Accepting request 1296683 from devel:languages:python:numeric

- Add patch ignore-userwarnings.patch:
  * Ignore any UserWarnings that arise, rather than to trying to swallow
    them with pytest.warns().

OBS-URL: https://build.opensuse.org/request/show/1296683
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-nibabel?expand=0&rev=15

ignore-userwarnings.patch

@@ -0,0 +1,41 @@
+From 3f40a3bc0c4bd996734576a15785ad0f769a963a Mon Sep 17 00:00:00 2001
+From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
+Date: Fri, 16 May 2025 14:25:24 -0400
+Subject: [PATCH 2/2] fix: Ignore warning that may not be emitted
+
+---
+ nibabel/tests/test_processing.py | 7 +++++--
+ 1 file changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/nibabel/tests/test_processing.py b/nibabel/tests/test_processing.py
+index f1a4f0a90..7e2cc4b16 100644
+--- a/nibabel/tests/test_processing.py
++++ b/nibabel/tests/test_processing.py
+@@ -9,6 +9,7 @@
+ """Testing processing module"""
+ 
+ import logging
++import warnings
+ from os.path import dirname
+ from os.path import join as pjoin
+ 
+@@ -169,7 +170,8 @@ def test_resample_from_to(caplog):
+     exp_out[1:, :, :] = data[1, :, :]
+     assert_almost_equal(out.dataobj, exp_out)
+     out = resample_from_to(img, trans_p_25_img)
+-    with pytest.warns(UserWarning):  # Suppress scipy warning
++    with warnings.catch_warnings():
++        warnings.simplefilter('ignore', UserWarning)
+         exp_out = spnd.affine_transform(data, [1, 1, 1], [-0.25, 0, 0], order=3)
+     assert_almost_equal(out.dataobj, exp_out)
+     # Test cval
+@@ -275,7 +277,8 @@ def test_resample_to_output(caplog):
+     assert_array_equal(out_img.dataobj, np.flipud(data))
+     # Subsample voxels
+     out_img = resample_to_output(Nifti1Image(data, np.diag([4, 5, 6, 1])))
+-    with pytest.warns(UserWarning):  # Suppress scipy warning
++    with warnings.catch_warnings():
++        warnings.simplefilter('ignore', UserWarning)
+         exp_out = spnd.affine_transform(data, [1 / 4, 1 / 5, 1 / 6], output_shape=(5, 11, 19))
+     assert_array_equal(out_img.dataobj, exp_out)
+     # Unsubsample with voxel sizes

nibabel-5.2.1.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b6c80b2e728e4bc2b65f1142d9b8d2287a9102a8bf8477e115ef0d8334559975
-size 4503320

nibabel-5.3.2.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0bdca6503b1c784b446c745a4542367de7756cfba0d72143b91f9ffb78be569b
+size 4504842

python-nibabel.changes

@@ -1,3 +1,50 @@
+-------------------------------------------------------------------
+Thu Jul 31 02:59:03 UTC 2025 - Steve Kowalik <steven.kowalik@suse.com>
+
+- Add patch ignore-userwarnings.patch:
+  * Ignore any UserWarnings that arise, rather than to trying to swallow
+    them with pytest.warns().
+
+-------------------------------------------------------------------
+Tue Nov 26 05:22:53 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com>
+
+- Update to 5.3.2:
+  * New features
+    + Update NIfTI extension protocol to include .content : bytes, .text :
+      str and .json : dict properties for accessing extension contents.
+  * Enhancements
+    + Ability to read data from many multiframe DICOM files that previously
+      generated errors
+    + nib-nifti-dx now supports NIfTI-2 files with a --nifti2 flag
+    + Update nibabel.streamlines.tractogram to support ragged arrays.
+    + Improve error message for for dicomwrapper errors in shape
+      calculation
+    + Support "flat" ASCII-encoded GIFTI DataArrays
+  * Bug fixes
+    + Fix location initialization/update in OrthoSlicer3D for permuted axes
+    + Fix DICOM scaling, making frame filtering explicit
+    + Fixed multiframe DICOM issue where data could be flipped along slice
+      dimension relative to the affine
+    + Fixed multiframe DICOM issue where image_position and the translation
+      component in the affine could be incorrect
+  * Maintenance
+    + Numpy 2.0 compatibility and addressing deprecations in numpy API
+    + Python 3.13 compatibility
+    + Testing on Python 3.13 with free-threading
+    + Proactively address deprecations in coming Python versions
+    + Replace nose-era setup() and teardown() functions with pytest
+      equivalents
+  * API changes and deprecations
+    + Raise HeaderDataError from set_qform if the affine fails to
+      decompose. This would previously result in numpy.linalgLinAlgError.
+    + The nibabel.onetime.auto_attr module can be replaced by
+      functoolscached_property in all supported versions of Python. This
+      alias may be removed in future versions.
+    + Removed the deprecated nisext (setuptools extensions) package.
+- Dropped patches, included upstream:
+  * support-pytest-8.patch
+  * support-numpy-2.patch
+
 -------------------------------------------------------------------
 Thu Jul 25 02:05:50 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com>
 

