Allow overriding model name during PySB import (#1801)

python/amici/petab_import.py

@@ -280,7 +280,7 @@ def import_petab_problem(
     :param model_name:
         Name of the generated model. If model file name was provided,
         this defaults to the file name without extension, otherwise
-        the SBML model ID will be used.
+        the model ID will be used.
 
     :param force_compile:
         Whether to compile the model even if the target folder is not empty,
@@ -303,12 +303,9 @@ def import_petab_problem(
     else:
         model_output_dir = os.path.abspath(model_output_dir)
 
-    if PysbPetabProblem and isinstance(petab_problem, PysbPetabProblem):
-        if model_name is None:
-            model_name = petab_problem.pysb_model.name
-        else:
-            raise ValueError(
-                "Argument model_name currently not allowed for pysb models")
+    if PysbPetabProblem and isinstance(petab_problem, PysbPetabProblem) \
+            and model_name is None:
+        model_name = petab_problem.pysb_model.name
     elif model_name is None:
         model_name = _create_model_name(model_output_dir)
 
@@ -333,6 +330,7 @@ def import_petab_problem(
         if PysbPetabProblem and isinstance(petab_problem, PysbPetabProblem):
             import_model_pysb(
                 petab_problem,
+                model_name=model_name,
                 model_output_dir=model_output_dir,
                 **kwargs)
         else:

python/amici/petab_import_pysb.py

@@ -314,6 +314,7 @@ def import_model_pysb(
         petab_problem: PysbPetabProblem,
         model_output_dir: Optional[Union[str, Path]] = None,
         verbose: Optional[Union[bool, int]] = True,
+        model_name: Optional[str] = None,
         **kwargs
 ) -> None:
     """
@@ -329,11 +330,13 @@ def import_model_pysb(
     :param verbose:
         Print/log extra information.
 
+    :param model_name:
+        Name of the generated model module
+
     :param kwargs:
         Additional keyword arguments to be passed to
         :meth:`amici.pysb_import.pysb2amici`.
     """
-
     set_log_level(logger, verbose)
 
     logger.info("Importing model ...")
@@ -374,7 +377,10 @@ def import_model_pysb(
             observable_table)
 
     from amici.pysb_import import pysb2amici
-    pysb2amici(pysb_model, model_output_dir, verbose=True,
+    pysb2amici(model=pysb_model,
+               output_dir=model_output_dir,
+               model_name=model_name,
+               verbose=True,
                observables=observables,
                sigmas=sigmas,
                constant_parameters=constant_parameters,

python/amici/pysb_import.py

@@ -51,6 +51,7 @@ def pysb2amici(
         # See https://github.com/AMICI-dev/AMICI/pull/1672
         cache_simplify: bool = False,
         generate_sensitivity_code: bool = True,
+        model_name: Optional[str] = None,
 ):
     r"""
     Generate AMICI C++ files for the provided model.
@@ -124,6 +125,10 @@ def pysb2amici(
     :param generate_sensitivity_code:
         if set to ``False``, code for sensitivity computation will not be
         generated
+
+    :param model_name:
+        Name for the generated model module. If None, :attr:`pysb.Model.name`
+        will be used.
     """
     if observables is None:
         observables = []
@@ -133,6 +138,8 @@ def pysb2amici(
     if sigmas is None:
         sigmas = {}
 
+    model_name = model_name or model.name
+
     set_log_level(logger, verbose)
     ode_model = ode_model_from_pysb_importer(
         model, constant_parameters=constant_parameters,
@@ -146,7 +153,7 @@ def pysb2amici(
     exporter = ODEExporter(
         ode_model,
         outdir=output_dir,
-        model_name=model.name,
+        model_name=model_name,
         verbose=verbose,
         assume_pow_positivity=assume_pow_positivity,
         compiler=compiler,