Merge branch 'refs/heads/main' into 68-makescaffoldgeneric-set-all-ca…

…rbons-to-wild-card-symbols-to-allow-a-substrcutre-search

# Conflicts:
#	molpipeline/mol2mol/scaffolds.py

molpipeline/abstract_pipeline_elements/core.py

@@ -97,21 +97,23 @@ class ABCPipelineElement(abc.ABC):
 
     def __init__(
         self,
-        name: str = "ABCPipelineElement",
+        name: Optional[str] = None,
         n_jobs: int = 1,
         uuid: Optional[str] = None,
     ) -> None:
         """Initialize ABCPipelineElement.
 
         Parameters
         ----------
-        name: str
+        name: Optional[str], optional (default=None)
             Name of PipelineElement
         n_jobs: int
             Number of cores used for processing.
         uuid: Optional[str]
             Unique identifier of the PipelineElement.
         """
+        if name is None:
+            name = self.__class__.__name__
         self.name = name
         self.n_jobs = n_jobs
         if uuid is None:
@@ -182,12 +184,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             "uuid": self.uuid,
         }
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """As the setter function cannot be assessed with super(), this method is implemented for inheritance.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Parameters to be set.
 
         Returns
@@ -338,15 +340,15 @@ class TransformingPipelineElement(ABCPipelineElement):
 
     def __init__(
         self,
-        name: str = "ABCPipelineElement",
+        name: Optional[str] = None,
         n_jobs: int = 1,
         uuid: Optional[str] = None,
     ) -> None:
         """Initialize ABCPipelineElement.
 
         Parameters
         ----------
-        name: str
+        name: Optional[str], optional (default=None)
             Name of PipelineElement
         n_jobs: int
             Number of cores used for processing.
@@ -377,12 +379,12 @@ def parameters(self) -> dict[str, Any]:
         return self.get_params()
 
     @parameters.setter
-    def parameters(self, **parameters: dict[str, Any]) -> None:
+    def parameters(self, **parameters: Any) -> None:
         """Set the parameters of the object.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Object parameters as a dictionary.
 
         Returns
@@ -616,25 +618,6 @@ class MolToMolPipelineElement(TransformingPipelineElement, abc.ABC):
     _input_type = "RDKitMol"
     _output_type = "RDKitMol"
 
-    def __init__(
-        self,
-        name: str = "MolToMolPipelineElement",
-        n_jobs: int = 1,
-        uuid: Optional[str] = None,
-    ) -> None:
-        """Initialize MolToMolPipelineElement.
-
-        Parameters
-        ----------
-        name: str
-            Name of the PipelineElement.
-        n_jobs: int
-            Number of cores used for processing.
-        uuid: Optional[str]
-            Unique identifier of the PipelineElement.
-        """
-        super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
-
     def transform(self, values: list[OptionalMol]) -> list[OptionalMol]:
         """Transform list of molecules to list of molecules.
 
@@ -700,25 +683,6 @@ class AnyToMolPipelineElement(TransformingPipelineElement, abc.ABC):
 
     _output_type = "RDKitMol"
 
-    def __init__(
-        self,
-        name: str = "AnyToMolPipelineElement",
-        n_jobs: int = 1,
-        uuid: Optional[str] = None,
-    ) -> None:
-        """Initialize AnyToMolPipelineElement.
-
-        Parameters
-        ----------
-        name: str
-            Name of the PipelineElement.
-        n_jobs: int
-            Number of cores used for processing.
-        uuid: Optional[str]
-            Unique identifier of the PipelineElement.
-        """
-        super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
-
     def transform(self, values: Any) -> list[OptionalMol]:
         """Transform list of instances to list of molecules.
 
@@ -756,25 +720,6 @@ class MolToAnyPipelineElement(TransformingPipelineElement, abc.ABC):
 
     _input_type = "RDKitMol"
 
-    def __init__(
-        self,
-        name: str = "MolToAnyPipelineElement",
-        n_jobs: int = 1,
-        uuid: Optional[str] = None,
-    ) -> None:
-        """Initialize MolToAnyPipelineElement.
-
-        Parameters
-        ----------
-        name: str
-            Name of the PipelineElement.
-        n_jobs: int
-            Number of cores used for processing.
-        uuid: Optional[str]
-            Unique identifier of the PipelineElement.
-        """
-        super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
-
     @abc.abstractmethod
     def pretransform_single(self, value: RDKitMol) -> Any:
         """Transform the molecule, but skip parameters learned during fitting.

molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py

@@ -140,12 +140,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
 
         return parameters
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set object parameters relevant for copying the class.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dictionary of parameter names and values.
 
