Merge tag '5.3.0'

5.3.0 (Tuesday 8 October 2024)

This release primarily adds support for Python 3.13 and Numpy 2.0.

NiBabel 6.0 will drop support for Numpy 1.x.

New features
------------
* Update NIfTI extension protocol to include ``.content : bytes``, ``.text : str`` and ``.json : dict``
  properties for accessing extension contents. Exceptions will be raised on ``.text`` and ``.json`` if
  conversion fails. (pr/1336) (CM)

Enhancements
------------
* Ability to read data from many multiframe DICOM files that previously generated errors (pr/1340)
  (Brendan Moloney, reviewed by CM)
* ``nib-nifti-dx`` now supports NIfTI-2 files with a ``--nifti2`` flag (pr/1323) (CM)
* Update :mod:`nibabel.streamlines.tractogram` to support ragged arrays. (pr/1291)
  (Serge Koudoro, reviewed by CM)
* Filter numpy ``UserWarning`` on ``np.finfo(np.longdouble)``. This can occur on
  Windows systems, but it's done in the context of checking for the problem that
  is being warned against, so there's no need to be noisy. (pr/1310)
  (Joshua Newton, reviewed by CM)
* Improve error message for for dicomwrapper errors in shape calculation (pr/1302)
  (YOH, reviewed by CM)
* Support "flat" ASCII-encoded GIFTI DataArrays (pr/1298) (PM, reviewed by CM)

Bug fixes
---------
* Fix location initialization/update in OrthoSlicer3D for permuted axes (pr/1319, pr/1350)
  (Guillaume Becq, reviewed by CM)
* Fix DICOM scaling, making frame filtering explicit (pr/1342) (Brendan Moloney, reviewed by CM)
* Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the
  affine (pr/1340) (Brendan Moloney, reviewed by CM)
* Fixed multiframe DICOM issue where ``image_position`` and the translation component in the
  ``affine`` could be incorrect (pr/1340) (Brendan Moloney, reviewed by CM)

Maintenance
-----------
* Numpy 2.0 compatibility and addressing deprecations in numpy API
  (pr/1304, pr/1330, pr/1331, pr/1334, pr/1337) (Jon Haitz Legarreta Gorroño, CM)
* Python 3.13 compatibility (pr/1315) (Sandro from the Fedora Project, reviewed by CM)
* Testing on Python 3.13 with free-threading (pr/1339) (CM)
* Testing on ARM64 Mac OS runners (pr/1320) (CM)
* Proactively address deprecations in coming Python versions (pr/1329, pr/1332, pr/1333)
  (Jon Haitz Legarreta Gorroño, reviewed by CM)
* Replace nose-era ``setup()`` and ``teardown()`` functions with pytest equivalents
  (pr/1325) (Sandro from the Fedora Project, reviewed by Étienne Mollier and CM)
* Transitioned from blue/isort/flake8 to `ruff <https://docs.astral.sh/ruff/>`__. (pr/1289)
  (Dimitri Papadopoulos, reviewed by CM)
* Vetted and added various rules to the ruff configuration for auto-formatting and style
  guide enforcement. (pr/1321, pr/1351, pr/1352, pr/1353, pr/1354, pr/1355, pr/1357, pr/1358,
  pr/1359, pr/1360, pr/1361, pr/1362, pr/1363, pr/1364, pr/1368, pr/1369)
  (Dimitri Papadopoulos, reviewed by CM)
* Fixing typos when found. (pr/1313, pr/1370) (MB, Dimitri Papadopoulos)
* Applied Repo-Review suggestions (Dimitri Papadopoulos, reviewed by CM)

API changes and deprecations
----------------------------
* Raise :class:`~nibabel.spatialimages.HeaderDataError` from
  :func:`~nibabel.nifti1.Nifti1Header.set_qform` if the affine fails to decompose.
  This would previously result in :class:`numpy.linalg.LinAlgError`. (pr/1227) (CM)
* The :func:`nibabel.onetime.auto_attr` module can be replaced by :func:`functools.cached_property`
  in all supported versions of Python. This alias may be removed in future versions. (pr/1341) (CM)
* Removed the deprecated ``nisext`` (setuptools extensions) package. (pr/1290) (CM, reviewed by MB)

