pestifer.core.example module

Defines the Example class for managing examples.

class pestifer.core.example.Example(*args, example_id: int, title: str, shortname: str, db_id: str | None = None, author_name: str | None = None, author_email: str | None = None, input: str | Path | None = None, auxiliary_inputs: list[str | Path] | None = None, outputs: list[str | Path] | None = None)

Bases: BaseObj

Represents an example.

author_email: str | None

author_name: str | None

auxiliary_inputs: list[str | Path] | None

db_id: str | None

example_id: int

folder_name_format: ClassVar[str] = 'ex{example_id:02d}'

format for the name of the root folder of each example

input: str | Path | None

inputs_subdir: ClassVar[str] = 'inputs'

property inputspath: Path

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': False}

Configuration for pydantic.BaseModel.

model_post_init(context: Any, /) → None

This function is meant to behave like a BaseModel method to initialize private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

• self – The BaseModel instance.

• context – The context.

outputs: list[str | Path] | None

outputs_subdir: ClassVar[str] = 'outputs'

property outputspath: Path

report_line(formatter='{:>7s}    {:>4s}  {:<30s}    {}') → str

Generate a formatted line for reporting the example.

Parameters:

formatter (str, optional) – A format string for the report. Default is a string that formats the index, name, pdbID, and title of the example.

Returns:

A formatted string representing the example.

Return type:

str

property rootfolderpath: Path

property scriptname: str

property scriptpath: Path

shortname: str

title: str

to_dict(ignore_none: bool = False) → dict

Convert the example to a dictionary representation.

Returns:

A dictionary containing the example’s attributes.

Return type:

dict

to_yaml() → str

Convert the example to a YAML string.

Returns:

A YAML representation of the example.

Return type:

str

update_options(author_name: str = None, author_email: str = None, auxiliary_inputs: list[str] = None, outputs: list[str] = None) → Example

Update the optional attributes of the example in place. Return the Example instance itself.

Parameters:

• author_name (str, optional) – The new name of the author of the example.

• author_email (str, optional) – The new email of the author of the example.

• auxiliary_inputs (list[str], optional) – A new list of auxiliary inputs for the example.

• outputs (list[str], optional) – A new list of outputs for the example.

Returns:

The updated Example instance.

Return type:

Example

class pestifer.core.example.ExampleList(initlist: Iterable[T] = ())

Bases: BaseObjList[Example]

Represents a list of examples.

Inherits from UserList to provide list-like behavior for managing examples.

append(example: Example)

Append an Example instance to the list.

Parameters:

example (Example) – The Example instance to append.

describe() → str

Abstract method to describe the contents of the BaseObjList. Subclasses should implement this method to provide a meaningful description.

classmethod from_list_of_dicts(examples_list) → ExampleList

Create an ExampleList from a list of dictionaries.

Parameters:

examples_list (list of dict) – A list of dictionaries, each representing an example.

Returns:

An instance of ExampleList containing the examples.

Return type:

ExampleList

from_yaml(yaml_str: str, overwrite: bool = False)

Load examples from a YAML string.

Parameters:

• yaml_str (str) – A YAML string containing the examples.

• overwrite (bool) – Whether to overwrite existing examples.

get_example_by_example_id(example_id: int) → Example

get_example_by_shortname(shortname: str) → Example

Get an example by its shortname.

Parameters:

name (str) – The name of the example to retrieve.

Returns:

The Example instance with the specified name or None if not found.

Return type:

Example

classmethod read_yaml(yaml_str: str)

Load examples from a YAML string.

Parameters:

yaml_str (str) – A YAML string containing the examples.

to_list_of_dicts() → list

Convert the list of examples to a list of dictionaries.

Returns:

A list of dictionaries, each representing an example.

Return type:

list

to_yaml() → str

Convert the list of examples to a YAML string.

Returns:

A YAML representation of the examples.

Return type:

str