from __future__ import annotations
import os
import shutil
from typing import TYPE_CHECKING
from .importer import PetabImporter
if TYPE_CHECKING:
import amici.petab_import_pysb
[docs]class PetabImporterPysb(PetabImporter):
"""Import for experimental PySB-based PEtab problems."""
[docs] def __init__(
self,
petab_problem: amici.petab_import_pysb.PysbPetabProblem,
output_folder: str = None,
):
"""
Initialize importer.
Parameters
----------
petab_problem:
Managing access to the model and data.
output_folder:
Folder to contain the amici model.
"""
super().__init__(
petab_problem,
model_name=petab_problem.pysb_model.name,
output_folder=output_folder,
validate_petab=False,
)
[docs] def compile_model(self, **kwargs):
"""
Compile the model.
If the output folder exists already, it is first deleted.
Parameters
----------
kwargs: Extra arguments passed to `amici.SbmlImporter.sbml2amici`.
"""
import amici.petab_import_pysb
# delete output directory
if os.path.exists(self.output_folder):
shutil.rmtree(self.output_folder)
amici.petab_import_pysb.import_model_pysb(
petab_problem=self.petab_problem,
model_output_dir=self.output_folder,
**kwargs,
)