Merge branch 'develop' into nearly_no_doxygen_attic

Author: ye-luo

.github/workflows/ci-github-actions-nexus.yaml

@@ -21,15 +21,15 @@ jobs:
 
     steps:
     - name: Checkout Action
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Setup Graphviz
       run: sudo apt-get install graphviz
 
     - name: Install uv and Setup Python ${{ matrix.python-version }}
-      uses: astral-sh/setup-uv@v7
+      uses: astral-sh/setup-uv@v8.3.0
       with:
-        version: "0.11.11"
+        version: "0.11.26"
         python-version: ${{ matrix.python-version }}
 
     - name: Install Project and All Dependencies
@@ -56,15 +56,15 @@ jobs:
 
     steps:
     - name: Checkout Action
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     - name: Setup Graphviz
       run: brew install graphviz
 
     - name: Install uv and Setup Python ${{ matrix.python-version }}
-      uses: astral-sh/setup-uv@v7
+      uses: astral-sh/setup-uv@v8.3.0
       with:
-        version: "0.11.11"
+        version: "0.11.26"
         python-version: ${{ matrix.python-version }}
 
     - name: Install Project and All Dependencies
@@ -73,7 +73,7 @@ jobs:
 
     - name: Downgrade to Minimum Versions (Python 3.10 only)
       if: contains(matrix.python-version, '3.10')
-      run: uv pip install numpy==1.22.0 scipy==1.8.0 spglib==1.16.0 cif2cell==2.1.0 pydot==2.0.0 seekpath==2.0.0
+      run: uv pip install numpy==1.22.0 scipy==1.8.0 spglib==1.16.0 cif2cell==2.1.0 pydot==2.0.0 seekpath==2.0.0 matplotlib==3.8.4
       working-directory: ./nexus
 
     - name: Run Nexus Tests

.github/workflows/ci-github-actions-self-hosted.yaml

@@ -71,7 +71,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
@@ -170,7 +170,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
@@ -266,7 +266,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
@@ -362,7 +362,7 @@ jobs:
 
       - name: Checkout PR branch
         if: steps.check.outputs.triggered == 'true'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{secrets.GITHUB_TOKEN}}
           repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}

.github/workflows/ci-github-actions-static.yaml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Configure
         run: tests/test_automation/github-actions/ci/run_step_static.sh configure

.github/workflows/ci-github-actions.yaml

@@ -128,7 +128,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Configure
         run: tests/test_automation/github-actions/ci/run_step.sh configure
@@ -167,7 +167,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Set Python Version
         uses: actions/setup-python@v6
@@ -229,7 +229,7 @@ jobs:
 
     steps:
       - name: Checkout Action
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Echo Debug
         run: |

.github/workflows/ghcr-develop.yaml

@@ -19,7 +19,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-centos10.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu22-clang.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu22-openmpi.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu22-serial.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4

.github/workflows/update-ghcr-ci-image-ubuntu24-openmpi.yaml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v4