diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5d34f39752..486b5e94fd 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -29,7 +29,7 @@ repos:
         exclude: ^source/3rdparty
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.6.8
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -52,10 +52,10 @@ repos:
       - id: blacken-docs
   # C++
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v18.1.8
+    rev: v19.1.0
     hooks:
       - id: clang-format
-        exclude: ^source/3rdparty|source/lib/src/gpu/cudart/.+\.inc
+        exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$)
   # markdown, yaml, CSS, javascript
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
@@ -146,7 +146,7 @@ repos:
         exclude: .pre-commit-config.yaml|source/lmp
   # customized pylint rules
   - repo: https://github.com/pylint-dev/pylint/
-    rev: v3.3.0
+    rev: v3.3.1
     hooks:
       - id: pylint
         entry: env PYTHONPATH=source/checker pylint
diff --git a/source/lib/include/gpu_cuda.h b/source/lib/include/gpu_cuda.h
index fb467674cb..9504a95b7a 100644
--- a/source/lib/include/gpu_cuda.h
+++ b/source/lib/include/gpu_cuda.h
@@ -18,8 +18,10 @@
 #define gpuMemset cudaMemset
 
 #define GPU_MAX_NBOR_SIZE 4096
-#define DPErrcheck(res) \
-  { DPAssert((res), __FILE__, __LINE__); }
+#define DPErrcheck(res)                  \
+  {                                      \
+    DPAssert((res), __FILE__, __LINE__); \
+  }
 inline void DPAssert(cudaError_t code,
                      const char *file,
                      int line,
@@ -54,8 +56,10 @@ inline void DPAssert(cudaError_t code,
   }
 }
 
-#define nborErrcheck(res) \
-  { nborAssert((res), __FILE__, __LINE__); }
+#define nborErrcheck(res)                  \
+  {                                        \
+    nborAssert((res), __FILE__, __LINE__); \
+  }
 inline void nborAssert(cudaError_t code,
                        const char *file,
                        int line,
diff --git a/source/lib/include/gpu_rocm.h b/source/lib/include/gpu_rocm.h
index fbd5e1ce3f..abb7ddfa62 100644
--- a/source/lib/include/gpu_rocm.h
+++ b/source/lib/include/gpu_rocm.h
@@ -20,8 +20,10 @@
 #define gpuMemcpyDeviceToDevice hipMemcpyDeviceToDevice
 #define gpuMemset hipMemset
 
-#define DPErrcheck(res) \
-  { DPAssert((res), __FILE__, __LINE__); }
+#define DPErrcheck(res)                  \
+  {                                      \
+    DPAssert((res), __FILE__, __LINE__); \
+  }
 inline void DPAssert(hipError_t code,
                      const char *file,
                      int line,
@@ -39,8 +41,10 @@ inline void DPAssert(hipError_t code,
   }
 }
 
-#define nborErrcheck(res) \
-  { nborAssert((res), __FILE__, __LINE__); }
+#define nborErrcheck(res)                  \
+  {                                        \
+    nborAssert((res), __FILE__, __LINE__); \
+  }
 inline void nborAssert(hipError_t code,
                        const char *file,
                        int line,