commit python-nibabel for openSUSE:Factory
Hello community,
here is the log from the commit of package python-nibabel for openSUSE:Factory
checked in at 2020-07-10 15:32:19
Comparing /work/SRC/openSUSE:Factory/python-nibabel (Old)
and /work/SRC/openSUSE:Factory/.python-nibabel.new.3060 (New)
Package is "python-nibabel"
Fri Jul 10 15:32:19 2020 rev:6 rq:819969 version:3.1.1
Changes:
--- /work/SRC/openSUSE:Factory/python-nibabel/python-nibabel.changes
2020-05-26 17:20:27.300121165 +0200
+++ /work/SRC/openSUSE:Factory/.python-nibabel.new.3060/python-nibabel.changes
2020-07-10 15:32:25.26502 +0200
@@ -1,0 +2,13 @@
+Fri Jul 10 09:06:52 UTC 2020 - Marketa Calabkova
+
+- Update to 3.1.1
+ * Conformation function (``processing.conform``) and CLI tool
+(``nib-conform``) to apply shape, orientation and zooms (pr/853) (Jakub
+Kaczmarzyk, reviewed by CM, YOH)
+ * Affine rescaling function (``affines.rescale_affine``) to update
+dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)
+ * ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
+(RM, reviewed by CM)
+- Add patch purge-nose.patch
+
+---
Old:
nibabel-3.0.1.tar.gz
New:
nibabel-3.1.1.tar.gz
purge-nose.patch
Other differences:
--
++ python-nibabel.spec ++
--- /var/tmp/diff_new_pack.WjkrEM/_old 2020-07-10 15:32:27.555134544 +0200
+++ /var/tmp/diff_new_pack.WjkrEM/_new 2020-07-10 15:32:27.555134544 +0200
@@ -18,14 +18,15 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define skip_python2 1
-%define binaries nib-dicomfs nib-diff nib-ls nib-nifti-dx nib-tck2trk
nib-trk2tck parrec2nii
+%define binaries nib-conform nib-dicomfs nib-diff nib-ls nib-nifti-dx
nib-tck2trk nib-trk2tck parrec2nii
Name: python-nibabel
-Version:3.0.1
+Version:3.1.1
Release:0
Summary:Tool to access multiple neuroimaging data formats
License:MIT
URL:https://nipy.org/nibabel
Source:
https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
+Patch0: purge-nose.patch
BuildRequires: %{python_module setuptools >= 30.3.0}
BuildRequires: %{pythons}
BuildRequires: fdupes
@@ -41,7 +42,6 @@
# SECTION test requirements
BuildRequires: %{python_module Pillow}
BuildRequires: %{python_module h5py}
-BuildRequires: %{python_module nose >= 0.11}
BuildRequires: %{python_module numpy >= 1.12}
BuildRequires: %{python_module pytest}
BuildRequires: %{python_module scipy}
@@ -58,6 +58,7 @@
%prep
%setup -q -n nibabel-%{version}
+%patch0 -p1
%build
%python_build
@@ -70,7 +71,7 @@
%python_expand %fdupes %{buildroot}%{$python_sitelib}
%check
-%python_expand nosetests-%{$python_bin_suffix} -v
+%pytest
%post
for b in %{binaries}; do
@@ -85,6 +86,7 @@
%files %{python_files}
%doc AUTHOR Changelog README.rst
%license COPYING
+%python_alternative %{_bindir}/nib-conform
%python_alternative %{_bindir}/nib-dicomfs
%python_alternative %{_bindir}/nib-diff
%python_alternative %{_bindir}/nib-ls
++ nibabel-3.0.1.tar.gz -> nibabel-3.1.1.tar.gz ++
22642 lines of diff (skipped)
++ purge-nose.patch ++
Index: nibabel-3.1.1/nisext/tests/test_sexts.py
===
--- nibabel-3.1.1.orig/nisext/tests/test_sexts.py
+++ nibabel-3.1.1/nisext/tests/test_sexts.py
@@ -6,7 +6,7 @@ import types
from ..sexts import package_check
-from nose.tools import assert_true, assert_false, assert_equal, assert_raises
+import pytest
FAKE_NAME = 'nisext_improbable'
