precommit formatting

src/allpairs.py

@@ -3,7 +3,10 @@
 
 import pandas as pd
 
-from src.interactome import convert_directed_to_undirected, readd_direction_col_undirected
+from src.interactome import (
+    convert_directed_to_undirected,
+    readd_direction_col_undirected,
+)
 from src.prm import PRM
 from src.util import prepare_volume, run_container
 

src/interactome.py

@@ -7,6 +7,7 @@
 
 import pandas as pd
 
+
 def convert_undirected_to_directed(df: pd.DataFrame) -> pd.DataFrame:
     """
     turns a graph into a fully directed graph
@@ -25,10 +26,10 @@ def convert_undirected_to_directed(df: pd.DataFrame) -> pd.DataFrame:
     new_df['Direction'] = 'D'
     df.loc[mask, 'Direction'] = 'D'
     df = pd.concat([df, new_df], ignore_index=True)
-    
+
     print("convert_undirected_to_directed")
     print(df)
-    
+
     return df
 
 
@@ -41,12 +42,12 @@ def convert_directed_to_undirected(df: pd.DataFrame) -> pd.DateOffset:
     @param df: input network df of edges, weights, and directionality
     @return a dataframe with no directed edges in Direction column
     """
-    
+
     df["Direction"] = "U"
-    
+
     print("convert_directed_to_undirected")
     print(df)
-    
+
     return df
 
 
@@ -61,10 +62,10 @@ def add_constant(df: pd.DataFrame, col_name: str, const: str) -> pd.DataFrame:
     """
 
     df.insert(df.shape[1], col_name, const)
-    
+
     print("add_constant")
     print(df)
-   
+
     return df
 
 
@@ -86,7 +87,7 @@ def add_directionality_constant(df: pd.DataFrame,  col_name: str, dir_const: str
 
     print("add_directionality_constant")
     print(df)
-    
+
     return df
 
 def readd_direction_col_mixed(df: pd.DataFrame, existing_direction_column: str, dir_const: str, undir_const: str) -> pd.DataFrame:
@@ -110,10 +111,10 @@ def readd_direction_col_mixed(df: pd.DataFrame, existing_direction_column: str,
 
     mask_dir = df[existing_direction_column] == dir_const
     df.loc[mask_dir, "Direction"] = "D"
-    
+
     print("readd_direction_col_mixed")
     print(df)
-    
+
     return df
 
 def readd_direction_col_undirected(df: pd.DataFrame) -> pd.DataFrame:
@@ -124,10 +125,10 @@ def readd_direction_col_undirected(df: pd.DataFrame) -> pd.DataFrame:
     @return a df with Direction column added back
     """
     df.insert(df.shape[1], "Direction", "U")
-    
+
     print("readd_direction_col_undirected")
     print(df)
-    
+
     return df
 
 def readd_direction_col_directed(df: pd.DataFrame) -> pd.DataFrame:
@@ -138,8 +139,8 @@ def readd_direction_col_directed(df: pd.DataFrame) -> pd.DataFrame:
     @return a df with Direction column added back
     """
     df.insert(df.shape[1], "Direction", "D")
-    
+
     print("readd_direction_col_directed")
     print(df)
-    
+
     return df

src/omicsintegrator2.py

@@ -4,7 +4,10 @@
 import docker
 import pandas as pd
 
-from src.interactome import convert_directed_to_undirected, readd_direction_col_undirected
+from src.interactome import (
+    convert_directed_to_undirected,
+    readd_direction_col_undirected,
+)
 from src.prm import PRM
 from src.util import prepare_path_docker
 

test/interactome/test_interactome.py

@@ -1,14 +1,15 @@
 from pathlib import Path
+
 import pandas as pd
 
 from src.interactome import (
-    convert_undirected_to_directed,
-    convert_directed_to_undirected,
     add_constant,
     add_directionality_constant,
+    convert_directed_to_undirected,
+    convert_undirected_to_directed,
+    readd_direction_col_directed,
     readd_direction_col_mixed,
     readd_direction_col_undirected,
-    readd_direction_col_directed,
 )
 
 IN_DIR = "test/interactome/input"
@@ -40,18 +41,18 @@ def add_const(self):
         df = add_constant(df, "const", "-")
         expected_df = pd.read_csv(EXPECTED_DIR+"add_const.csv", sep='\t')
         assert df.equals(expected_df)
-        
+
     def add_directionality_const(self):
         df = pd.read_csv(IN_DIR+ 'test-network.csv', sep='\t')
         df = add_directionality_constant(df, "direct", "pd", "pp")
         expected_df = pd.read_csv(EXPECTED_DIR+"add_directionality_const.csv", sep='\t')
         assert df.equals(expected_df)
 
     def readd_col_mixed(self):
-        None
+        assert True
 
     def readd_col_undir(self):
-        None
+        assert True
 
     def readd_col_dir(self):
-        None
+        assert True