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here is the log from the commit of package python-scikit-image for
openSUSE:Factory checked in at 2024-06-07 15:05:24
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-scikit-image (Old)
and /work/SRC/openSUSE:Factory/.python-scikit-image.new.24587 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-scikit-image"
Fri Jun 7 15:05:24 2024 rev:20 rq:1179164 version:0.23.2
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-scikit-image/python-scikit-image.changes
2024-03-20 21:16:58.059826640 +0100
+++
/work/SRC/openSUSE:Factory/.python-scikit-image.new.24587/python-scikit-image.changes
2024-06-07 15:06:02.933635306 +0200
@@ -1,0 +2,97 @@
+Thu Jun 6 17:13:16 UTC 2024 - Ben Greiner <c...@bnavigator.de>
+
+- Add skimage-pr7414-np2.patch gh#scikit-image/scikit-image#7414
+
+-------------------------------------------------------------------
+Sun May 5 14:31:34 UTC 2024 - Ben Greiner <c...@bnavigator.de>
+
+- Update to 0.23.2
+ ## Bug Fixes
+ * Make sure skimage.util.img_as_ubyte supports the edge case
+ where dtype('uint64').type of the provided image is
+ np.ulonglong instead of np.uint64 (#7392).
+ ## Documentation
+ * Add date to 0.23.1 release notes (#7384).
+ * Fix docstring of connectivity parameter in
+ skimage.segmentation.watershed (#7360).
+ ## Infrastructure
+ * Ignore Sphinx warning about unpickable cache (#7400).
+ * Simplify instructions on changelist in PR template (#7401).
+ ## Maintenance
+ * Use numpy.inf instead of deprecated numpy.infty (#7386).
+ * Update Ruff config (#7387).
+ * Update matrix and names of Azure pipelines configuration
+ (#7390).
+ * Use upload- and download-artifact v4 (#7389).
+ * Ignore arch specific cast warnings originating from astype in
+ tests (#7393).
+ * Update link to numpydoc example.py (#7395).
+- Release 0.23.1/0.23.0
+ ## Highlights
+ * Ensure skimage.morphology.closing and
+ skimage.morphology.opening are extensive and anti-extensive,
+ respectively, if the footprint is not mirror symmetric (#6695).
+ * Add parameter mode to binary_erosion, binary_dilation,
+ binary_opening and binary_closing in skimage.morphology. These
+ new parameters determine how array borders are handled (#6695).
+ * Add parameters mode and cval to erosion, dilation, opening,
+ closing, white_tophat, and black_tophat in skimage.morphology.
+ These new parameters determine how array borders are handled
+ (#6695).
+ * Speedup skimage.util.map_array by parallelization with Cython's
+ prange (#7266).
+ ## New Features
+ * Add new intensity_std property to skimage.measure.regionprops
+ which computes the standard deviation of the intensity in a
+ region (#6712).
+ * Add parameter mode to binary_erosion, binary_dilation,
+ binary_opening and binary_closing in skimage.morphology. These
+ new parameters determine how array borders are handled (#6695).
+ * Add functions mirror_footprint and pad_footprint to
+ skimage.morphology (#6695).
+ * Add parameters mode and cval to erosion, dilation, opening,
+ closing, white_tophat, and black_tophat in skimage.morphology.
+ These new parameters determine how array borders are handled
+ (#6695).
+ * Add new parameter spacing to segmentation.expand_labels to
+ support anisotropic images (#7080).
+ ## API Changes
+ * Drop support for Python 3.9 (#7217).
+ * Parameters shift_x and shift_y in skimage.morphology.erosion
+ and skimage.morphology.dilation are deprecated. Use
+ pad_footprint or modify the footprint manually instead (#6695).
+ * Remove unexpected value scaling in
+ skimage.morphology.skeletonize_3d for non-binary input images.
+ skeletonize_3d now always returns a binary array like similar
+ functions (#7095).
+ * Deprecate function skimage.feature.plot_matches in favor of
+ skimage.feature.plot_matched_features (#7255).
+ * Deprecate skimage.morphology.skeletonize_3d in favor of just
+ skimage.morphology.skeletonize (#7094).
+ * Deprecate parameter output in skimage.filters.gaussian; use out
+ instead (#7225).
+ * Change the default value of the parameters shift_x, shift_y and
+ shift_z from False to 0 in the skimage.filters.rank functions.
+ This has not impact on the results. Warn in case boolean shifts
+ are provided from now on (#7320).