assert FAKE_NAME not in sys.modules
@@ -15,7 +15,8 @@ FAKE_MODULE = types.ModuleType('nisext_f
def test_package_check():
# Try to use a required package - raise error
-assert_raises(RuntimeError, package_check, FAKE_NAME)
+with pytest.raises(RuntimeError):
+package_check(FAKE_NAME)
# Optional, log.warn
package_check(FAKE_NAME, optional=True)
# Can also pass a string
@@ -29,7 +30,8 @@ def test_package_check():
FAKE_MODULE.__version__ = '0.2'
package_check(FAKE_NAME, version='0.2')
# fails when version not good enough
-assert_raises(RuntimeError, package_check, FAKE_NAME, '0.3')
+with pytest.raises(RuntimeError):
+package_check(FAKE_NAME, '0.3')
# Unless optional in which case log.warns
package_check(FAKE_NAME, version='0.3', optional=True)
# Might do custom version check
@@ -40,78 +42,63 @@ def test_package_check():
def test_package_check_setuptools():
# If setuptools arg not None, missing package just adds it to arg
-assert_raises(RuntimeError,
commit python-nibabel for openSUSE:Factory
Hello community,
here is the log from the commit of package python-nibabel for openSUSE:Factory
checked in at 2020-05-26 17:20:23
Comparing /work/SRC/openSUSE:Factory/python-nibabel (Old)
and /work/SRC/openSUSE:Factory/.python-nibabel.new.2738 (New)
Package is "python-nibabel"
Tue May 26 17:20:23 2020 rev:5 rq:808042 version:3.0.1
Changes:
--- /work/SRC/openSUSE:Factory/python-nibabel/python-nibabel.changes
2020-03-06 21:28:05.401579389 +0100
+++ /work/SRC/openSUSE:Factory/.python-nibabel.new.2738/python-nibabel.changes
2020-05-26 17:20:27.300121165 +0200
@@ -1,0 +2,5 @@
+Thu May 21 10:56:36 UTC 2020 - Petr Gajdos
+
+- %python3_only -> %python_alternative
+
+---
Other differences:
--
++ python-nibabel.spec ++
--- /var/tmp/diff_new_pack.g5VgP7/_old 2020-05-26 17:20:28.012122696 +0200
+++ /var/tmp/diff_new_pack.g5VgP7/_new 2020-05-26 17:20:28.016122705 +0200
@@ -18,6 +18,7 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define skip_python2 1
+%define binaries nib-dicomfs nib-diff nib-ls nib-nifti-dx nib-tck2trk
nib-trk2tck parrec2nii
Name: python-nibabel
Version:3.0.1
Release:0
@@ -30,6 +31,8 @@
BuildRequires: fdupes
BuildRequires: python-rpm-macros
Requires: python-numpy >= 1.12
+Requires(post): update-alternatives
+Requires(postun): update-alternatives
Recommends: python-Pillow
Recommends: python-dicom >= 0.9.9
Recommends: python-h5py
@@ -61,21 +64,34 @@
%install
%python_install
+for b in %{binaries}; do
+ %python_clone -a %{buildroot}%{_bindir}/$b
+done
%python_expand %fdupes %{buildroot}%{$python_sitelib}
%check
%python_expand nosetests-%{$python_bin_suffix} -v
+%post
+for b in %{binaries}; do
+ %python_install_alternative $b
+done
+
+%postun
+for b in %{binaries}; do
+ %python_uninstall_alternative $b
+done
+
%files %{python_files}
%doc AUTHOR Changelog README.rst
%license COPYING
-%python3_only %{_bindir}/nib-dicomfs
-%python3_only %{_bindir}/nib-diff
-%python3_only %{_bindir}/nib-ls
-%python3_only %{_bindir}/nib-nifti-dx
-%python3_only %{_bindir}/nib-tck2trk
-%python3_only %{_bindir}/nib-trk2tck
-%python3_only %{_bindir}/parrec2nii
+%python_alternative %{_bindir}/nib-dicomfs
+%python_alternative %{_bindir}/nib-diff
+%python_alternative %{_bindir}/nib-ls
+%python_alternative %{_bindir}/nib-nifti-dx
