linting

molpipeline/mol2any/mol2concatinated_vector.py

@@ -164,7 +164,7 @@ def _set_element_execution_details(
         else:
             self._output_type = "mixed"
         self._requires_fitting = any(
-            element[1]._requires_fitting for element in element_list
+            element[1]._requires_fitting for element in element_list  # type: ignore[protected-access]
         )
 
     def get_params(self, deep: bool = True) -> dict[str, Any]:
@@ -197,22 +197,21 @@ def get_params(self, deep: bool = True) -> dict[str, Any]:
 
         return parameters
 
-    def set_params(self, **parameters: Any) -> Self:
-        """Set parameters.
+    def _set_element_list(
+        self, parameter_copy: dict[str, Any], **parameters: Any
+    ) -> tuple[dict[str, Any], dict[str, Any]]:
+        """Set the element list and run necessary configurations.
 
         Parameters
         ----------
-        parameters: Any
-            Parameters to set.
+        element_list: list[tuple[str, MolToAnyPipelineElement]]
+            List of pipeline elements.
 
-        Returns
-        -------
-        Self
-            Mol2ConcatenatedVector object with updated parameters.
+        Raises
+        ------
+        ValueError
+            If element_list is empty.
         """
-        parameter_copy = dict(parameters)
-
-        # handle element_list
         element_list = parameter_copy.pop("element_list", None)
         if element_list is not None:
             self._element_list = element_list
@@ -240,6 +239,27 @@ def set_params(self, **parameters: Any) -> Self:
             _ = parameter_copy.pop(to_delete, None)
         for step, params in step_params.items():
             step_dict[step].set_params(**params)
+        return parameter_copy, parameters
+
+    def set_params(self, **parameters: Any) -> Self:
+        """Set parameters.
+
+        Parameters
+        ----------
+        parameters: Any
+            Parameters to set.
+
+        Returns
+        -------
+        Self
+            Mol2ConcatenatedVector object with updated parameters.
+        """
+        parameter_copy = dict(parameters)
+
+        # handle element_list
+        parameter_copy, parameters = self._set_element_list(
+            parameter_copy, **parameters
+        )
 
         # handle use_feature_names_prefix
         use_feature_names_prefix = parameter_copy.pop("use_feature_names_prefix", None)

tests/test_elements/test_mol2any/test_mol2concatenated.py

@@ -11,6 +11,7 @@
 from sklearn.preprocessing import StandardScaler
 
 from molpipeline import Pipeline
+from molpipeline.abstract_pipeline_elements.core import MolToAnyPipelineElement
 from molpipeline.any2mol import SmilesToMol
 from molpipeline.mol2any import (
     MolToConcatenatedVector,
@@ -234,7 +235,7 @@ def test_features_names(self) -> None:  # pylint: disable-msg=too-many-locals
 
     def test_logging_feature_names_uniqueness(self) -> None:
         """Test that a warning is logged when feature names are not unique."""
-        elements = [
+        elements: list[tuple[str, MolToAnyPipelineElement]] = [
             (
                 "MorganFP",
                 MolToMorganFP(n_bits=17),
@@ -282,7 +283,7 @@ def test_logging_feature_names_uniqueness(self) -> None:
 
     def test_getter_setter(self) -> None:
         """Test getter and setter methods."""
-        elements = [
+        elements: list[tuple[str, MolToAnyPipelineElement]] = [
             (
                 "MorganFP",
                 MolToMorganFP(n_bits=17),

tests/utils/logging.py

@@ -1,15 +1,18 @@
 """Test utils for logging."""
 
+from __future__ import annotations
+
 from contextlib import contextmanager
 from typing import Generator
 
+import loguru
 from loguru import logger
 
 
 @contextmanager
 def capture_logs(
     level="INFO", format="{level}:{name}:{message}"
-) -> Generator[list[str], None, None]:
+) -> Generator[list[loguru.Message], None, None]:  # ign
     """Capture loguru-based logs.
 
     Custom context manager to test loguru-based logs. For details and usage examples,
@@ -24,10 +27,15 @@ def capture_logs(
 
     Yields
     -------
-    list[str]
+    list[loguru.Message]
+        List of log messages
+
+    Returns
+    -------
+    Generator[list[loguru.Message], None, None]
         List of log messages
     """
-    output: list[str] = []
+    output: list[loguru.Message] = []
     handler_id = logger.add(output.append, level=level, format=format)
     yield output
     logger.remove(handler_id)