Merge pull request #291 from cschlaffner/pre-commit-for-all-files

Fix existing code style inconsistencies using pre-commit hooks

protzilla/constants/workflow_meta.json

@@ -475,7 +475,7 @@
             }
           },
           {
-            "graph_type_quantites": {
+            "graph_type_quantities": {
               "name": "Graph type Imputed Values:",
               "type": "categorical",
               "categories": [
@@ -522,7 +522,7 @@
             }
           },
           {
-            "graph_type_quantites": {
+            "graph_type_quantities": {
               "name": "Graph type Imputed Values:",
               "type": "categorical",
               "categories": [
@@ -569,7 +569,7 @@
             }
           },
           {
-            "graph_type_quantites": {
+            "graph_type_quantities": {
               "name": "Graph type Imputed Values:",
               "type": "categorical",
               "categories": [
@@ -619,7 +619,7 @@
             }
           },
           {
-            "graph_type_quantites": {
+            "graph_type_quantities": {
               "name": "Graph type Imputed Values:",
               "type": "categorical",
               "categories": [
@@ -666,7 +666,7 @@
             }
           },
           {
-            "graph_type_quantites": {
+            "graph_type_quantities": {
               "name": "Graph type - Imputed Values:",
               "type": "categorical",
               "categories": [

protzilla/data_analysis/differential_expression_linear_model.py

@@ -4,7 +4,6 @@
 import pandas as pd
 import statsmodels.api as sm
 from django.contrib import messages
-from scipy import stats
 
 from .differential_expression_helper import apply_multiple_testing_correction
 

protzilla/data_analysis/dimension_reduction.py

@@ -1,4 +1,3 @@
-import numpy as np
 import pandas as pd
 from django.contrib import messages
 from sklearn.manifold import TSNE

protzilla/data_analysis/model_evaluation_plots.py

@@ -1,5 +1,4 @@
 import matplotlib.pyplot as plt
-import pandas as pd
 from sklearn.metrics import PrecisionRecallDisplay, RocCurveDisplay
 
 from protzilla.data_analysis.classification_helper import encode_labels

protzilla/data_integration/database_download.py

@@ -1,11 +1,11 @@
+import json
 import re
+from datetime import date
 from pathlib import Path
 
 import requests
 from requests.adapters import HTTPAdapter, Retry
 from tqdm import tqdm
-from datetime import date
-import json
 
 # cannot be imported form constants as package cannot be found
 external_data_path = Path(__file__).parent.parent.parent / "user_data" / "external_data"

protzilla/data_preprocessing/imputation.py

@@ -221,41 +221,43 @@ def by_min_per_dataset(
     return intensity_df_copy, dict()
 
 
-def by_knn_plot(df, result_df, current_out, graph_type, graph_type_quantites, group_by):
+def by_knn_plot(
+    df, result_df, current_out, graph_type, graph_type_quantities, group_by
+):
     return _build_box_hist_plot(
-        df, result_df, graph_type, graph_type_quantites, group_by
+        df, result_df, graph_type, graph_type_quantities, group_by
     )
 
 
 def by_simple_imputer_plot(
-    df, result_df, current_out, graph_type, graph_type_quantites, group_by
+    df, result_df, current_out, graph_type, graph_type_quantities, group_by
 ):
     return _build_box_hist_plot(
-        df, result_df, graph_type, graph_type_quantites, group_by
+        df, result_df, graph_type, graph_type_quantities, group_by
     )
 
 
 def by_min_per_sample_plot(
-    df, result_df, current_out, graph_type, graph_type_quantites, group_by
+    df, result_df, current_out, graph_type, graph_type_quantities, group_by
 ):
     return _build_box_hist_plot(
-        df, result_df, graph_type, graph_type_quantites, group_by
+        df, result_df, graph_type, graph_type_quantities, group_by
     )
 
 
 def by_min_per_protein_plot(
-    df, result_df, current_out, graph_type, graph_type_quantites, group_by
+    df, result_df, current_out, graph_type, graph_type_quantities, group_by
 ):
     return _build_box_hist_plot(
-        df, result_df, graph_type, graph_type_quantites, group_by
+        df, result_df, graph_type, graph_type_quantities, group_by
     )
 
 
 def by_min_per_dataset_plot(
-    df, result_df, current_out, graph_type, graph_type_quantites, group_by
+    df, result_df, current_out, graph_type, graph_type_quantities, group_by
 ):
     return _build_box_hist_plot(
-        df, result_df, graph_type, graph_type_quantites, group_by
+        df, result_df, graph_type, graph_type_quantities, group_by
     )
 
