Updated test to use mordred_filtered features. Added arguments to def…

…ault true and default false lists
ATOMScience-org · Jan 21, 2025 · 8feea36 · 8feea36
1 parent 53d3f74
commit 8feea36
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Showing 4 changed files with 18 additions and 12 deletions.
diff --git a/atomsci/ddm/pipeline/parameter_parser.py b/atomsci/ddm/pipeline/parameter_parser.py
@@ -775,8 +775,11 @@ def dict_to_list(inp_dictionary,replace_spaces=False):
     temp_list_to_command_line = []
 
     # Special case handling for arguments that are False or True by default
-    default_false = ['previously_split','use_shortlist','datastore', 'save_results','verbose', 'hyperparam', 'split_only', 'is_ki', 'production'] 
-    default_true = ['transformers','previously_featurized','uncertainty', 'rerun']
+    default_false = ['previously_split','use_shortlist','datastore', 'save_results','verbose', 'hyperparam', 'split_only', 'is_ki', 'production',
+                     'robustscaler_unit_variance'] 
+    default_true = ['transformers','previously_featurized','uncertainty', 'rerun',
+                    'robustscaler_with_centering', 'robustscaler_with_scaling',
+                    'powertransformer_standardize']
     for key, value in inp_dictionary.items():
         if key in default_false:
             true_options = ['True','true','ture','TRUE','Ture']

diff --git a/atomsci/ddm/test/integrative/balancing_trans/jsons/PowerTransformer_transformer.json b/atomsci/ddm/test/integrative/balancing_trans/jsons/PowerTransformer_transformer.json
@@ -15,7 +15,8 @@
         "system": "LC",
         "transformers": "True",
         "model_type": "NN",
-        "featurizer": "ecfp",
+        "featurizer": "computed_descriptors",
+        "descriptor_type": "rdkit_raw",
         "feature_transform_type": "PowerTransformer",
         "learning_rate": ".0007",
         "layer_sizes": "20,10",

diff --git a/atomsci/ddm/test/integrative/balancing_trans/jsons/RobustScaler_transformer.json b/atomsci/ddm/test/integrative/balancing_trans/jsons/RobustScaler_transformer.json
@@ -15,11 +15,12 @@
         "system": "LC",
         "transformers": "True",
         "model_type": "NN",
-        "featurizer": "ecfp",
+        "featurizer": "computed_descriptors",
+        "descriptor_type": "rdkit_raw",
         "feature_transform_type": "RobustScaler",
         "robustscaler_with_center": "True",
         "robustscaler_with_scaling": "True",
-        "robustscaler_with_quartile_range": "30.0,80.0",
+        "robustscaler_quartile_range": "30.0,80.0",
         "robustscaler_unit_variance": "True",
         "learning_rate": ".0007",
         "layer_sizes": "20,10",

diff --git a/atomsci/ddm/test/integrative/balancing_trans/test_balancing_transformer.py b/atomsci/ddm/test/integrative/balancing_trans/test_balancing_transformer.py
@@ -345,9 +345,9 @@ def test_sklearn_transformers():
 
     robustscaler_pipe = make_pipeline(robustscaler_params)
     transformers_x = robustscaler_pipe.model_wrapper.transformers_x
-    assert len(transformers_x)==1
-    assert isinstance(transformers_x[0], trans.SklearnTransformerWrapper)
-    assert isinstance(transformers_x[0].sklearn_transformer, RobustScaler)
+    assert len(transformers_x[0])==1
+    assert isinstance(transformers_x[0][0], trans.SklearnTransformerWrapper)
+    assert isinstance(transformers_x[0][0].sklearn_transformer, RobustScaler)
 
     powertransformer_params = read_params(
         make_relative_to_file('jsons/PowerTransformer_transformer.json'),
@@ -357,12 +357,13 @@ def test_sklearn_transformers():
 
     powertransformer_pipe = make_pipeline(powertransformer_params)
     transformers_x = powertransformer_pipe.model_wrapper.transformers_x
-    assert len(transformers_x)==1
-    assert isinstance(transformers_x[0], trans.SklearnTransformerWrapper)
-    assert isinstance(transformers_x[0].sklearn_transformer, PowerTransformer)
+    assert len(transformers_x[0])==1
+    assert isinstance(transformers_x[0][0], trans.SklearnTransformerWrapper)
+    assert isinstance(transformers_x[0][0].sklearn_transformer, PowerTransformer)
 
 if __name__ == '__main__':
-    test_kfold_regression_transformers()
+    test_sklearn_transformers()
+    #test_kfold_regression_transformers()
     #test_kfold_transformers()
     #test_all_transformers()
     #test_balancing_transformer()