Realize dev features

molpipeline/abstract_pipeline_elements/core.py

@@ -6,16 +6,9 @@
 import copy
 import inspect
 from collections.abc import Iterable
-from typing import Any, NamedTuple, Union
-
-try:
-    from typing import Self  # type: ignore[attr-defined]
-except ImportError:
-    from typing_extensions import Self
-
+from typing import Any, NamedTuple, Self
 from uuid import uuid4
 
-import numpy as np
 from joblib import Parallel, delayed
 from loguru import logger
 from rdkit import Chem
@@ -55,7 +48,7 @@ def __repr__(self) -> str:
         )
 
 
-OptionalMol = Union[RDKitMol, InvalidInstance]
+OptionalMol = RDKitMol | InvalidInstance
 
 
 class RemovedInstance:  # pylint: disable=too-few-public-methods
@@ -209,11 +202,6 @@ def set_params(self, **parameters: Any) -> Self:
             setattr(self, att_name, att_value)
         return self
 
-    @property
-    def additional_attributes(self) -> dict[str, Any]:
-        """Any attribute relevant for recreating and exact copy, which is not a parameter."""
-        return {}
-
     @property
     def n_jobs(self) -> int:
         """Get the number of cores."""
@@ -236,12 +224,6 @@ def requires_fitting(self) -> bool:
         """Return whether the object requires fitting or not."""
         return self._requires_fitting
 
-    def finish(self) -> None:
-        """Inform object that iteration has been finished. Does in most cases nothing.
-
-        Called after all transform singles have been processed. From MolPipeline
-        """
-
     def fit(self, values: Any, labels: Any = None) -> Self:
         """Fit object to input_values.
 
@@ -391,29 +373,6 @@ def parameters(self, parameters: Any) -> None:
         """
         self.set_params(**parameters)
 
-    def copy(self) -> Self:
-        """Copy the object.
-
-        Raises
-        ------
-        AssertionError
-            If the object cannot be copied.
-
-        Returns
-        -------
-        Self
-            Copy of the object.
-
-        """
-        recreated_object = self.__class__(**self.parameters)
-        for key, value in self.additional_attributes.items():
-            if not hasattr(recreated_object, key):
-                raise AssertionError(
-                    f"Cannot set attribute {key} on {self.__class__.__name__}. This should not happen!"
-                )
-            setattr(recreated_object, key, copy.copy(value))
-        return recreated_object
-
     def fit_to_result(self, values: Any) -> Self:
         """Fit object to result of transformed values.
 
@@ -589,32 +548,8 @@ def transform(self, values: Any) -> Any:
         output_rows = self.pretransform(values)
         output_rows = self.finalize_list(output_rows)
         output = self.assemble_output(output_rows)
-        self.finish()
         return output
 
-    def to_json(self) -> dict[str, Any]:
-        """Return all defining attributes of object as dict.
-
-        Returns
-        -------
-        dict[str, Any]
-            A dictionary with all attributes necessary to initialize a object with same parameters.
-        """
-        json_dict: dict[str, Any] = {
-            "__name__": self.__class__.__name__,
-            "__module__": self.__class__.__module__,
-        }
-        json_dict.update(self.parameters)
-        if self.additional_attributes:
-            adittional_attributes = {}
-            for key, value in self.additional_attributes.items():
-                if isinstance(value, np.ndarray):
-                    adittional_attributes[key] = value.tolist()
-                else:
-                    adittional_attributes[key] = value
-            json_dict["additional_attributes"] = adittional_attributes
-        return json_dict
-
 
 class MolToMolPipelineElement(TransformingPipelineElement, abc.ABC):
     """Abstract PipelineElement where input and outputs are molecules."""