Fix importing PetabImporter without jax and sciml extras (#3141)

* Fix importing PetabImporter without jax extras

Closes #3140.

* local h5py import

Author: dweindl

CHANGELOG.md

@@ -4,7 +4,15 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v1.X Series
 
-### v1.0.0 (unreleased)
+### v1.0.1
+
+**Fixes**
+
+* Fixed an issue that resulted in failure to import the `PetabImporter` if
+  the jax-dependencies weren't installed.
+
+
+### v1.0.0
 
 **BREAKING CHANGES**
 
@@ -39,7 +47,7 @@ The following functionality has been removed without replacement:
   fixed parameters as "fixed parameters", "constant parameters",
   or "constants". This has now been harmonized to "free" and "fixed" across the
   API. E.g., `Model.setParameters()` is now `Model.set_free_parameters()`.
-* `ReturnDataView.posteq_numsteps` and `ReturnDataView.posteq_numsteps` now
+* `ReturnDataView.posteq_numsteps` and `ReturnDataView.preeq_numsteps` now
   return a one-dimensional array of shape `(num_timepoints,)` instead of a
   two-dimensional array of shape `(1, num_timepoints)`.
 * `ReturnDataView.posteq_status` and `ReturnDataView.preeq_status` now

python/sdist/amici/importers/petab/__init__.py

@@ -21,10 +21,4 @@
 passing a :class:`petab.v1.Problem` instance to the PEtab v2 import functions.
 """
 
-# FIXME: for some tests (petab-sciml, maybe petab-v1-pysb) we still rely on an
-#   old PEtab version on which the petab v2 import does not work.
-#   Once those tests are updated, we can remove this try-except block.
-try:
-    from ._petab_importer import *  # noqa: F403, F401
-except ImportError:
-    pass
+from ._petab_importer import *  # noqa: F403, F401

python/sdist/amici/importers/petab/_petab_importer.py

@@ -24,7 +24,6 @@
 from amici._symbolic import DEModel, Event
 from amici.importers.utils import MeasurementChannel, amici_time_symbol
 from amici.logging import get_logger
-from amici.sim.jax.petab import JAXProblem
 
 from .v1._sbml_import import _add_global_parameter
 
@@ -594,7 +593,7 @@ def create_model(self) -> amici.sim.sundials.Model:
 
     def create_simulator(
         self, force_import: bool = False
-    ) -> amici.sim.sundials.petab.PetabSimulator:
+    ) -> amici.sim.sundials.petab.PetabSimulator | amici.sim.jax.JAXProblem:
         """
         Create a PEtab simulator for the imported model.
 
@@ -607,6 +606,9 @@ def create_simulator(
         if self._jax:
             model_module = self.import_module(force_import=force_import)
             model = model_module.Model()
+
+            from amici.sim.jax.petab import JAXProblem
+
             return JAXProblem(model, self.petab_problem)
 
         model = self.import_module(force_import=force_import).get_model()

python/sdist/amici/sim/jax/petab.py

@@ -10,7 +10,6 @@
 
 import diffrax
 import equinox as eqx
-import h5py
 import jax.lax
 import jax.numpy as jnp
 import jaxtyping as jt
@@ -593,6 +592,9 @@ def _load_parameter_arrays_from_files(self) -> dict:
             "array_files", []
         )
 
+        import h5py
+
+        # TODO(performance): Avoid opening each file multiple times
         return {
             file_spec.split("_")[0]: h5py.File(file_spec, "r")["parameters"][
                 file_spec.split("_")[0]
@@ -615,6 +617,9 @@ def _load_input_arrays_from_files(self) -> dict:
             "array_files", []
         )
 
+        import h5py
+
+        # TODO(performance): Avoid opening each file multiple times
         return {
             file_spec.split("_")[0]: h5py.File(file_spec, "r")["inputs"]
             for file_spec in array_files