Merge branch 'galaxyproject:dev' into job-completion-email-citation

Author: Syrinx55

.github/workflows/api.yaml

@@ -47,7 +47,7 @@ jobs:
         run: |
           echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false

.github/workflows/bioblend.yaml

@@ -35,13 +35,13 @@ jobs:
         galaxy_python_version: ['3.9']
     steps:
       - name: Checkout Galaxy
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
           path: galaxy
           persist-credentials: false
       - name: Checkout Bioblend
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           repository: galaxyproject/bioblend
           path: bioblend

.github/workflows/build_client.yaml

@@ -11,7 +11,7 @@ jobs:
     outputs:
       commit-id: ${{ steps.client-commit.outputs.commit }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false

.github/workflows/build_container_image.yaml

@@ -14,7 +14,7 @@ jobs:
     name: Build container image for GHCR
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
@@ -79,7 +79,7 @@ jobs:
       tag: ${{ steps.branch.outputs.name }}
       version: ${{ steps.version.outputs.version }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       - uses: actions/setup-python@v4
@@ -235,7 +235,7 @@ jobs:
     if: startsWith(github.ref, 'refs/tags/')
     steps:
       - name: Checkout Galaxy Helm chart
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           repository: galaxyproject/galaxy-helm
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/check_test_class_names.yaml

@@ -16,7 +16,7 @@ jobs:
       matrix:
         python-version: ['3.9']
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       - uses: actions/setup-python@v6

.github/workflows/client-unit.yaml

@@ -15,7 +15,7 @@ jobs:
   client-unit-test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
       - name: Read Node.js version

.github/workflows/codeql-analysis.yml

@@ -40,7 +40,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           persist-credentials: false
 

.github/workflows/converter_tests.yaml

@@ -30,12 +30,12 @@ jobs:
         run: |
           echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false
       - name: Clone galaxyproject/galaxy-test-data
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           repository: galaxyproject/galaxy-test-data
           path: galaxy-test-data

.github/workflows/cwl_conformance.yaml

@@ -39,7 +39,7 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false

.github/workflows/db_indexes.yaml

@@ -41,7 +41,7 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           path: 'galaxy root'
           persist-credentials: false