From a70ab5417143806330f00b59fd9e28537b6ebe3e Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 5 Sep 2024 14:30:03 -0400
Subject: [PATCH 1/3] TYP: Ignore overzealous warning for min/max with numpy
 scalars

---
 nibabel/volumeutils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabel/volumeutils.py b/nibabel/volumeutils.py
index 29b954dbb..c2387f094 100644
--- a/nibabel/volumeutils.py
+++ b/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

From a1fff406a18313ff67f9ed6abd9fce58dbb65e59 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 5 Sep 2024 14:32:04 -0400
Subject: [PATCH 2/3] Update pre-commit config

---
 .pre-commit-config.yaml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b348393a4..4f49318eb 100644
--- a/.pre-commit-config.yaml
+++ b/.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:

From e2fe1903f73c4c58865af34fd2ab8781c58ab7e8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sat, 7 Sep 2024 12:16:47 -0400
Subject: [PATCH 3/3] typ: Ignore Pointset.__rmatmul__/ndarray.__matmul__
 inconsistency

---
 nibabel/pointset.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nibabel/pointset.py b/nibabel/pointset.py
index 70a802480..889a8c70c 100644
--- a/nibabel/pointset.py
+++ b/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.