Merge branch 'main' into 58-test-python-313

molpipeline/utils/comparison.py

@@ -32,6 +32,8 @@ def remove_irrelevant_params(params: _T) -> _T:
     if isinstance(params, dict):
         params_new = {}
         for key, value in params.items():
+            if not isinstance(key, str):
+                continue
             if key.split("__")[-1] in irrelevant_params:
                 continue
             params_new[key] = remove_irrelevant_params(value)

tests/test_utils/test_comparison.py

@@ -1,20 +1,30 @@
 """Test the comparison functions."""
 
+from typing import Callable
 from unittest import TestCase
 
+from molpipeline import Pipeline
 from molpipeline.utils.comparison import check_pipelines_equivalent
-from tests.utils.default_models import get_morgan_physchem_rf_pipeline
+from tests.utils.default_models import (
+    get_morgan_physchem_rf_pipeline,
+    get_standardization_pipeline,
+)
 
 
 class TestComparison(TestCase):
     """Test if functional equivalent pipelines are detected as such."""
 
     def test_are_equal(self) -> None:
         """Test if two equivalent pipelines are detected as such."""
-
-        pipeline_a = get_morgan_physchem_rf_pipeline()
-        pipeline_b = get_morgan_physchem_rf_pipeline()
-        self.assertTrue(check_pipelines_equivalent(pipeline_a, pipeline_b))
+        # Test standardization pipelines
+        pipline_method_list: list[Callable[[int], Pipeline]] = [
+            get_standardization_pipeline,
+            get_morgan_physchem_rf_pipeline,
+        ]
+        for pipeline_method in pipline_method_list:
+            pipeline_a = pipeline_method(1)
+            pipeline_b = pipeline_method(1)
+            self.assertTrue(check_pipelines_equivalent(pipeline_a, pipeline_b))
 
     def test_are_not_equal(self) -> None:
         """Test if two different pipelines are detected as such."""

tests/utils/default_models.py

@@ -9,13 +9,30 @@
     MolToConcatenatedVector,
     MolToMorganFP,
     MolToRDKitPhysChem,
+    MolToSmiles,
 )
+from molpipeline.mol2mol import (
+    EmptyMoleculeFilter,
+    FragmentDeduplicator,
+    MetalDisconnector,
+    MixtureFilter,
+    SaltRemover,
+    StereoRemover,
+    TautomerCanonicalizer,
+    Uncharger,
+)
+from molpipeline.mol2mol.filter import ElementFilter
 from molpipeline.post_prediction import PostPredictionWrapper
 
 
-def get_morgan_physchem_rf_pipeline() -> Pipeline:
+def get_morgan_physchem_rf_pipeline(n_jobs: int = 1) -> Pipeline:
     """Get a pipeline combining Morgan fingerprints and physicochemical properties with a RandomForestClassifier.
 
+    Parameters
+    ----------
+    n_jobs: int, default=-1
+        Number of parallel jobs to use.
+
     Returns
     -------
     Pipeline
@@ -35,14 +52,52 @@ def get_morgan_physchem_rf_pipeline() -> Pipeline:
                 ),
             ),
             ("error_filter", error_filter),
-            ("rf", RandomForestClassifier()),
+            ("rf", RandomForestClassifier(n_jobs=n_jobs)),
             (
                 "filter_reinserter",
                 PostPredictionWrapper(
                     FilterReinserter.from_error_filter(error_filter, None)
                 ),
             ),
         ],
-        n_jobs=1,
+        n_jobs=n_jobs,
     )
     return pipeline
+
+
+def get_standardization_pipeline(n_jobs: int = 1) -> Pipeline:
+    """Get the standardization pipeline.
+
+    Parameters
+    ----------
+    n_jobs: int, optional (default=-1)
+        The number of jobs to use for standardization.
+        In case of -1, all available CPUs are used.
+
+    Returns
+    -------
+    Pipeline
+        The standardization pipeline.
+    """
+    error_filter = ErrorFilter(filter_everything=True)
+    # Set up pipeline
+    standardization_pipeline = Pipeline(
+        [
+            ("smi2mol", SmilesToMol()),
+            ("metal_disconnector", MetalDisconnector()),
+            ("salt_remover", SaltRemover()),
+            ("element_filter", ElementFilter()),
+            ("uncharge1", Uncharger()),
+            ("canonical_tautomer", TautomerCanonicalizer()),
+            ("uncharge2", Uncharger()),
+            ("stereo_remover", StereoRemover()),
+            ("fragment_deduplicator", FragmentDeduplicator()),
+            ("mixture_remover", MixtureFilter()),
+            ("empty_molecule_remover", EmptyMoleculeFilter()),
+            ("mol2smi", MolToSmiles()),
+            ("error_filter", error_filter),
+            ("error_replacer", FilterReinserter.from_error_filter(error_filter, None)),
+        ],
+        n_jobs=n_jobs,
+    )
+    return standardization_pipeline