diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
index 82d1452d37..ff1be3145d 100644
--- a/.github/workflows/deploy_branch.yml
+++ b/.github/workflows/deploy_branch.yml
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -31,7 +31,7 @@ jobs:
         scripts/buildSdist.sh
 
     - name: "Upload artifact: sdist"
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: sdist
         path: python/sdist/dist/amici-*.gz
diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
index cd9257818d..c520896a70 100644
--- a/.github/workflows/deploy_protected.yml
+++ b/.github/workflows/deploy_protected.yml
@@ -25,10 +25,10 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v2
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
index 975f8aa5b8..de7a073cc2 100644
--- a/.github/workflows/deploy_release.yml
+++ b/.github/workflows/deploy_release.yml
@@ -23,11 +23,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
index 3bf4cc3c1e..ab29938a12 100644
--- a/.github/workflows/test_benchmark_collection_models.yml
+++ b/.github/workflows/test_benchmark_collection_models.yml
@@ -29,11 +29,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -66,9 +66,9 @@ jobs:
           && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
 
     # upload results
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
-        name: computation times
+        name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
         path: |
           tests/benchmark-models/computation_times.csv
           tests/benchmark-models/computation_times.png
diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
index 7a60aa99d5..a4fe10de22 100644
--- a/.github/workflows/test_doc.yml
+++ b/.github/workflows/test_doc.yml
@@ -24,11 +24,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Set up doxygen
@@ -47,11 +47,11 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - 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 166616b434..0c624a33e5 100644
--- a/.github/workflows/test_install.yml
+++ b/.github/workflows/test_install.yml
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -54,11 +54,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -87,11 +87,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - 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 914ce19f09..46185e9d45 100644
--- a/.github/workflows/test_matlab.yml
+++ b/.github/workflows/test_matlab.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - 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 c306e0333a..c02245224c 100644
--- a/.github/workflows/test_performance.yml
+++ b/.github/workflows/test_performance.yml
@@ -27,11 +27,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -64,7 +64,7 @@ jobs:
         AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
 
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: model_performance_test
         path: model_performance_test
diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
index a4791536e9..c167c927fa 100644
--- a/.github/workflows/test_petab_test_suite.yml
+++ b/.github/workflows/test_petab_test_suite.yml
@@ -26,11 +26,11 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 20
 
@@ -86,7 +86,7 @@ jobs:
 
       - name: Codecov
         if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-        uses: codecov/codecov-action@v3.1.0
+        uses: codecov/codecov-action@v3.1.4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml
diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml
index 68675c578a..fecda3edb0 100644
--- a/.github/workflows/test_pypi.yml
+++ b/.github/workflows/test_pypi.yml
@@ -36,7 +36,7 @@ jobs:
           fi
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
index 5aa47173b8..10ba5b0a0f 100644
--- a/.github/workflows/test_python_cplusplus.yml
+++ b/.github/workflows/test_python_cplusplus.yml
@@ -19,11 +19,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -67,7 +67,7 @@ jobs:
 
     - name: Codecov Python
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v3.1.4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: build/coverage_py.xml
@@ -87,7 +87,7 @@ jobs:
 
     - name: Codecov CPP
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v3.1.4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
@@ -114,11 +114,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -142,7 +142,7 @@ jobs:
 
     - name: Codecov Python
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v3.1.4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: build/coverage_py.xml
@@ -162,7 +162,7 @@ jobs:
 
     - name: Codecov CPP
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v3.1.4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
@@ -190,11 +190,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -224,11 +224,11 @@ jobs:
 
     steps:
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Install dependencies
@@ -266,11 +266,11 @@ jobs:
 
     steps:
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Install dependencies
diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
index 9290cd0c1a..5f9d96d295 100644
--- a/.github/workflows/test_python_ver_matrix.yml
+++ b/.github/workflows/test_python_ver_matrix.yml
@@ -33,11 +33,11 @@ jobs:
     - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
index ee123a233b..df7fd4a01e 100644
--- a/.github/workflows/test_sbml_semantic_test_suite.yml
+++ b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -33,11 +33,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
 
@@ -48,14 +48,14 @@ jobs:
     - run: AMICI_PARALLEL_COMPILE="" ./scripts/run-SBMLTestsuite.sh ${{ matrix.cases }}
 
     - name: "Upload artifact: SBML semantic test suite results"
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: amici-semantic-results
+        name: amici-semantic-results-${{ matrix.cases }}
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v3.1.4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage_SBMLSuite.xml
diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
index 32eea2e0c0..034945d461 100644
--- a/.github/workflows/test_valgrind.yml
+++ b/.github/workflows/test_valgrind.yml
@@ -25,11 +25,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Install apt dependencies
@@ -64,11 +64,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Install apt dependencies
diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
index 9dc13efbea..fbd91ce73a 100644
--- a/.github/workflows/test_windows.yml
+++ b/.github/workflows/test_windows.yml
@@ -31,11 +31,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - shell: bash
@@ -61,7 +61,7 @@ jobs:
       shell: powershell
       run: scripts/installOpenBLAS
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: OpenBLAS
         path: C:\BLAS\OpenBLAS