Fix AttributeError in petab_import_pysb with petab==0.2.0 (#2079)

* Fix AttributeError in petab_import_pysb with petab==0.2.0

Closes  #2078

* petab>=0.2.0

Author: dweindl

python/sdist/amici/petab_import_pysb.py

@@ -9,16 +9,16 @@
 import os
 from itertools import chain
 from pathlib import Path
-from typing import Dict, Iterable, Optional, Tuple, Union
+from typing import Dict, Iterable, Optional, Union
 
-import libsbml
 import petab
 import pysb
 import sympy as sp
 from petab.C import (CONDITION_FILES, CONDITION_NAME, FORMAT_VERSION,
                      MEASUREMENT_FILES, NOISE_FORMULA, OBSERVABLE_FILES,
                      OBSERVABLE_FORMULA, PARAMETER_FILE, SBML_FILES,
                      VISUALIZATION_FILES)
+from petab.models.sbml_model import SbmlModel
 
 from .logging import get_logger, log_execution_time, set_log_level
 
@@ -56,7 +56,7 @@ def __init__(self, pysb_model: 'pysb.Model' = None, *args, **kwargs):
         self._add_observation_model()
 
         if self.pysb_model is not None:
-            self.sbml_document, self.sbml_model = \
+            self.model = \
                 create_dummy_sbml(
                     self.pysb_model,
                     observable_ids=self.observable_df.index.values
@@ -252,17 +252,16 @@ def from_yaml(yaml_config: Union[Dict, Path, str],
 def create_dummy_sbml(
         pysb_model: 'pysb.Model',
         observable_ids: Optional[Iterable[str]] = None
-) -> Tuple['libsbml.Model', 'libsbml.SBMLDocument']:
+) -> SbmlModel:
     """Create SBML dummy model for to use PySB models with PEtab.
 
     Model must at least contain PEtab problem parameter and noise parameters
     for observables.
 
     :param pysb_model: PySB model
     :param observable_ids: Observable IDs
-    :return: A dummy SBML model and document.
+    :return: A dummy petab SBML model.
     """
-
     import libsbml
 
     document = libsbml.SBMLDocument(3, 1)
@@ -305,7 +304,7 @@ def create_dummy_sbml(
         s.setCompartment('dummy_compartment')
         s.setConstant(False)
 
-    return document, dummy_sbml_model
+    return SbmlModel(sbml_model=dummy_sbml_model, sbml_document=document)
 
 
 @log_execution_time('Importing PEtab model', logger)

python/sdist/setup.cfg

@@ -44,7 +44,7 @@ include_package_data = True
 zip_safe = False
 
 [options.extras_require]
-petab = petab>=0.1.27
+petab = petab>=0.2.0
 pysb = pysb>=1.13.1
 test =
     pytest