* tag '5.3.0':
  MNT: Update release notes translator
  STY: ruff check --fix
  MNT: Remove workarounds used for Python 3.8 support
  MNT: Update support matrix for Python and numpy
  DOC: Remove end year from copyright
  DOC: Update mailmap and contributor list
  DOC: Update Zenodo contributors
  DOC: Update changelog

.github/workflows/test.yml

@@ -113,17 +113,17 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         architecture: ['x64', 'x86', 'arm64']
         dependencies: ['full', 'pre']
         include:
           # Basic dependencies only
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: 3.9
             dependencies: 'none'
           # Absolute minimum dependencies
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: 3.9
             dependencies: 'min'
           # NoGIL
           - os: ubuntu-latest
@@ -153,10 +153,10 @@ jobs:
           - os: macos-13
             dependencies: pre
           # Drop pre tests for SPEC-0-unsupported Python versions
-          - python-version: '3.8'
-            dependencies: pre
           - python-version: '3.9'
             dependencies: pre
+          - python-version: '3.10'
+            dependencies: pre
 
     env:
       DEPENDS: ${{ matrix.dependencies }}

.mailmap

@@ -75,6 +75,7 @@ Oliver P. Hinds <[email protected]>
 Or Duek <[email protected]>
 Oscar Esteban <[email protected]>
 Paul McCarthy <[email protected]> <[email protected]>
+Paul McCarthy <[email protected]> <[email protected]>
 Reinder Vos de Wael <[email protected]> <[email protected]>
 Roberto Guidotti <[email protected]>
 Roberto Guidotti <[email protected]> <[email protected]>

.zenodo.json

@@ -25,6 +25,11 @@
       "name": "Cipollini, Ben",
       "orcid": "0000-0002-7782-0790"
     },
+    {
+      "affiliation": "CEA",
+      "name": "Papadopoulos Orfanos, Dimitri",
+      "orcid": "0000-0002-1242-8990"
+    },
     {
       "name": "McCarthy, Paul"
     },
@@ -78,13 +83,11 @@
       "orcid": "0000-0001-7159-1387"
     },
     {
-      "name": "Wang, Hao-Ting",
-      "orcid": "0000-0003-4078-2038"
+      "name": "Moloney, Brendan"
     },
     {
-      "affiliation": "CEA",
-      "name": "Papadopoulos Orfanos, Dimitri",
-      "orcid": "0000-0002-1242-8990"
+      "name": "Wang, Hao-Ting",
+      "orcid": "0000-0003-4078-2038"
     },
     {
       "affiliation": "Harvard University - Psychology",
@@ -123,9 +126,6 @@
     {
       "name": "S\u00f3lon, Anibal"
     },
-    {
-      "name": "Moloney, Brendan"
-    },
     {
       "name": "Morency, F\u00e9lix C."
     },
@@ -177,6 +177,11 @@
     {
       "name": "Van, Andrew"
     },
+    {
+      "affiliation": "Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School",
+      "name": "Legarreta, Jon Haitz",
+      "orcid": "0000-0002-9661-1396"
+    },
     {
       "affiliation": "Google",
       "name": "Gorgolewski, Krzysztof J.",
@@ -203,6 +208,9 @@
     {
       "name": "Baker, Eric M."
     },
+    {
+      "name": "Koudoro, Serge"
+    },
     {
       "name": "Hayashi, Soichi"
     },
@@ -220,14 +228,14 @@
       "name": "Esteban, Oscar",
       "orcid": "0000-0001-8435-6191"
     },
-    {
-      "name": "Koudoro, Serge"
-    },
     {
       "affiliation": "University College London",
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
       "orcid": "0000-0001-9090-3024"
     },
+    {
+      "name": "Becq, Guillaume"
+    },
     {
       "name": "Dock\u00e8s, J\u00e9r\u00f4me"
     },
@@ -270,9 +278,9 @@
       "orcid": "0000-0003-1076-5122"
     },
     {
-      "affiliation": "Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School",
-      "name": "Legarreta, Jon Haitz",
-      "orcid": "0000-0002-9661-1396"
+      "affiliation": "Polytechnique Montr\u00e9al, Montr\u00e9al, CA",
+      "name": "Newton, Joshua",
+      "orcid": "0009-0005-6963-3812"
     },
     {
       "name": "Hahn, Kevin S."
@@ -285,6 +293,9 @@
     {
       "name": "Hinds, Oliver P."
     },
+    {
+      "name": "Sandro"
+    },
     {
       "name": "Fauber, Bennet"
     },
@@ -391,11 +402,6 @@
     },
     {
       "name": "freec84"
-    },
-    {
-      "affiliation": "Polytechnique Montréal, Montréal, CA",
-      "name": "Newton, Joshua",
-      "orcid": "0009-0005-6963-3812"
     }
   ],
   "keywords": [