         Returns
@@ -160,7 +160,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
                 raise ValueError(
                     f"return_as has to be one of {get_args(OutputDatatype)}! (Received: {return_as})"
                 )
-            self._return_as = return_as  # type: ignore
+            self._return_as = return_as
         super().set_params(**parameter_dict_copy)
         return self
 
@@ -300,12 +300,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
 
         return parameters
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set object parameters relevant for copying the class.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dictionary of parameter names and values.
 
         Returns
@@ -398,12 +398,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
         parameters.pop("fill_value", None)
         return parameters
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dictionary of parameter names and values.
 
         Returns
@@ -417,7 +417,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
 
         # explicitly check for None, since 0 is a valid value
         if radius is not None:
-            self._radius = radius  # type: ignore
+            self._radius = radius
         # explicitly check for None, since False is a valid value
         if use_features is not None:
             self._use_features = bool(use_features)

molpipeline/abstract_pipeline_elements/mol2any/mol2floatvector.py

@@ -107,12 +107,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             params["standardizer"] = self._standardizer
         return params
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dictionary with parameter names and corresponding values.
 
         Returns
@@ -123,7 +123,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         parameter_copy = dict(parameters)
         standardizer = parameter_copy.pop("standardizer", None)
         if standardizer is not None:
-            self._standardizer = standardizer  # type: ignore
+            self._standardizer = standardizer
         super().set_params(**parameter_copy)
         return self
 

molpipeline/any2mol/bin2mol.py

@@ -2,8 +2,6 @@
 
 from __future__ import annotations
 
-from typing import Optional
-
 from rdkit import Chem
 
 from molpipeline.abstract_pipeline_elements.core import (
@@ -16,25 +14,6 @@
 class BinaryToMol(AnyToMolPipelineElement):
     """Transforms binary string representation to RDKit Mol objects."""
 
-    def __init__(
-        self,
-        name: str = "bin2mol",
-        n_jobs: int = 1,
-        uuid: Optional[str] = None,
-    ) -> None:
-        """Initialize BinaryToMol.
-
-        Parameters
-        ----------
-        name: str, optional (default="bin2mol")
-            Name of PipelineElement.
-        n_jobs: int, optional (default=1)
-            Number of cores used.
-        uuid: str | None, optional (default=None)
-            UUID of the pipeline element. If None, a random UUID is generated.
-        """
-        super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
-
     def pretransform_single(self, value: str) -> OptionalMol:
         """Transform binary string to molecule.
 

molpipeline/any2mol/sdf2mol.py

@@ -71,12 +71,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             params["identifier"] = self.identifier
         return params
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters of the object.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dictionary containing all parameters defining the object.
 
         Returns
@@ -86,7 +86,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         """
         super().set_params(**parameters)
         if "identifier" in parameters:
-            self.identifier = parameters["identifier"]  # type: ignore
+            self.identifier = parameters["identifier"]
         return self
 
     def finish(self) -> None:

molpipeline/any2mol/smiles2mol.py

@@ -2,8 +2,6 @@
 
 from __future__ import annotations
 
-from typing import Optional
-
 from rdkit import Chem
 
 from molpipeline.abstract_pipeline_elements.any2mol.string2mol import (
@@ -16,25 +14,6 @@
 class SmilesToMol(_StringToMolPipelineElement):
     """Transforms Smiles to RDKit Mol objects."""
 
-    def __init__(
-        self,
-        name: str = "smiles2mol",
-        n_jobs: int = 1,
-        uuid: Optional[str] = None,
-    ) -> None:
-        """Initialize SmilesToMol.
-
-        Parameters
-        ----------
-        name: str, optional (default="smiles2mol")
-            Name of PipelineElement.
-        n_jobs: int, optional (default=1)
-            Number of cores used.
-        uuid: str | None, optional (default=None)
-            UUID of the pipeline element. If None, a random UUID is generated.
-        """
-        super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
-
     def pretransform_single(self, value: str) -> OptionalMol:
         """Transform Smiles string to molecule.
 

molpipeline/error_handling.py

@@ -127,12 +127,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             params["element_ids"] = self.element_ids
         return params
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters for this element.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dict of arameters to set.
 
         Returns
@@ -508,12 +508,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             params["fill_value"] = self.fill_value
         return params
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters for this element.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Parameter dict.
 
         Returns