Merge pull request #1346 from effigies/fix/minmax-types

TYP: Address some recent numpy/mypy type complaints

Author: effigies

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ".*/data/.*"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,15 +13,18 @@ repos:
       - id: check-merge-conflict
       - id: check-vcs-permalinks
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.6.4
     hooks:
       - id: ruff
-        args: [--fix, --show-fixes, --exit-non-zero-on-fix]
+        args: [ --fix ]
         exclude: = ["doc", "tools"]
       - id: ruff-format
         exclude: = ["doc", "tools"]
+      - id: ruff
+        args: [ --select, ISC001, --fix ]
+        exclude: = ["doc", "tools"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing
@@ -36,7 +39,7 @@ repos:
         args: ["nibabel"]
         pass_filenames: false
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         additional_dependencies:

nibabel/pointset.py

@@ -101,7 +101,11 @@ def dim(self) -> int:
         """The dimensionality of the space the coordinates are in"""
         return self.coordinates.shape[1] - self.homogeneous
 
-    def __rmatmul__(self, affine: np.ndarray) -> Self:
+    # Use __rmatmul__ to prefer to compose affines. Mypy does not like that
+    # this conflicts with ndarray.__matmul__. We will need some more feedback
+    # on how this plays out for type-checking or code suggestions before we
+    # can do better than ignore.
+    def __rmatmul__(self, affine: np.ndarray) -> Self:  # type: ignore[misc]
         """Apply an affine transformation to the pointset
 
         This will return a new pointset with an updated affine matrix only.

nibabel/volumeutils.py

@@ -624,7 +624,7 @@ def array_to_file(
             # pre scale thresholds
             mn, mx = _dt_min_max(in_dtype, mn, mx)
             mn_out, mx_out = _dt_min_max(out_dtype)
-            pre_clips = max(mn, mn_out), min(mx, mx_out)
+            pre_clips = max(mn, mn_out), min(mx, mx_out)  # type: ignore[type-var]
             return _write_data(data, fileobj, out_dtype, order, pre_clips=pre_clips)
         # In any case, we do not want to check for nans because we've already
         # disallowed scaling that generates nans