Fix wrong typing that caused thousands of type ignores

molpipeline/abstract_pipeline_elements/core.py

@@ -184,12 +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
@@ -379,12 +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

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/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/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

molpipeline/mol2any/mol2concatinated_vector.py

@@ -113,12 +113,12 @@ 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 parameters.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Parameters to set.
 
         Returns
@@ -129,7 +129,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         parameter_copy = dict(parameters)
         element_list = parameter_copy.pop("element_list", None)
         if element_list is not None:
-            self._element_list = element_list  # type: ignore
+            self._element_list = element_list
         step_params: dict[str, dict[str, Any]] = {}
         step_dict = dict(self._element_list)
         to_delete_list = []

molpipeline/mol2any/mol2morgan_fingerprint.py

@@ -104,12 +104,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             parameters["n_bits"] = self._n_bits
         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
@@ -120,7 +120,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         parameter_copy = dict(parameters)
         n_bits = parameter_copy.pop("n_bits", None)
         if n_bits is not None:
-            self._n_bits = n_bits  # type: ignore
+            self._n_bits = n_bits
         super().set_params(**parameter_copy)
 
         return self

molpipeline/mol2any/mol2net_charge.py

@@ -145,12 +145,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             parent_dict["charge_policy"] = self._charge_method
         return parent_dict
 
-    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
             Parameters to set
 
         Returns
@@ -161,6 +161,6 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         parameters_shallow_copy = dict(parameters)
         charge_policy = parameters_shallow_copy.pop("charge_policy", None)
         if charge_policy is not None:
-            self._charge_method = charge_policy  # type: ignore
+            self._charge_method = charge_policy
         super().set_params(**parameters_shallow_copy)
         return self

molpipeline/mol2any/mol2path_fingerprint.py

@@ -152,12 +152,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             parameters["n_bits"] = self._n_bits
         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
@@ -168,36 +168,36 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         parameter_copy = dict(parameters)
         min_path = parameter_copy.pop("min_path", None)
         if min_path is not None:
-            self._min_path = min_path  # type: ignore
+            self._min_path = min_path
         max_path = parameter_copy.pop("max_path", None)
         if max_path is not None:
-            self._max_path = max_path  # type: ignore
+            self._max_path = max_path
         use_hs = parameter_copy.pop("use_hs", None)
         if use_hs is not None:
-            self._use_hs = use_hs  # type: ignore
+            self._use_hs = use_hs
         branched_paths = parameter_copy.pop("branched_paths", None)
         if branched_paths is not None:
-            self._branched_paths = branched_paths  # type: ignore
+            self._branched_paths = branched_paths
         use_bond_order = parameter_copy.pop("use_bond_order", None)
         if use_bond_order is not None:
-            self._use_bond_order = use_bond_order  # type: ignore
+            self._use_bond_order = use_bond_order
         count_simulation = parameter_copy.pop("count_simulation", None)
         if count_simulation is not None:
-            self._count_simulation = count_simulation  # type: ignore
+            self._count_simulation = count_simulation
         count_bounds = parameter_copy.pop("count_bounds", None)
         if count_bounds is not None:
-            self._count_bounds = count_bounds  # type: ignore
+            self._count_bounds = count_bounds
         num_bits_per_feature = parameter_copy.pop("num_bits_per_feature", None)
         if num_bits_per_feature is not None:
-            self._num_bits_per_feature = num_bits_per_feature  # type: ignore
+            self._num_bits_per_feature = num_bits_per_feature
         atom_invariants_generator = parameter_copy.pop(
             "atom_invariants_generator", None
         )
         if atom_invariants_generator is not None:
             self._atom_invariants_generator = atom_invariants_generator
         n_bits = parameter_copy.pop("n_bits", None)  # pylint: disable=duplicate-code
         if n_bits is not None:
-            self._n_bits = n_bits  # type: ignore
+            self._n_bits = n_bits
         super().set_params(**parameter_copy)
         return self
 

molpipeline/mol2any/mol2rdkit_phys_chem.py

@@ -170,12 +170,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             parent_dict["log_exceptions"] = self._log_exceptions
         return parent_dict
 
-    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
             Parameters to set
 
         Returns

molpipeline/mol2mol/filter.py

@@ -88,12 +88,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             params["allowed_element_numbers"] = self.allowed_element_numbers
         return params
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters of ElementFilter.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Parameters to set.
 
         Returns
@@ -103,7 +103,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         """
         parameter_copy = dict(parameters)
         if "allowed_element_numbers" in parameter_copy:
-            self.allowed_element_numbers = parameter_copy.pop("allowed_element_numbers")  # type: ignore
+            self.allowed_element_numbers = parameter_copy.pop("allowed_element_numbers")
         super().set_params(**parameter_copy)
         return self
 

molpipeline/mol2mol/reaction.py

@@ -91,12 +91,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             parameters["handle_multi"] = self.handle_multi
         return parameters
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set the parameters.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Dictionary containing parameters to be set.
 
         Returns
@@ -108,9 +108,9 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         if "reaction" in parameters:
             self.reaction = parameters["reaction"]
         if "additive_list" in parameters:
-            self.additive_list = parameters["additive_list"]  # type: ignore
+            self.additive_list = parameters["additive_list"]
         if "handle_multi" in parameters:
-            self.handle_multi = parameters["handle_multi"]  # type: ignore
+            self.handle_multi = parameters["handle_multi"]
         return self
 
     @property

molpipeline/mol2mol/standardization.py

@@ -400,12 +400,12 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
             params["solvent_smiles_list"] = self.solvent_smiles_list
         return params
 
-    def set_params(self, **parameters: dict[str, Any]) -> Self:
+    def set_params(self, **parameters: Any) -> Self:
         """Set parameters of pipeline element.
 
         Parameters
         ----------
-        parameters: dict[str, Any]
+        parameters: Any
             Parameters to set.
 
         Returns
@@ -416,7 +416,7 @@ def set_params(self, **parameters: dict[str, Any]) -> Self:
         param_copy = dict(parameters)
         solvent_smiles_list = param_copy.pop("solvent_smiles_list", None)
         if solvent_smiles_list is not None:
-            self.solvent_smiles_list = solvent_smiles_list  # type: ignore
+            self.solvent_smiles_list = solvent_smiles_list
         super().set_params(**param_copy)
         return self