Fix linting errors (#114)

* adapt _fit to match sklearn >= 1.6

* check type

* change type casting

* reduce used vars

* overhaul typing

* use new variable

* dont override variable type and ignore too many return statements

* ignore types

* generalize type

* Add typing

* ignore error

* do not reuse var

* decode file

* ignore that Hash functions cannot be found

* false positive

* type cast

* ignore rdkit typing

* add type

* improve docstring

* remove invalid dtype param

molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py

@@ -238,12 +238,12 @@ def __init__(
         self.counted = counted
 
     @abc.abstractmethod
-    def _get_fp_generator(self) -> rdFingerprintGenerator.FingeprintGenerator64:
+    def _get_fp_generator(self) -> rdFingerprintGenerator.FingerprintGenerator64:
         """Get fingerprint generator.
 
         Returns
         -------
-        rdFingerprintGenerator.FingeprintGenerator64
+        rdFingerprintGenerator.FingerprintGenerator64
             Fingerprint generator.
         """
 

molpipeline/abstract_pipeline_elements/mol2mol/filter.py

@@ -170,7 +170,9 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
         params["filter_elements"] = self.filter_elements
         return params
 
-    def pretransform_single(self, value: RDKitMol) -> OptionalMol:
+    def pretransform_single(  # pylint: disable=too-many-return-statements
+        self, value: RDKitMol
+    ) -> OptionalMol:
         """Invalidate or validate molecule based on specified filter.
 
         There are four possible scenarios:
@@ -195,7 +197,7 @@ def pretransform_single(self, value: RDKitMol) -> OptionalMol:
                 # For "any" mode we can return early if a match is found
                 if self.mode == "any":
                     if not self.keep_matches:
-                        value = InvalidInstance(
+                        return InvalidInstance(
                             self.uuid,
                             f"Molecule contains forbidden filter element {filter_element}.",
                             self.name,
@@ -205,7 +207,7 @@ def pretransform_single(self, value: RDKitMol) -> OptionalMol:
                 # For "all" mode we can return early if a match is not found
                 if self.mode == "all":
                     if self.keep_matches:
-                        value = InvalidInstance(
+                        return InvalidInstance(
                             self.uuid,
                             f"Molecule does not contain required filter element {filter_element}.",
                             self.name,
@@ -216,7 +218,7 @@ def pretransform_single(self, value: RDKitMol) -> OptionalMol:
         # If mode is "any", finishing the loop means no match was found
         if self.mode == "any":
             if self.keep_matches:
-                value = InvalidInstance(
+                return InvalidInstance(
                     self.uuid,
                     "Molecule does not match any of the required filter elements.",
                     self.name,
@@ -226,7 +228,7 @@ def pretransform_single(self, value: RDKitMol) -> OptionalMol:
 
         if self.mode == "all":
             if not self.keep_matches:
-                value = InvalidInstance(
+                return InvalidInstance(
                     self.uuid,
                     "Molecule matches all forbidden filter elements.",
                     self.name,

molpipeline/any2mol/sdf2mol.py

@@ -120,6 +120,6 @@ def pretransform_single(self, value: str) -> OptionalMol:
                 self.name,
             )
         if self.identifier == "smiles":
-            mol.SetProp("identifier", self.mol_counter)
+            mol.SetProp("identifier", str(self.mol_counter))
         self.mol_counter += 1
         return mol