Changelog

@@ -25,31 +25,72 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
-Upcoming release (To be determined)
-===================================
+5.3.0 (Tuesday 8 October 2024)
+==============================
+
+This release primarily adds support for Python 3.13 and Numpy 2.0.
+
+NiBabel 6.0 will drop support for Numpy 1.x.
 
 New features
 ------------
+* Update NIfTI extension protocol to include ``.content : bytes``, ``.text : str`` and ``.json : dict``
+  properties for accessing extension contents. Exceptions will be raised on ``.text`` and ``.json`` if
+  conversion fails. (pr/1336) (CM)
 
 Enhancements
 ------------
- * Ability to read data from many multiframe DICOM files that previously generated errors
+* Ability to read data from many multiframe DICOM files that previously generated errors (pr/1340)
+  (Brendan Moloney, reviewed by CM)
+* ``nib-nifti-dx`` now supports NIfTI-2 files with a ``--nifti2`` flag (pr/1323) (CM)
+* Update :mod:`nibabel.streamlines.tractogram` to support ragged arrays. (pr/1291)
+  (Serge Koudoro, reviewed by CM)
+* Filter numpy ``UserWarning`` on ``np.finfo(np.longdouble)``. This can occur on
+  Windows systems, but it's done in the context of checking for the problem that
+  is being warned against, so there's no need to be noisy. (pr/1310)
+  (Joshua Newton, reviewed by CM)
+* Improve error message for for dicomwrapper errors in shape calculation (pr/1302)
+  (YOH, reviewed by CM)
+* Support "flat" ASCII-encoded GIFTI DataArrays (pr/1298) (PM, reviewed by CM)
 
 Bug fixes
 ---------
- * Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the
-   affine
- * Fixed multiframe DICOM issue where ``image_position`` and the translation component in the
-   ``affine`` could be incorrect
-
-Documentation
--------------
+* Fix location initialization/update in OrthoSlicer3D for permuted axes (pr/1319, pr/1350)
+  (Guillaume Becq, reviewed by CM)
+* Fix DICOM scaling, making frame filtering explicit (pr/1342) (Brendan Moloney, reviewed by CM)
+* Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the
+  affine (pr/1340) (Brendan Moloney, reviewed by CM)
+* Fixed multiframe DICOM issue where ``image_position`` and the translation component in the
+  ``affine`` could be incorrect (pr/1340) (Brendan Moloney, reviewed by CM)
 