python-nibabel.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python-nibabel
 #
-# Copyright (c) 2024 SUSE LLC
+# Copyright (c) 2025 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -18,17 +18,15 @@
 
 %define binaries nib-conform nib-convert nib-dicomfs nib-diff nib-ls nib-nifti-dx nib-roi nib-stats nib-tck2trk nib-trk2tck parrec2nii
 Name:           python-nibabel
-Version:        5.2.1
+Version:        5.3.2
 Release:        0
 Summary:        Tool to access multiple neuroimaging data formats
 License:        MIT
 URL:            https://nipy.org/nibabel
 # SourceRepository: https://github.com/nipy/nibabel
 Source:         https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
-# PATCH-FIX-UPSTREAM gh#nipy/nibabel#1325
-Patch0:         support-pytest-8.patch
-# PATCH-FIX-UPSTREAM gh#nipy/nibabel#1304
-Patch1:         support-numpy-2.patch
+# PATCH-FIX-UPSTREAM One commit of gh#nipy/nibabel#1416
+Patch0:         ignore-userwarnings.patch
 BuildRequires:  %{python_module base >= 3.8}
 BuildRequires:  %{python_module hatch-vcs}
 BuildRequires:  %{python_module hatchling}
@@ -37,7 +35,12 @@ BuildRequires:  fdupes
 BuildRequires:  python-rpm-macros
 Requires:       python-numpy >= 1.20
 Requires:       python-packaging => 17
-Requires:       (python-importlib-resources >= 1.3 if python-base < 3.9)
+%if 0%{?python_version_nodots} < 312
+Requires:       python-importlib-resources >= 5.12
+%endif
+%if 0%{?python_version_nodots} < 313
+Requires:       python-typing-extensions >= 4.6
+%endif
 Requires(post): update-alternatives
 Requires(postun): update-alternatives
 Recommends:     python-Pillow
@@ -48,7 +51,7 @@ BuildArch:      noarch
 # SECTION test requirements
 BuildRequires:  %{python_module Pillow}
 BuildRequires:  %{python_module h5py}
-BuildRequires:  %{python_module importlib-resources >= 1.3 if %python-base < 3.9}
+BuildRequires:  %{python_module importlib-resources >= 5.12 if %python-base < 3.12}
 BuildRequires:  %{python_module numpy >= 1.20}
 BuildRequires:  %{python_module packaging >= 17}
 BuildRequires:  %{python_module pydicom >= 1}
@@ -57,6 +60,7 @@ BuildRequires:  %{python_module pytest-httpserver}
 BuildRequires:  %{python_module pytest-xdist}
 BuildRequires:  %{python_module pytest}
 BuildRequires:  %{python_module scipy}
+BuildRequires:  %{python_module typing-extensions >= 4.6 if %python-base < 3.13}
 BuildRequires:  %{pythons}
 BuildRequires:  git-core
 # /SECTION
@@ -101,7 +105,6 @@ done
 %license COPYING
 %{expand:%(for b in %{binaries}; do echo "%%python_alternative %%{_bindir}/$b"; done)}
 %{python_sitelib}/nibabel
-%{python_sitelib}/nisext
 %{python_sitelib}/nibabel-%{version}.dist-info
 
