Bump actions/checkout from 4 to 5 (#2937)

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: dependabot[bot]

.github/workflows/deploy_branch.yml

@@ -17,7 +17,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
 

.github/workflows/deploy_protected.yml

@@ -41,7 +41,7 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v3

.github/workflows/deploy_release.yml

@@ -27,7 +27,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
 
@@ -79,7 +79,7 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.11"
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v3

.github/workflows/test_benchmark_collection_models.yml

@@ -30,7 +30,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
 
@@ -107,7 +107,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
 

.github/workflows/test_doc.yml

@@ -26,7 +26,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - name: Set up doxygen
@@ -49,7 +49,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

.github/workflows/test_install.yml

@@ -19,7 +19,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -60,7 +60,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -93,7 +93,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

.github/workflows/test_matlab.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

.github/workflows/test_performance.yml

@@ -22,7 +22,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
 

.github/workflows/test_petab_test_suite.yml

@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 20
 

.github/workflows/test_python_cplusplus.yml

@@ -31,7 +31,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         lfs: true
     - run: git fetch --prune --unshallow
@@ -140,7 +140,7 @@ jobs:
           ~/.cache/pooch
         key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -223,7 +223,7 @@ jobs:
           ~/.cache/pooch
         key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -254,7 +254,7 @@ jobs:
       with:
         python-version: "3.11"
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         lfs: true
 
@@ -319,7 +319,7 @@ jobs:
       with:
         python-version: "3.11"
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         lfs: true
     - run: git fetch --prune --unshallow