diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
index fac3a06995..6ec6a89b93 100644
--- a/.github/workflows/deploy_branch.yml
+++ b/.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
 
diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
index 513bf17f1d..80b5225a15 100644
--- a/.github/workflows/deploy_protected.yml
+++ b/.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
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
index 4287d88bca..b7588133e8 100644
--- a/.github/workflows/deploy_release.yml
+++ b/.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
diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
index 0e94766bb7..31a3d2ae5e 100644
--- a/.github/workflows/test_benchmark_collection_models.yml
+++ b/.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
 
diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
index ca19f4d149..851cd1c81f 100644
--- a/.github/workflows/test_doc.yml
+++ b/.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
diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
index 262565ab32..5bc5df6fb0 100644
--- a/.github/workflows/test_install.yml
+++ b/.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
diff --git a/.github/workflows/test_matlab.yml b/.github/workflows/test_matlab.yml
index 252113d57a..10cf07565a 100644
--- a/.github/workflows/test_matlab.yml
+++ b/.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
diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
index 9ccd78506d..0239d712a9 100644
--- a/.github/workflows/test_performance.yml
+++ b/.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
 
diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
index edd9676e1e..5df669167f 100644
--- a/.github/workflows/test_petab_test_suite.yml
+++ b/.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
 
diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
index a74c05f29c..e7d7fd8700 100644
--- a/.github/workflows/test_python_cplusplus.yml
+++ b/.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
diff --git a/.github/workflows/test_python_nogil.yml b/.github/workflows/test_python_nogil.yml
index d4f49c79b6..ad1fc42a28 100644
--- a/.github/workflows/test_python_nogil.yml
+++ b/.github/workflows/test_python_nogil.yml
@@ -20,7 +20,7 @@ jobs:
       with:
         python-version: '3.13'
         freethreaded: true
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
     - name: Install apt dependencies
diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
index 9897ed9184..eb67ef8d37 100644
--- a/.github/workflows/test_python_ver_matrix.yml
+++ b/.github/workflows/test_python_ver_matrix.yml
@@ -35,7 +35,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 20
         lfs: true
diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
index 37d0179d7d..da9872411d 100644
--- a/.github/workflows/test_sbml_semantic_test_suite.yml
+++ b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -36,7 +36,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 1
 
diff --git a/.github/workflows/test_sbml_semantic_test_suite_jax.yml b/.github/workflows/test_sbml_semantic_test_suite_jax.yml
index a39a9eec68..4c1b3c5321 100644
--- a/.github/workflows/test_sbml_semantic_test_suite_jax.yml
+++ b/.github/workflows/test_sbml_semantic_test_suite_jax.yml
@@ -32,7 +32,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 1
 
diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
index e61ed5533d..504f5036f5 100644
--- a/.github/workflows/test_valgrind.yml
+++ b/.github/workflows/test_valgrind.yml
@@ -37,14 +37,14 @@ jobs:
 
     - name: Checkout code (scheduled)
       if: github.event_name == 'schedule'
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         ref: main
         lfs: true
 
     - name: Checkout code (manual, push, pull request)
       if: github.event_name != 'schedule'
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         lfs: true
 
@@ -89,7 +89,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         lfs: true
     - run: git fetch --prune --unshallow
diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
index 5b93e5a0dc..baae8c1436 100644
--- a/.github/workflows/test_windows.yml
+++ b/.github/workflows/test_windows.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