Accepting request 819969 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/819969
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-nibabel?expand=0&rev=6

nibabel-3.0.1.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:d38c657eca6ae3d246db9019549be5448b7a0a6683240c96bff2cebf91b7d422
-size 4615979

nibabel-3.1.1.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b5efff77c81affbed2a85a038fb7948669b088b4a87ff6fdf358f83acf4b39ce
+size 4617212

purge-nose.patch

@@ -0,0 +1,189 @@
+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, package_check, FAKE_NAME, setuptools_args=None)
++    with pytest.raises(RuntimeError):
++        package_check(FAKE_NAME, setuptools_args=None)
+     def pkg_chk_sta(*args, **kwargs):
+         st_args = {}
+         package_check(*args, setuptools_args=st_args, **kwargs)
+         return st_args
+-    assert_equal(pkg_chk_sta(FAKE_NAME),
+-                 {'install_requires': ['nisext_improbable']})
++    assert pkg_chk_sta(FAKE_NAME) == {'install_requires': ['nisext_improbable']}
+     # Check that this gets appended to existing value
+     old_sta = {'install_requires': ['something']}
+     package_check(FAKE_NAME, setuptools_args=old_sta)
+-    assert_equal(old_sta,
+-                 {'install_requires': ['something', 'nisext_improbable']})
++    assert old_sta == {'install_requires': ['something', 'nisext_improbable']}
+     # That existing value as string gets converted to a list
+     old_sta = {'install_requires': 'something'}
+     package_check(FAKE_NAME, setuptools_args=old_sta)
+-    assert_equal(old_sta,
+-                 {'install_requires': ['something', 'nisext_improbable']})
++    assert old_sta == {'install_requires': ['something', 'nisext_improbable']}
+     # Optional, add to extras_require
+-    assert_equal(pkg_chk_sta(FAKE_NAME, optional='something'),
+-                 {'extras_require': {'something': ['nisext_improbable']}})
++    assert pkg_chk_sta(FAKE_NAME, optional='something') == {'extras_require': {'something': ['nisext_improbable']}}
+     # Check that this gets appended to existing value
+     old_sta = {'extras_require': {'something': ['amodule']}}
+     package_check(FAKE_NAME, optional='something', setuptools_args=old_sta)
+-    assert_equal(old_sta,
+-                 {'extras_require':
+-                  {'something': ['amodule', 'nisext_improbable']}})
++    assert old_sta == {'extras_require': {'something': ['amodule', 'nisext_improbable']}}
+     # That string gets converted to a list here too
+     old_sta = {'extras_require': {'something': 'amodule'}}
+     package_check(FAKE_NAME, optional='something', setuptools_args=old_sta)
+-    assert_equal(old_sta,
+-                 {'extras_require':
+-                  {'something': ['amodule', 'nisext_improbable']}})
++    assert old_sta == {'extras_require':
++                  {'something': ['amodule', 'nisext_improbable']}}
+     # But optional has to be a string if not empty and setuptools_args defined
+-    assert_raises(RuntimeError,
+-                  package_check, FAKE_NAME, optional=True, setuptools_args={})
++    with pytest.raises(RuntimeError):
++        package_check(FAKE_NAME, optional=True, setuptools_args={})
+     try:
+         # Make a package
+         sys.modules[FAKE_NAME] = FAKE_MODULE
+         # No install_requires because we already have it
+-        assert_equal(pkg_chk_sta(FAKE_NAME), {})
++        assert pkg_chk_sta(FAKE_NAME) == {}
+         # A fake version still works
+         FAKE_MODULE.__version__ = '0.2'
+-        assert_equal(pkg_chk_sta(FAKE_NAME, version='0.2'), {})
++        assert pkg_chk_sta(FAKE_NAME, version='0.2') == {}
+         # goes into install requires when version not good enough
+         exp_spec = [FAKE_NAME + '>=0.3']
+-        assert_equal(pkg_chk_sta(FAKE_NAME, version='0.3'),
+-                     {'install_requires': exp_spec})
++        assert pkg_chk_sta(FAKE_NAME, version='0.3') == {'install_requires': exp_spec}
+         # Unless optional in which case goes into extras_require
+         package_check(FAKE_NAME, version='0.2', version_getter=lambda x: '0.2')
+-        assert_equal(
+-            pkg_chk_sta(FAKE_NAME, version='0.3', optional='afeature'),
+-            {'extras_require': {'afeature': exp_spec}})
++        assert pkg_chk_sta(FAKE_NAME, version='0.3', optional='afeature') == {'extras_require': {'afeature': exp_spec}}
