black formatting (rule change 2026)

Author: aretaon

autoprot/analysis/PCA.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 from typing import Union, Literal
 
 import pandas as pd

autoprot/analysis/clustering.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 import os
 import warnings
 from typing import Union, Literal

autoprot/analysis/functional.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 from functools import reduce
 from importlib import resources
 from typing import Union, Literal, List, Dict, Any, Tuple

autoprot/analysis/qc.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 from typing import Literal
 from datetime import date
 
@@ -233,21 +234,17 @@ def missed_cleavages(df_evidence, enzyme="Trypsin/P", save=True, ax=None, title=
     today = date.today().isoformat()
 
     if "Experiment" not in df_evidence.columns.tolist():
-        print(
-            "Warning: Column [Experiment] either not unique or missing,\n\
-              column [Raw file] used"
-        )
+        print("Warning: Column [Experiment] either not unique or missing,\n\
+              column [Raw file] used")
         experiments = list(set((df_evidence["Raw file"])))
     else:
         experiments = list(set((df_evidence["Experiment"])))
 
     rawfiles = list(set((df_evidence["Raw file"])))
     if len(experiments) != len(rawfiles):
         experiments = rawfiles
-        print(
-            "Warning: Column [Experiment] either not unique or missing,\n\
-              column [Raw file] used"
-        )
+        print("Warning: Column [Experiment] either not unique or missing,\n\
+              column [Raw file] used")
 
     # calculate miss cleavage for each raw file in df_evidence
     df_missed_cleavage_summary = pd.DataFrame()
@@ -604,10 +601,8 @@ def dimethyl_labeling_efficieny(df_evidence, label, save=True) -> pd.DataFrame:
         experiments = list((df_evidence["Experiment"].unique()))
     else:
         experiments = list((df_evidence["Raw file"].unique()))
-        print(
-            "Warning: Column [Experiment] either not unique or missing,\n\
-              column [Raw file] used"
-        )
+        print("Warning: Column [Experiment] either not unique or missing,\n\
+              column [Raw file] used")
 
     df_labeling_eff = pd.DataFrame()
 

autoprot/analysis/stat_test.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 import os
 
 import numpy as np

autoprot/analysis/stats.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 import pandas as pd
 import numpy as np
 import matplotlib.pylab as plt

autoprot/preprocessing/annotation.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 import os
 import re
 from importlib import resources

autoprot/preprocessing/filtering.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 import functools
 
 import numpy as np
@@ -15,7 +16,6 @@
 from autoprot.decorators import report
 from .. import r_helper
 
-
 RFUNCTIONS, R = r_helper.return_r_path()
 
 

autoprot/preprocessing/imputation.py

@@ -6,6 +6,7 @@
 
 @documentation: Julian
 """
+
 import numpy as np
 import pandas as pd
 from subprocess import run, PIPE, STDOUT

autoprot/preprocessing/transformation.py

@@ -10,6 +10,7 @@
 Julian Bender <julian.bender@uni-wuerzburg.de>
 Johannes Zimmermann <johannes.zimmermann@uni-wuerzburg.de>
 """
+
 import collections
 import re
 import warnings