petab_select.model

The Model class.

Functions

default_compare(model0, model1, criterion[, ...])

Compare two calibrated models by their criterion values.

Classes

Model(**data)

A model.

ModelBase(**data)

Definition of the standardized model.

ModelHash(**data)

The model hash.

VirtualModelBase(**data)

Sufficient information for the virtual initial model.
class petab_select.model.Model(**data)[source]

A model.

__init__(**data)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

compute_criterion(criterion, raise_on_failure=True)[source]

Compute a criterion value for the model.

The value will also be stored, which will overwrite any previously stored value for the criterion.

Parameters:

  • criterion (Criterion) – The criterion.

  • raise_on_failure (bool) – Whether to raise a ValueError if the criterion could not be computed. If False, None is returned.

Return type:

float

Returns:

The criterion value.

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

  • include (Set[int] | Set[str] | Mapping[int, Any] | Mapping[str, Any] | None) – Optional set or mapping specifying which fields to include in the copied model.

  • exclude (Set[int] | Set[str] | Mapping[int, Any] | Mapping[str, Any] | None) – Optional set or mapping specifying which fields to exclude in the copied model.

  • update (Optional[Dict[str, Any]]) – Optional dictionary of field-value pairs to override field values in the copied model.

  • deep (bool) – If True, the values of fields that are Pydantic models will be deep-copied.

Return type:

Self

Returns:

A copy of the model with included, excluded and updated fields as specified.

criteria: dict[Criterion, float]

The criterion values of the calibrated model (e.g. AIC).

estimated_parameters: dict[str, float] | None

The parameter estimates of the calibrated model (always unscaled).

static from_yaml(filename, model_subspace_petab_problem=None)[source]

Load a model from a YAML file.

Parameters:

  • filename (Union[str, Path]) – The filename.

  • model_subspace_petab_problem (Problem | None) – A preloaded copy of the PEtab problem of the model subspace that this model belongs to.

Return type:

Model

get_criterion(criterion, compute=True, raise_on_failure=True)[source]

Get a criterion value for the model.

Parameters:

  • criterion (Criterion) – The criterion.

  • compute (bool) – Whether to attempt computing the criterion value. For example, the AIC can be computed if the likelihood is available.

  • raise_on_failure (bool) – Whether to raise a ValueError if the criterion could not be computed. If False, None is returned.

Return type:

float | None

Returns:

The criterion value, or None if it is not available.

get_estimated_parameter_ids(full=True)[source]

Get estimated parameter IDs.

Parameters:

full (bool) – Whether to provide all IDs, including additional parameters that are not part of the model selection problem but estimated.

Return type:

list[str]

get_hash()[source]

Deprecated. Use Model.hash instead.

Return type:

ModelHash

get_parameter_values(parameter_ids=None)[source]

Get parameter values.

Includes ESTIMATE for parameters that should be estimated.

Parameters:

parameter_ids (list[str] | None) – The IDs of parameters that values will be returned for. Order is maintained. Defaults to the model subspace PEtab problem parameters (including those not part of the model selection problem).

Return type:

list[Union[float, int, Literal['estimate']]]

Returns:

The values of parameters.

has_criterion(criterion)[source]

Check whether a value for a criterion has been set.

Return type:

bool

property hash: ModelHash

Get the model hash.

iteration: int | None

The iteration of model selection that calibrated this model.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note

model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

  • _fields_set (set[str] | None) – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.

  • values (Any) – Trusted or pre-validated data dictionary.

Return type:

Self

Returns:

A new instance of the Model class with validated data.

model_copy(*, update=None, deep=False)
!!! abstract “Usage Documentation”

[model_copy](../concepts/models.md#model-copy)

Returns a copy of the model.

!!! note

The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

  • update (Mapping[str, Any] | None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

  • deep (bool) – Set to True to make a deep copy of the model.

Return type:

Self

Returns:

New model instance.

model_dump(*, mode='python', include=None, exclude=None, context=None, by_alias=None, exclude_unset=False, exclude_defaults=False, exclude_none=False, exclude_computed_fields=False, round_trip=False, warnings=True, fallback=None, serialize_as_any=False)
!!! abstract “Usage Documentation”

[model_dump](../concepts/serialization.md#python-mode)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

  • mode (Union[Literal['json', 'python'], str]) – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

  • include (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – A set of fields to include in the output.

  • exclude (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – A set of fields to exclude from the output.

  • context (Any | None) – Additional context to pass to the serializer.

  • by_alias (bool | None) – Whether to use the field’s alias in the dictionary key if defined.

  • exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

  • exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

  • exclude_none (bool) – Whether to exclude fields that have a value of None.

  • exclude_computed_fields (bool) – Whether to exclude computed fields. While this can be useful for round-tripping, it is usually recommended to use the dedicated round_trip parameter instead.

  • round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

  • warnings (Union[bool, Literal['none', 'warn', 'error']]) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

  • fallback (Optional[Callable[[Any], Any]]) – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.

  • serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Return type:

dict[str, Any]

Returns:

A dictionary representation of the model.

model_dump_json(*, indent=None, ensure_ascii=False, include=None, exclude=None, context=None, by_alias=None, exclude_unset=False, exclude_defaults=False, exclude_none=False, exclude_computed_fields=False, round_trip=False, warnings=True, fallback=None, serialize_as_any=False)
!!! abstract “Usage Documentation”

[model_dump_json](../concepts/serialization.md#json-mode)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

  • indent (int | None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

  • ensure_ascii (bool) – If True, the output is guaranteed to have all incoming non-ASCII characters escaped. If False (the default), these characters will be output as-is.

  • include (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – Field(s) to include in the JSON output.

  • exclude (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – Field(s) to exclude from the JSON output.

  • context (Any | None) – Additional context to pass to the serializer.

  • by_alias (bool | None) – Whether to serialize using field aliases.

  • exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

  • exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

  • exclude_none (bool) – Whether to exclude fields that have a value of None.

  • exclude_computed_fields (bool) – Whether to exclude computed fields. While this can be useful for round-tripping, it is usually recommended to use the dedicated round_trip parameter instead.

  • round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

  • warnings (Union[bool, Literal['none', 'warn', 'error']]) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

  • fallback (Optional[Callable[[Any], Any]]) – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.

  • serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Return type:

str

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Returns:

A dictionary of extra fields, or None if config.extra is not set to “allow”.

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,

i.e. that were not filled from defaults.

model_hash: ModelHash

The model hash (treat as read-only after initialization).

model_id: str

The model ID.

classmethod model_json_schema(by_alias=True, ref_template='#/$defs/{model}', schema_generator=<class 'pydantic.json_schema.GenerateJsonSchema'>, mode='validation', *, union_format='any_of')

Generates a JSON schema for a model class.

Parameters:

  • by_alias (bool) – Whether to use attribute aliases or not.

  • ref_template (str) – The reference template.

  • union_format (Literal['any_of', 'primitive_type_array']) –

    The format to use when combining schemas from unions together. Can be one of:

    keyword to combine schemas (the default). - ‘primitive_type_array’: Use the [type](https://json-schema.org/understanding-json-schema/reference/type) keyword as an array of strings, containing each type of the combination. If any of the schemas is not a primitive type (string, boolean, null, integer or number) or contains constraints/metadata, falls back to any_of.

  • schema_generator (type[GenerateJsonSchema]) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

  • mode (Literal['validation', 'serialization']) – The mode in which to generate the schema.

Return type:

dict[str, Any]

Returns:

The JSON schema for the given model class.

model_label: str | None

The model label (e.g. for plotting).

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:

params (tuple[type[Any], ...]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Return type:

str

Returns:

String representing the new class where params are passed to cls as type variables.

Raises:

TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(_Model__context)[source]

Add additional instance attributes.

Return type:

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

  • force (bool) – Whether to force the rebuilding of the model schema, defaults to False.

  • raise_errors (bool) – Whether to raise errors, defaults to True.

  • _parent_namespace_depth (int) – The depth level of the parent namespace, defaults to 2.

  • _types_namespace (Mapping[str, Any] | None) – The types namespace, defaults to None.

Return type:

bool | None

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

model_subspace_id: str

The ID of the subspace that this model belongs to.

model_subspace_indices: list[int]

The location of this model in its subspace.

model_subspace_petab_yaml: Path | None

The location of the base PEtab problem for the model subspace.

N.B.: Not the PEtab problem for this model specifically! Use Model.to_petab() to get the model-specific PEtab problem.

classmethod model_validate(obj, *, strict=None, extra=None, from_attributes=None, context=None, by_alias=None, by_name=None)

Validate a pydantic model instance.

Parameters:

  • obj (Any) – The object to validate.

  • strict (bool | None) – Whether to enforce types strictly.

  • extra (Optional[Literal['allow', 'ignore', 'forbid']]) – Whether to ignore, allow, or forbid extra data during model validation. See the [extra configuration value][pydantic.ConfigDict.extra] for details.

  • from_attributes (bool | None) – Whether to extract data from object attributes.

  • context (Any | None) – Additional context to pass to the validator.

  • by_alias (bool | None) – Whether to use the field’s alias when validating against the provided input data.

  • by_name (bool | None) – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Return type:

Self

Returns:

The validated model instance.

classmethod model_validate_json(json_data, *, strict=None, extra=None, context=None, by_alias=None, by_name=None)
!!! abstract “Usage Documentation”

[JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

  • json_data (str | bytes | bytearray) – The JSON data to validate.

  • strict (bool | None) – Whether to enforce types strictly.

  • extra (Optional[Literal['allow', 'ignore', 'forbid']]) – Whether to ignore, allow, or forbid extra data during model validation. See the [extra configuration value][pydantic.ConfigDict.extra] for details.

  • context (Any | None) – Extra variables to pass to the validator.

  • by_alias (bool | None) – Whether to use the field’s alias when validating against the provided input data.

  • by_name (bool | None) – Whether to use the field’s name when validating against the provided input data.

Return type:

Self

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj, *, strict=None, extra=None, context=None, by_alias=None, by_name=None)

Validate the given object with string data against the Pydantic model.

Parameters:

  • obj (Any) – The object containing string data to validate.

  • strict (bool | None) – Whether to enforce types strictly.

  • extra (Optional[Literal['allow', 'ignore', 'forbid']]) – Whether to ignore, allow, or forbid extra data during model validation. See the [extra configuration value][pydantic.ConfigDict.extra] for details.

  • context (Any | None) – Extra variables to pass to the validator.

  • by_alias (bool | None) – Whether to use the field’s alias when validating against the provided input data.

  • by_name (bool | None) – Whether to use the field’s name when validating against the provided input data.

Return type:

Self

Returns:

The validated Pydantic model.

parameters: dict[str, float | int | Literal[ESTIMATE]]

PEtab problem parameters overrides for this model.

For example, fixes parameters to certain values, or sets them to be estimated.

predecessor_model_hash: ModelHash

The predecessor model hash.

resolve_paths(root_path)

Resolve all paths to be relative to root_path.

Return type:

None

set_criterion(criterion, value)[source]

Set a criterion value.

Return type:

None

set_estimated_parameters(estimated_parameters, scaled=False)[source]

Set parameter estimates.

Parameters:

  • estimated_parameters (dict[str, float]) – The estimated parameters.

  • scaled (bool) – Whether the parameter estimates are on the scale defined in the PEtab problem (True), or unscaled (False).

Return type:

None

set_relative_paths(root_path)

Change all paths to be relative to root_path.

Return type:

None

to_petab(output_path=None, set_estimated_parameters=None)[source]

Generate the PEtab problem for this model.

Parameters:

  • output_path (Union[str, Path]) – If specified, the PEtab tables will be written to disk, inside this directory.

  • set_estimated_parameters (bool | None) – Whether to implement Model.estimated_parameters as the nominal values of the PEtab problem parameter table. Defaults to True if Model.estimated_parameters is set.

Return type:

dict[str, Union[Problem, str, Path]]

Returns:

The PEtab problem. Also returns the path of the PEtab problem YAML file, if output_path is specified.

to_yaml(filename)

Save a model to a YAML file.

All paths will be made relative to the filename directory.

Parameters:

filename (Union[str, Path]) – Location of the YAML file.

Return type:

None

class petab_select.model.ModelHash(**data)[source]

The model hash.

The model hash is designed to be human-readable and able to be converted back into the corresponding model. Currently, if two models from two different model subspaces are actually the same PEtab problem, they will still have different model hashes.

__init__(**data)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`python {test="skip" lint="skip"} data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

  • include (Set[int] | Set[str] | Mapping[int, Any] | Mapping[str, Any] | None) – Optional set or mapping specifying which fields to include in the copied model.

  • exclude (Set[int] | Set[str] | Mapping[int, Any] | Mapping[str, Any] | None) – Optional set or mapping specifying which fields to exclude in the copied model.

  • update (Optional[Dict[str, Any]]) – Optional dictionary of field-value pairs to override field values in the copied model.

  • deep (bool) – If True, the values of fields that are Pydantic models will be deep-copied.

Return type:

Self

Returns:

A copy of the model with included, excluded and updated fields as specified.

get_model(problem)[source]

Get the model that a hash corresponds to.

Parameters:

problem (Problem) – The Problem that will be used to look up the model.

Return type:

Model

Returns:

The model.

static hash_model_subspace_indices(model_subspace_indices)[source]

Hash the location of a model in its subspace.

Parameters:

model_subspace_indices (list[int]) – The location (indices) of the model in its subspace.

Return type:

str

Returns:

The hash.

static kwargs_from_str(hash_str)[source]

Convert a model hash string into constructor kwargs.

Return type:

dict[str, str]

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note

model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

  • _fields_set (set[str] | None) – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.

  • values (Any) – Trusted or pre-validated data dictionary.

Return type:

Self

Returns:

A new instance of the Model class with validated data.

model_copy(*, update=None, deep=False)
!!! abstract “Usage Documentation”

[model_copy](../concepts/models.md#model-copy)

Returns a copy of the model.

!!! note

The underlying instance’s [__dict__][object.__dict__] attribute is copied. This might have unexpected side effects if you store anything in it, on top of the model fields (e.g. the value of [cached properties][functools.cached_property]).

Parameters:

  • update (Mapping[str, Any] | None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

  • deep (bool) – Set to True to make a deep copy of the model.

Return type:

Self

Returns:

New model instance.

model_dump(*, mode='python', include=None, exclude=None, context=None, by_alias=None, exclude_unset=False, exclude_defaults=False, exclude_none=False, exclude_computed_fields=False, round_trip=False, warnings=True, fallback=None, serialize_as_any=False)
!!! abstract “Usage Documentation”

[model_dump](../concepts/serialization.md#python-mode)

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

  • mode (Union[Literal['json', 'python'], str]) – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

  • include (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – A set of fields to include in the output.

  • exclude (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – A set of fields to exclude from the output.

  • context (Any | None) – Additional context to pass to the serializer.

  • by_alias (bool | None) – Whether to use the field’s alias in the dictionary key if defined.

  • exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

  • exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

  • exclude_none (bool) – Whether to exclude fields that have a value of None.

  • exclude_computed_fields (bool) – Whether to exclude computed fields. While this can be useful for round-tripping, it is usually recommended to use the dedicated round_trip parameter instead.

  • round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

  • warnings (Union[bool, Literal['none', 'warn', 'error']]) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

  • fallback (Optional[Callable[[Any], Any]]) – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.

  • serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Return type:

dict[str, Any]

Returns:

A dictionary representation of the model.

model_dump_json(*, indent=None, ensure_ascii=False, include=None, exclude=None, context=None, by_alias=None, exclude_unset=False, exclude_defaults=False, exclude_none=False, exclude_computed_fields=False, round_trip=False, warnings=True, fallback=None, serialize_as_any=False)
!!! abstract “Usage Documentation”

[model_dump_json](../concepts/serialization.md#json-mode)

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

  • indent (int | None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

  • ensure_ascii (bool) – If True, the output is guaranteed to have all incoming non-ASCII characters escaped. If False (the default), these characters will be output as-is.

  • include (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – Field(s) to include in the JSON output.

  • exclude (Union[set[int], set[str], Mapping[int, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], Mapping[str, Union[set[int], set[str], Mapping[int, Union[IncEx, bool]], Mapping[str, Union[IncEx, bool]], bool]], None]) – Field(s) to exclude from the JSON output.

  • context (Any | None) – Additional context to pass to the serializer.

  • by_alias (bool | None) – Whether to serialize using field aliases.

  • exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

  • exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

  • exclude_none (bool) – Whether to exclude fields that have a value of None.

  • exclude_computed_fields (bool) – Whether to exclude computed fields. While this can be useful for round-tripping, it is usually recommended to use the dedicated round_trip parameter instead.

  • round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

  • warnings (Union[bool, Literal['none', 'warn', 'error']]) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

  • fallback (Optional[Callable[[Any], Any]]) – A function to call when an unknown value is encountered. If not provided, a [PydanticSerializationError][pydantic_core.PydanticSerializationError] error is raised.

  • serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Return type:

str

Returns:

A JSON string representation of the model.

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Returns:

A dictionary of extra fields, or None if config.extra is not set to “allow”.

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set,

i.e. that were not filled from defaults.

classmethod model_json_schema(by_alias=True, ref_template='#/$defs/{model}', schema_generator=<class 'pydantic.json_schema.GenerateJsonSchema'>, mode='validation', *, union_format='any_of')

Generates a JSON schema for a model class.

Parameters:

  • by_alias (bool) – Whether to use attribute aliases or not.

  • ref_template (str) – The reference template.

