REL: 5.2.0

.mailmap

@@ -1,79 +1,87 @@
 # Prevent git from showing duplicate names with commands like "git shortlog"
 # See the manpage of git-shortlog for details.
 # The syntax is:
-# Name that should be used <email that should be used> Bad name <bad email>
 #
-# You can skip Bad name if it is the same as the one that should be used, and is unique.
+# Good Name <good email> [[Bad Name] <bad email>]
+#
+# If multiple names are mapped to the good email, a line without any bad
+# emails will consolidate these names.
+# Likewise, any name mapped to a bad email will be converted to the good name.
+#
+# A contributor with three emails and inconsistent names could be mapped like this:
+#
+# Good Name <email1>
+# Good Name <email1> <email2>
+# Good Name <email1> <email3>
+#
+# If a contributor uses an email that is not unique to them, you will need their
+# name.
+#
+# Good Name <good email>
+# Good Name <good email> Good Name <ambiguous email>
 #
 # This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
 # gives no duplicates.
-Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]>
+Alexandre Gramfort <[email protected]> <[email protected]>
 Anibal Sólon <[email protected]>
-Ariel Rokem <[email protected]> arokem <[email protected]>
-B. Nolan Nichols <[email protected]> Nolan Nichols <[email protected]>
-Basile Pinsard <[email protected]> bpinsard <[email protected]>
-Basile Pinsard <[email protected]> bpinsard <[email protected]>
-Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
+Ariel Rokem <[email protected]>
+B. Nolan Nichols <[email protected]>
+Basile Pinsard <[email protected]>
+Basile Pinsard <[email protected]> <[email protected]>
+Ben Cipollini <[email protected]> <[email protected]>
 Benjamin C Darwin <[email protected]>
-Bertrand Thirion <[email protected]> bthirion <[email protected]>
+Bertrand Thirion <[email protected]>
 Cameron Riddell <[email protected]> <[email protected]>
-Christian Haselgrove <[email protected]> Christian Haselgrove <[email protected]>
-Christopher J. Markiewicz <[email protected]> Chris Johnson <[email protected]>
-Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
-Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
-Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
-Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
-Cindee Madison <[email protected]> CindeeM <[email protected]>
-Cindee Madison <[email protected]> cindeem <[email protected]>
-Demian Wassermann <[email protected]> Demian Wassermann <[email protected]>
+Christian Haselgrove <[email protected]> <[email protected]>
+Christopher J. Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Cindee Madison <[email protected]>
+Demian Wassermann <[email protected]> <[email protected]>
 Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
 Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
-Eric Larson <[email protected]> Eric89GXL <[email protected]>
-Eric Larson <[email protected]> larsoner <[email protected]>
+Eric Larson <[email protected]>
 Fabian Perez <[email protected]>
-Fernando Pérez-García <[email protected]> Fernando <[email protected]>
-Félix C. Morency <[email protected]> Felix C. Morency <[email protected]>
-Félix C. Morency <[email protected]> Félix C. Morency <[email protected]>
-Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
-Gregory R. Lee <[email protected]> Gregory R. Lee <[email protected]>
