forked from pool/python-nibabel
Accepting request 1147056 from home:bnavigator:branches:devel:languages:python:numeric
- Update to 5.2.0 ## New features * Add generic Pointset and regularly spaced Grid data structures in preparation for coordinate transformation and resampling (#1251) (CM, reviewed by Oscar Esteban) ## Enhancements * Add copy method to ArrayProxy (#1255) (CM, reviewed by Paul McCarthy) * Permit to_xml to pass keyword arguments to tostring (#1258) (CM) * Allow user expansion (e.g., ~/...) in strings passed to functions that accept paths (#1260) (Reinder Vos de Wael, reviewed by CM) * Expand CIFTI-2 brain structures to permit synonyms (#1256) (CM, reviewed by Mathias Goncalves) * Annotate SpatialImage as accepting affine=None argument (#1253) (Blake Dewey, reviewed by CM) * Warn on invalid MINC2 spacing declarations, treat as missing (#1237) (Peter Suter, reviewed by CM) * Refactor find_private_section for improved readability and maintainability (#1228) (MB, reviewed by CM) ## API changes and deprecations * The nibabel.pydicom_compat module is deprecated and will be removed in NiBabel 7.0. (#1280) * The int_to_float and as_int functions are no longer needed to work around NumPy deficiencies and have been deprecated (#1272) (CM, reviewed by EL) - Release 5.1 ## Enhancements * Make imagestats available with import nibabel (pr/1208) (Fabian Perez, reviewed by CM) * Use symmetric threshold for identifying unit quaternions on qform calculations (pr/1182) (CM, reviewed by MB) * Type annotations for nibabel.loadsave (pr/1213) and nibabel.spatialimages.SpatialImage APIs (pr/1179), nibabel.deprecated, nibabel.deprecator, nibabel.onetime and nibabel.optpkg modules (pr/1188), nibabel.volumeutils (pr/1189), nibabel.filename_parser and nibabel.openers (pr/1197) (CM, reviewed by Zvi Baratz) - Release 5.0 ## New features * SerializableImage now has to_stream() and from_stream() methods to read/write streams implementing the io.IOBase interface. A from_url() method enables loading images from URLs. (pr/1129) (CM, reviewed by MB) * TrkFile supports TRKv3, an undocumented but generally compatible variant of TRKv2. (pr/1125) (CM) ## Enhancements * Support multiline header fields in TCKFile (pr/1175) (CM, reviewed by Matt Cieslak) * Make layout order an initialization parameter of ArrayProxy (pr/1131) (CM, reviewed by MB) * Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by Zvi Baratz) ## API changes and deprecations * Passing an int64 array to Nifti1Image without a header or dtype argument will raise a ValueError. (pr/1173) (CM) * tmpdirs.TemporaryDirectory is deprecated in favor of tempfile.TemporaryDirectory. (pr/1172) (CM, reviewed by Zvi Baratz) * The nisext package is deprecated and will be removed in NiBabel 6.0. (pr/1170) (CM, reviewed by MB) * Drop support for Python 3.7, Numpy < 1.19 (pr/1177) (CM) * The following deprecated functions and methods will now raise ExpiredDeprecationErrors - nibabel.loadsave.read_img_data - nibabel.dataobj_images.DataobjImage.get_data - nibabel.loadsave.guessed_image_type - nibabel.onetime.setattr_on_read - nibabel.orientations.flip_axis * Modules, classes and functions that expired at 4.0 were fully removed. ExpiredDeprecationError will now be AttributeError. OBS-URL: https://build.opensuse.org/request/show/1147056 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-nibabel?expand=0&rev=20
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version https://git-lfs.github.com/spec/v1
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-------------------------------------------------------------------
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Thu Feb 15 16:13:37 UTC 2024 - Ben Greiner <code@bnavigator.de>
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- Update to 5.2.0
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## New features
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* Add generic Pointset and regularly spaced Grid data structures
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in preparation for coordinate transformation and resampling
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(#1251) (CM, reviewed by Oscar Esteban)
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## Enhancements
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* Add copy method to ArrayProxy (#1255) (CM, reviewed by Paul
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McCarthy)
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* Permit to_xml to pass keyword arguments to tostring (#1258)
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(CM)
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* Allow user expansion (e.g., ~/...) in strings passed to
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functions that accept paths (#1260) (Reinder Vos de Wael,
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reviewed by CM)
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* Expand CIFTI-2 brain structures to permit synonyms (#1256) (CM,
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reviewed by Mathias Goncalves)
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* Annotate SpatialImage as accepting affine=None argument (#1253)
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(Blake Dewey, reviewed by CM)
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* Warn on invalid MINC2 spacing declarations, treat as missing
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(#1237) (Peter Suter, reviewed by CM)
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* Refactor find_private_section for improved readability and
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maintainability (#1228) (MB, reviewed by CM)
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## API changes and deprecations
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* The nibabel.pydicom_compat module is deprecated and will be
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removed in NiBabel 7.0. (#1280)
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* The int_to_float and as_int functions are no longer needed to
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work around NumPy deficiencies and have been deprecated (#1272)
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(CM, reviewed by EL)
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- Release 5.1
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## Enhancements
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* Make imagestats available with import nibabel (pr/1208) (Fabian
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Perez, reviewed by CM)
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* Use symmetric threshold for identifying unit quaternions on
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qform calculations (pr/1182) (CM, reviewed by MB)
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* Type annotations for nibabel.loadsave (pr/1213) and
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nibabel.spatialimages.SpatialImage APIs (pr/1179),
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nibabel.deprecated, nibabel.deprecator, nibabel.onetime and
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nibabel.optpkg modules (pr/1188), nibabel.volumeutils
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(pr/1189), nibabel.filename_parser and nibabel.openers
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(pr/1197) (CM, reviewed by Zvi Baratz)
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- Release 5.0
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## New features
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* SerializableImage now has to_stream() and from_stream() methods
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to read/write streams implementing the io.IOBase interface. A
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from_url() method enables loading images from URLs. (pr/1129)
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(CM, reviewed by MB)
