Plotting capabilities

Pipeline plots use fieldless capability mixins. They can be added to existing Pydantic operation or analysis classes without changing those classes’ constructors or serialized settings.

Lifecycle mixins

class phenotypic.abc_.plotting.PhtPlot

Bases: object

Methods-only mixin for saveable figures and complete reports.

PhtPlot has no fields, constructor, abstract methods, or persistent instance state. It can therefore be combined with an existing Pydantic model without changing that model’s schema or serialization.

Subject-taking figure methods receive a subject passed to inspect or report. Helpers that already hold their subject may instead override _figure_subject() and declare subject-free figure methods.

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

class phenotypic.abc_.plotting.PlotImage

Bases: PhtPlot

Mark a plot for refresh after one image completes its pipeline stage.

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

class phenotypic.abc_.plotting.PlotMeas

Bases: PhtPlot

Mark a plot for refresh after the measurements mirror is updated.

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

class phenotypic.abc_.plotting.PlotAnalysis

Bases: PhtPlot

Mark a plot for refresh after its selected analysis input is updated.

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

class phenotypic.abc_.plotting.PlotQc

Bases: PhtPlot

Mark a plot for refresh after its selected input or QC state changes.

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

Figure composition

class phenotypic.abc_.plotting.Control(label: str, kind: Literal['float', 'select', 'bool', 'text'], default: Any, bounds: tuple[float, float] | None = None, step: float | None = None, options: tuple[Any, ...] | None = None, help: str | None = None)

Bases: object

Renderer-neutral input bound to a figure method keyword argument.

Controls are bound by identity. Reusing one Control instance across figure methods creates one shared control, while equal but distinct instances remain independent.

Parameters:

• label (str) – Human-readable control label.

• kind (Literal['float', 'select', 'bool', 'text']) – Control renderer kind.

• default (Any) – Initial value for the control.

• bounds (tuple[float, float] | None) – Required (low, high) range for a float control.

• step (float | None) – Optional step for a float control.

• options (tuple[Any, ...] | None) – Required allowed values for a select control.

• help (str | None) – Optional help text.

Raises:

ValueError – If the default or kind-specific settings are invalid.

bounds: tuple[float, float] | None = None

default: Any

help: str | None = None

kind: Literal['float', 'select', 'bool', 'text']

label: str

options: tuple[Any, ...] | None = None

step: float | None = None

class phenotypic.abc_.plotting.FigureSpec(title: str, section: str, controls: dict[str, Control], description: Any, primary: bool, name: str, method: Callable[..., 'go.Figure'], wants_subject: bool, subject_param: str | None, order: int)

Bases: object

Metadata attached to a method by figure().

Parameters:

• title (str)

• section (str)

• controls (dict[str, Control])

• description (Any)

• primary (bool)

• name (str)

• method (Callable[..., 'go.Figure'])

• wants_subject (bool)

• subject_param (str | None)

• order (int)

title

Human-readable figure title.

Type:

str

section

Grouping tag used by report adapters.

Type:

str

controls

Mapping from method keyword to its control.

Type:

dict[str, Control]

description

Optional renderer-neutral explanatory content.

Type:

Any

primary

Whether this is the default PhtPlot.inspect() figure.

Type:

bool

name

Decorated method name.

Type:

str

method

Wrapped, theme-applying method.

Type:

Callable[…, ‘go.Figure’]

wants_subject

Whether the method accepts a positional subject.

Type:

bool

subject_param

Positional subject parameter name, if present.

Type:

str | None

order

Definition-order index.

Type:

int

controls: dict[str, Control]

description: Any

method: Callable[..., 'go.Figure']

name: str

order: int

primary: bool

section: str

subject_param: str | None

title: str

wants_subject: bool

phenotypic.abc_.plotting.figure(*, title: str, section: str = 'default', controls: dict[str, Control] | None = None, description: Any = None, primary: bool = False) → Callable[[Callable[..., 'go.Figure']], Callable[..., 'go.Figure']]

Mark a method as a figure builder and lazily apply the house theme.

A figure method may accept a subject as its first positional parameter. Any positional parameter not named by controls is treated as the subject. Plot-specific parameters that are not subjects must therefore be keyword-only.

Parameters:

• title (str) – Human-readable figure title.

• section (str) – Grouping tag used by report adapters.

• controls (dict[str, Control] | None) – Mapping from method keyword to renderer-neutral control.

