upgrade actions/checkout@v3 to v4

.github/workflows/ci.yaml

@@ -56,7 +56,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -85,7 +85,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5
@@ -129,7 +129,7 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5

.github/workflows/enable_ci_workflows.yml

@@ -8,7 +8,7 @@ jobs:
     name: Enable CI workflows
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: run Python script

.github/workflows/setup.yml

@@ -79,7 +79,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks

.github/workflows/test_workflows.yml

@@ -60,7 +60,7 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5

.github/workflows/usegalaxy-star-installation.yml

@@ -9,7 +9,7 @@ jobs:
   workflow-install:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Cache downloads
         uses: actions/cache@v4
         with:

.github/workflows/workflow_test.yml

@@ -24,7 +24,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5
@@ -114,7 +114,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5