+         # Might do custom version check
+-        assert_equal(
+-            pkg_chk_sta(FAKE_NAME,
++        assert pkg_chk_sta(FAKE_NAME,
+                         version='0.2',
+-                        version_getter=lambda x: '0.2'),
+-            {})
++                        version_getter=lambda x: '0.2') == {}
+         # If the version check fails, put into requires
+         bad_getter = lambda x: x.not_an_attribute
+         exp_spec = [FAKE_NAME + '>=0.2']
+-        assert_equal(
+-            pkg_chk_sta(FAKE_NAME,
++        assert pkg_chk_sta(FAKE_NAME,
+                         version='0.2',
+-                        version_getter=bad_getter),
+-            {'install_requires': exp_spec})
++                        version_getter=bad_getter) == {'install_requires': exp_spec}
+         # Likewise for optional dependency
+-        assert_equal(
+-            pkg_chk_sta(FAKE_NAME,
++        assert pkg_chk_sta(FAKE_NAME,
+                         version='0.2',
+                         optional='afeature',
+-                        version_getter=bad_getter),
+-            {'extras_require': {'afeature': [FAKE_NAME + '>=0.2']}})
++                        version_getter=bad_getter) == {'extras_require': {'afeature': [FAKE_NAME + '>=0.2']}}
+     finally:
+         del sys.modules[FAKE_NAME]
+Index: nibabel-3.1.1/nisext/tests/test_testers.py
+===================================================================
+--- nibabel-3.1.1.orig/nisext/tests/test_testers.py
++++ nibabel-3.1.1/nisext/tests/test_testers.py
+@@ -6,38 +6,37 @@ from os.path import dirname, pathsep
+ 
+ from ..testers import back_tick, run_mod_cmd, PYTHON
+ 
+-from nose.tools import assert_true, assert_equal, assert_raises
+-
++import pytest
+ 
+ def test_back_tick():
+     cmd = '{0} -c "print(\'Hello\')"'.format(PYTHON)
+-    assert_equal(back_tick(cmd), "Hello")
+-    assert_equal(back_tick(cmd, ret_err=True), ("Hello", ""))
+-    assert_equal(back_tick(cmd, True, False), (b"Hello", b""))
++    assert back_tick(cmd) == "Hello"
++    assert back_tick(cmd, ret_err=True) == ("Hello", "")
++    assert back_tick(cmd, True, False) == (b"Hello", b"")
+     cmd = '{0} -c "raise ValueError()"'.format(PYTHON)
+-    assert_raises(RuntimeError, back_tick, cmd)
++    with pytest.raises(RuntimeError):
++        back_tick(cmd)
+ 
+ 
+ def test_run_mod_cmd():
+     mod = 'os'
+     mod_dir = dirname(os.__file__)
+-    assert_equal(run_mod_cmd(mod, mod_dir, "print('Hello')", None, False),
+-                 ("Hello", ""))
++    assert run_mod_cmd(mod, mod_dir, "print('Hello')", None, False) == ("Hello", "")
+     sout, serr = run_mod_cmd(mod, mod_dir, "print('Hello again')")
+-    assert_equal(serr, '')
++    assert serr == ''
+     mod_file, out_str = [s.strip() for s in sout.split('\n')]
+-    assert_true(mod_file.startswith(mod_dir))
+-    assert_equal(out_str, 'Hello again')
++    assert mod_file.startswith(mod_dir)
++    assert out_str == 'Hello again'
+     sout, serr = run_mod_cmd(mod,
+                              mod_dir,
+                              "print(os.environ['PATH'])",
+                              None,
+                              False)
+-    assert_equal(serr, '')
++    assert serr == ''
+     sout2, serr = run_mod_cmd(mod,
+                               mod_dir,
+                               "print(os.environ['PATH'])",
+                               'pth2',
+                               False)
+-    assert_equal(serr, '')
+-    assert_equal(sout2, '"pth2"' + pathsep + sout)
++    assert serr == ''
++    assert sout2 == '"pth2"' + pathsep + sout

python-nibabel.changes

@@ -1,3 +1,16 @@
+-------------------------------------------------------------------
+Fri Jul 10 09:06:52 UTC 2020 - Marketa Calabkova <mcalabkova@suse.com>
+
+- 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
+
 -------------------------------------------------------------------
 Thu May 21 10:56:36 UTC 2020 - Petr Gajdos <pgajdos@suse.com>
 

python-nibabel.spec

@@ -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 @@ BuildArch:      noarch
 # 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 @@ very limited support for DICOM.
 
 %prep
 %setup -q -n nibabel-%{version}
+%patch0 -p1
 
 %build
 %python_build
@@ -70,7 +71,7 @@ done
 %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 @@ done
 %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