Nibabel

===============================

Bug-fix release in the 5.0.x series.

Bug fixes
---------
* Support ragged voxel arrays in
:class:`~nibabel.cifti2.cifti2_axes.ParcelsAxis` (pr/1194) (Michiel Cottaar,
reviewed by CM)
* Return to cwd on exception in :class:`~nibabel.tmpdirs.InTemporaryDirectory`
(pr/1184) (CM)

Maintenance
-----------
* Add ``py.typed`` to module root to enable use of types in downstream
projects (CM, reviewed by Fernando Pérez-Garcia)
* Cache git-archive separately from Python packages in GitHub Actions
(pr/1186) (CM, reviewed by Zvi Baratz)

=============================

New feature release in the 5.0.x series.

New features
------------
* :class:`~nibabel.filebasedimages.SerializableImage` now has
:meth:`~nibabel.filebasedimages.SerializableImage.to_stream()` and
:meth:`~nibabel.filebasedimages.SerializableImage.from_stream()` methods to
read/write streams implementing the :class:`~io.IOBase` interface. A
:meth:`~nibabel.filebasedimages.SerializableImage.from_url()` method
enables loading images from URLs. (pr/1129) (CM, reviewed by MB)
* :class:`~nibabel.streamlines.trk.TrkFile` supports TRKv3, an
undocumented but generally compatible variant of TRKv2. (pr/1125) (CM)

Enhancements
------------
* Support multiline header fields in :class:`~nibabel.streamlines.tck.TCKFile`
(pr/1175) (CM, reviewed by Matt Cieslak)
* Make layout order an initialization parameter of
:class:`~nibabel.arrayproxy.ArrayProxy` (pr/1131) (CM, reviewed by MB)
* Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by
Zvi Baratz)

Bug fixes
---------
* Handle extension/file-format mismatches implemented incompletely in pr/1013
(pr/1138) (CM, reviewed by Thomas Phil)
* Improve handling of invalid TCK files, which could sometimes cause an
infinite loop (pr/1140) (Anibal Solon, reviewed by CM)
* Clean up ECAT test case that left filehandle open and failed to use class
variables (pr/1155) (Dimitri Papadopoulos, reviewed by CM)

Maintenance
-----------
* Simplify TCK reading code by assuming files are open in binary mode
(pr/1142) (Anibal Solon, reviewed by MC, CM)
* Code support for tests covering deprecated functionality (pr/1159) (CM)
* Miscellaneous code cleanups (pr/1148, pr/1149, pr/1153, pr/1154, pr/1156)
(Dimitri Papadopoulos, reviewed by CM)
* Update CI to build, test and deploy PyPI artifacts (pr/1134) (CM, reviewed
by MB)
* Transition from ``setup.cfg`` to ``pyproject.toml`` package configuration
(pr/1133) (CM, reviewed by MB)
* Addressed race conditions preventing running tests with pytest-xdist_.
(pr/1157, pr/1158) (CM, reviewed by Christian Haselgrove)
* Apply blue_ and isort_ auto-formatters and provide pre-commit_ configuration
to reduce human burden of style guidelines. (pr/1124, pr/1165, pr/1169)
(CM and Zvi Baratz)
* Manage versioning with setuptools_scm_ (pr/1171) (CM, reviewed by Zvi Baratz)
* Reduce installed package size by excluding very large test file (pr/1176)
(CM, reviewed by Zvi Baratz)

API changes and deprecations
----------------------------
* Passing an ``int64`` array to :class:`~nibabel.nifti1.Nifti1Image` without a
header or dtype argument will raise a ``ValueError``. (pr/1173) (CM)
* :class:`nibabel.tmpdirs.TemporaryDirectory` is deprecated in favor of
:class:`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
``ExpiredDeprecationError``\s

* :func:`nibabel.loadsave.read_img_data`
* :meth:`nibabel.dataobj_images.DataobjImage.get_data`
* :func:`nibabel.loadsave.guessed_image_type`
* :func:`nibabel.onetime.setattr_on_read`
* :func:`nibabel.orientations.flip_axis`

* Modules, classes and functions that expired at 4.0 were fully removed.
``ExpiredDeprecationError``\s will now be ``AttributeError``\s.

.. _blue: https://blue.readthedocs.io
.. _isort: https://pycqa.github.io/isort/
.. _pre-commit: https://pre-commit.com/
.. _pytest-xdist: https://pytest-xdist.readthedocs.io
.. _setuptools_scm: https://github.com/pypa/setuptools_scm

================================

Bug-fix release in the 4.0.x series.

Bug fixes
---------
* Make ``GiftiMetaData.data`` a list proxy, deprecate (pr/1127) (CM, reviewed
by Hao-Ting Wang)

Maintenance
-----------
* Finalize deprecation of ``ArrayWriter.to_fileobj(nan2zero=...)`` argument
(pr/1126) (CM)

=============================

Bug-fix release in the 4.0.x series.

Bug fixes
---------
* Finalize 4.0 deprecations, converting tests expecting ``DeprecationWarning`` to
expected ``ExpiredDeprecationError`` (pr/1117) (CM)

Maintenance
-----------
* Suppress new numpy warning on nan-to-int cast (pr/1118) (CM, reviewed by MB)

=============================

New feature release in the 4.0.x series.

