Merge branch 'develop' into jax_export

.github/workflows/test_benchmark_collection_models.yml

@@ -52,23 +52,28 @@ jobs:
         AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis,jax]
 
-    - run: |
+    - name: Install test dependencies
+      run: |
         python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
-        &&  python3 -m pip install -U sympy
+        &&  python3 -m pip install -U sympy \
+        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git
 
-    # retrieve test models
-    - name: Download and test benchmark collection
+    - name: Download benchmark collection
       run: |
         pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python \
           && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
 
-    # run gradient checks
-    - name: Run Gradient Checks
+    - name: Run tests
+      env:
+        AMICI_PARALLEL_COMPILE: ""
+      run: |
+          cd tests/benchmark-models && pytest --durations=10
+
+    # collect & upload results
+    - name: Aggregate results
       run: |
-        pip install git+https://github.com/ICB-DCM/fiddy.git \
-          && cd tests/benchmark-models && pytest --durations=10 ./test_petab_benchmark.py
+          cd tests/benchmark-models && python3 evaluate_benchmark.py
 
-    # upload results
     - uses: actions/upload-artifact@v4
       with:
         name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}

.github/workflows/test_python_cplusplus.yml

@@ -242,6 +242,8 @@ jobs:
   macos_cpp_py:
     name: Tests MacOS C++/Python
     runs-on: macos-latest
+    env:
+      PYTHONFAULTHANDLER: "1"
 
     steps:
     - name: Set up Python
@@ -295,6 +297,8 @@ jobs:
   macos_python:
     name: Tests MacOS Python
     runs-on: macos-latest
+    env:
+      PYTHONFAULTHANDLER: "1"
 
     steps:
     - name: Cache