+%python_alternative %{_bindir}/nib-tck2trk
+%python_alternative %{_bindir}/nib-trk2tck
+%python_alternative %{_bindir}/parrec2nii
%{python_sitelib}/*
%changelog
commit python-nibabel for openSUSE:Factory
Hello community,
here is the log from the commit of package python-nibabel for openSUSE:Factory
checked in at 2020-03-06 21:28:03
Comparing /work/SRC/openSUSE:Factory/python-nibabel (Old)
and /work/SRC/openSUSE:Factory/.python-nibabel.new.26092 (New)
Package is "python-nibabel"
Fri Mar 6 21:28:03 2020 rev:4 rq:782024 version:3.0.1
Changes:
--- /work/SRC/openSUSE:Factory/python-nibabel/python-nibabel.changes
2019-11-20 10:29:04.462584248 +0100
+++ /work/SRC/openSUSE:Factory/.python-nibabel.new.26092/python-nibabel.changes
2020-03-06 21:28:05.401579389 +0100
@@ -1,0 +2,13 @@
+Fri Mar 6 08:07:25 UTC 2020 - Tomáš Chvátal
+
+- Update to 3.0.1:
+ * Test failed by using array method on tuple. (pr/860) (Ben Darwin, reviewed
by CM)
+ * Validate ExpiredDeprecationErrors, promoted by 3.0 release from
DeprecationWarnings. (pr/857) (CM)
+ * Improve testing of data scaling in ArrayProxy API (pr/847) (CM, reviewed
by Alejandro de la Vega)
+ * Document SpatialImage.slicer interface (pr/846) (CM)
+ * get_fdata(dtype=np.float32) will attempt to avoid casting data to
np.float64 when scaling parameters would otherwise promote the data type
unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
+ * ArraySequence now supports a large set of Python operators to combine or
update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM,
MB)
+ * Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags
(pr/818) (Henry Braun, reviewed by CM)
+ * Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov,
reviewed by MB)
+
+---
Old:
nibabel-2.5.1.tar.gz
New:
nibabel-3.0.1.tar.gz
Other differences:
--
++ python-nibabel.spec ++
--- /var/tmp/diff_new_pack.bJwJR1/_old 2020-03-06 21:28:05.997579756 +0100
+++ /var/tmp/diff_new_pack.bJwJR1/_new 2020-03-06 21:28:06.001579759 +0100
@@ -1,7 +1,7 @@
#
# spec file for package python-nibabel
#
-# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2020 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -17,30 +17,32 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
+%define skip_python2 1
Name: python-nibabel
-Version:2.5.1
+Version:3.0.1
Release:0
Summary:Tool to access multiple neuroimaging data formats
License:MIT
URL:https://nipy.org/nibabel
Source:
https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
BuildRequires: %{python_module setuptools >= 30.3.0}
+BuildRequires: %{pythons}
BuildRequires: fdupes
BuildRequires: python-rpm-macros
-Requires: python-numpy >= 1.8
-Requires: python-six >= 1.3
+Requires: python-numpy >= 1.12
+Recommends: python-Pillow
Recommends: python-dicom >= 0.9.9
+Recommends: python-h5py
+Recommends: python-scipy
BuildArch: noarch
# SECTION test requirements
-BuildRequires: %{python_module mock}
-BuildRequires: %{python_module nose >= 0.10.1}
-BuildRequires: %{python_module numpy >= 1.8}
-BuildRequires: %{python_module six >= 1.3}
-BuildRequires: python-bz2file
+BuildRequires: %{python_module Pillow}
+BuildRequires: %{python_module h5py}
+BuildRequires: %{python_module nose >= 0.11}
+BuildRequires: %{python_module numpy >= 1.12}
+BuildRequires: %{python_module pytest}