• description (Any) – Optional renderer-neutral explanatory content.

• primary (bool) – Whether this is the default figure returned by inspect.

Returns:

A decorator for a Plotly figure-building method.

Raises:

ValueError – If a control key does not name a method parameter.

Return type:

Callable[[Callable[…, ‘go.Figure’]], Callable[…, ‘go.Figure’]]

class phenotypic.abc_.plotting.BoundFigures(provider: PhtPlot, subject: Any)

Bases: object

Transient subject binding for a PhtPlot.

Image subjects are held weakly so a notebook widget cannot extend the lifetime of a complete plate image. Aggregate subjects such as measurement tables are held strongly because they are compact, reusable plot inputs. Figures are rendered on demand rather than cached across control values.

Parameters:

• provider (PhtPlot) – Plot provider whose figures will be rendered.

• subject (Any) – Runtime subject bound to those figures.

render(spec: FigureSpec, **control_values: Any) → go.Figure

Render a figure for the supplied control values.

Parameters:

• spec (FigureSpec) – Figure metadata to render.

• **control_values (Any) – Control values passed to the figure method.

Returns:

The themed Plotly figure.

Return type:

go.Figure

specs() → list[FigureSpec]

Return provider figures in definition order.

Return type:

list[FigureSpec]

property subject: Any

Return the bound runtime subject.

Plot outputs

phenotypic.abc_.plotting.FigureLike = typing.Any

Special type indicating an unconstrained type.

• Any is compatible with every type.

• Any assumed to have all methods.

• All values assumed to be instances of Any.

Note that all the above statements are true from the point of view of static type checkers. At runtime, Any should not be used with instance checks.

class phenotypic.abc_.plotting.PlotOutput(pages: tuple[PlotPage, ...])

Bases: object

Ordered pages returned by a plotting invocation.

Parameters:

pages (tuple[PlotPage, ...])

pages: tuple[PlotPage, ...]

class phenotypic.abc_.plotting.PlotPage(key: str, figure: ~typing.Any, label: str | None = None, metadata: ~typing.Mapping[str, str | int | float | bool | None] = <factory>)

Bases: object

One independently saveable figure page.

Parameters:

• key (str) – Stable logical page key.

• figure (Any) – Plotly or Matplotlib figure.

• label (str | None) – Optional human-readable page label.

• metadata (Mapping[str, str | int | float | bool | None]) – Immutable-by-convention selector metadata.

figure: Any

key: str

label: str | None = None

metadata: Mapping[str, str | int | float | bool | None]

phenotypic.abc_.plotting.canonical_group_key(pairs: list[tuple[str, Any]]) → str

Encode typed grouping pairs without ambiguous string concatenation.

Integer, float, temporal, and string values retain distinct tags. Numeric and temporal payloads use canonical strings so JSON encoder settings and platform formatting cannot change a page identity.

Parameters:

pairs (list[tuple[str, Any]])

Return type:

str

Built-in plots

class phenotypic.plotting.PlotDiagnostics

Bases: BaseModel, PlotImage

Build image-quality diagnostics from a weakly bound call-time image.

classmethod __get_pydantic_json_schema__(core_schema: CoreSchema, handler: GetJsonSchemaHandler, /) → JsonSchemaValue

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs: Any) → None

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after basic class initialization is complete. In particular, attributes like model_fields will be present when this is called, but forward annotations are not guaranteed to be resolved yet, meaning that creating an instance of the class may fail.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by Pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by Pydantic.

Return type:

None

Note

You may want to override [__pydantic_on_complete__()][pydantic.main.BaseModel.__pydantic_on_complete__] instead, which is called once the class and its fields are fully initialized and ready for validation.

classmethod __pydantic_on_complete__() → None

This is called once the class and its fields are fully initialized and ready to be used.

This typically happens when the class is created (just before [__pydantic_init_subclass__()][pydantic.main.BaseModel.__pydantic_init_subclass__] is called on the superclass), except when forward annotations are used that could not immediately be resolved. In that case, it will be called later, when the model is rebuilt automatically or explicitly using [model_rebuild()][pydantic.main.BaseModel.model_rebuild].

Return type:

None

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

Self

classmethod from_orm(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self

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.

Returns:

A new instance of the Model class with validated data.

