Fix handling truth values of filtering columns in pandas

src/add_dti_annotations.py

@@ -118,7 +118,7 @@ def add_dti_annotations(
                     dataset.drug_mechanism_pairs_set
                 )
             )
-            & (dataset.df_result["therapeutic_target"] == True)
+            & (dataset.df_result["therapeutic_target"])
         ),
         "DTI",
     ] = "DT"
@@ -133,7 +133,7 @@ def add_dti_annotations(
                     dataset.drug_mechanism_pairs_set
                 )
             )
-            & (dataset.df_result["therapeutic_target"] == False)
+            & ~(dataset.df_result["therapeutic_target"])
         ),
         "DTI",
     ] = "NDT"

src/add_filtering_columns.py

@@ -159,9 +159,9 @@ def add_subset_filtering_columns(
         dataset.df_result[col_name] = False
         dataset.df_result.loc[(dataset.df_result.index.isin(df.index)), col_name] = True
         # check that filtering works
-        assert dataset.df_result[dataset.df_result[col_name] == True][
-            df.columns
-        ].equals(df), f"Filtering is not accurate for {col_name}."
+        assert dataset.df_result[dataset.df_result[col_name]][df.columns].equals(
+            df
+        ), f"Filtering is not accurate for {col_name}."
 
     if logging.DEBUG >= logging.root.level:
         for [df_subset, subset_desc] in subsets:
@@ -200,9 +200,7 @@ def add_filtering_columns(
     # consider only binding assays
     # assay description = binding
     desc = "B"
-    df_combined_subset = dataset.df_result[
-        dataset.df_result["keep_for_binding"] == True
-    ].copy()
+    df_combined_subset = dataset.df_result[dataset.df_result["keep_for_binding"]].copy()
     add_subset_filtering_columns(
         df_combined_subset,
         dataset,

src/get_drug_mechanism_ct_pairs.py

@@ -314,7 +314,7 @@ def add_drug_mechanism_ct_pairs(dataset: Dataset, chembl_con: sqlite3.Connection
     dataset.df_result.loc[
         (
             (dataset.df_result["pchembl_value_mean_B"].notnull())
-            | (dataset.df_result["pair_mutation_in_dm_table"] == True)
+            | (dataset.df_result["pair_mutation_in_dm_table"])
         ),
         "keep_for_binding",
     ] = True

src/sanity_checks.py

@@ -51,7 +51,7 @@ def check_pairs_without_pchembl_are_in_drug_mechanisms(df_result: pd.DataFrame):
     ]:
         assert df_result[(df_result[pchembl_col].isnull())].equals(
             df_result[
-                (df_result["pair_mutation_in_dm_table"] == True)
+                (df_result["pair_mutation_in_dm_table"])
                 & (df_result[pchembl_col].isnull())
             ]
         ), f"Missing pchembl value in column {pchembl_col}"