+BuildRequires: %{python_module scipy}
# /SECTION
-%ifpython2
-Requires: python-bz2file
-%endif
%python_subpackages
%description
@@ -62,7 +64,7 @@
%python_expand %fdupes %{buildroot}%{$python_sitelib}
%check
-%python_expand nosetests-%{$python_bin_suffix} nibabel
+%python_expand nosetests-%{$python_bin_suffix} -v
%files %{python_files}
%doc AUTHOR Changelog README.rst
++ nibabel-2.5.1.tar.gz -> nibabel-3.0.1.tar.gz ++
11510 lines of diff (skipped)
commit python-nibabel for openSUSE:Factory
Hello community,
here is the log from the commit of package python-nibabel for openSUSE:Factory
checked in at 2019-11-20 10:28:41
Comparing /work/SRC/openSUSE:Factory/python-nibabel (Old)
and /work/SRC/openSUSE:Factory/.python-nibabel.new.26869 (New)
Package is "python-nibabel"
Wed Nov 20 10:28:41 2019 rev:3 rq:749762 version:2.5.1
Changes:
--- /work/SRC/openSUSE:Factory/python-nibabel/python-nibabel.changes
2019-07-30 12:39:15.166935099 +0200
+++ /work/SRC/openSUSE:Factory/.python-nibabel.new.26869/python-nibabel.changes
2019-11-20 10:29:04.462584248 +0100
@@ -1,0 +2,36 @@
+Tue Nov 19 20:41:07 UTC 2019 - Todd R
+
+- Update to version 2.5.1
+ + Enhancements
+* Ignore endianness in ``nib-diff`` if values match
+ + Bug fixes
+* Correctly handle Philips DICOMs w/ derived volume
+* Raise CSA tag limit to 1000, parametrize for future relaxing
+* Coerce data types to match NIfTI intent codes when writing GIFTI data
+ arrays
+ + Maintenance
+* Require h5py 2.10 for Windows + Python < 3.6 to resolve unexpected dtypes
+ in Minc2 data
+ + API changes and deprecations
+* Deprecate ``nicom.dicomwrappers.Wrapper.get_affine()`` in favor of
``affine``
+ property; final removal in nibabel 4.0
+- Update to version 2.5.0
+ + Enhancements
+* Add SerializableImage class with to/from_bytes methods
+* Check CIFTI-2 data shape matches shape described by header
+ + Bug fixes
+* Handle stricter numpy casting rules in tests
+* TRK header fields flipped in files written on big-endian systems
+* Load multiframe ECAT images with Python 3
+ + Maintenance
+* Fix CodeCov paths on Appveyor for more accurate coverage
+* Move to setuptools and reduce use ``nisext`` functions
+* Better handle test setup/teardown
+ + API changes and deprecations
+* Effect threatened warnings and set some deprecation timelines
+* Trackvis methods now default to v2 formats
+* ``nibabel.trackvis`` scheduled for removal in nibabel 4.0
+* ``nibabel.minc`` and ``nibabel.MincImage`` will be removed in nibabel 3.0
+- Drop upstream-included fix_numpy_1_17.patch
+
+---
Old:
fix_numpy_1_17.patch
nibabel-2.4.1.tar.gz
New:
nibabel-2.5.1.tar.gz
Other differences:
--
++ python-nibabel.spec ++
--- /var/tmp/diff_new_pack.rK5Ki7/_old 2019-11-20 10:29:06.370584629 +0100
+++ /var/tmp/diff_new_pack.rK5Ki7/_new 2019-11-20 10:29:06.370584629 +0100
@@ -12,38 +12,35 @@
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
-# Please submit bugfixes or comments via http://bugs.opensuse.org/
+# Please submit bugfixes or comments via https://bugs.opensuse.org/
+#
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-nibabel
-Version:2.4.1
+Version:2.5.1
Release:0
-License:MIT
Summary:Tool to access multiple neuroimaging data formats
-Url:http://nipy.org/nibabel
-Group: Development/Languages/Python
+License:MIT
