fixing minor warnings that appeared while running pytest

xomicsdatascience · Mar 19, 2024 · 3c0fac4 · 3c0fac4
1 parent 7071a01
commit 3c0fac4
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/src/zodiaq/scoring/quantificationFunctions.py b/src/zodiaq/scoring/quantificationFunctions.py
@@ -2,14 +2,13 @@
 import numpy as np
 from zodiaq.utils import format_protein_string_to_list
 from .idpickerFunctions import initialize__format_peptide_protein_connections
-from scipy import mean
 from collections import defaultdict
 from itertools import chain
 import scipy.linalg as linalg
 
 
 def calculate_ion_count_from_peptides_of_protein(ionCountList):
-    return mean(ionCountList)
+    return np.mean(ionCountList)
 
 
 def calculate_ion_count_for_each_protein_in_protein_fdr_df(proteinDf):

diff --git a/tests/system/system_tests/scoring/testFileContentCreators/MaccScoresBreakdown.py b/tests/system/system_tests/scoring/testFileContentCreators/MaccScoresBreakdown.py
@@ -22,11 +22,11 @@ def _create_input_template_for_scoring_module(self):
         )
         duplicatePeptideInputDf["zLIB"] = [2] * len(duplicatePeptideInputDf.index)
         allDecoyDf = self._create_input_for_all_decoys()
-        firstDecoyLayerInputDf = allDecoyDf.iloc[:2]
+        firstDecoyLayerInputDf = allDecoyDf.iloc[:2].copy()
         firstDecoyLayerInputDf["rank"] = [3] * len(firstDecoyLayerInputDf.index)
-        secondDecoyLayerInputDf = allDecoyDf.iloc[2:4]
+        secondDecoyLayerInputDf = allDecoyDf.iloc[2:4].copy()
         secondDecoyLayerInputDf["rank"] = [4] * len(secondDecoyLayerInputDf.index)
-        thirdDecoyLayerInputDf = allDecoyDf.iloc[4:]
+        thirdDecoyLayerInputDf = allDecoyDf.iloc[4:].copy()
         thirdDecoyLayerInputDf["rank"] = [5] * len(thirdDecoyLayerInputDf.index)
         extraSpectralInputDf = self._create_input_for_generic_peptides(
             rank=6, startingRow=200

diff --git a/...s/system/system_tests/scoring/testFileContentCreators/ProteinCosineEvalScoresBreakdown.py b/...s/system/system_tests/scoring/testFileContentCreators/ProteinCosineEvalScoresBreakdown.py
@@ -21,9 +21,9 @@ def _create_input_template_for_scoring_module(self):
         )
         peptideInputDf = self._create_input_for_generic_peptides(rank=2, startingRow=2)
         allDecoyDf = self._create_input_for_all_decoys(numRows=3)
-        firstDecoyLayerInputDf = allDecoyDf.iloc[:2]
+        firstDecoyLayerInputDf = allDecoyDf.iloc[:2].copy()
         firstDecoyLayerInputDf["rank"] = [3] * len(firstDecoyLayerInputDf.index)
-        secondDecoyLayerInputDf = allDecoyDf.iloc[2:]
+        secondDecoyLayerInputDf = allDecoyDf.iloc[2:].copy()
         secondDecoyLayerInputDf["rank"] = [4] * len(secondDecoyLayerInputDf.index)
         self.inputDf = pd.concat(
             [