 Maintenance
 -----------
+* Numpy 2.0 compatibility and addressing deprecations in numpy API
+  (pr/1304, pr/1330, pr/1331, pr/1334, pr/1337) (Jon Haitz Legarreta Gorroño, CM)
+* Python 3.13 compatibility (pr/1315) (Sandro from the Fedora Project, reviewed by CM)
+* Testing on Python 3.13 with free-threading (pr/1339) (CM)
+* Testing on ARM64 Mac OS runners (pr/1320) (CM)
+* Proactively address deprecations in coming Python versions (pr/1329, pr/1332, pr/1333)
+  (Jon Haitz Legarreta Gorroño, reviewed by CM)
+* Replace nose-era ``setup()`` and ``teardown()`` functions with pytest equivalents
+  (pr/1325) (Sandro from the Fedora Project, reviewed by Étienne Mollier and CM)
+* Transitioned from blue/isort/flake8 to `ruff <https://docs.astral.sh/ruff/>`__. (pr/1289)
+  (Dimitri Papadopoulos, reviewed by CM)
+* Vetted and added various rules to the ruff configuration for auto-formatting and style
+  guide enforcement. (pr/1321, pr/1351, pr/1352, pr/1353, pr/1354, pr/1355, pr/1357, pr/1358,
+  pr/1359, pr/1360, pr/1361, pr/1362, pr/1363, pr/1364, pr/1368, pr/1369)
+  (Dimitri Papadopoulos, reviewed by CM)
+* Fixing typos when found. (pr/1313, pr/1370) (MB, Dimitri Papadopoulos)
+* Applied Repo-Review suggestions (Dimitri Papadopoulos, reviewed by CM)
 
 API changes and deprecations
 ----------------------------
+* Raise :class:`~nibabel.spatialimages.HeaderDataError` from
+  :func:`~nibabel.nifti1.Nifti1Header.set_qform` if the affine fails to decompose.
+  This would previously result in :class:`numpy.linalg.LinAlgError`. (pr/1227) (CM)
+* The :func:`nibabel.onetime.auto_attr` module can be replaced by :func:`functools.cached_property`
+  in all supported versions of Python. This alias may be removed in future versions. (pr/1341) (CM)
+* Removed the deprecated ``nisext`` (setuptools extensions) package. (pr/1290) (CM, reviewed by MB)
 
 
 5.2.1 (Monday 26 February 2024)

doc/source/conf.py

@@ -102,7 +102,7 @@
 
 # General information about the project.
 project = 'NiBabel'
-copyright = f"2006-2023, {authors['name']} <{authors['email']}>"
+copyright = f"2006, {authors['name']} <{authors['email']}>"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/index.rst

@@ -130,6 +130,9 @@ contributed code and discussion (in rough order of appearance):
 * Reinder Vos de Wael
 * Peter Suter
 * Blake Dewey
+* Guillaume Becq
+* Joshua Newton
+* Sandro from the Fedora Project
 
 License reprise
 ===============

doc/source/installation.rst

@@ -81,16 +81,16 @@ is for you.
 Requirements
 ------------
 
-.. check these against pyproject.toml
-
-*  Python_ 3.8 or greater
-*  NumPy_ 1.20 or greater
-*  Packaging_ 17.0 or greater
-*  importlib-resources_ 1.3 or greater (or Python 3.9+)
-*  SciPy_ (optional, for full SPM-ANALYZE support)
-*  h5py_ (optional, for MINC2 support)
-*  PyDICOM_ 1.0.0 or greater (optional, for DICOM support)
-*  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
+.. check these against pyproject.toml / tox.ini
+
+*  Python_ 3.9 or greater
+*  NumPy_ 1.22 or greater
+*  Packaging_ 20.0 or greater
+*  importlib-resources_ 5.12 or greater (or Python 3.12+)
+*  SciPy_ 1.8 or greater (optional, for full SPM-ANALYZE support)
+*  h5py_ 3.5 or greater (optional, for MINC2 support)
+*  PyDICOM_ 2.3.0 or greater (optional, for DICOM support)
+*  `Python Imaging Library`_ 8.4 or greater (optional, for PNG conversion in DICOMFS)
 *  pytest_ (optional, to run the tests)
 *  sphinx_ (optional, to build the documentation)
 

