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DOC: Update changelog
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Changelog

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@@ -25,6 +25,89 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
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References like "pr/298" refer to github pull request numbers.
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5.0.0 (Monday 9 January 2023)
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=============================
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New feature release in the 5.0.x series.
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New features
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------------
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* :class:`~nibabel.filebasedimages.SerializableImage` now has
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:meth:`~nibabel.filebasedimages.SerializableImage.to_stream()` and
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:meth:`~nibabel.filebasedimages.SerializableImage.from_stream()` methods to
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read/write streams implementing the :class:`~io.IOBase` interface. A
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:meth:`~nibabel.filebasedimages.SerializableImage.from_url()` method
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enables loading images from URLs. (pr/1129) (CM, reviewed by MB)
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* :class:`~nibabel.streamlines.trk.TrkFile` supports TRKv3, an
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undocumented but generally compatible variant of TRKv2. (pr/1125) (CM)
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Enhancements
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------------
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* Support multiline header fields in :class:`~nibabel.streamlines.tck.TCKFile`
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(pr/1175) (CM, reviewed by Matt Cieslak)
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* Make layout order an initialization parameter of
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:class:`~nibabel.arrayproxy.ArrayProxy` (pr/1131) (CM, reviewed by MB)
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* Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by
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Zvi Baratz)
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Bug fixes
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---------
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* Handle extension/file-format mismatches implemented incompletely in pr/1013
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(pr/1138) (CM, reviewed by Thomas Phil)
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* Improve handling of invalid TCK files, which could sometimes cause an
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infinite loop (pr/1140) (Anibal Solon, reviewed by CM)
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* Clean up ECAT test case that left filehandle open and failed to use class
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variables (pr/1155) (Dimitri Papadopoulos, reviewed by CM)
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Maintenance
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-----------
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* Simplify TCK reading code by assuming files are open in binary mode
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(pr/1142) (Anibal Solon, reviewed by MC, CM)
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* Code support for tests covering deprecated functionality (pr/1159) (CM)
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* Miscellaneous code cleanups (pr/1148, pr/1149, pr/1153, pr/1154, pr/1156)
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(Dimitri Papadopoulos, reviewed by CM)
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* Update CI to build, test and deploy PyPI artifacts (pr/1134) (CM, reviewed
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by MB)
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* Transition from ``setup.cfg`` to ``pyproject.toml`` package configuration
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(pr/1133) (CM, reviewed by MB)
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* Addressed race conditions preventing running tests with pytest-xdist_.
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(pr/1157, pr/1158) (CM, reviewed by Christian Haselgrove)
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* Apply blue_ and isort_ auto-formatters and provide pre-commit_ configuration
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to reduce human burden of style guidelines. (pr/1124, pr/1165, pr/1169)
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(CM and Zvi Baratz)
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* Manage versioning with setuptools_scm_ (pr/1171) (CM, reviewed by Zvi Baratz)
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* Reduce installed package size by excluding very large test file (pr/1176)
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(CM, reviewed by Zvi Baratz)
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API changes and deprecations
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----------------------------
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* Passing an ``int64`` array to :class:`~nibabel.nifti1.Nifti1Image` without a
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header or dtype argument will raise a ``ValueError``. (pr/1173) (CM)
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* :class:`nibabel.tmpdirs.TemporaryDirectory` is deprecated in favor of
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:class:`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 6.0.
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(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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``ExpiredDeprecationError``\s
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* :func:`nibabel.loadsave.read_img_data`
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* :meth:`nibabel.dataobj_images.DataobjImage.get_data`
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* :func:`nibabel.loadsave.guessed_image_type`
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* :func:`nibabel.onetime.setattr_on_read`
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* :func:`nibabel.orientations.flip_axis`
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* Modules, classes and functions that expired at 4.0 were fully removed.
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``ExpiredDeprecationError``\s will now be ``AttributeError``\s.
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.. _blue: https://blue.readthedocs.io
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.. _isort: https://pycqa.github.io/isort/
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.. _pre-commit: https://pre-commit.com/
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.. _pytest-xdist: https://pytest-xdist.readthedocs.io
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.. _setuptools_scm: https://github.com/pypa/setuptools_scm
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4.0.2 (Wednesday 31 August 2022)
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================================
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