New features
------------
* ``nib-convert`` CLI tool to make image type and data dtype conversion accessible
via the command line. (pr/1113) (CM, reviewed by Ariel Rokem)
* Add ``'mask'``, ``'compat'`` and ``'smallest'`` dtype aliases to NIfTI images
to allow for dtype specifications that can depend on the contents of the data.
``'mask'`` is a synonym for ``uint8``. ``'compat'`` will find the nearest
Analyze-compatible (therefore widely supported) dtype that will not truncate
the data. ``'smallest'`` attempts to find the smallest integer dtype that will
contain the data. (pr/1096) (CM, reviewed by Chris Rorden and Josh Teves)
* Add ``dtype`` arguments to ``Cifti2Image`` (pr/1111) (CM)
* Allow dtypes to be passed to Analyze-like images at ``__init__()`` and
``to_filename()`` to provide better control over output images. (pr/1082)
(CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes, and MB)
* Allow compressed GIFTI images (MB, reviewed by CM)
* Add zstd compression support (pr/1005) (Andrew Van, reviewed by CM)
* Support ``ExternalFileBinary`` GIFTI data arrays (PM, reviewed by CM)

Enhancements
------------
* Document ``InTemporaryDirectory`` as non-thread-safe (pr/1103) (Jacob Roberts,
reviewed by MB)
* Unify Caret-XML-style metadata structure (GiftiMetaData, Cifti2MetaData)
as dict-like (pr/1091) (CM, reviewed by Josh Teves and Hao-Ting Wang)
* Add ``__repr__`` methods to GIFTI objects (pr/1092) (CM,
reviewed by Josh Teves and Hao-Ting Wang)
* Create gzip header deterministically by default (pr/1024) (CM, reviewed by YOH)
* Provide clear error message when files with zip extensions don't match
file contents (pr/1013) (Jérôme Dockès, reviewed by CM)

Bug fixes
---------
* Re-import externals/netcdf.py from scipy to resolve numpy API change (pr/1110)
(CM)
* Resize ArraySequence.data without helper function to avoid reference increment
(pr/1093) (MC, reviewed by CM)

Maintenance
-----------
* Update submodule URLs to use https over git protocol (pr/1097) (CM)
* Published BIAP 9: CoordinateImage API (pr/1084) (CM)
* Drop uses of deprecated ``distutils`` (pr/1073) (CM, reviewed by MB)
* Suppress LGTM false alarm "Clear-text logging of sensitive information"
(pr/1052) (Dimitri Papadopoulos, reviewed by CM)
* Test on Python 3.10 (pr/1047) (CM)
* Fix typos found by codespell (pr/1040, pr/1044)
(Dimitri Papadopoulos, reviewed by CM)
* Run stable tests weekly, pre-release tests nightly (pr/1025) (CM)
* Documentation updates to establish/clarify governance and decision
making (pr/1019, pr/1020, pr/1022, pr/1018, pr/1017, pr/1016) (MB and CM)

API changes and deprecations
----------------------------
* Writing NIfTIs with 64-bit integer dtypes is getting harder.
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.
(pr/1082) (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes,
and MB)
* Drop support for Python 3.6, Numpy < 1.17 (pr/1079) (CM)
* Fully removed the following APIs, which have raised errors on use
since 3.0 (pr/980) (CM, reviewed by Jonathan Daniel)

* ``nibabel.trackvis``
* ``nibabel.volumeutils.calculate_scale``
* ``nibabel.volumeutils.can_cast``
* ``nibabel.volumeutils.scale_min_max``
* ``nibabel.dataobj_images.DataobjImage.get_shape``
* ``nibabel.minc1.MincImage`` (use ``Minc1Image``)
* ``nibabel.minc1.MincFile`` (use ``Minc1File``)
* ``nibabel.filebasedimages.FileBasedImage.from_files``
* ``nibabel.filebasedimages.FileBasedImage.filespec_to_files``
* ``nibabel.filebasedimages.FileBasedImage.to_filespec``
* ``nibabel.filebasedimages.FileBasedImage.to_files``
* ``nibabel.arrayproxy.ArrayProxy.header``
* ``keep_file_open=="auto"`` parameter to load method (now must be boolean)

==============================

Bug fix release in the 3.2.x series.

Bug fixes
---------
* Reshape CIFTI-2 affines to 4x4 when encoded as row-major sequence (pr/1059)
(Andrew Van, reviewed by CM)
* Suggest nibabel.save() on calls to deprecated giftiio.write() (pr/1055)
(Anibal Solon, reviewed by CM)
* Various bugs and style issues detected by LGTM (pr/1043, pr/1048)
(Dimitri Papadopoulos, reviewed by CM)
* Resolve unclosed file warning in GiftiImage (pr/1038) (Lea Waller, reviewed by CM)
* Fix typos preventing deprecation warnings from being raised (pr/991)
(Jonathan Daniel, reviewed by MB)
* Work around numpy SystemError to maintain expected error types (pr/1051) (CM)
* Use more constrained mock when testing optpkg (pr/983) (CM, reviewed by YOH)

Maintenance
-----------
* Add setuptools requirement to match usage (pr/1009)
(Tomáš Hrnčiar, reviewed by CM)
* Fix grammar of headings in CoC (pr/996) (MB, reviewed by CM, Ariel Rokem)
* Set minimum pydicom to 1.0.0 (pr/1050) (CM)
* Submit coverage to codecov via pinned PyPI package (pr/1008) (CM)
* Upgrade versioneer to 0.19 (pr/967) (CM)
* Migrate to GitHub actions (pr/972) (CM, reviewed by Serge Koudoro)