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python-nibabel
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File python-nibabel.changes of Package python-nibabel
------------------------------------------------------------------- Thu Jul 25 02:05:50 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com> - Remove numpy upper bound. - Add patch support-numpy-2.patch: * Use np.asarray() to support NumPy 2 as well. ------------------------------------------------------------------- Mon Jul 22 05:51:49 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com> - Switch to autosetup macro. - Restrict numpy to < 2 because it isn't currently supported. - Add patch support-pytest-8.patch: * Use pytest setup/teardown methods. ------------------------------------------------------------------- Mon Mar 25 20:12:25 UTC 2024 - Dirk Müller <dmueller@suse.com> - update to 5.2.1: * Support "flat" ASCII-encoded GIFTI DataArrays (pr/1298) (PM, reviewed by CM) * Tolerate missing ``git`` when reporting version info (pr/1286) * Handle Siemens XA30 derived DWI DICOMs (pr/1296) * Add tool for generating GitHub-friendly release notes * Accommodate pytest 8 changes (pr/1297) (CM) ------------------------------------------------------------------- Thu Feb 15 16:13:37 UTC 2024 - Ben Greiner <code@bnavigator.de> - 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. ------------------------------------------------------------------- Thu Oct 6 14:07:18 UTC 2022 - Markéta Machová <mmachova@suse.com> - Update to 4.0.2 * many changes, see Changelog * nib-convert CLI tool to make image type and data dtype conversion accessible via the command line. * Allow dtypes to be passed to Analyze-like images at __init__() and to_filename() * Allow compressed GIFTI images * Add zstd compression support * Test on Python 3.10 * Passing (u)int64 arrays to Nifti1Image and subclasses will warn unless a header or dtype option is passed; in the future this will become an error. Additionally, passing int or 'int' to set_data_dtype() now raises an error, requiring an explicit numpy dtype to make 64-bit integer images. * Drop support for Python 3.6, Numpy < 1.17 * Fully removed the APIs, which have raised errors on use since 3.0 - Drop upstreamed 983.patch and purge-nose.patch ------------------------------------------------------------------- Wed Mar 31 09:09:56 UTC 2021 - Guillaume GARDET <guillaume.gardet@opensuse.org> - Add upstream patch to fix test on Backports:SLE-15-SP3: * 983.patch ------------------------------------------------------------------- Fri Feb 12 14:37:36 UTC 2021 - Dirk Müller <dmueller@suse.com> - skip python 36 ------------------------------------------------------------------- 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> - %python3_only -> %python_alternative ------------------------------------------------------------------- Fri Mar 6 08:07:25 UTC 2020 - Tomáš Chvátal <tchvatal@suse.com> - 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) ------------------------------------------------------------------- Tue Nov 19 20:41:07 UTC 2019 - Todd R <toddrme2178@gmail.com> - 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 ------------------------------------------------------------------- Mon Jul 29 18:56:10 UTC 2019 - Todd R <toddrme2178@gmail.com> - Add fix_numpy_1_17.patch to fix building with numpy 1.17.0 From: gh#/nipy/nibabel#768 ------------------------------------------------------------------- Fri Jul 26 14:21:33 UTC 2019 - Todd R <toddrme2178@gmail.com> - Initial version
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