Upgrade CI actions to latest major versions (Node.js 24)

.github/workflows/CI.yml

@@ -81,7 +81,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Setup Miniforge Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           environment-file: environment.yml
           miniforge-variant: Miniforge3
@@ -109,7 +109,7 @@ jobs:
 
       - name: Setup Juliaup
         if: matrix.include-rms == 'with RMS'
-        uses: julia-actions/install-juliaup@v2
+        uses: julia-actions/install-juliaup@v3
         with:
           channel: '1.10'
 
@@ -148,7 +148,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Setup Miniforge Python 3.9
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           environment-file: environment.yml
           miniforge-variant: Miniforge3
@@ -179,7 +179,7 @@ jobs:
           conda create --name rmg_env_without_rms -f environment.yml
 
       - name: Setup Juliaup
-        uses: julia-actions/install-juliaup@v2
+        uses: julia-actions/install-juliaup@v3
         with:
           channel: '1.10'
 
@@ -214,7 +214,7 @@ jobs:
       # Upload Regression Results as Failed if above step failed
       - name: Upload Failed Results
         if: ${{ failure() && steps.regression-execution.conclusion == 'failure' }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: failed_regression_results
           path: |
@@ -224,7 +224,7 @@ jobs:
       - name: Upload Results as Reference
         # upload the results for scheduled CI (on main) and pushes to main
         if: ${{ env.REFERENCE_JOB == 'true' }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: stable_regression_results
           path: |
@@ -233,7 +233,7 @@ jobs:
       # Upload Regression Results as Dynamic if Push to non-main Branch
       - name: Upload Results as Dynamic
         if: ${{ env.REFERENCE_JOB == 'false' }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: dynamic_regression_results
           path: |
@@ -259,7 +259,7 @@ jobs:
 
       - name: Retrieve Stable Regression Results
         if: ${{ env.REFERENCE_JOB == 'false' }}
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
         # download stable regression results
           run-id: ${{ env.CI_RUN_ID }}
@@ -391,14 +391,14 @@ jobs:
 
       - name: Upload regression summary artifact
         # the annotate workflow uses this artifact to add a comment to the PR
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         if: ${{ github.event_name == 'pull_request' }}
         with:
           name: regression_summary
           path: summary.txt
 
       - name: Upload Comparison Results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: regression_test_comparison_results
           path: |
@@ -423,20 +423,20 @@ jobs:
       (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == 'ReactionMechanismGenerator/RMG-Py')
     steps:
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
 
       - name: Login to Docker Hub
         if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build (and Push if on main)
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         env:
           BUILDKIT_PROGRESS: plain
         with:

.github/workflows/annotate.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
       - run: echo 'The triggering workflow passed'
       - name: 'Download regression_summary artifact'
-        uses: actions/github-script@v8
+        uses: actions/github-script@v9
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -51,10 +51,10 @@ jobs:
           sed -i '1d' summary.txt
 
       - name: Write summary to pull request as a comment
-        uses: thollander/actions-comment-pull-request@v2
+        uses: thollander/actions-comment-pull-request@v3
         with:
-          filePath: summary.txt
-          pr_number: ${{ env.PR_NUMBER }}
+          file-path: summary.txt
+          pr-number: ${{ env.PR_NUMBER }}
 
       - name: Report the github.event.workflow_run as json
         if: ${{ failure() }}

.github/workflows/conda_build.yml

@@ -48,7 +48,7 @@ jobs:
       - uses: actions/checkout@v6
 
       - name: Setup Miniforge
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           miniforge-variant: Miniforge3
           miniforge-version: latest

.github/workflows/docs.yml

@@ -28,7 +28,7 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Miniforge Python 3.11
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           environment-file: environment.yml
           miniforge-variant: Miniforge3