 %changelog

support-numpy-2.patch

@@ -1,36 +0,0 @@
-From 2bad8cce331976af3e8b42cecaed76bb075ee8b3 Mon Sep 17 00:00:00 2001
-From: Chris Markiewicz <effigies@gmail.com>
-Date: Tue, 5 Mar 2024 08:16:05 -0500
-Subject: [PATCH] FIX: Use np.asarray instead of np.array(..., copy=False)
-
----
- nibabel/affines.py | 2 +-
- nibabel/casting.py | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/nibabel/affines.py b/nibabel/affines.py
-index 05fdd7bb5..1478fd2dc 100644
---- a/nibabel/affines.py
-+++ b/nibabel/affines.py
-@@ -365,7 +365,7 @@ def rescale_affine(affine, shape, zooms, new_shape=None):
-         A new affine transform with the specified voxel sizes
- 
-     """
--    shape = np.array(shape, copy=False)
-+    shape = np.asarray(shape)
-     new_shape = np.array(new_shape if new_shape is not None else shape)
- 
-     s = voxel_sizes(affine)
-diff --git a/nibabel/casting.py b/nibabel/casting.py
-index f3e04f30f..09015135f 100644
---- a/nibabel/casting.py
-+++ b/nibabel/casting.py
-@@ -611,7 +611,7 @@ def int_abs(arr):
-     >>> int_abs(np.array([-128, 127], dtype=np.float32))
-     array([128., 127.], dtype=float32)
-     """
--    arr = np.array(arr, copy=False)
-+    arr = np.asarray(arr)
-     dt = arr.dtype
-     if dt.kind == 'u':
-         return arr

support-pytest-8.patch

@@ -1,60 +0,0 @@
-From 82c8588528d5a06fd0dfc99e3cbb83d5cc299e2b Mon Sep 17 00:00:00 2001
-From: Sandro <devel@penguinpee.nl>
-Date: Wed, 29 May 2024 00:20:34 +0200
-Subject: [PATCH] Replace deprecated setup() and teardown()
-
-Those were compatibility functions for porting from nose. They are now
-deprecated and have been removed from pytest.
-
-This will make all tests compatible with pytests 8.x.
----
- nibabel/streamlines/tests/test_streamlines.py | 2 +-
- nibabel/tests/test_deprecated.py              | 4 ++--
- nibabel/tests/test_dft.py                     | 2 +-
- 3 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/nibabel/streamlines/tests/test_streamlines.py b/nibabel/streamlines/tests/test_streamlines.py
-index f0bd9c7c4..53a43c393 100644
---- a/nibabel/streamlines/tests/test_streamlines.py
-+++ b/nibabel/streamlines/tests/test_streamlines.py
-@@ -20,7 +20,7 @@
- DATA = {}
- 
- 
--def setup():
-+def setup_module():
-     global DATA
-     DATA['empty_filenames'] = [pjoin(data_path, 'empty' + ext) for ext in FORMATS.keys()]
-     DATA['simple_filenames'] = [pjoin(data_path, 'simple' + ext) for ext in FORMATS.keys()]
-diff --git a/nibabel/tests/test_deprecated.py b/nibabel/tests/test_deprecated.py
-index f1c3d517c..01636632e 100644
---- a/nibabel/tests/test_deprecated.py
-+++ b/nibabel/tests/test_deprecated.py
-@@ -14,12 +14,12 @@
- from nibabel.tests.test_deprecator import TestDeprecatorFunc as _TestDF
- 
- 
--def setup():
-+def setup_module():
-     # Hack nibabel version string
-     pkg_info.cmp_pkg_version.__defaults__ = ('2.0',)
- 
- 
--def teardown():
-+def teardown_module():
-     # Hack nibabel version string back again
-     pkg_info.cmp_pkg_version.__defaults__ = (pkg_info.__version__,)
- 
-diff --git a/nibabel/tests/test_dft.py b/nibabel/tests/test_dft.py
-index 654af9827..6c6695b16 100644
---- a/nibabel/tests/test_dft.py
-+++ b/nibabel/tests/test_dft.py
-@@ -26,7 +26,7 @@
- data_dir = pjoin(dirname(__file__), 'data')
- 
- 
--def setUpModule():
-+def setup_module():
-     if os.name == 'nt':
-         raise unittest.SkipTest('FUSE not available for windows, skipping dft tests')
-     if not have_dicom: