTransform against docstring algorithm.
+diff -ur a/tests/skimage/transform/test_radon_transform.py b/tests/skimage/transform/test_radon_transform.py
+--- a/tests/skimage/transform/test_radon_transform.py	2026-09-08 16:40:21.642151944 +0200
++++ b/tests/skimage/transform/test_radon_transform.py	2026-09-08 16:46:46.306964028 +0200
+@@ -143,11 +143,11 @@
+ 
+ @pytest.mark.parametrize(
+     "size, theta, circle",
+-    itertools.product(
++    list(itertools.product(
+         sizes_for_test_iradon_center,
+         thetas_for_test_iradon_center,
+         circles_for_test_iradon_center,
+-    ),
++    )),
+ )
+ def test_iradon_center(size, theta, circle):
+     check_iradon_center(size, theta, circle)
+@@ -252,7 +252,7 @@
+ 
+ 
+ @pytest.mark.parametrize(
+-    "shape, coordinate", generate_test_data_for_radon_iradon_minimal(shapes)
++    "shape, coordinate", list(generate_test_data_for_radon_iradon_minimal(shapes))
+ )
+ def test_radon_iradon_minimal(shape, coordinate):
+     check_radon_iradon_minimal(shape, coordinate)
+@@ -373,7 +373,7 @@
+ 
+ @pytest.mark.parametrize(
+     "shape, interpolation, output_size",
+-    itertools.product(shapes_radon_iradon_circle, interpolations, output_sizes),
++    list(itertools.product(shapes_radon_iradon_circle, interpolations, output_sizes)),
+ )
+ def test_radon_iradon_circle(shape, interpolation, output_size):
+     check_radon_iradon_circle(interpolation, shape, output_size)
+diff -ur a/tests/skimage/util/test_dtype.py b/tests/skimage/util/test_dtype.py
+--- a/tests/skimage/util/test_dtype.py	2026-09-08 16:40:21.642526756 +0200
++++ b/tests/skimage/util/test_dtype.py	2026-09-08 16:47:26.352700023 +0200
+@@ -39,7 +39,7 @@
+     assert x.dtype == dtype
+ 
+ 
+-@parametrize("dtype, f_and_dt", itertools.product(dtype_range, img_funcs_and_types))
++@parametrize("dtype, f_and_dt", list(itertools.product(dtype_range, img_funcs_and_types)))
+ def test_range(dtype, f_and_dt):
+     imin, imax = dtype_range[dtype]
+     x = np.linspace(imin, imax, 10).astype(dtype)

diff --git a/python-scikit-image.spec b/python-scikit-image.spec
index 4987af5..f4a37a4 100644
--- a/python-scikit-image.spec
+++ b/python-scikit-image.spec
@@ -7,7 +7,7 @@
 
 Name: python-scikit-image
 Version: 0.26.0
-Release: 4%{?dist}
+Release: 5%{?dist}
 Summary: Image processing in Python
 # The following files are BSD 2 clauses, the rest BSD 3 clauses
 # skimage/graph/_mcp.pyx
@@ -24,6 +24,11 @@ Source1: scikit-image-data-20260521.tar.xz
 # Rebased from: https://github.com/scikit-image/scikit-image/commit/9d8daba419249
 Patch: fix-pillow-Image-getdata-deprecation.patch
 
+# .shape cant be used in numpy>= 2.5 instead of reshape, backported
+Patch: fix-numpy25.patch
+# can't use iterators in pytest parametrize
+Patch: pytest-param-iterators.patch
+
 # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval
 ExcludeArch:    %{ix86}
 
@@ -49,12 +54,13 @@ BuildRequires: %{py3_dist astropy}
 BuildRequires: %{py3_dist dask}
 BuildRequires: %{py3_dist matplotlib}
 BuildRequires: %{py3_dist numpydoc}
+BuildRequires: %{py3_dist pillow}
 BuildRequires: %{py3_dist pooch}
 BuildRequires: %{py3_dist PyWavelets}
+BuildRequires: %{py3_dist scikit-learn}
 # Unpackaged optional test deps
 #BuildRequires: %%{py3_dist imread}
 #BuildRequires: %%{py3_dist SimpleITK}
-#BuildRequires: %%{py3_dist sklearn}
 %endif
 Obsoletes: %{srcname}-tools < 0.20.0
 
@@ -93,7 +99,17 @@ export XDG_CONFIG_HOME=$PWD
 # We deselect tests that require network data
 # Needs pytest_pretty
 rm -f tests/conftest.py
-%pytest -v \
+%pytest -W "default::DeprecationWarning" \
+  --deselect="tests/skimage/measure/test_fit.py::test_ellipse_model_estimate" \
+  --deselect="tests/skimage/measure/test_fit.py::test_ellipse_parameter_stability" \
+  --deselect="tests/skimage/io/test_pil.py::test_all_mono" \
+  --deselect="tests/skimage/measure/test_fit.py::test_circle_model_estimate" \
+  --deselect="tests/skimage/measure/test_fit.py::test_circle_model_int_overflow" \
+  --deselect="tests/skimage/measure/test_fit.py::test_circle_model_estimate_from_small_scale_data" \
+  --deselect="tests/skimage/measure/test_fit.py::test_ellipse_model_estimate_from_data" \
+  --deselect="tests/skimage/measure/test_fit.py::test_ellipse_model_estimate_from_far_shifted_data" \
+  --deselect="tests/skimage/measure/test_fit.py::test_init_estimate_deprecations" \
+  --deselect="tests/skimage/transform/test_geometric.py::test_polynomial_weighted_estimation" \
   --deselect="tests/skimage/data/test_data.py::test_brain_3d" \
   --deselect="tests/skimage/data/test_data.py::test_download_all_with_pooch" \
   --deselect="tests/skimage/data/test_data.py::test_kidney_3d_multichannel" \
@@ -118,6 +134,7 @@ rm -f tests/conftest.py
   tests/skimage
 %endif
 
+
 %files -n python3-%{srcname} -f %{pyproject_files}
 %doc CONTRIBUTORS.md README.md SECURITY.md
 %license LICENSE.txt