flake8 corrections

Author: jmarinllao

src/diffupath/cli.py

@@ -255,8 +255,6 @@ def evaluate(
             graph,
             kernel,
             k=iterations)
-
-
     else:
         raise ValueError("The comparison method provided not match any provided method.")
 

src/diffupath/cross_validation.py

@@ -95,7 +95,6 @@ def cross_validation_by_subgraph(data_input,
             if universe_kernel is None:
                 universe_kernel = kernel
 
-
             input_diff, validation_diff = _get_random_cv_split_input_and_validation(data_input[type],
                                                                                     kernel)
             input_diff_universe, validation_diff_universe = _get_random_cv_split_input_and_validation(data_input[type],

src/diffupath/pathme_processing.py

@@ -13,7 +13,9 @@
 
 def calculate_database_sets_as_dict(nodes, database):
     gene_nodes, mirna_nodes, metabolite_nodes, bp_nodes = calculate_database_sets(nodes, database)
-    return {'gene_nodes': gene_nodes, 'mirna_nodes': mirna_nodes, 'metabolite_nodes': metabolite_nodes,
+    return {'gene_nodes': gene_nodes,
+            'mirna_nodes': mirna_nodes,
+            'metabolite_nodes': metabolite_nodes,
             'bp_nodes': bp_nodes}
 
 

src/diffupath/topological_analyses.py

@@ -2,9 +2,8 @@
 
 """Topological analyses."""
 
-from collections import defaultdict
-
 import warnings
+from collections import defaultdict
 
 import networkx as nx
 import numpy as np
@@ -19,16 +18,17 @@ def generate_pagerank_baseline(graph: nx.Graph, background_mat: Matrix) -> Matri
     pagerank_scores = nx.pagerank(graph)
 
     if len(pagerank_scores.values()) != len(background_mat.mat):
-        warnings.warn('The provided graph do not match the kernel nodes amount. '
-                       'The nodes will be matched (deleting and filling missing) according to the reference Matrix.')
+        warnings.warn(
+            'The provided graph do not match the kernel nodes amount. The nodes will be matched (deleting and filling missing) according to the reference Matrix.')
 
     return Matrix(mat=np.array(
         list(pagerank_scores.values())).reshape(
         (len(list(pagerank_scores.values())), 1)
     ),
         rows_labels=list(pagerank_scores.keys()),
         cols_labels=['PageRank']
-    ).match_delete_rows(background_mat.rows_labels).match_missing_rows(background_mat.rows_labels).match_rows(background_mat)
+    ).match_delete_rows(background_mat.rows_labels).match_missing_rows(background_mat.rows_labels).match_rows(
+        background_mat)
 
 
 def resistance_distance(G=None, M=None, normalized=False):

src/diffupath/views.py

@@ -111,7 +111,7 @@ def show_venn_diagram(
     intersections_len = [len(intersection) for name, intersection in intersections.items()]
 
     plt.figure(figsize=(17, 8))
-    v = venn3(subsets=intersections_len, set_labels=set_labels)
+    _ = venn3(subsets=intersections_len, set_labels=set_labels)
 
     plt.show()