 
@@ -264,7 +266,7 @@ def number_of_imputed_values(input_df, result_df):
 
 
 def _build_box_hist_plot(
-    df, result_df, graph_type, graph_type_quantites, group_by
+    df, result_df, graph_type, graph_type_quantities, group_by
 ) -> list[Figure]:
     """
     This function creates two visualisations:
@@ -300,13 +302,13 @@ def _build_box_hist_plot(
         abs(len(df)),
         number_of_imputed_values(df, result_df),
     ]
-    if graph_type_quantites == "Bar chart":
+    if graph_type_quantities == "Bar chart":
         fig2 = create_bar_plot(
             names_of_sectors=["Non-imputed values", "Imputed values"],
             values_of_sectors=values_of_sectors,
             heading="Number of Imputed Values",
         )
-    elif graph_type_quantites == "Pie chart":
+    elif graph_type_quantities == "Pie chart":
         fig2 = create_pie_plot(
             names_of_sectors=["Non-imputed values", "Imputed values"],
             values_of_sectors=values_of_sectors,

protzilla/history.py

@@ -1,5 +1,4 @@
 import json
-import os
 import shutil
 from dataclasses import dataclass
 from pathlib import Path

tests/protzilla/data_analysis/test_dimension_reduction.py

@@ -1,4 +1,3 @@
-import numpy as np
 import pandas as pd
 import pytest
 

tests/protzilla/importing/test_ms_data_import.py

@@ -1,8 +1,8 @@
+from unittest.mock import patch
+
 import numpy as np
 import pandas as pd
 import pytest
-from unittest.mock import patch
-
 
 from protzilla.constants.paths import PROJECT_PATH
 from protzilla.importing import ms_data_import

tests/protzilla/test_run.py

@@ -251,7 +251,9 @@ def test_export_plot(tests_folder_name):
     run.perform_calculation(data_preprocessing.imputation.by_min_per_sample, {})
     run.create_plot(
         data_preprocessing.imputation.by_min_per_sample_plot,
-        dict(graph_type="Boxplot", graph_type_quantites="Bar chart", group_by="Sample"),
+        dict(
+            graph_type="Boxplot", graph_type_quantities="Bar chart", group_by="Sample"
+        ),
     )
     assert len(run.plots) > 1
     for plot in run.export_plots("tiff"):

tests/protzilla/test_run_helper.py

@@ -1,5 +1,5 @@
 import copy
-from unittest.mock import MagicMock, Mock, patch
+from unittest.mock import MagicMock, Mock
 
 import pandas as pd
 import pytest

tests/protzilla/test_runner.py

@@ -176,7 +176,7 @@ def test_serialize_workflow_graphs():
     serial_imputation_graphs = {
         "graph_type": "Bar chart",
         "group_by": "Sample",
-        "graph_type_quantites": "Pie chart",
+        "graph_type_quantities": "Pie chart",
     }
 
     serial_filter_graphs = {"graph_type": "Pie chart"}

tests/test_workflows/example_workflow.json

@@ -57,7 +57,7 @@
               "group_by": "Sample"
             },
             {
-              "graph_type_quantites": "Pie chart"
+              "graph_type_quantities": "Pie chart"
             }
           ]
         },

tests/test_workflows/wrong_parameters.json

@@ -18,7 +18,7 @@
               "group_by": "Sample"
             },
             {
-              "graph_type_quantites": "Bar chart"
+              "graph_type_quantities": "Bar chart"
             }
           ]
         }

ui/main/views.py

@@ -1,7 +1,8 @@
-import shutil
-import pandas
 import json
+import shutil
 from datetime import date
+
+import pandas
 from django.contrib import messages
 from django.http import HttpResponseRedirect
 from django.shortcuts import redirect, render

user_data/workflows/BA46_VolcanoPlot.json

@@ -59,7 +59,7 @@
               "group_by": "Sample"
             },
             {
-              "graph_type_quantites": "Pie chart"
+              "graph_type_quantities": "Pie chart"
             }
           ],
           "output_name": null

user_data/workflows/enrichment_analysis.json

@@ -57,7 +57,7 @@
               "group_by": "Sample"
             },
             {
-              "graph_type_quantites": "Pie chart"
+              "graph_type_quantities": "Pie chart"
             }
           ]
         },

user_data/workflows/standard.json

@@ -57,7 +57,7 @@
               "group_by": "Sample"
             },
             {
-              "graph_type_quantites": "Pie chart"
+              "graph_type_quantities": "Pie chart"
             }
           ]
         },

user_data/workflows/workflow_gsea.json

@@ -61,7 +61,7 @@
               "group_by": "Sample"
             },
             {
-              "graph_type_quantites": "Pie chart"
+              "graph_type_quantities": "Pie chart"
             }
           ],
           "output_name": null