Merge branch 'main' into bes/petabv2_jax

Author: BSnelling

python/sdist/amici/jax/petab.py

@@ -314,8 +314,8 @@ def _get_measurements(
         for col in [petabv1.OBSERVABLE_PARAMETERS, petabv1.NOISE_PARAMETERS]:
             n_pars[col] = 0
             if col in self._petab_problem.measurement_df:
-                if np.issubdtype(
-                    self._petab_problem.measurement_df[col].dtype, np.number
+                if pd.api.types.is_numeric_dtype(
+                    self._petab_problem.measurement_df[col].dtype
                 ):
                     n_pars[col] = 1 - int(
                         self._petab_problem.measurement_df[col].isna().all()
@@ -416,7 +416,7 @@ def get_parameter_override(x):
                     mat_numeric = jnp.ones((len(m), n_pars[col]))
                     par_mask = np.zeros_like(mat_numeric, dtype=bool)
                     par_index = np.zeros_like(mat_numeric, dtype=int)
-                elif np.issubdtype(m[col].dtype, np.number):
+                elif pd.api.types.is_numeric_dtype(m[col].dtype):
                     mat_numeric = np.expand_dims(m[col].values, axis=1)
                     par_mask = np.zeros_like(mat_numeric, dtype=bool)
                     par_index = np.zeros_like(mat_numeric, dtype=int)

tests/benchmark_models/test_petab_benchmark_jax.py

@@ -1,6 +1,7 @@
 import logging
 from functools import partial
 
+import diffrax
 import equinox as eqx
 import jax
 import jax.numpy as jnp
@@ -23,8 +24,6 @@
     settings,
 )
 
-import diffrax
-
 jax.config.update("jax_enable_x64", True)
 
 
@@ -38,7 +37,12 @@ def test_jax_llh(benchmark_problem):
         benchmark_problem
     )
 
-    to_skip = ["Smith_BMCSystBiol2013", "Oliveira_NatCommun2021", "SalazarCavazos_MBoC2020"]
+    to_skip = [
+        "Liu_IFACPapersOnLine2025",
+        "Oliveira_NatCommun2021",
+        "SalazarCavazos_MBoC2020",
+        "Smith_BMCSystBiol2013",
+    ]
     if problem_id in to_skip:
         pytest.skip(
             f"Skipping {problem_id} due to non-supported events in JAX."
@@ -133,7 +137,7 @@ def test_jax_llh(benchmark_problem):
             )
         else:
             llh_jax, _ = beartype(run_simulations)(jax_problem)
-
+            
         np.testing.assert_allclose(
             llh_jax,
             llh_amici,