Merge tag '5.3.2'

5.3.2 (Wednesday 23 October 2024)

Bug-fix release in the 5.3.x series.

Bug fixes
---------
* Restore MRS extension type to Nifti1Extension to maintain backwards compatibility.
  (pr/1380) (CM)

Author: effigies

Changelog

@@ -25,6 +25,29 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+5.3.2 (Wednesday 23 October 2024)
+=================================
+
+Bug-fix release in the 5.3.x series.
+
+Bug fixes
+---------
+* Restore MRS extension type to Nifti1Extension to maintain backwards compatibility.
+  (pr/1380) (CM)
+
+
+5.3.1 (Tuesday 15 October 2024)
+===============================
+
+Bug-fix release in the 5.3.x series.
+
+Bug fixes
+---------
+* Restore access to private attribute ``Nifti1Extension._content`` to unbreak subclasses
+  that did not use public accessor methods. (pr/1378) (CM, reviewed by Basile Pinsard)
+* Remove test order dependency in ``test_api_validators`` (pr/1377) (CM)
+
+
 5.3.0 (Tuesday 8 October 2024)
 ==============================
 
@@ -34,9 +57,9 @@ 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)
+* Update NIfTI extension protocol to include ``.content : bytes``, ``.text : str`` and
+  ``.json() : dict`` properties/methods for accessing extension contents.
+  Exceptions will be raised on ``.text`` and ``.json()`` if conversion fails. (pr/1336) (CM)
 
 Enhancements
 ------------

nibabel/nifti1.py

@@ -326,7 +326,7 @@ class NiftiExtension(ty.Generic[T]):
 
     code: int
     encoding: str | None = None
-    _content: bytes
+    _raw: bytes
     _object: T | None = None
 
     def __init__(
@@ -351,10 +351,14 @@ def __init__(
             self.code = extension_codes.code[code]  # type: ignore[assignment]
         except KeyError:
             self.code = code  # type: ignore[assignment]
-        self._content = content
+        self._raw = content
         if object is not None:
             self._object = object
 
+    @property
+    def _content(self):
+        return self.get_object()
+
     @classmethod
     def from_bytes(cls, content: bytes) -> Self:
         """Create an extension from raw bytes.
@@ -394,15 +398,15 @@ def _sync(self) -> None:
         and updates the bytes representation accordingly.
         """
         if self._object is not None:
-            self._content = self._mangle(self._object)
+            self._raw = self._mangle(self._object)
 
     def __repr__(self) -> str:
         try:
             code = extension_codes.label[self.code]
         except KeyError:
             # deal with unknown codes
             code = self.code
-        return f'{self.__class__.__name__}({code}, {self._content!r})'
+        return f'{self.__class__.__name__}({code}, {self._raw!r})'
 
     def __eq__(self, other: object) -> bool:
         return (
@@ -425,7 +429,7 @@ def get_code(self):
     def content(self) -> bytes:
         """Return the extension content as raw bytes."""
         self._sync()
-        return self._content
+        return self._raw
 
     @property
     def text(self) -> str:
@@ -452,7 +456,7 @@ def get_object(self) -> T:
         instead.
         """
         if self._object is None:
-            self._object = self._unmangle(self._content)
+            self._object = self._unmangle(self._raw)
         return self._object
 
     # Backwards compatibility
@@ -488,7 +492,7 @@ def write_to(self, fileobj: ty.BinaryIO, byteswap: bool = False) -> None:
             extinfo = extinfo.byteswap()
         fileobj.write(extinfo.tobytes())
         # followed by the actual extension content, synced above
-        fileobj.write(self._content)
+        fileobj.write(self._raw)
         # be nice and zero out remaining part of the extension till the
         # next 16 byte border
         pad = extstart + rawsize - fileobj.tell()
@@ -671,7 +675,7 @@ def _mangle(self, dataset: DicomDataset) -> bytes:
         (38, 'eval', NiftiExtension),
         (40, 'matlab', NiftiExtension),
         (42, 'quantiphyse', NiftiExtension),
-        (44, 'mrs', NiftiExtension[dict[str, ty.Any]]),
+        (44, 'mrs', Nifti1Extension),
     ),
     fields=('code', 'label', 'handler'),
 )

nibabel/tests/test_nifti1.py

@@ -1250,6 +1250,33 @@ def test_extension_content_access():
     assert json_ext.json() == {'a': 1}
 
 
+def test_legacy_underscore_content():
+    """Verify that subclasses that depended on access to ._content continue to work."""
+    import io
+    import json
+
+    class MyLegacyExtension(Nifti1Extension):
+        def _mangle(self, value):
+            return json.dumps(value).encode()
+
+        def _unmangle(self, value):
+            if isinstance(value, bytes):
+                value = value.decode()
+            return json.loads(value)
+
+    ext = MyLegacyExtension(0, '{}')
+
+    assert isinstance(ext._content, dict)
+    # Object identity is not broken by multiple accesses
+    assert ext._content is ext._content
+
+    ext._content['val'] = 1
+
+    fobj = io.BytesIO()
+    ext.write_to(fobj)
+    assert fobj.getvalue() == b'\x20\x00\x00\x00\x00\x00\x00\x00{"val": 1}' + bytes(14)
+
+
 def test_extension_codes():
     for k in extension_codes.keys():
         Nifti1Extension(k, 'somevalue')