Bump the actions group with 8 updates

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
     name: Lint (ruff)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: astral-sh/ruff-action@v3
         with:
           args: "check ."
@@ -34,21 +34,21 @@ jobs:
     steps:
       # 1. Checkout T3 (The repo running this CI)
       - name: Checkout T3
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           path: T3
 
       # 2. Checkout ARC (Dependency)
       - name: Checkout ARC
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/ARC
           ref: linear_ts
           path: ARC
 
       # 3. Checkout RMG Database
       - name: Checkout RMG Database
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/RMG-database
           path: RMG-database
@@ -57,7 +57,7 @@ jobs:
 
       # 4. Checkout RMG-Py (needed at runtime for the rmg_env subprocess)
       - name: Checkout RMG-Py
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/RMG-Py
           path: RMG-Py
@@ -77,7 +77,7 @@ jobs:
 
       # 6. Setup T3 Environment
       - name: Set up micromamba (t3_env)
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: t3_env
           environment-file: T3/environment.yml
@@ -86,7 +86,7 @@ jobs:
 
       # 7. Setup RMG Environment (rmg_env) — required by all T3 tests that
       - name: Set up micromamba (rmg_env)
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: rmg_env
           environment-file: RMG-Py/environment.yml
@@ -148,7 +148,7 @@ jobs:
 
       # 9. Upload Coverage
       - name: Upload coverage data
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: T3/coverage.xml

.github/workflows/codeql.yml

@@ -25,18 +25,18 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         queries: security-and-quality
 
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
+      uses: github/codeql-action/autobuild@v4
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/docker_build.yml

@@ -49,12 +49,12 @@ jobs:
           docker-images: false
           swap-storage: false
       - name: Checkout
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3.0.0
+        uses: docker/setup-buildx-action@v4.0.0
       # Add steps for CI checks of the Dockerfile
       - name: Build Docker Image (No Push)
-        uses: docker/build-push-action@v5.1.0
+        uses: docker/build-push-action@v7.1.0
         with:
           context: .
           file: ./Dockerfile
@@ -65,7 +65,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6
       - name: Free Disk Space (Ubuntu)
         uses: jlumbroso/free-disk-space@main
         with:
@@ -82,21 +82,21 @@ jobs:
           docker-images: false
           swap-storage: false
       - name: Login to Docker Hub
-        uses: docker/login-action@v3.0.0
+        uses: docker/login-action@v4.1.0
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3.0.0
+        uses: docker/setup-buildx-action@v4.0.0
       - name: Build and push RMG-Py
-        uses: docker/build-push-action@v5.0.0
+        uses: docker/build-push-action@v7.1.0
         with:
           context: .
           file: ./devtools/Dockerfile_rmgpy
           push: true
           tags: ${{ secrets.DOCKERHUB_USERNAME }}/rmgpy:latest
       - name: Build and push T3
-        uses: docker/build-push-action@v5.0.0
+        uses: docker/build-push-action@v7.1.0
         with:
           context: .
           file: ./Dockerfile

.github/workflows/gh-pages.yml

@@ -18,10 +18,10 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
           cache: pip