code review comments

Author: JochenSiegWork

molpipeline/mol2any/mol2concatinated_vector.py

@@ -315,7 +315,7 @@ def assemble_output(
         """
         values = list(value_list)
         if len(values) == 0:
-            return np.empty((0, 0), dtype=np.float64)
+            return np.empty((0, self.n_features), dtype=np.float64)
         return np.vstack(values)
 
     def transform(self, values: list[RDKitMol]) -> npt.NDArray[np.float64]:

tests/test_elements/test_mol2any/test_mol2concatenated.py

@@ -11,9 +11,6 @@
 from sklearn.preprocessing import StandardScaler
 
 from molpipeline import ErrorFilter, Pipeline
-
-if TYPE_CHECKING:
-    from molpipeline.abstract_pipeline_elements.core import MolToAnyPipelineElement
 from molpipeline.any2mol import SmilesToMol
 from molpipeline.mol2any import (
     Mol2PathFP,
@@ -26,6 +23,9 @@
 from tests.utils.fingerprints import fingerprints_to_numpy
 from tests.utils.logging import capture_logs
 
+if TYPE_CHECKING:
+    from molpipeline.abstract_pipeline_elements.core import MolToAnyPipelineElement
+
 
 class TestConcatenatedFingerprint(unittest.TestCase):
     """Unittest for MolToConcatenatedVector."""

tests/test_elements/test_mol2any/test_mol2rdkit_phys_chem.py

@@ -417,7 +417,7 @@ def test_empty_result(self) -> None:
                 "C1=NC(N)=[Se]=C1",  # fails PhysChem calculation
             ],
         )
-        self.assertIsNotNone(pipeline)
+        self.assertIsNotNone(pipeline)  # test for ruff to not have a staticmethod
 
         # test with a molecule that fails the PhysChem calculation and with standardizer
         pipeline = Pipeline(
@@ -439,7 +439,7 @@ def test_empty_result(self) -> None:
                 "C1=NC(N)=[Se]=C1",  # fails PhysChem calculation
             ],
         )
-        self.assertIsNotNone(pipeline)
+        self.assertIsNotNone(pipeline)  # test for ruff to not have a staticmethod
 
     def test_empty_descriptor_list(self) -> None:
         """Test that an empty descriptor list raises ValueError."""