nibabel/__init__.py

@@ -170,10 +170,7 @@ def bench(label=None, verbose=1, extra_argv=None):
     code : ExitCode
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
-    try:
-        from importlib.resources import as_file, files
-    except ImportError:
-        from importlib_resources import as_file, files
+    from importlib.resources import as_file, files
 
     args = []
     if extra_argv is not None:

nibabel/conftest.py

@@ -10,10 +10,7 @@
 
 @pytest.fixture(scope='session', autouse=True)
 def legacy_printoptions():
-    from packaging.version import Version
-
-    if Version(np.__version__) >= Version('1.22'):
-        np.set_printoptions(legacy='1.21')
+    np.set_printoptions(legacy='1.21')
 
 
 @pytest.fixture
@@ -24,7 +21,7 @@ def max_digits():
         orig_max_str_digits = sys.get_int_max_str_digits()
         yield sys.set_int_max_str_digits
         sys.set_int_max_str_digits(orig_max_str_digits)
-    except AttributeError:  # pragma: no cover
+    except AttributeError:  # PY310 # pragma: no cover
         # Nothing to do for versions of Python that lack these methods
         # They were added as DoS protection in Python 3.11 and backported to
         # some other versions.

nibabel/filebasedimages.py

@@ -23,7 +23,7 @@
 if ty.TYPE_CHECKING:
     from .filename_parser import ExtensionSpec, FileSpec
 
-FileSniff = ty.Tuple[bytes, str]
+FileSniff = tuple[bytes, str]
 
 ImgT = ty.TypeVar('ImgT', bound='FileBasedImage')
 HdrT = ty.TypeVar('HdrT', bound='FileBasedHeader')

nibabel/nicom/ascconv.py

@@ -90,10 +90,7 @@ def assign2atoms(assign_ast, default_class=int):
             target = target.value
             prev_target_type = OrderedDict
         elif isinstance(target, ast.Subscript):
-            if isinstance(target.slice, ast.Constant):  # PY39
-                index = target.slice.value
-            else:  # PY38
-                index = target.slice.value.n
+            index = target.slice.value
             atoms.append(Atom(target, prev_target_type, index))
             target = target.value
             prev_target_type = list

nibabel/nifti1.py

@@ -671,7 +671,7 @@ def _mangle(self, dataset: DicomDataset) -> bytes:
         (38, 'eval', NiftiExtension),
         (40, 'matlab', NiftiExtension),
         (42, 'quantiphyse', NiftiExtension),
-        (44, 'mrs', NiftiExtension[ty.Dict[str, ty.Any]]),
+        (44, 'mrs', NiftiExtension[dict[str, ty.Any]]),
     ),
     fields=('code', 'label', 'handler'),
 )

nibabel/spatialimages.py

@@ -133,6 +133,7 @@
 from __future__ import annotations
 
 import typing as ty
+from functools import cache
 from typing import Literal
 
 import numpy as np
@@ -145,11 +146,6 @@
 from .viewers import OrthoSlicer3D
 from .volumeutils import shape_zoom_affine
 
-try:
-    from functools import cache
-except ImportError:  # PY38
-    from functools import lru_cache as cache
-
 if ty.TYPE_CHECKING:
     import io
     from collections.abc import Sequence

nibabel/testing/__init__.py

@@ -17,6 +17,7 @@
 import unittest
 import warnings
 from contextlib import nullcontext
+from importlib.resources import as_file, files
 from itertools import zip_longest
 
 import numpy as np
@@ -29,11 +30,6 @@
 if ty.TYPE_CHECKING:
     from importlib.resources.abc import Traversable
 
-try:
-    from importlib.resources import as_file, files
-except ImportError:  # PY38
-    from importlib_resources import as_file, files
-
 
 def get_test_data(
     subdir: ty.Literal['gifti', 'nicom', 'externals'] | None = None,