diff --git a/python/sdist/amici/petab_import_pysb.py b/python/sdist/amici/petab_import_pysb.py index 796aa3bee0..4d2f146a74 100644 --- a/python/sdist/amici/petab_import_pysb.py +++ b/python/sdist/amici/petab_import_pysb.py @@ -9,9 +9,8 @@ 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 @@ -19,6 +18,7 @@ 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 @@ -252,7 +252,7 @@ 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 @@ -260,9 +260,8 @@ def create_dummy_sbml( :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) diff --git a/python/sdist/setup.cfg b/python/sdist/setup.cfg index cb9338612f..26255e77be 100644 --- a/python/sdist/setup.cfg +++ b/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