+ * Performance
+ * Add lazy loading to skimage.metrics module (#7211).
+ * Speedup skimage.util.map_array by parallelization with Cython's
+ prange (#7266).
+ ## Bug Fixes
+ * Add exception to avoid surprising result when image is too
+ small for the given parameters in skimage.feature.hog (#7153).
+ * Ensure skimage.morphology.closing and
+ skimage.morphology.opening are extensive and anti-extensive,
+ respectively, if the footprint is not mirror symmetric (#6695).
+ * Avoid a TypeError in
+ skimage.registration.phase_cross_correlation when the real-time
+ shift cannot be determined (disambiguate=True). Display a
+ warning instead (#7259).
+ * Fix logic in skimage.graph.pixel_graph which raised a TypeError
+ when the parameter edge_function was provided without a mask
+ (#7310).
+ * Ensure cache stays empty when cache=False is passed to
+ skimage.measure.regionprops (#7333).
+
+-------------------------------------------------------------------
Old:
----
scikit_image-0.22.0.tar.gz
New:
----
scikit_image-0.23.2.tar.gz
skimage-pr7414-np2.patch
BETA DEBUG BEGIN:
New:
- Add skimage-pr7414-np2.patch gh#scikit-image/scikit-image#7414
BETA DEBUG END:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-scikit-image.spec ++++++
--- /var/tmp/diff_new_pack.2A9QLh/_old 2024-06-07 15:06:04.117678440 +0200
+++ /var/tmp/diff_new_pack.2A9QLh/_new 2024-06-07 15:06:04.121678586 +0200
@@ -26,16 +26,19 @@
%bcond_with test
%endif
Name: python-scikit-image%{psuffix}
-Version: 0.22.0
+Version: 0.23.2
Release: 0
Summary: Collection of algorithms for image processing in Python
License: BSD-3-Clause
URL: https://scikit-image.org/
+# SourceRepository: https://github.com/scikit-image/scikit-image
Source0:
https://files.pythonhosted.org/packages/source/s/scikit-image/%{srcname}-%{version}.tar.gz
-BuildRequires: %{python_module Cython >= 0.29.21}
-BuildRequires: %{python_module devel >= 3.7}
-BuildRequires: %{python_module meson-python}
-BuildRequires: %{python_module numpy-devel >= 1.21.1}
+# PATCH-FIX-UPSTREAM skimage-pr7414-np2.patch gh#scikit-image/scikit-image#7414
+Patch0:
https://github.com/scikit-image/scikit-image/pull/7414.patch#/skimage-pr7414-np2.patch
+BuildRequires: %{python_module Cython >= 3.0.4}
+BuildRequires: %{python_module devel >= 3.10}
+BuildRequires: %{python_module meson-python >= 0.15}
+BuildRequires: %{python_module numpy-devel >= 1.23}
BuildRequires: %{python_module packaging >= 20}
BuildRequires: %{python_module pip}
BuildRequires: %{python_module pythran}
@@ -45,14 +48,14 @@
BuildRequires: freeimage-devel
BuildRequires: gcc-c++
BuildRequires: python-rpm-macros
-Requires: python-Pillow >= 9.0.1
+Requires: python-Pillow >= 9.1
Requires: python-PyWavelets >= 1.1.1
-Requires: python-imageio >= 2.7
-Requires: python-lazy-loader >= 0.2
+Requires: python-imageio >= 2.33
+Requires: python-lazy-loader >= 0.4
Requires: python-networkx >= 2.8
-Requires: python-numpy >= 1.21.1
+Requires: python-numpy >= 1.23
Requires: python-packaging >= 21.0
-Requires: python-scipy >= 1.8
+Requires: python-scipy >= 1.9
Requires: python-tifffile >= 2022.8.12
Requires(post): update-alternatives
Requires(postun): update-alternatives
@@ -62,12 +65,12 @@
Recommends: python-cloudpickle >= 0.2.1
Recommends: python-dask-array >= 1.0.0
Recommends: python-imread >= 0.5.1
-Recommends: python-matplotlib >= 3.0.3
+Recommends: python-matplotlib >= 3.6
Recommends: python-pooch >= 1.3.0
Recommends: python-pyamg
%if %{with test}
BuildRequires: %{python_module dask-array >= 1.0.0}
-BuildRequires: %{python_module matplotlib >= 3.0.3}
+BuildRequires: %{python_module matplotlib >= 3.6}
BuildRequires: %{python_module numpydoc}
BuildRequires: %{python_module pytest >= 4.0}
BuildRequires: %{python_module pytest-localserver}
@@ -85,6 +88,7 @@
%if !%{with test}
%autosetup -p1 -n %{srcname}-%{version}
sed -Ei "1{s@/usr/bin/env python@%{_bindir}/python3@}"
./skimage/_build_utils/*.py
+chmod -x skimage/measure/{__init__,_find_contours}.py
%else