Return type:

Self

classmethod model_json_schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}', schema_generator: type[~pydantic.json_schema.GenerateJsonSchema] = <class 'pydantic.json_schema.GenerateJsonSchema'>, mode: ~typing.Literal['validation', 'serialization'] = 'validation', *, union_format: ~typing.Literal['any_of', 'primitive_type_array'] = 'any_of') → dict[str, Any]

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:

  • ’any_of’: Use the [anyOf](https://json-schema.org/understanding-json-schema/reference/combining#anyOf)

  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.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str

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.

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.

Return type:

str

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | 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 (MappingNamespace | None) – The types namespace, defaults to 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.

Return type:

bool | None

classmethod model_validate(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, from_attributes: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

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

• extra (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated model instance.

Return type:

Self

classmethod model_validate_json(json_data: str | bytes | bytearray, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

!!! 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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Raises:

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

Return type:

Self

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Return type:

Self

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• path (str | Path)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod parse_obj(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod update_forward_refs(**localns: Any) → None

Parameters:

localns (Any)

Return type:

None

classmethod validate(value: Any) → Self

Parameters:

value (Any)

Return type:

Self

__copy__() → Self

Returns a shallow copy of the model.

Return type:

Self

__deepcopy__(memo: dict[int, Any] | None = None) → Self

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

Self

__init__(**data: Any) → None

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.

Parameters:

data (Any)

Return type:

None

__iter__() → Generator[tuple[str, Any], None, None]

So dict(model) works.

Return type:

Generator[tuple[str, Any], None, None]

__pretty__(fmt: Callable[[Any], Any], **kwargs: Any) → Generator[Any]

Used by devtools (https://python-devtools.helpmanual.io/) to pretty print objects.

Parameters:

• fmt (Callable[[Any], Any])

• kwargs (Any)

Return type:

Generator[Any]

__repr_name__() → str

Name of the instance’s class, used in __repr__.

Return type:

str

__repr_recursion__(object: Any) → str

Returns the string representation of a recursive object.

Parameters:

object (Any)

Return type:

str

__rich_repr__() → RichReprResult

Used by Rich (https://rich.readthedocs.io/en/stable/pretty.html) to pretty print objects.

Return type:

RichReprResult

copy(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, update: Dict[str, Any] | None = None, deep: bool = False) → Self

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 (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – 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.

Returns:

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

Return type:

Self

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

fig_background_estimate(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_contrast_metrics(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_detection_matrix(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_gradient_magnitude(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_intensity_histogram(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_local_contrast_map(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_local_variance(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_noise_autocorrelation(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_orientation_coherence(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_power_spectral_density(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_quality_summary(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

fig_ridge_response(subject: Any, **controls: Any) → Any

Parameters:

• subject (Any)

• controls (Any)

Return type:

Any

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

• encoder (Callable[[Any], Any] | None)

• models_as_dict (bool)

• dumps_kwargs (Any)

Return type:

str

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self

!!! 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.

Returns:

New model instance.

Return type:

Self

model_dump(*, mode: Literal['json', 'python'] | str = 'python', include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → dict[str, Any]

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A dictionary representation of the model.

Return type:

dict[str, Any]

model_dump_json(*, indent: int | None = None, ensure_ascii: bool = False, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → str

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A JSON string representation of the model.

Return type:

str

model_post_init(context: Any, /) → None

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.

Parameters:

context (Any)

Return type:

None

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

model_computed_fields = {}

model_config: ClassVar[ConfigDict] = {'extra': 'forbid'}

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

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”.

model_fields = {}

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.

class phenotypic.plotting.PlotDetectModes

Bases: BaseModel, PlotImage

Compare every registered detection mode for a supplied image.

classmethod __get_pydantic_json_schema__(core_schema: CoreSchema, handler: GetJsonSchemaHandler, /) → JsonSchemaValue

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs: Any) → None

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after basic class initialization is complete. In particular, attributes like model_fields will be present when this is called, but forward annotations are not guaranteed to be resolved yet, meaning that creating an instance of the class may fail.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by Pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by Pydantic.

Return type:

None

Note

You may want to override [__pydantic_on_complete__()][pydantic.main.BaseModel.__pydantic_on_complete__] instead, which is called once the class and its fields are fully initialized and ready for validation.

classmethod __pydantic_on_complete__() → None

This is called once the class and its fields are fully initialized and ready to be used.

This typically happens when the class is created (just before [__pydantic_init_subclass__()][pydantic.main.BaseModel.__pydantic_init_subclass__] is called on the superclass), except when forward annotations are used that could not immediately be resolved. In that case, it will be called later, when the model is rebuilt automatically or explicitly using [model_rebuild()][pydantic.main.BaseModel.model_rebuild].

Return type:

None

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

Self

classmethod from_orm(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self

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.

Returns:

A new instance of the Model class with validated data.

Return type:

Self

classmethod model_json_schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}', schema_generator: type[~pydantic.json_schema.GenerateJsonSchema] = <class 'pydantic.json_schema.GenerateJsonSchema'>, mode: ~typing.Literal['validation', 'serialization'] = 'validation', *, union_format: ~typing.Literal['any_of', 'primitive_type_array'] = 'any_of') → dict[str, Any]

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:

  • ’any_of’: Use the [anyOf](https://json-schema.org/understanding-json-schema/reference/combining#anyOf)

  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.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str

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.

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.

Return type:

str

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | 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 (MappingNamespace | None) – The types namespace, defaults to 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.

Return type:

bool | None

classmethod model_validate(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, from_attributes: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

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

• extra (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated model instance.

Return type:

Self

classmethod model_validate_json(json_data: str | bytes | bytearray, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

!!! 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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Raises:

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

Return type:

Self

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Return type:

Self

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• path (str | Path)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod parse_obj(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod update_forward_refs(**localns: Any) → None

Parameters:

localns (Any)

Return type:

None

classmethod validate(value: Any) → Self

Parameters:

value (Any)

Return type:

Self

__copy__() → Self

Returns a shallow copy of the model.

Return type:

Self

__deepcopy__(memo: dict[int, Any] | None = None) → Self

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

Self

__init__(**data: Any) → None

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.

Parameters:

data (Any)

Return type:

None

__iter__() → Generator[tuple[str, Any], None, None]

So dict(model) works.

Return type:

Generator[tuple[str, Any], None, None]

__pretty__(fmt: Callable[[Any], Any], **kwargs: Any) → Generator[Any]

Used by devtools (https://python-devtools.helpmanual.io/) to pretty print objects.

Parameters:

• fmt (Callable[[Any], Any])

• kwargs (Any)

Return type:

Generator[Any]

__repr_name__() → str

Name of the instance’s class, used in __repr__.

Return type:

str

__repr_recursion__(object: Any) → str

Returns the string representation of a recursive object.

Parameters:

object (Any)

Return type:

str

__rich_repr__() → RichReprResult

Used by Rich (https://rich.readthedocs.io/en/stable/pretty.html) to pretty print objects.

Return type:

RichReprResult

copy(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, update: Dict[str, Any] | None = None, deep: bool = False) → Self

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 (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – 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.

Returns:

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

Return type:

Self

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → Any

Return the primary saveable figure.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• for_save (bool) – Forwarded when the selected figure accepts it.

• **overrides (Any) – Values overriding declared control defaults.

Returns:

The themed primary figure. Multi-page producers may override this method and return a runtime plotting output.

Raises:

ValueError – If an override is not a declared control.

Return type:

Any

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

• encoder (Callable[[Any], Any] | None)

• models_as_dict (bool)

• dumps_kwargs (Any)

Return type:

str

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self

!!! 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.

Returns:

New model instance.

Return type:

Self

model_dump(*, mode: Literal['json', 'python'] | str = 'python', include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → dict[str, Any]

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A dictionary representation of the model.

Return type:

dict[str, Any]

model_dump_json(*, indent: int | None = None, ensure_ascii: bool = False, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → str

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A JSON string representation of the model.

Return type:

str

model_post_init(context: Any, /) → None

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.

Parameters:

context (Any)

Return type:

None

report(subject: Any = None, **overrides: Any) → Any

Return the complete composed or interactive report.

Parameters:

• subject (Any) – Runtime subject, or None to use held subject state.

• **overrides (Any) – Reserved for specialized report implementations.

Returns:

A composed Plotly figure when all figures are control-free, or an ipywidgets report when any figure declares controls.

Raises:

• RuntimeError – If no figure methods are declared.

• ValueError – If the base report receives overrides. Concrete plots may override this method to expose report-specific parameters.

Return type:

Any

model_computed_fields = {}

model_config: ClassVar[ConfigDict] = {'extra': 'forbid'}

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

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”.

model_fields = {}

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.

class phenotypic.plotting.PlotMeasTimeSeries(*, page_by: ~typing.Annotated[list[str], _ColumnRefMarker('measurements')] = <factory>, environment_by: ~typing.Annotated[list[str], _ColumnRefMarker('measurements')], replicate_by: ~typing.Annotated[list[str], _ColumnRefMarker('measurements')], time: ~typing.Annotated[str, _ColumnRefMarker('measurements')] = 'MetadataCulture_Time', measurements: ~typing.Annotated[list[str], _ColumnRefMarker('measurements')] = <factory>, connect: bool = True)

Bases: BaseModel, PlotMeas

Plot replicate scatter time series across grouped environments.

Each page is one genetic grouping, each row is a measurement, and each column is one environmental grouping. Replicates remain separate traces; values are never averaged or otherwise aggregated.

Parameters:

• page_by (Annotated[list[str], _ColumnRefMarker('measurements')]) – Columns defining separate figure pages.

• environment_by (Annotated[list[str], _ColumnRefMarker('measurements')]) – Columns defining subplot columns within a page.

• replicate_by (Annotated[list[str], _ColumnRefMarker('measurements')]) – Columns identifying biological or technical replicates.

• time (Annotated[str, _ColumnRefMarker('measurements')]) – Numeric or ordered time column used on the x-axis.

• measurements (Annotated[list[str], _ColumnRefMarker('measurements')]) – Numeric measurement columns. An empty list selects eligible columns automatically.

• connect (bool) – Whether to connect points within each replicate trace.

classmethod __get_pydantic_json_schema__(core_schema: CoreSchema, handler: GetJsonSchemaHandler, /) → JsonSchemaValue

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs: Any) → None

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after basic class initialization is complete. In particular, attributes like model_fields will be present when this is called, but forward annotations are not guaranteed to be resolved yet, meaning that creating an instance of the class may fail.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by Pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by Pydantic.

Return type:

None

Note

You may want to override [__pydantic_on_complete__()][pydantic.main.BaseModel.__pydantic_on_complete__] instead, which is called once the class and its fields are fully initialized and ready for validation.

classmethod __pydantic_on_complete__() → None

This is called once the class and its fields are fully initialized and ready to be used.

This typically happens when the class is created (just before [__pydantic_init_subclass__()][pydantic.main.BaseModel.__pydantic_init_subclass__] is called on the superclass), except when forward annotations are used that could not immediately be resolved. In that case, it will be called later, when the model is rebuilt automatically or explicitly using [model_rebuild()][pydantic.main.BaseModel.model_rebuild].

Return type:

None

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

Self

classmethod from_orm(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self

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.

Returns:

A new instance of the Model class with validated data.

Return type:

Self

classmethod model_json_schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}', schema_generator: type[~pydantic.json_schema.GenerateJsonSchema] = <class 'pydantic.json_schema.GenerateJsonSchema'>, mode: ~typing.Literal['validation', 'serialization'] = 'validation', *, union_format: ~typing.Literal['any_of', 'primitive_type_array'] = 'any_of') → dict[str, Any]

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:

  • ’any_of’: Use the [anyOf](https://json-schema.org/understanding-json-schema/reference/combining#anyOf)

  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.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str

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.

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.

Return type:

str

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | 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 (MappingNamespace | None) – The types namespace, defaults to 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.

Return type:

bool | None

classmethod model_validate(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, from_attributes: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

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

• extra (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated model instance.

Return type:

Self

classmethod model_validate_json(json_data: str | bytes | bytearray, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

!!! 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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Raises:

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

Return type:

Self

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Return type:

Self

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• path (str | Path)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod parse_obj(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod update_forward_refs(**localns: Any) → None

Parameters:

localns (Any)

Return type:

None

classmethod validate(value: Any) → Self

Parameters:

value (Any)

Return type:

Self

__copy__() → Self

Returns a shallow copy of the model.

Return type:

Self

__deepcopy__(memo: dict[int, Any] | None = None) → Self

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

Self

__init__(**data: Any) → None

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.

Parameters:

data (Any)

Return type:

None

__iter__() → Generator[tuple[str, Any], None, None]

So dict(model) works.

Return type:

Generator[tuple[str, Any], None, None]

__pretty__(fmt: Callable[[Any], Any], **kwargs: Any) → Generator[Any]

Used by devtools (https://python-devtools.helpmanual.io/) to pretty print objects.

Parameters:

• fmt (Callable[[Any], Any])

• kwargs (Any)

Return type:

Generator[Any]

__repr_name__() → str

Name of the instance’s class, used in __repr__.

Return type:

str

__repr_recursion__(object: Any) → str

Returns the string representation of a recursive object.

Parameters:

object (Any)

Return type:

str

__rich_repr__() → RichReprResult

Used by Rich (https://rich.readthedocs.io/en/stable/pretty.html) to pretty print objects.

Return type:

RichReprResult

copy(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, update: Dict[str, Any] | None = None, deep: bool = False) → Self

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 (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – 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.

Returns:

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

Return type:

Self

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → PlotOutput

Build one Plotly page per configured page grouping.

Parameters:

• subject (Any) – Current measurement mirror as a pandas DataFrame.

• for_save (bool) – Accepted for the common plotting contract. Plot geometry is identical for interactive and saved output.

• **overrides (Any) – Optional field-value overrides for this invocation.

Returns:

Ordered multi-page output. Empty input returns no pages.

Return type:

PlotOutput

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

• encoder (Callable[[Any], Any] | None)

• models_as_dict (bool)

• dumps_kwargs (Any)

Return type:

str

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self

!!! 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.

Returns:

New model instance.

Return type:

Self

model_dump(*, mode: Literal['json', 'python'] | str = 'python', include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → dict[str, Any]

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A dictionary representation of the model.

Return type:

dict[str, Any]

model_dump_json(*, indent: int | None = None, ensure_ascii: bool = False, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → str

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A JSON string representation of the model.

Return type:

str

model_post_init(context: Any, /) → None

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.

Parameters:

context (Any)

Return type:

None

report(subject: Any = None, **overrides: Any) → PlotOutput

Return the complete multi-page report.

Parameters:

• subject (Any)

• overrides (Any)

Return type:

PlotOutput

connect: bool

environment_by: ColumnRefList

measurements: ColumnRefList

model_computed_fields = {}

model_config: ClassVar[ConfigDict] = {'extra': 'forbid'}

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

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”.

model_fields = {'connect': FieldInfo(annotation=bool, required=False, default=True), 'environment_by': FieldInfo(annotation=list[str], required=True, metadata=[_ColumnRefMarker('measurements')]), 'measurements': FieldInfo(annotation=list[str], required=False, default_factory=list, metadata=[_ColumnRefMarker('measurements')]), 'page_by': FieldInfo(annotation=list[str], required=False, default_factory=<lambda>, metadata=[_ColumnRefMarker('measurements')]), 'replicate_by': FieldInfo(annotation=list[str], required=True, metadata=[_ColumnRefMarker('measurements')]), 'time': FieldInfo(annotation=str, required=False, default='MetadataCulture_Time', metadata=[_ColumnRefMarker('measurements')])}

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.

page_by: ColumnRefList

replicate_by: ColumnRefList

time: ColumnRef

class phenotypic.plotting.PlotColonyMetricOverTime(*, on: ~typing.Annotated[str, _ColumnRefMarker('measurements')], strain_label: ~typing.Annotated[str, _ColumnRefMarker('measurements')] = 'MetadataGenetic_Strain', groupby: ~typing.Annotated[list[str], _ColumnRefMarker('measurements')] = <factory>, replicate_label: ~typing.Annotated[str, _ColumnRefMarker('measurements')] = 'MetadataSample_BioReplicate', time: ~typing.Annotated[str, _ColumnRefMarker('measurements')] = 'MetadataCulture_Time', connect: bool = True)

Bases: BaseModel, PlotMeas

Plot one colony metric over time by strain and environment.

The plot emits one page per strain, one subplot column per environmental group, and one trace per replicate. Values are never aggregated. on accepts any numeric measurement column, so the same class can visualize radius, area, intensity, or a custom numeric colony metric.

Parameters:

• on (Annotated[str, _ColumnRefMarker('measurements')]) – Numeric measurement column plotted on the y-axis.

• strain_label (Annotated[str, _ColumnRefMarker('measurements')]) – Column defining the strain on each figure page.

• groupby (Annotated[list[str], _ColumnRefMarker('measurements')]) – Columns defining the subplot groups on each page. Defaults to growth medium.

• replicate_label (Annotated[str, _ColumnRefMarker('measurements')]) – Column identifying replicate traces. Defaults to the biological replicate identifier.

• time (Annotated[str, _ColumnRefMarker('measurements')]) – Numeric or ordered time column used on the x-axis.

• connect (bool) – Whether to connect points within each replicate trace.

classmethod __get_pydantic_json_schema__(core_schema: CoreSchema, handler: GetJsonSchemaHandler, /) → JsonSchemaValue

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs: Any) → None

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after basic class initialization is complete. In particular, attributes like model_fields will be present when this is called, but forward annotations are not guaranteed to be resolved yet, meaning that creating an instance of the class may fail.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by Pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by Pydantic.

Return type:

None

Note

You may want to override [__pydantic_on_complete__()][pydantic.main.BaseModel.__pydantic_on_complete__] instead, which is called once the class and its fields are fully initialized and ready for validation.

classmethod __pydantic_on_complete__() → None

This is called once the class and its fields are fully initialized and ready to be used.

This typically happens when the class is created (just before [__pydantic_init_subclass__()][pydantic.main.BaseModel.__pydantic_init_subclass__] is called on the superclass), except when forward annotations are used that could not immediately be resolved. In that case, it will be called later, when the model is rebuilt automatically or explicitly using [model_rebuild()][pydantic.main.BaseModel.model_rebuild].

Return type:

None

classmethod construct(_fields_set: set[str] | None = None, **values: Any) → Self

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

Self

classmethod from_orm(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod model_construct(_fields_set: set[str] | None = None, **values: Any) → Self

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.

Returns:

A new instance of the Model class with validated data.

Return type:

Self

classmethod model_json_schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}', schema_generator: type[~pydantic.json_schema.GenerateJsonSchema] = <class 'pydantic.json_schema.GenerateJsonSchema'>, mode: ~typing.Literal['validation', 'serialization'] = 'validation', *, union_format: ~typing.Literal['any_of', 'primitive_type_array'] = 'any_of') → dict[str, Any]

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:

  • ’any_of’: Use the [anyOf](https://json-schema.org/understanding-json-schema/reference/combining#anyOf)

  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.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params: tuple[type[Any], ...]) → str

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.

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.

Return type:

str

classmethod model_rebuild(*, force: bool = False, raise_errors: bool = True, _parent_namespace_depth: int = 2, _types_namespace: MappingNamespace | None = None) → bool | 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 (MappingNamespace | None) – The types namespace, defaults to 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.

Return type:

bool | None

classmethod model_validate(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, from_attributes: bool | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

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

• extra (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated model instance.

Return type:

Self

classmethod model_validate_json(json_data: str | bytes | bytearray, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

!!! 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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Raises:

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

Return type:

Self

classmethod model_validate_strings(obj: Any, *, strict: bool | None = None, extra: Literal['allow', 'ignore', 'forbid'] | None = None, context: Any | None = None, by_alias: bool | None = None, by_name: bool | None = None) → Self

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 (Literal['allow', 'ignore', 'forbid'] | None) – 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.

Returns:

The validated Pydantic model.

Return type:

Self

classmethod parse_file(path: str | Path, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• path (str | Path)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod parse_obj(obj: Any) → Self

Parameters:

obj (Any)

Return type:

Self

classmethod parse_raw(b: str | bytes, *, content_type: str | None = None, encoding: str = 'utf8', proto: DeprecatedParseProtocol | None = None, allow_pickle: bool = False) → Self

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (DeprecatedParseProtocol | None)

• allow_pickle (bool)

Return type:

Self

classmethod schema(by_alias: bool = True, ref_template: str = '#/$defs/{model}') → Dict[str, Any]

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias: bool = True, ref_template: str = '#/$defs/{model}', **dumps_kwargs: Any) → str

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod update_forward_refs(**localns: Any) → None

Parameters:

localns (Any)

Return type:

None

classmethod validate(value: Any) → Self

Parameters:

value (Any)

Return type:

Self

__copy__() → Self

Returns a shallow copy of the model.

Return type:

Self

__deepcopy__(memo: dict[int, Any] | None = None) → Self

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

Self

__init__(**data: Any) → None

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.

Parameters:

data (Any)

Return type:

None

__iter__() → Generator[tuple[str, Any], None, None]

So dict(model) works.

Return type:

Generator[tuple[str, Any], None, None]

__pretty__(fmt: Callable[[Any], Any], **kwargs: Any) → Generator[Any]

Used by devtools (https://python-devtools.helpmanual.io/) to pretty print objects.

Parameters:

• fmt (Callable[[Any], Any])

• kwargs (Any)

Return type:

Generator[Any]

__repr_name__() → str

Name of the instance’s class, used in __repr__.

Return type:

str

__repr_recursion__(object: Any) → str

Returns the string representation of a recursive object.

Parameters:

object (Any)

Return type:

str

__rich_repr__() → RichReprResult

Used by Rich (https://rich.readthedocs.io/en/stable/pretty.html) to pretty print objects.

Return type:

RichReprResult

copy(*, include: AbstractSetIntStr | MappingIntStrAny | None = None, exclude: AbstractSetIntStr | MappingIntStrAny | None = None, update: Dict[str, Any] | None = None, deep: bool = False) → Self

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 (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (AbstractSetIntStr | MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – 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.

Returns:

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

Return type:

Self

dict(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False) → Dict[str, Any]

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

figures(subject: Any = None) → BoundFigures

Bind a subject to figures for use by a renderer adapter.

Parameters:

subject (Any)

Return type:

BoundFigures

inspect(subject: Any = None, *, for_save: bool = False, **overrides: Any) → PlotOutput

Build one page per configured colony grouping.

Parameters:

• subject (Any) – Current measurement mirror as a pandas DataFrame.

• for_save (bool) – Accepted for the common plotting contract.

• **overrides (Any) – Optional field-value overrides for this invocation.

Returns:

Ordered multi-page time-series output.

Return type:

PlotOutput

iter_figures() → list[FigureSpec]

Return all visible figure specs in definition order.

Figure discovery follows normal Python override rules across the MRO. An undecorated override removes an inherited figure, while a decorated override retains the inherited figure’s position.

Return type:

list[FigureSpec]

json(*, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, by_alias: bool = False, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, encoder: Callable[[Any], Any] | None = PydanticUndefined, models_as_dict: bool = PydanticUndefined, **dumps_kwargs: Any) → str

Parameters:

• include (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

• encoder (Callable[[Any], Any] | None)

• models_as_dict (bool)

• dumps_kwargs (Any)

Return type:

str

model_copy(*, update: Mapping[str, Any] | None = None, deep: bool = False) → Self

!!! 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.

Returns:

New model instance.

Return type:

Self

model_dump(*, mode: Literal['json', 'python'] | str = 'python', include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → dict[str, Any]

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A dictionary representation of the model.

Return type:

dict[str, Any]

model_dump_json(*, indent: int | None = None, ensure_ascii: bool = False, include: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, exclude: set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | None = None, context: Any | None = None, by_alias: bool | None = None, exclude_unset: bool = False, exclude_defaults: bool = False, exclude_none: bool = False, exclude_computed_fields: bool = False, round_trip: bool = False, warnings: bool | Literal['none', 'warn', 'error'] = True, fallback: Callable[[Any], Any] | None = None, serialize_as_any: bool = False) → str

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

• exclude (set[int] | set[str] | Mapping[int, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, IncEx | bool] | bool] | Mapping[str, set[int] | set[str] | Mapping[int, IncEx | bool] | Mapping[str, 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 (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 (Callable[[Any], Any] | None) – 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.

Returns:

A JSON string representation of the model.

Return type:

str

model_post_init(context: Any, /) → None

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.

Parameters:

context (Any)

Return type:

None

report(subject: Any = None, **overrides: Any) → PlotOutput

Return the complete multi-page metric report.

Parameters:

• subject (Any)

• overrides (Any)

Return type:

PlotOutput

connect: bool

groupby: ColumnRefList

model_computed_fields = {}

model_config: ClassVar[ConfigDict] = {'extra': 'forbid'}

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

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”.

model_fields = {'connect': FieldInfo(annotation=bool, required=False, default=True), 'groupby': FieldInfo(annotation=list[str], required=False, default_factory=<lambda>, metadata=[_ColumnRefMarker('measurements')]), 'on': FieldInfo(annotation=str, required=True, metadata=[_ColumnRefMarker('measurements')]), 'replicate_label': FieldInfo(annotation=str, required=False, default='MetadataSample_BioReplicate', metadata=[_ColumnRefMarker('measurements')]), 'strain_label': FieldInfo(annotation=str, required=False, default='MetadataGenetic_Strain', metadata=[_ColumnRefMarker('measurements')]), 'time': FieldInfo(annotation=str, required=False, default='MetadataCulture_Time', metadata=[_ColumnRefMarker('measurements')])}

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.

on: ColumnRef

replicate_label: ColumnRef

strain_label: ColumnRef

time: ColumnRef