-Ian Nimmo-Smith <[email protected]> Ian Nimmo-Smith <[email protected]>
-Jaakko Leppäkangas <[email protected]> jaeilepp <[email protected]>
-Jacob Roberts <[email protected]>
+Fernando Pérez-García <[email protected]>
+Félix C. Morency <[email protected]> <[email protected]>
+Gael Varoquaux <[email protected]>
+Gregory R. Lee <[email protected]> <[email protected]>
+Ian Nimmo-Smith <[email protected]> <[email protected]>
+Jaakko Leppäkangas <[email protected]>
 Jacob Roberts <[email protected]> <[email protected]>
-Jakub Kaczmarzyk <[email protected]>
 Jakub Kaczmarzyk <[email protected]> <[email protected]>
-Jasper J.F. van den Bosch <[email protected]> Jasper <[email protected]>
-Jean-Baptiste Poline <[email protected]> jbpoline <[email protected]>
+Jasper J.F. van den Bosch <[email protected]>
+Jean-Baptiste Poline <[email protected]>
 Jérôme Dockès <[email protected]>
-Jon Haitz Legarreta <[email protected]> Jon Haitz Legarreta Gorroño <[email protected]>
-Jonathan Daniel <[email protected]>
+Jon Haitz Legarreta <[email protected]>
 Jonathan Daniel <[email protected]> <[email protected]>
-Kesshi Jordan <[email protected]> kesshijordan <[email protected]>
-Kevin S. Hahn <[email protected]> Kevin S. Hahn <[email protected]>
-Konstantinos Raktivan <[email protected]> constracti <[email protected]>
-Krish Subramaniam <[email protected]> Krish Subramaniam <[email protected]>
+Kesshi Jordan <[email protected]>
+Kevin S. Hahn <[email protected]> <[email protected]>
+Konstantinos Raktivan <[email protected]>
+Krish Subramaniam <[email protected]> <[email protected]>
 Krzysztof J. Gorgolewski <[email protected]>
 Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
-Marc-Alexandre Côté <[email protected]> Marc-Alexandre Cote <[email protected]>
+Marc-Alexandre Côté <[email protected]>
 Mathias Goncalves <[email protected]>
 Mathias Goncalves <[email protected]> <[email protected]>
-Matthew Cieslak <[email protected]> Matt Cieslak <[email protected]>
+Mathieu Scheltienne <[email protected]> <[email protected]>
+Matthew Cieslak <[email protected]>
 Michael Hanke <[email protected]> <mhanke-guest@82381867-18eb-0310-98a2-9474e637aba2>
 Michael Hanke <[email protected]> <[email protected]>
-Michiel Cottaar <[email protected]>
 Michiel Cottaar <[email protected]> <[email protected]>
 Michiel Cottaar <[email protected]> <[email protected]>
-Ly Nguyen <[email protected]> lxn2 <[email protected]>
-Oliver P. Hinds <[email protected]> ohinds <[email protected]>
+Ly Nguyen <[email protected]> <[email protected]>
+Oliver P. Hinds <[email protected]>
 Or Duek <[email protected]>
 Oscar Esteban <[email protected]>
-Paul McCarthy <[email protected]> Paul McCarthy <[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]>
-Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
-Serge Koudoro <[email protected]> skoudoro <[email protected]>
+Satrajit Ghosh <[email protected]> <[email protected]>
+Serge Koudoro <[email protected]>
 Stephan Gerhard <[email protected]> Stephan Gerhard <[email protected]>
-Thomas Roos <[email protected]> Roosted7 <[email protected]>
-Venkateswara Reddy Reddam <[email protected]> R3DDY97 <[email protected]>
+Thomas Roos <[email protected]>
+Venkateswara Reddy Reddam <[email protected]>
+Yaroslav O. Halchenko <[email protected]>
 Yaroslav O. Halchenko <[email protected]> <yoh-guest@82381867-18eb-0310-98a2-9474e637aba2>
-Yaroslav O. Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>