%setup -q -c scikit-image-%{version}-test -D -T
%endif
@@ -97,9 +101,7 @@
%install
%if !%{with test}
%pyproject_install
-%{python_expand %fdupes %{buildroot}%{$python_sitearch}
-chmod -x
%{buildroot}%{$python_sitearch}/skimage/measure/{__init__,_find_contours}.py
-}
+%python_expand %fdupes %{buildroot}%{$python_sitearch}
%endif
%if %{with test}
++++++ scikit_image-0.22.0.tar.gz -> scikit_image-0.23.2.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-scikit-image/scikit_image-0.22.0.tar.gz
/work/SRC/openSUSE:Factory/.python-scikit-image.new.24587/scikit_image-0.23.2.tar.gz
differ: char 5, line 1
++++++ skimage-pr7414-np2.patch ++++++
>From 24e84822508a886c0433875889608f7aa31848ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <la...@mailbox.org>
Date: Tue, 7 May 2024 20:07:48 +0200
Subject: [PATCH 1/5] Fix NumPy2 dtype promotion issues in pywt dependent code
---
skimage/metrics/simple_metrics.py | 1 +
skimage/restoration/_denoise.py | 4 +++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/skimage/metrics/simple_metrics.py
b/skimage/metrics/simple_metrics.py
index 37cd69ee1c9..7bb13acf189 100644
--- a/skimage/metrics/simple_metrics.py
+++ b/skimage/metrics/simple_metrics.py
@@ -164,6 +164,7 @@ def peak_signal_noise_ratio(image_true, image_test, *,
data_range=None):
image_true, image_test = _as_floats(image_true, image_test)
err = mean_squared_error(image_true, image_test)
+ data_range = float(data_range) # prevent overflow for small integer types
return 10 * np.log10((data_range**2) / err)
diff --git a/skimage/restoration/_denoise.py b/skimage/restoration/_denoise.py
index 791a8c9f25b..4f4a235ac40 100644
--- a/skimage/restoration/_denoise.py
+++ b/skimage/restoration/_denoise.py
@@ -788,7 +788,9 @@ def _wavelet_threshold(
for thresh, level in zip(threshold, dcoeffs)
]
denoised_coeffs = [coeffs[0]] + denoised_detail
- return pywt.waverecn(denoised_coeffs, wavelet)[original_extent]
+ out = pywt.waverecn(denoised_coeffs, wavelet)[original_extent]
+ out = out.astype(image.dtype)
+ return out
def _scale_sigma_and_image_consistently(image, sigma, multichannel,
rescale_sigma):
>From bfbf88aad4fbd04b3657c682266d43aa0fe01ec4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <lagru+git...@mailbox.org>
Date: Wed, 8 May 2024 00:17:00 +0200
Subject: [PATCH 2/5] Update skimage/metrics/simple_metrics.py
Co-authored-by: Mark Harfouche <mark.harfou...@gmail.com>
---
skimage/metrics/simple_metrics.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/skimage/metrics/simple_metrics.py
b/skimage/metrics/simple_metrics.py
index 7bb13acf189..6a255ed4211 100644
--- a/skimage/metrics/simple_metrics.py
+++ b/skimage/metrics/simple_metrics.py
@@ -164,8 +164,7 @@ def peak_signal_noise_ratio(image_true, image_test, *,
data_range=None):
image_true, image_test = _as_floats(image_true, image_test)
err = mean_squared_error(image_true, image_test)
- data_range = float(data_range) # prevent overflow for small integer types
- return 10 * np.log10((data_range**2) / err)
+ return 20 * np.log10(data_range / err)
def _pad_to(arr, shape):
>From b90376cbfbbfdf7d3a8f910b4fec03621b3cc2a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <la...@mailbox.org>
Date: Wed, 8 May 2024 00:41:34 +0200
Subject: [PATCH 3/5] Catch and warn about pyamg not supporting NumPy 2 yet
---
TODO.txt | 4 ++++
pyproject.toml | 1 +
skimage/segmentation/random_walker_segmentation.py | 10 ++++++++++
3 files changed, 15 insertions(+)
diff --git a/TODO.txt b/TODO.txt
index f8b35a6ea39..476f160dcd2 100644
--- a/TODO.txt
+++ b/TODO.txt
@@ -27,6 +27,10 @@ Other
skimage/exposure/tests/test_exposure.py::test_rescale_nan_warning
* Finalize ``skimage.future.manual_segmentation`` API,
see https://github.com/scikit-image/scikit-image/issues/2624
+* Remove ``except AttributeError`` block in
+ ``skimage/segmentation/random_walker_segmentation.py`` as well as the
warning filter
+ in ``pyproject.toml``, once pyamg supports NumPy 2
+ (see https://github.com/pyamg/pyamg/issues/406).
