Refactor benchmark collection tests (#2569)

* Refactor tests/benchmark-models/test_benchmark_collection.sh into pytest cases
* Unify with gradient checks in `tests/benchmark-models/test_petab_benchmark.py`
* Test some additional benchmark problems

For now, just consolidating the old tests. To be cleaned up further later on.

Closes #2510.

.github/workflows/test_benchmark_collection_models.yml

@@ -52,25 +52,28 @@ jobs:
         AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
-    - 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: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
-          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
-          && pip3 install -e $BENCHMARK_COLLECTION/../src/python \
-          && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
+          && python3 -m pip install -e Benchmark-Models-PEtab/src/python
+
+    - name: Run tests
+      env:
+        AMICI_PARALLEL_COMPILE: ""
+      run: |
+          cd tests/benchmark-models && pytest --durations=10
 
-    # run gradient checks
-    - name: Run Gradient Checks
+    # 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 }}