diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
index 3f8f75be52..f4846e7c53 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@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 20
 
diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
index b88c17a143..7402604de8 100644
--- a/.github/workflows/deploy_protected.yml
+++ b/.github/workflows/deploy_protected.yml
@@ -41,7 +41,7 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - 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 95cd047ef3..675e61cd54 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@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 20
 
@@ -76,7 +76,7 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: "3.11"
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - 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 652b7e740b..a6a868dbf8 100644
--- a/.github/workflows/test_benchmark_collection_models.yml
+++ b/.github/workflows/test_benchmark_collection_models.yml
@@ -31,7 +31,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 20
 
@@ -108,7 +108,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 20
 
diff --git a/.github/workflows/test_conda_install.yml b/.github/workflows/test_conda_install.yml
index 9a1db741f5..6367214c2f 100644
--- a/.github/workflows/test_conda_install.yml
+++ b/.github/workflows/test_conda_install.yml
@@ -17,7 +17,7 @@ jobs:
         python-version: ['3.11', '3.12', '3.13']
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
index 8a66c05861..d5e162473c 100644
--- a/.github/workflows/test_doc.yml
+++ b/.github/workflows/test_doc.yml
@@ -27,7 +27,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - run: git fetch --prune --unshallow
 
     - name: Set up doxygen
@@ -50,7 +50,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - 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 bc3d1200fb..45d527bf82 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@v5
+    - uses: actions/checkout@v6
     - 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@v5
+    - uses: actions/checkout@v6
     - 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@v5
+    - uses: actions/checkout@v6
     - 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 7439a9bf26..1a3c872a22 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@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 20
 
diff --git a/.github/workflows/test_petab_sciml.yml b/.github/workflows/test_petab_sciml.yml
index 720015a321..30d646fece 100644
--- a/.github/workflows/test_petab_sciml.yml
+++ b/.github/workflows/test_petab_sciml.yml
@@ -29,7 +29,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 20
 
diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
index 0c305876fc..3d86715996 100644
--- a/.github/workflows/test_petab_test_suite.yml
+++ b/.github/workflows/test_petab_test_suite.yml
@@ -29,7 +29,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 20
 
@@ -136,7 +136,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 20
 
diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
index 799ffbbdc2..d5ddaf5221 100644
--- a/.github/workflows/test_python_cplusplus.yml
+++ b/.github/workflows/test_python_cplusplus.yml
@@ -32,7 +32,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         lfs: true
     - run: git fetch --prune --unshallow
@@ -143,7 +143,7 @@ jobs:
           ~/.cache/pooch
         key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -228,7 +228,7 @@ jobs:
           ~/.cache/pooch
         key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -259,7 +259,7 @@ jobs:
       with:
         python-version: "3.11"
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         lfs: true
 
@@ -326,7 +326,7 @@ jobs:
       with:
         python-version: "3.11"
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       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 e04f3b2c44..2ddb0b429b 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@v5
+    - uses: actions/checkout@v6
       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 3f665031be..2777f0ed85 100644
--- a/.github/workflows/test_python_ver_matrix.yml
+++ b/.github/workflows/test_python_ver_matrix.yml
@@ -37,7 +37,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       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 891ddb91d4..29b00ea929 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@v5
+    - uses: actions/checkout@v6
       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 a7f95507c5..d9af9235ce 100644
--- a/.github/workflows/test_sbml_semantic_test_suite_jax.yml
+++ b/.github/workflows/test_sbml_semantic_test_suite_jax.yml
@@ -33,7 +33,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 1
 
diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
index 098fcce03f..e0e3c4dfc0 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@v5
+      uses: actions/checkout@v6
       with:
         ref: main
         lfs: true
 
     - name: Checkout code (manual, push, pull request)
       if: github.event_name != 'schedule'
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         lfs: true
 
@@ -89,7 +89,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         lfs: true
     - run: git fetch --prune --unshallow
diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
index 76487d1a38..fb7db0fc53 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@v5
+    - uses: actions/checkout@v6
       with:
         lfs: true
     - run: git fetch --prune --unshallow