Post numpy 2
------------
diff --git a/pyproject.toml b/pyproject.toml
index 9e839b4b098..0ff6f176e9e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -195,6 +195,7 @@ python_classes = ["Test*", "*Suite"]
python_functions = ["time_*", "test_*", "peakmem_*"]
filterwarnings = [
"error",
+ 'default:.*pyamg, which cannot \(yet\) be imported with NumPy
>=2:RuntimeWarning'
]
[tool.coverage.run]
diff --git a/skimage/segmentation/random_walker_segmentation.py
b/skimage/segmentation/random_walker_segmentation.py
index c4dd2fe314b..d5c2cabcff7 100644
--- a/skimage/segmentation/random_walker_segmentation.py
+++ b/skimage/segmentation/random_walker_segmentation.py
@@ -43,6 +43,16 @@ def new_del(self):
amg_loaded = True
except ImportError:
amg_loaded = False
+except AttributeError as e:
+ if "`np.deprecate` was removed" not in e.args[0]:
+ raise e
+ warn(
+ "found optional dependency pyamg, which cannot (yet) be imported with "
+ "NumPy >=2 and will be treated as if not available",
+ RuntimeWarning,
+ )
+ amg_loaded = False
+
from ..util import img_as_float
>From ad081e184464f74be2057060812d5ba745317b1d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <la...@mailbox.org>
Date: Wed, 8 May 2024 00:50:28 +0200
Subject: [PATCH 4/5] Revert "Update skimage/metrics/simple_metrics.py"
This reverts commit bfbf88aad4fbd04b3657c682266d43aa0fe01ec4.
---
skimage/metrics/simple_metrics.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/skimage/metrics/simple_metrics.py
b/skimage/metrics/simple_metrics.py
index 6a255ed4211..7bb13acf189 100644
--- a/skimage/metrics/simple_metrics.py
+++ b/skimage/metrics/simple_metrics.py
@@ -164,7 +164,8 @@ def peak_signal_noise_ratio(image_true, image_test, *,
data_range=None):
image_true, image_test = _as_floats(image_true, image_test)
err = mean_squared_error(image_true, image_test)
- return 20 * np.log10(data_range / err)
+ data_range = float(data_range) # prevent overflow for small integer types
+ return 10 * np.log10((data_range**2) / err)
def _pad_to(arr, shape):
>From 05d585cff4ccdef84db024fc1c99841b9fb57a38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lars=20Gr=C3=BCter?= <la...@mailbox.org>
Date: Wed, 8 May 2024 10:14:40 +0200
Subject: [PATCH 5/5] Simplify except block a little bit
---
.../random_walker_segmentation.py | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/skimage/segmentation/random_walker_segmentation.py
b/skimage/segmentation/random_walker_segmentation.py
index d5c2cabcff7..68d7c46cd1d 100644
--- a/skimage/segmentation/random_walker_segmentation.py
+++ b/skimage/segmentation/random_walker_segmentation.py
@@ -43,15 +43,16 @@ def new_del(self):
amg_loaded = True
except ImportError:
amg_loaded = False
-except AttributeError as e:
- if "`np.deprecate` was removed" not in e.args[0]:
- raise e
- warn(
- "found optional dependency pyamg, which cannot (yet) be imported with "
- "NumPy >=2 and will be treated as if not available",
- RuntimeWarning,
- )
- amg_loaded = False
+except AttributeError as error:
+ if "`np.deprecate` was removed" in error.args[0]:
+ warn(
+ "found optional dependency pyamg, which cannot (yet) be imported
with "
+ "NumPy >=2 and will be treated as if not available",
+ RuntimeWarning,
+ )
+ amg_loaded = False
+ else:
+ raise error
from ..util import img_as_float
