amici.petab.pysb_import

PySB-PEtab Import

Import a model in the PySB-adapted petab (https://github.com/PEtab-dev/PEtab) format into AMICI.

Functions

import_model_pysb(petab_problem[, ...])

Create AMICI model from PySB-PEtab problem

amici.petab.pysb_import.import_model_pysb(petab_problem, model_output_dir=None, verbose=True, model_name=None, jax=False, **kwargs)[source]

Create AMICI model from PySB-PEtab problem

Parameters:

petab_problem (petab.v1.problem.Problem) – PySB PEtab problem
model_output_dir (str | pathlib.Path | None) – Directory to write the model code to. Will be created if doesn’t exist. Defaults to current directory.
verbose (bool | int | None) – Print/log extra information.
model_name (str | None) – Name of the generated model module
jax (bool) – Whether to generate JAX code instead of C++ code.
kwargs – Additional keyword arguments to be passed to amici.pysb_import.pysb2amici().

Return type:

None