remove copy method

Author: c-w-feldmann

molpipeline/abstract_pipeline_elements/core.py

@@ -18,7 +18,7 @@
 from joblib import Parallel, delayed
 from loguru import logger
 from rdkit import Chem
-from rdkit.Chem import Mol as RDKitMol  # pylint: disable=no-name-in-module
+from rdkit.Chem import Mol as RDKitMol
 
 from molpipeline.utils.multi_proc import check_available_cores
 
@@ -393,23 +393,6 @@ def parameters(self, **parameters: Any) -> None:
         """
         self.set_params(**parameters)
 
-    def copy(self) -> Self:
-        """Copy the object.
-
-        Returns
-        -------
-        Self
-            Copy of the object.
-        """
-        recreated_object = self.__class__(**self.parameters)
-        for key, value in self.additional_attributes.items():
-            if not hasattr(recreated_object, key):
-                raise AssertionError(
-                    f"Cannot set attribute {key} on {self.__class__.__name__}. This should not happen!"
-                )
-            setattr(recreated_object, key, copy.copy(value))
-        return recreated_object
-
     def fit_to_result(self, values: Any) -> Self:
         """Fit object to result of transformed values.
 

tests/test_elements/test_mol2any/test_mol2maccs_key_fingerprint.py

@@ -6,6 +6,7 @@
 from typing import Any
 
 import numpy as np
+from sklearn.base import clone
 
 from molpipeline import Pipeline
 from molpipeline.any2mol import SmilesToMol
@@ -32,7 +33,7 @@ def test_can_be_constructed(self) -> None:
         None
         """
         mol_fp = MolToMACCSFP()
-        mol_fp_copy = mol_fp.copy()
+        mol_fp_copy = clone(mol_fp)
         self.assertTrue(mol_fp_copy is not mol_fp)
         for key, value in mol_fp.get_params().items():
             self.assertEqual(value, mol_fp_copy.get_params()[key])

tests/test_elements/test_mol2any/test_mol2morgan_fingerprint.py

@@ -6,6 +6,7 @@
 from typing import Any
 
 import numpy as np
+from sklearn.base import clone
 
 from molpipeline import Pipeline
 from molpipeline.any2mol import SmilesToMol
@@ -22,15 +23,15 @@
 class TestMol2MorganFingerprint(unittest.TestCase):
     """Unittest for MolToFoldedMorganFingerprint, which calculates folded Morgan Fingerprints."""
 
-    def test_can_be_constructed(self) -> None:
+    def test_clone(self) -> None:
         """Test if the MolToFoldedMorganFingerprint pipeline element can be constructed.
 
         Returns
         -------
         None
         """
         mol_fp = MolToMorganFP()
-        mol_fp_copy = mol_fp.copy()
+        mol_fp_copy = clone(mol_fp)
         self.assertTrue(mol_fp_copy is not mol_fp)
         for key, value in mol_fp.get_params().items():
             self.assertEqual(value, mol_fp_copy.get_params()[key])

tests/test_elements/test_mol2any/test_mol2path_fingerprint.py

@@ -6,6 +6,7 @@
 from typing import Any
 
 import numpy as np
+from sklearn.base import clone
 
 from molpipeline import Pipeline
 from molpipeline.any2mol import SmilesToMol
@@ -23,15 +24,15 @@
 class TestMol2PathFingerprint(unittest.TestCase):
     """Unittest for Mol2PathFP, which calculates the RDKit Path Fingerprint."""
 
-    def test_can_be_constructed(self) -> None:
-        """Test if the Mol2PathFP pipeline element can be constructed.
+    def test_clone(self) -> None:
+        """Test if the Mol2PathFP pipeline element can be cloned.
 
         Returns
         -------
         None
         """
         mol_fp = Mol2PathFP()
-        mol_fp_copy = mol_fp.copy()
+        mol_fp_copy = clone(mol_fp)
         self.assertTrue(mol_fp_copy is not mol_fp)
         for key, value in mol_fp.get_params().items():
             self.assertEqual(value, mol_fp_copy.get_params()[key])