More informative exceptions (#3037)

* doc: Skip petab-sciml for now

GitHub Action runners run out of disk space when installing petab-sciml with all its huge dependencies.
Don't install that for now. So far, it's not used anywhere for the documentation build as far as I can see.
This won't prevent enabling intersphinx later on.

* More informative exceptions

* Add more context to exceptions
* Convert `NotImplementedError`s during SBML import to `SBMLException` as done in other places
* Catch simulation errors early

Author: dweindl

python/sdist/amici/exporters/sundials/de_export.py

@@ -285,7 +285,13 @@ def _generate_c_code(self) -> None:
 
             if func_info.generate_body:
                 dec = log_execution_time(f"writing {func_name}.cpp", logger)
-                dec(self._write_function_file)(func_name)
+                try:
+                    dec(self._write_function_file)(func_name)
+                except Exception as e:
+                    e.add_note(
+                        f"Error while generating function '{func_name}'"
+                    )
+                    raise
 
         for name in self.model.sym_names():
             # only generate for those that have nontrivial implementation,

python/sdist/amici/gradient_check.py

@@ -133,17 +133,22 @@ def check_finite_difference(
         else:
             raise NotImplementedError()
 
-        _check_close(
-            sensi,
-            fd,
-            atol=atol,
-            rtol=rtol,
-            field=field,
-            ip=ip,
-            parameter_id=model.get_free_parameter_ids()[ip]
-            if model.has_free_parameter_ids()
-            else None,
-        )
+        try:
+            _check_close(
+                sensi,
+                fd,
+                atol=atol,
+                rtol=rtol,
+                field=field,
+                ip=ip,
+                parameter_id=model.get_free_parameter_ids()[ip]
+                if model.has_free_parameter_ids()
+                else None,
+            )
+        except Exception as e:
+            sm = SensitivityMethod(solver.get_sensitivity_method())
+            e.add_note(f"Sensitivity method was {sm!r}")
+            raise e
 
     solver.set_sensitivity_order(og_sensitivity_order)
     model.set_free_parameters(og_parameters)

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

@@ -278,6 +278,7 @@ def pysb2amici(
         compiler=compiler,
         generate_sensitivity_code=generate_sensitivity_code,
     )
+    # TODO: remove with https://github.com/AMICI-dev/AMICI/issues/3035
     # Sympy code optimizations are incompatible with PySB objects, as
     #  `pysb.Observable` comes with its own `.match` which overrides
     #  `sympy.Basic.match()`, breaking `sympy.codegen.rewriting.optimize`.

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

@@ -401,17 +401,23 @@ def sbml2amici(
             DEExporter,
         )
 
-        exporter = DEExporter(
-            ode_model,
-            model_name=model_name,
-            outdir=output_dir,
-            verbose=verbose,
-            assume_pow_positivity=assume_pow_positivity,
-            compiler=compiler,
-            allow_reinit_fixpar_initcond=allow_reinit_fixpar_initcond,
-            generate_sensitivity_code=generate_sensitivity_code,
-        )
-        exporter.generate_model_code()
+        try:
+            exporter = DEExporter(
+                ode_model,
+                model_name=model_name,
+                outdir=output_dir,
+                verbose=verbose,
+                assume_pow_positivity=assume_pow_positivity,
+                compiler=compiler,
+                allow_reinit_fixpar_initcond=allow_reinit_fixpar_initcond,
+                generate_sensitivity_code=generate_sensitivity_code,
+            )
+            exporter.generate_model_code()
+        except NotImplementedError as e:
+            raise SBMLException(
+                "The SBML model contains features that are currently not "
+                "supported by the AMICI SBML importer."
+            ) from e
 
         if compile:
             if not has_clibs:

tests/petab_test_suite/test_petab_v2_suite.py

@@ -9,6 +9,7 @@
 import pytest
 from _pytest.outcomes import Skipped
 from amici import (
+    AMICI_SUCCESS,
     SensitivityMethod,
     SensitivityOrder,
 )
@@ -78,6 +79,10 @@ def _test_case(case, model_type, version, jax):
     ret = ps.simulate(problem_parameters=problem_parameters)
 
     rdatas = ret[RDATAS]
+    for rdata in rdatas:
+        assert rdata.status == AMICI_SUCCESS, (
+            f"Simulation failed for {rdata.id}"
+        )
     chi2 = sum(rdata.chi2 for rdata in rdatas)
     llh = ret[LLH]
     simulation_df = rdatas_to_simulation_df(rdatas, ps.model, pi.petab_problem)