+URL:https://nipy.org/nibabel
Source:
https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
-# PATCH-FIX-UPSTREAM fix_numpy_1_17.patch gh#/nipy/nibabel#768
-Patch1: fix_numpy_1_17.patch
BuildRequires: %{python_module setuptools >= 30.3.0}
BuildRequires: fdupes
BuildRequires: python-rpm-macros
+Requires: python-numpy >= 1.8
+Requires: python-six >= 1.3
+Recommends: python-dicom >= 0.9.9
+BuildArch: noarch
# SECTION test requirements
-BuildRequires: %{python_module numpy >= 1.8}
BuildRequires: %{python_module mock}
BuildRequires: %{python_module nose >= 0.10.1}
+BuildRequires: %{python_module numpy >= 1.8}
BuildRequires: %{python_module six >= 1.3}
BuildRequires: python-bz2file
# /SECTION
-Requires: python-numpy >= 1.8
-Requires: python-six >= 1.3
%ifpython2
Requires: python-bz2file
%endif
-Recommends: python-dicom >= 0.9.9
-BuildArch: noarch
-
%python_subpackages
%description
@@ -56,7 +53,6 @@
%prep
%setup -q -n nibabel-%{version}
-%patch1 -p1
%build
%python_build
++ nibabel-2.4.1.tar.gz -> nibabel-2.5.1.tar.gz ++
2561 lines of diff (skipped)
commit python-nibabel for openSUSE:Factory
Hello community,
here is the log from the commit of package python-nibabel for openSUSE:Factory
checked in at 2019-07-30 12:39:09
Comparing /work/SRC/openSUSE:Factory/python-nibabel (Old)
and /work/SRC/openSUSE:Factory/.python-nibabel.new.4126 (New)
Package is "python-nibabel"
Tue Jul 30 12:39:09 2019 rev:2 rq:719706 version:2.4.1
Changes:
--- /work/SRC/openSUSE:Factory/python-nibabel/python-nibabel.changes
2019-07-28 10:22:01.592568758 +0200
+++ /work/SRC/openSUSE:Factory/.python-nibabel.new.4126/python-nibabel.changes
2019-07-30 12:39:15.166935099 +0200
@@ -1,0 +2,6 @@
+Mon Jul 29 18:56:10 UTC 2019 - Todd R
+
+- Add fix_numpy_1_17.patch to fix building with numpy 1.17.0
+ From: gh#/nipy/nibabel#768
+
+---
New:
fix_numpy_1_17.patch
Other differences:
--
++ python-nibabel.spec ++
--- /var/tmp/diff_new_pack.xn8MQZ/_old 2019-07-30 12:39:20.266934252 +0200
+++ /var/tmp/diff_new_pack.xn8MQZ/_new 2019-07-30 12:39:20.266934252 +0200
@@ -24,6 +24,8 @@
Url:http://nipy.org/nibabel
Group: Development/Languages/Python
Source:
https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
+# PATCH-FIX-UPSTREAM fix_numpy_1_17.patch gh#/nipy/nibabel#768
+Patch1: fix_numpy_1_17.patch
BuildRequires: %{python_module setuptools >= 30.3.0}
BuildRequires: fdupes
BuildRequires: python-rpm-macros
@@ -54,6 +56,7 @@
%prep
%setup -q -n nibabel-%{version}
+%patch1 -p1
%build
%python_build
++ fix_numpy_1_17.patch ++
>From 86b4fbedfb6919fab4e3ffe21536c5df2633c57b Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz"
Date: Sat, 15 Jun 2019 14:28:04 +0200
Subject: [PATCH] FIX/TEST: Numpy casting rules have gotten more strict, raise
different exception
---
nibabel/tests/test_volumeutils.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/nibabel/tests/test_volumeutils.py
b/nibabel/tests/test_volumeutils.py
index 06df9eb6a..fcdc5c271 100644
--- a/nibabel/tests/test_volumeutils.py
+++ b/nibabel/tests/test_volumeutils.py
@@ -700,7 +700,7 @@ def test_a2f_non_numeric():
# Some versions of numpy can cast structured types to float, others not
try:
arr.astype(float)
-except ValueError:
+except (TypeError, ValueError):
pass
else:
back_arr = write_return(arr, fobj, float)
