petab.v1.models.model

PEtab model abstraction

Functions

model_factory(filepath_or_buffer, model_language)

Create a PEtab model instance from the given model

Classes

Model()

Base class for wrappers for any PEtab-supported model type

class petab.v1.models.model.Model[source]

Bases: ABC

Base class for wrappers for any PEtab-supported model type

abstractmethod static from_file(filepath_or_buffer: Any, model_id: str, base_path: str | Path = None) → Model[source]

Load the model from the given path/URL

Parameters:

filepath_or_buffer – Absolute or relative path/URL to the model file. If relative, it is interpreted relative to base_path, if given.
base_path – Base path for relative paths in the model file.
model_id – Model ID

Returns:

A Model instance holding the given model

abstractmethod get_free_parameter_ids_with_values() → Iterable[tuple[str, float]][source]

Get free model parameters along with their values

Returns:: Iterator over tuples of (parameter_id, parameter_value)

abstractmethod get_parameter_ids() → Iterable[str][source]

Get all parameter IDs from this model

Returns:: Iterator over model parameter IDs

abstractmethod get_parameter_value(id_: str) → float[source]

Get a parameter value

Parameters:: id – ID of the parameter whose value is to be returned
Raises:: ValueError – If no parameter with the given ID exists
Returns:: The value of the given parameter as specified in the model

abstractmethod get_valid_ids_for_condition_table() → Iterable[str][source]

Get IDs of all model entities that are allowed to occur as columns in the PEtab conditions table.

Returns:: Iterator over model entity IDs

abstractmethod get_valid_parameters_for_parameter_table() → Iterable[str][source]

Get IDs of all parameters that are allowed to occur in the PEtab parameters table

Returns:: Iterator over parameter IDs

abstractmethod has_entity_with_id(entity_id) → bool[source]

Check if there is a model entity with the given ID

Parameters:: entity_id – ID to check for
Returns:: True, if there is an entity with the given ID, False otherwise

abstractmethod is_state_variable(id_: str) → bool[source]: Check whether the given ID corresponds to a model state variable

abstractmethod is_valid() → bool[source]

Validate this model

Returns:: True if the model is valid, False if there are errors in this model

abstract property model_id

abstractmethod symbol_allowed_in_observable_formula(id_: str) → bool[source]

Check if the given ID is allowed to be used in observable and noise formulas

Returns:: True, if allowed, False otherwise

abstractmethod to_file(filename: str | Path | None = None)[source]

Save the model to the given file

Parameters:: filename – Destination filename

abstract class property type_id

petab.v1.models.model.model_factory(filepath_or_buffer: Any, model_language: str, model_id: str = None, base_path: str | Path = None) → Model[source]

Create a PEtab model instance from the given model

Parameters:

filepath_or_buffer – Path/URL of the model. Absolute or relative to base_path if given.
base_path – Base path for relative paths in the model file.
model_language – PEtab model language ID for the given model
model_id – PEtab model ID for the given model

Returns:

A Model instance representing the given model