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* TrkFile supports TRKv3, an undocumented but generally
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compatible variant of TRKv2. (pr/1125) (CM)
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## Enhancements
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* Support multiline header fields in TCKFile (pr/1175) (CM,
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reviewed by Matt Cieslak)
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* Make layout order an initialization parameter of ArrayProxy
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(pr/1131) (CM, reviewed by MB)
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* Initial support for type annotations. (pr/1115, pr/1178) (CM,
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reviewed by Zvi Baratz)
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## API changes and deprecations
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* Passing an int64 array to Nifti1Image without a header or dtype
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argument will raise a ValueError. (pr/1173) (CM)
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* tmpdirs.TemporaryDirectory is deprecated in favor of
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tempfile.TemporaryDirectory. (pr/1172) (CM, reviewed by Zvi
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Baratz)
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* The nisext package is deprecated and will be removed in NiBabel
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6.0. (pr/1170) (CM, reviewed by MB)
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* Drop support for Python 3.7, Numpy < 1.19 (pr/1177) (CM)
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* The following deprecated functions and methods will now raise
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ExpiredDeprecationErrors
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- nibabel.loadsave.read_img_data
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- nibabel.dataobj_images.DataobjImage.get_data
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- nibabel.loadsave.guessed_image_type
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- nibabel.onetime.setattr_on_read
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- nibabel.orientations.flip_axis
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* Modules, classes and functions that expired at 4.0 were fully
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removed. ExpiredDeprecationError will now be
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AttributeError.
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-------------------------------------------------------------------
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-------------------------------------------------------------------
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Thu Oct 6 14:07:18 UTC 2022 - Markéta Machová <mmachova@suse.com>
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Thu Oct 6 14:07:18 UTC 2022 - Markéta Machová <mmachova@suse.com>
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@ -1,7 +1,7 @@
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#
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#
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# spec file for package python-nibabel
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# spec file for package python-nibabel
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#
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#
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# Copyright (c) 2022 SUSE LLC
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# Copyright (c) 2024 SUSE LLC
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#
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#
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# All modifications and additions to the file contributed by third parties
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# remain the property of their copyright owners, unless otherwise agreed
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@ -16,35 +16,45 @@
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#
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#
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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%define skip_python2 1
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%define skip_python36 1
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%define binaries nib-conform nib-convert nib-dicomfs nib-diff nib-ls nib-nifti-dx nib-roi nib-stats nib-tck2trk nib-trk2tck parrec2nii
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%define binaries nib-conform nib-convert nib-dicomfs nib-diff nib-ls nib-nifti-dx nib-roi nib-stats nib-tck2trk nib-trk2tck parrec2nii
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Name: python-nibabel
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Name: python-nibabel
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Version: 4.0.2
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Version: 5.2.0
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Release: 0
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Release: 0
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Summary: Tool to access multiple neuroimaging data formats
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Summary: Tool to access multiple neuroimaging data formats
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License: MIT
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License: MIT
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URL: https://nipy.org/nibabel
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URL: https://nipy.org/nibabel
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# SourceRepository: https://github.com/nipy/nibabel
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Source: https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
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Source: https://files.pythonhosted.org/packages/source/n/nibabel/nibabel-%{version}.tar.gz
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BuildRequires: %{python_module setuptools >= 30.3.0}
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BuildRequires: %{python_module base >= 3.8}
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BuildRequires: %{pythons}
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BuildRequires: %{python_module hatch-vcs}
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BuildRequires: %{python_module hatchling}
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BuildRequires: %{python_module pip}
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BuildRequires: fdupes
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BuildRequires: fdupes
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BuildRequires: python-rpm-macros
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BuildRequires: python-rpm-macros
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Requires: python-numpy >= 1.17
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Requires: python-numpy >= 1.20
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Requires: python-packaging => 17
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Requires: (python-importlib-resources >= 1.3 if python-base < 3.9)
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Requires(post): update-alternatives
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Requires(post): update-alternatives
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Requires(postun):update-alternatives
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Requires(postun): update-alternatives
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Recommends: python-Pillow
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Recommends: python-Pillow
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Recommends: python-dicom >= 0.9.9
