Don't persist credentials when checking out repositories (#7353)

Author: nsoranzo

.github/workflows/ci.yaml

@@ -58,7 +58,7 @@ jobs:
       run: pip install wheel
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -86,7 +86,7 @@ jobs:
     steps:
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
@@ -132,11 +132,9 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    # checkout the repository
-    # and use it as the current working directory
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}

.github/workflows/pr.yaml

@@ -81,6 +81,7 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
+        persist-credentials: false
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -113,7 +114,7 @@ jobs:
     steps:
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
@@ -160,7 +161,7 @@ jobs:
     steps:
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
@@ -192,7 +193,7 @@ jobs:
     steps:
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
@@ -228,6 +229,7 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
+        persist-credentials: false
     - name: Check file sizes
       run: |
         touch file_size_report.txt
@@ -270,7 +272,7 @@ jobs:
     steps:
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
@@ -372,7 +374,7 @@ jobs:
     steps:
     - uses: actions/checkout@v5
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}