Sync develop to master

.github/codeql-config.yml

@@ -0,0 +1,28 @@
+# Query filters to include or exclude specific queries
+query-filters:
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-short-global-name/
+      id: cpp/short-global-name
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-commented-out-code/ 
+      id: cpp/commented-out-code
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-poorly-documented-function/
+      id: cpp/poorly-documented-function
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-trivial-switch/
+      id: cpp/trivial-switch
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-irregular-enum-init/
+      id: cpp/irregular-enum-init
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-guarded-free/
+      id: cpp/guarded-free
+
+# Directories to scan for vulnerabilities
+paths:
+  - src  # Main source directory
+
+# Directories and files to ignore during the scan
+paths-ignore:
+  - tests # Test directory

.github/workflows/clang-format-check.yml

@@ -7,9 +7,9 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Run clang-format style check for C programs.
-      uses: DoozyX/[email protected].2
+      uses: DoozyX/[email protected]
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp'

.github/workflows/clang-format-fix.yml

@@ -8,9 +8,9 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Run clang-format style check for C programs.
-      uses: DoozyX/[email protected].2
+      uses: DoozyX/[email protected]
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp'

.github/workflows/h5bench-hdf5-1.10.4.yml

@@ -24,7 +24,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -223,7 +223,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test
           path: build/storage/**/std*

.github/workflows/h5bench-hdf5-1.10.7.yml

@@ -24,7 +24,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -223,7 +223,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test
           path: build/h5bench_e3sm-prefix/src/h5bench_e3sm-stamp/*

.github/workflows/h5bench-hdf5-1.10.8.yml

@@ -24,7 +24,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -223,7 +223,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test
           path: build/storage/**/std*

.github/workflows/h5bench-hdf5-1.12.0.yml

@@ -24,7 +24,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -258,7 +258,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test
           path: build/storage/**/std*

.github/workflows/h5bench-hdf5-1.14.0.yml

@@ -24,7 +24,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -513,7 +513,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test
           path: build*/storage/**/std*

.github/workflows/h5bench-hdf5-1.14.1.yml

@@ -24,7 +24,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -513,7 +513,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: test
           path: build*/storage/**/std*