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Recommends: python-h5py
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Recommends: python-h5py
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Recommends: python-pydicom >= 1
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Recommends: python-scipy
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Recommends: python-scipy
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BuildArch: noarch
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BuildArch: noarch
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# SECTION test requirements
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# SECTION test requirements
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BuildRequires: %{python_module Pillow}
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BuildRequires: %{python_module Pillow}
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BuildRequires: %{python_module h5py}
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BuildRequires: %{python_module h5py}
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BuildRequires: %{python_module numpy >= 1.17}
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BuildRequires: %{python_module importlib-resources >= 1.3 if %python-base < 3.9}
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BuildRequires: %{python_module numpy >= 1.20}
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BuildRequires: %{python_module packaging >= 17}
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BuildRequires: %{python_module pydicom >= 1}
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BuildRequires: %{python_module pytest-doctestplus}
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BuildRequires: %{python_module pytest-httpserver}
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BuildRequires: %{python_module pytest-xdist}
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BuildRequires: %{python_module pytest}
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BuildRequires: %{python_module pytest}
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BuildRequires: %{python_module scipy}
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BuildRequires: %{python_module scipy}
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BuildRequires: %{pythons}
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BuildRequires: git-core
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# /SECTION
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# /SECTION
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%python_subpackages
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%python_subpackages
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%prep
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%prep
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%setup -q -n nibabel-%{version}
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%setup -q -n nibabel-%{version}
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find nibabel -name .gitignore -delete
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sed -i '1{/^!#/d}' nibabel/cmdline/*.py
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chmod a-x nibabel/cmdline/*.py
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chmod a-x nibabel/tests/data/umass_anonymized.PAR nibabel/gifti/tests/data/gzipbase64.gii nibabel/nicom/dicomwrappers.py nibabel/nicom/tests/test_dicomwrappers.py
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%build
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%build
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%python_build
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%pyproject_wheel
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%install
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%install
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%python_install
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%pyproject_install
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for b in %{binaries}; do
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for b in %{binaries}; do
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%python_clone -a %{buildroot}%{_bindir}/$b
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%python_clone -a %{buildroot}%{_bindir}/$b
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done
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done
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%python_expand %fdupes %{buildroot}%{$python_sitelib}
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%python_expand %fdupes %{buildroot}%{$python_sitelib}
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%check
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%check
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%pytest
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%pytest -n auto -rsfE
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%post
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%post
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for b in %{binaries}; do
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%{expand:%(for b in %{binaries}; do echo "%%python_install_alternative $b"; done)}
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%python_install_alternative $b
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done
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%postun
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%postun
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for b in %{binaries}; do
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%{expand:%(for b in %{binaries}; do echo "%%python_uninstall_alternative $b"; done)}
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%python_uninstall_alternative $b
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done
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%files %{python_files}
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%files %{python_files}
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%doc AUTHOR Changelog README.rst
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%doc AUTHOR Changelog README.rst
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%license COPYING
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%license COPYING
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%python_alternative %{_bindir}/nib-conform
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%{expand:%(for b in %{binaries}; do echo "%%python_alternative %%{_bindir}/$b"; done)}
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%python_alternative %{_bindir}/nib-convert
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%{python_sitelib}/nibabel
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%python_alternative %{_bindir}/nib-dicomfs
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%{python_sitelib}/nisext
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%python_alternative %{_bindir}/nib-diff
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%{python_sitelib}/nibabel-%{version}.dist-info
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%python_alternative %{_bindir}/nib-ls
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%python_alternative %{_bindir}/nib-nifti-dx
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%python_alternative %{_bindir}/nib-roi
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%python_alternative %{_bindir}/nib-stats
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%python_alternative %{_bindir}/nib-tck2trk
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%python_alternative %{_bindir}/nib-trk2tck
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%python_alternative %{_bindir}/parrec2nii
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%{python_sitelib}/*
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%changelog
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%changelog
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