Update nibabel to 4.0.2

[pyup-bot]

This PR updates nibabel from 3.0.1 to 4.0.2.

Changelog

4.0.2

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

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)

4.0.1

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

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)

4.0.0

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

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)

3.2.2

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

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)

3.2.1

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

Bug fix release in the 3.2.x series.

Maintenance
-----------
* Drop references to builtin types in Numpy namespace like ``np.float``
(pr/964) (EL, reviewed by CM)
* Ensure compatibility with Python 3.9 (pr/963) (CM)

3.2.0

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

New feature release in the 3.2.x series.

New features
------------
* ``nib-stats`` CLI tool to expose new ``nibabel.imagestats`` API. Initial
implementation of volume calculations, a la ``fslstats -V``. (Julian Klug,
reviewed by CM and GitHub user 0rC0)
* ``nib-roi`` CLI tool to crop images and/or flip axes (pr/947) (CM, reviewed
by Chris Cheng and Mathias Goncalves)
* Parser for Siemens "ASCCONV" text format (pr/896) (Brendan Moloney and MB,
reviewed by CM)

Enhancements
------------
* Drop confusing mention of ``img.to_filename()`` in getting started guide
(pr/946) (Fernando Pérez-Garcia, reviewed by MB, CM)
* Implement ``to_bytes()``/``from_bytes()`` methods for ``Cifti2Image``
(pr/938) (CM, reviewed by Mathias Goncalves)
* Clean up of DICOM documentation (pr/910) (Jonathan Daniel, reviewed by MB)

Bug fixes
---------
* Use canvas manager API to set title in ``OrthoSlicer3D`` (pr/958) (EL,
reviewed by CM)
* Record units as seconds parrec2nii; previously set TR to seconds but
retained msec units (pr/931) (CM, reviewed by MB)
* Reflect on-disk dimensions in NIfTI-2 view of CIFTI-2 images (pr/930)
(Mathias Goncalves and CM)
* Fix outdated Python 2 and Sympy code in DICOM derivations (pr/911) (MB,
reviewed by CM)
* Change string with invalid escape to raw string (pr/909) (EL, reviewed
by MB)

Maintenance
-----------
* Fix typo in docs (pr/955) (Carl Gauthier, reviewed by CM)
* Purge nose from nisext tests (pr/934) (Markéta Calábková, reviewed by CM)
* Suppress expected warnings in tests (pr/949) (CM, reviewed by Dorota
Jarecka)
* Various cleanups and modernizations (pr/916, pr/917, pr/918, pr/919)
(Jonathan Daniel, reviewed by CM)
* SVG logo for improved appearance in with zooming (pr/914) (Jonathan Daniel,
reviewed by CM)

API changes and deprecations
----------------------------
* Drop support for Numpy < 1.13 (pr/922) (CM)
* Warn on use of ``onetime.setattr_on_read``, which has been a deprecated
alias of ``auto_attr`` (pr/948) (CM, reviewed by Ariel Rokem)

3.1.1

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

Bug-fix release in the 3.1.x series.

These are small compatibility fixes that support ARM64 architecture and
``indexed_gzip>=1.3.0``.

Bug fixes
---------
* Detect ``IndexedGzipFile`` as compressed file type (pr/925) (PM, reviewed by
CM)
* Correctly cast ``nan`` when testing ``array_to_file``, fixing ARM64 builds
(pr/862) (CM, reviewed by MB)

3.1.0

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

New feature release in the 3.1.x series.

New features
------------
* 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)

Bug fixes
---------
* Delay import of h5py until needed (pr/889) (YOH, reviewed by CM)

Maintenance
-----------
* Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
* Tests converted from nose to pytest (pr/865 + many sub-PRs)
(Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon,
and Or Duek)

API changes and deprecations
----------------------------
* ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
(RM, reviewed by CM)

3.0.2

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

Bug fixes
---------
* Attempt to find versioneer version when building docs (pr/894) (CM)
* Delay import of h5py until needed (backport of pr/889) (YOH, reviewed by CM)

Maintenance
-----------
* Fix typo in documentation (backport of pr/893) (Zvi Baratz, reviewed by CM)
* Set minimum matplotlib to 1.5.3 to ensure wheels are available on all
supported Python versions. (backport of pr/887) (CM)
* Remove ``pyproject.toml`` for now. (issue/859) (CM)

Links

• PyPI: https://pypi.org/project/nibabel
• Changelog: https://pyup.io/changelogs/nibabel/
• Repo: https://github.com/nipy/nibabel
• Homepage: https://nipy.org/nibabel