  • union_format (Literal['any_of', 'primitive_type_array']) –

    The format to use when combining schemas from unions together. Can be one of:

    keyword to combine schemas (the default). - ‘primitive_type_array’: Use the [type](https://json-schema.org/understanding-json-schema/reference/type) keyword as an array of strings, containing each type of the combination. If any of the schemas is not a primitive type (string, boolean, null, integer or number) or contains constraints/metadata, falls back to any_of.

  • schema_generator (type[GenerateJsonSchema]) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

  • mode (Literal['validation', 'serialization']) – The mode in which to generate the schema.

Return type:

dict[str, Any]

Returns:

The JSON schema for the given model class.

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:

params (tuple[type[Any], ...]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Return type:

str

Returns:

String representing the new class where params are passed to cls as type variables.

Raises:

TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(context, /)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

Return type:

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

  • force (bool) – Whether to force the rebuilding of the model schema, defaults to False.

  • raise_errors (bool) – Whether to raise errors, defaults to True.

  • _parent_namespace_depth (int) – The depth level of the parent namespace, defaults to 2.

  • _types_namespace (Mapping[str, Any] | None) – The types namespace, defaults to None.

Return type:

bool | None

Returns:

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

model_subspace_id: str

The ID of the model subspace of the model.

Unique up to a single model space.

model_subspace_indices_hash: str

A hash of the location of the model in its model subspace.

Unique up to a single model subspace.

classmethod model_validate(obj, *, strict=None, extra=None, from_attributes=None, context=None, by_alias=None, by_name=None)

Validate a pydantic model instance.

Parameters:

  • obj (Any) – The object to validate.

  • strict (bool | None) – Whether to enforce types strictly.

  • extra (Optional[Literal['allow', 'ignore', 'forbid']]) – Whether to ignore, allow, or forbid extra data during model validation. See the [extra configuration value][pydantic.ConfigDict.extra] for details.

  • from_attributes (bool | None) – Whether to extract data from object attributes.

  • context (Any | None) – Additional context to pass to the validator.

  • by_alias (bool | None) – Whether to use the field’s alias when validating against the provided input data.

  • by_name (bool | None) – Whether to use the field’s name when validating against the provided input data.

Raises:

ValidationError – If the object could not be validated.

Return type:

Self

Returns:

The validated model instance.

classmethod model_validate_json(json_data, *, strict=None, extra=None, context=None, by_alias=None, by_name=None)
!!! abstract “Usage Documentation”

[JSON Parsing](../concepts/json.md#json-parsing)

Validate the given JSON data against the Pydantic model.

Parameters:

  • json_data (str | bytes | bytearray) – The JSON data to validate.

  • strict (bool | None) – Whether to enforce types strictly.

  • extra (Optional[Literal['allow', 'ignore', 'forbid']]) – Whether to ignore, allow, or forbid extra data during model validation. See the [extra configuration value][pydantic.ConfigDict.extra] for details.

  • context (Any | None) – Extra variables to pass to the validator.

  • by_alias (bool | None) – Whether to use the field’s alias when validating against the provided input data.

  • by_name (bool | None) – Whether to use the field’s name when validating against the provided input data.

Return type:

Self

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

classmethod model_validate_strings(obj, *, strict=None, extra=None, context=None, by_alias=None, by_name=None)

Validate the given object with string data against the Pydantic model.

Parameters:

  • obj (Any) – The object containing string data to validate.

  • strict (bool | None) – Whether to enforce types strictly.

  • extra (Optional[Literal['allow', 'ignore', 'forbid']]) – Whether to ignore, allow, or forbid extra data during model validation. See the [extra configuration value][pydantic.ConfigDict.extra] for details.

  • context (Any | None) – Extra variables to pass to the validator.

  • by_alias (bool | None) – Whether to use the field’s alias when validating against the provided input data.

  • by_name (bool | None) – Whether to use the field’s name when validating against the provided input data.

Return type:

Self

Returns:

The validated Pydantic model.

unhash_model_subspace_indices()[source]

Get the location of a model in its subspace.

Return type:

list[int]

Returns:

The location, as indices of the subspace.

petab_select.model.default_compare(model0, model1, criterion, criterion_threshold=0)[source]

Compare two calibrated models by their criterion values.

It is assumed that the model model0 provides a value for the criterion criterion, or is the VIRTUAL_INITIAL_MODEL.

Parameters:

  • model0 (Model) – The original model.

  • model1 (Model) – The new model.

  • criterion (Criterion) – The criterion.

  • criterion_threshold (float) – The non-negative value by which the new model must improve on the original model.

Return type:

bool

Returns:

True` if ``model1 has a better criterion value than model0, else False.