chore: pre-commit autoupdate, address fresh typecheck errors

.pre-commit-config.yaml

@@ -13,15 +13,15 @@ repos:
       - id: check-merge-conflict
       - id: check-vcs-permalinks
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.1
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [ --fix ]
         exclude: = ["doc", "tools"]
       - id: ruff-format
         exclude: = ["doc", "tools"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.15.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing
@@ -36,7 +36,7 @@ repos:
         args: ["nibabel"]
         pass_filenames: false
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:

.readthedocs.yaml

@@ -9,14 +9,13 @@ build:
       - asdf plugin add uv
       - asdf install uv latest
       - asdf global uv latest
-      # Turn `python -m virtualenv` into `python -c pass`
-      - truncate --size 0 $( dirname $( uv python find ) )/../lib/python3*/site-packages/virtualenv/__main__.py
-    post_create_environment:
+    create_environment:
       - uv venv $READTHEDOCS_VIRTUALENV_PATH
-      # Turn `python -m pip` into `python -c pass`
-      - truncate --size 0 $( ls -d $READTHEDOCS_VIRTUALENV_PATH/lib/python3* )/site-packages/pip.py
-    post_install:
+    install:
       # Use a cache dir in the same mount to halve the install time
       - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache .[doc]
     pre_build:
       - ( cd doc; python tools/build_modref_templates.py nibabel source/reference False )
+
+sphinx:
+  configuration: doc/source/conf.py

nibabel/deprecated.py

@@ -9,7 +9,11 @@
 from .pkg_info import cmp_pkg_version
 
 if ty.TYPE_CHECKING:
+    # PY39: ParamSpec is available in Python 3.10+
     P = ty.ParamSpec('P')
+else:
+    # Just to keep the runtime happy
+    P = ty.TypeVar('P')
 
 
 class ModuleProxy:
@@ -44,7 +48,7 @@ def __repr__(self) -> str:
         return f'<module proxy for {self._module_name}>'
 
 
-class FutureWarningMixin:
+class FutureWarningMixin(ty.Generic[P]):
     """Insert FutureWarning for object creation
 
     Examples

nibabel/nifti1.py

@@ -843,7 +843,7 @@ class Nifti1Header(SpmAnalyzeHeader):
     single_magic = b'n+1'
 
     # Quaternion threshold near 0, based on float32 precision
-    quaternion_threshold = np.finfo(np.float32).eps * 3
+    quaternion_threshold: np.floating = np.finfo(np.float32).eps * 3
 
     def __init__(self, binaryblock=None, endianness=None, check=True, extensions=()):
         """Initialize header from binary data block and extensions"""

nibabel/tests/test_proxy_api.py

@@ -166,6 +166,10 @@ def validate_array_interface_with_dtype(self, pmaker, params):
                 assert_dt_equal(out.dtype, np.dtype(dtype))
                 # Shape matches expected shape
                 assert out.shape == params['shape']
+                del out
+            del direct
+
+        del orig
 
         if context is not None:
             context.__exit__()

nibabel/volumeutils.py

@@ -35,8 +35,8 @@
     DT = ty.TypeVar('DT', bound=np.generic)
 
 sys_is_le = sys.byteorder == 'little'
-native_code = '<' if sys_is_le else '>'
-swapped_code = '>' if sys_is_le else '<'
+native_code: ty.Literal['<', '>'] = '<' if sys_is_le else '>'
+swapped_code: ty.Literal['<', '>'] = '>' if sys_is_le else '<'
 
 _endian_codes = (  # numpy code, aliases
     ('<', 'little', 'l', 'le', 'L', 'LE'),