skip some more tests and reinstate more specific implicit triggers check

Author: BSnelling

.github/workflows/test_petab_test_suite.yml

@@ -186,7 +186,7 @@ jobs:
         run: |
           source ./venv/bin/activate \
             && python3 -m pip uninstall -y petab \
-            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@8dc6c1c4b801fba5acc35fcd25308a659d01050e \
+            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@d57d9fed8d8d5f8592e76d0b15676e05397c3b4b \
             && python3 -m pip install git+https://github.com/pysb/pysb@master \
             && python3 -m pip install sympy>=1.12.1
 

python/sdist/amici/_symbolic/de_model.py

@@ -2724,7 +2724,7 @@ def has_implicit_event_assignments(self) -> bool:
         :return:
             boolean indicating if event assignments with implicit triggers are present
         """
-        return any(event.updates_state and not event.has_explicit_trigger_times({}) for event in self._events)
+        return any(event.updates_state and event._implicit_symbols() for event in self._events)
 
     def toposort_expressions(
         self, reorder: bool = True

python/sdist/amici/_symbolic/de_model_components.py

@@ -875,6 +875,15 @@ def get_trigger_times(self) -> set[sp.Expr]:
         time points at which the event triggers.
         """
         return set(self._t_root)
+    
+    def _implicit_symbols(self):
+        symbols = [str(s) for s in list(self.get_val().free_symbols)]
+        implicit_symbols = []
+        for s in symbols:
+            if (s.startswith("_petab_") and "indicator" in s) or s == "t":
+                continue
+            implicit_symbols.append(s)
+        return len(implicit_symbols) > 0
 
     @property
     def uses_values_from_trigger_time(self) -> bool:

python/sdist/amici/jax/ode_export.py

@@ -161,10 +161,10 @@ def __init__(
                 "The JAX backend does not support simultaneous events because event priorities are not supported."
             )
 
-        # if ode_model.has_implicit_event_assignments():
-        #     raise NotImplementedError(
-        #         "The JAX backend does not support event assignments with implicit triggers."
-        #     )
+        if ode_model.has_implicit_event_assignments():
+            raise NotImplementedError(
+                "The JAX backend does not support event assignments with implicit triggers."
+            )
 
         self.verbose: bool = logger.getEffectiveLevel() <= logging.DEBUG
 

python/tests/test_jax.py

@@ -284,21 +284,27 @@ def check_fields_jax(
 def test_preequilibration_failure(lotka_volterra):  # noqa: F811
     petab_problem = lotka_volterra
     # oscillating system, preequilibation should fail when interaction is active
-    with TemporaryDirectoryWinSafe(prefix="normal") as model_dir:
-        jax_problem = import_petab_problem(
-            petab_problem, jax=True, output_dir=model_dir
-        )
-        r = run_simulations(jax_problem)
-        assert not np.isinf(r[0].item())
-    petab_problem.measurement_df[PREEQUILIBRATION_CONDITION_ID] = (
-        petab_problem.measurement_df[SIMULATION_CONDITION_ID]
-    )
-    with TemporaryDirectoryWinSafe(prefix="failure") as model_dir:
-        jax_problem = import_petab_problem(
-            petab_problem, jax=True, output_dir=model_dir
+
+    try:
+        with TemporaryDirectoryWinSafe(prefix="normal") as model_dir:
+            jax_problem = import_petab_problem(
+                petab_problem, jax=True, output_dir=model_dir
+            )
+            r = run_simulations(jax_problem)
+            assert not np.isinf(r[0].item())
+        petab_problem.measurement_df[PREEQUILIBRATION_CONDITION_ID] = (
+            petab_problem.measurement_df[SIMULATION_CONDITION_ID]
         )
-        r = run_simulations(jax_problem)
-        assert np.isinf(r[0].item())
+        with TemporaryDirectoryWinSafe(prefix="failure") as model_dir:
+            jax_problem = import_petab_problem(
+                petab_problem, jax=True, output_dir=model_dir
+            )
+            r = run_simulations(jax_problem)
+            assert np.isinf(r[0].item())
+    except (TypeError, NotImplementedError) as err:
+        if "run_simulations does not support PEtab v1 problems" in str(err):
+            pytest.skip(str(err))
+        raise err
 
 
 @skip_on_valgrind

tests/benchmark_models/test_petab_benchmark_jax.py

@@ -151,7 +151,9 @@ def test_jax_llh(benchmark_problem):
                 atol=1e-2,
                 err_msg=f"SLLH mismatch for {problem_id}, {dict(zip(jax_problem.parameter_ids, sllh_jax.parameters))}",
             )
-    except TypeError as err:
+    except (NotImplementedError, TypeError) as err:
         if "run_simulations does not support PEtab v1 problems" in str(err):
             pytest.skip(str(err))
+        if "The JAX backend does not support simultaneous events" in str(err):
+            pytest.skip(str(err))
         raise err