.zenodo.json

@@ -38,6 +38,11 @@
       "name": "Cheng, Christopher P.",
       "orcid": "0000-0001-9112-9464"
     },
+    {
+      "affiliation": "University of Washington: Seattle, WA, United States",
+      "name": "Larson, Eric",
+      "orcid": "0000-0003-4782-5360"
+    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
@@ -48,11 +53,6 @@
       "name": "Cottaar, Michiel",
       "orcid": "0000-0003-4679-7724"
     },
-    {
-      "affiliation": "University of Washington: Seattle, WA, United States",
-      "name": "Larson, Eric",
-      "orcid": "0000-0003-4782-5360"
-    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
@@ -81,6 +81,11 @@
       "name": "Wang, Hao-Ting",
       "orcid": "0000-0003-4078-2038"
     },
+    {
+      "affiliation": "CEA",
+      "name": "Papadopoulos Orfanos, Dimitri",
+      "orcid": "0000-0002-1242-8990"
+    },
     {
       "affiliation": "Harvard University - Psychology",
       "name": "Kastman, Erik",
@@ -108,12 +113,12 @@
       "orcid": "0000-0003-0679-1985"
     },
     {
-      "name": "Madison, Cindee"
+      "affiliation": "Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland",
+      "name": "Mathieu Scheltienne",
+      "orcid": "0000-0001-8316-7436"
     },
     {
-      "affiliation": "CEA",
-      "name": "Papadopoulos Orfanos, Dimitri",
-      "orcid": "0000-0002-1242-8990"
+      "name": "Madison, Cindee"
     },
     {
       "name": "S\u00f3lon, Anibal"
@@ -187,6 +192,9 @@
       "name": "Klug, Julian",
       "orcid": "0000-0002-4849-9811"
     },
+    {
+      "name": "Vos de Wael, Reinder"
+    },
     {
       "affiliation": "SRI International",
       "name": "Nichols, B. Nolan",
@@ -238,6 +246,9 @@
     {
       "name": "Nguyen, Ly"
     },
+    {
+      "name": "Suter, Peter"
+    },
     {
       "affiliation": "BrainSpec, Boston, MA",
       "name": "Reddigari, Samir",
@@ -277,6 +288,9 @@
     {
       "name": "Fauber, Bennet"
     },
+    {
+      "name": "Dewey, Blake"
+    },
     {
       "name": "Perez, Fabian"
     },
@@ -377,15 +391,7 @@
     },
     {
       "name": "freec84"
-    },
-    {
-      "name": "Suter, Peter"
     }
-    {
-      "affiliation": "Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland",
-      "name": "Mathieu Scheltienne",
-      "orcid": "0000-0001-8316-7436"
-    },
   ],
   "keywords": [
     "neuroimaging"

Changelog

@@ -25,6 +25,79 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+5.2.0 (Monday 11 December 2023)
+===============================
+
+New feature release in the 5.2.x series.
+
+This release requires a minimum Python of 3.8 and NumPy 1.20, and has been
+tested up to Python 3.12 and NumPy 1.26.
+
+New features
+------------
+* Add generic :class:`~nibabel.pointset.Pointset` and regularly spaced
+  :class:`~nibabel.pointset.NDGrid` data structures in preparation for coordinate
+  transformation and resampling (pr/1251) (CM, reviewed by Oscar Esteban)
+
+Enhancements
+------------
+* Add :meth:`~nibabel.arrayproxy.ArrayProxy.copy` method to
+  :class:`~nibabel.arrayproxy.ArrayProxy` (pr/1255) (CM, reviewed by Paul McCarthy)
+* Permit :meth:`~nibabel.xmlutils.XmlSerializable.to_xml` to pass keyword
+  arguments to :meth:`~xml.etree.ElementTree.ElementTree.tostring` (pr/1258)
+  (CM)
+* Allow user expansion (e.g., ``~/...``) in strings passed to functions that
+  accept paths (pr/1260) (Reinder Vos de Wael, reviewed by CM)
+* Expand CIFTI-2 brain structures to permit synonyms (pr/1256) (CM, reviewed
+  by Mathias Goncalves)
+* Annotate :class:`~nibabel.spatialimages.SpatialImage` as accepting
+  ``affine=None`` argument (pr/1253) (Blake Dewey, reviewed by CM)
+* Warn on invalid MINC2 spacing declarations, treat as missing (pr/1237)
+  (Peter Suter, reviewed by CM)
+* Refactor :func:`~nibabel.nicom.utils.find_private_element` for improved
+  readability and maintainability (pr/1228) (MB, reviewed by CM)
+
+Bug fixes
+---------
+* Resolve test failure related to randomly generated invalid case (pr/1221) (CM)
+
+Documentation
+-------------
+* Remove references to NiPy data packages from documentation (pr/1275)
+  (Dimitri Papadopoulos, reviewed by CM, MB)
+
+Maintenance
+-----------
+* Quality of life improvements for CI, including color output and OIDC publishing
+  (pr/1282) (CM)
+* Patch for NumPy 2.0 pre-release compatibility (pr/1250) (Mathieu
+  Scheltienne and EL, reviewed by CM)
+* Add spellchecking to tox, CI and pre-commit (pr/1266) (CM)
+* Add py312-dev-x64 environment to Tox to test NumPy 2.0 pre-release
+  compatibility (pr/1267) (CM, reviewed by EL)
+* Resurrect tox configuration to cover development workflows and CI checks
+  (pr/1262) (CM)
+* Updates for Python 3.12 support (pr/1247, pr/1261, pr/1273) (CM)
+* Remove uses of deprecated ``numpy.compat.py3k`` module (pr/1243) (Eric
+  Larson, reviewed by CM)
+* Various fixes for typos and style issues detected by Codespell, pyupgrade and
+  refurb (pr/1263, pr/1269, pr/1270, pr/1271, pr/1276) (Dimitri Papadopoulos,
+  reviewed by CM)
+* Use stable argsorts in PARREC tests to ensure consistent behavior on systems
+  with AVX512 SIMD instructions and numpy 1.25 (pr/1234) (CM)
+* Resolve CodeCov submission failures (pr/1224) (CM)
+* Link to logo with full URL to avoid broken links in PyPI (pr/1218) (CM,
+  reviewed by Zvi Baratz)
+
+API changes and deprecations
+----------------------------
+* The :mod:`nibabel.pydicom_compat` module is deprecated and will be removed
+  in NiBabel 7.0. (pr/1280)
+* The :func:`~nibabel.casting.int_to_float` and :func:`~nibabel.casting.as_int`
+  functions are no longer needed to work around NumPy deficiencies and have been
+  deprecated (pr/1272) (CM, reviewed by EL)
+
+
 5.1.0 (Monday 3 April 2023)
 ===========================
 

README.rst

@@ -123,6 +123,27 @@ For more information on previous releases, see the `release archive`_ or
 .. _release archive: https://github.com/nipy/NiBabel/releases
 .. _development changelog: https://nipy.org/nibabel/changelog.html
 
+Testing
+=======
+
+During development, we recommend using tox_ to run nibabel tests::
+
+    git clone https://github.com/nipy/nibabel.git
+    cd nibabel
+    tox
+
+To test an installed version of nibabel, install the test dependencies
+and run pytest_::
+
+    pip install nibabel[test]
+    pytest --pyargs nibabel
+
+For more information, consult the `developer guidelines`_.
+
+.. _tox: https://tox.wiki
+.. _pytest: https://docs.pytest.org
+.. _developer guidelines: https://nipy.org/nibabel/devel/devguide.html
+
 Mailing List
 ============
 

doc-requirements.txt

@@ -1,7 +1,7 @@
 # Auto-generated by tools/update_requirements.py
 -r requirements.txt
-matplotlib >= 1.5.3
+sphinx
+matplotlib>=1.5.3
 numpydoc
-sphinx ~= 5.3
 texext
-tomli; python_version < "3.11"
+tomli; python_version < '3.11'

doc/source/index.rst

@@ -55,6 +55,7 @@ contributed code and discussion (in rough order of appearance):
 * JB Poline
 * Basile Pinsard
 * `Satrajit Ghosh`_
+* Eric Larson
 * `Nolan Nichols`_
 * Ly Nguyen
 * Philippe Gervais
@@ -126,6 +127,9 @@ contributed code and discussion (in rough order of appearance):
 * Horea Christian
 * Fabian Perez
 * Mathieu Scheltienne
+* Reinder Vos de Wael
+* Peter Suter
+* Blake Dewey
 
 License reprise
 ===============

nibabel/openers.py

@@ -78,12 +78,6 @@ def __init__(
             mtime=mtime,
         )
 
-    def seek(self, pos: int, whence: int = 0, /) -> int:
-        # Work around bug (gh-180111) in Python 3.12rc1, where seeking without
-        # flushing can cause write of excess null bytes
-        self.flush()
-        return super().seek(pos, whence)
-
 
 def _gzip_open(
     filename: str,