1 files changed, 31 insertions, 16 deletions
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index 98be0123..3571580b 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -18,22 +18,28 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2017 Inria"
 __license__ = "MIT"
 
-parser = argparse.ArgumentParser(description='RipsComplex creation from '
-                                 'a correlation matrix read in a csv file.',
-                                 epilog='Example: '
-                                 'example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py '
-                                 '-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3'
-                                 '- Constructs a Rips complex with the '
-                                 'correlation matrix from the given csv file.')
+parser = argparse.ArgumentParser(
+    description="RipsComplex creation from " "a correlation matrix read in a csv file.",
+    epilog="Example: "
+    "example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py "
+    "-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3"
+    "- Constructs a Rips complex with the "
+    "correlation matrix from the given csv file.",
+)
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band", type=float, default=0.)
-parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+parser.add_argument("-b", "--band", type=float, default=0.0)
+parser.add_argument(
+    "--no-diagram",
+    default=False,
+    action="store_true",
+    help="Flag for not to display the diagrams",
+)
 
 args = parser.parse_args()
 
-if not (-1. < args.min_edge_correlation < 1.):
+if not (-1.0 < args.min_edge_correlation < 1.0):
     print("Wrong value of the treshold corelation (should be between -1 and 1).")
     sys.exit(1)
 
@@ -48,12 +54,18 @@ print("RipsComplex creation from correlation matrix read in a csv file")
 message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation)
 print(message)
 
-correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file)
+correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
+    csv_file=args.file
+)
 # Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
-distance_matrix = [[1.-correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))] for i in range(len(correlation_matrix))]
-
-rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix,
-                                 max_edge_length=1.-args.min_edge_correlation)
+distance_matrix = [
+    [1.0 - correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))]
+    for i in range(len(correlation_matrix))
+]
+
+rips_complex = gudhi.RipsComplex(
+    distance_matrix=distance_matrix, max_edge_length=1.0 - args.min_edge_correlation
+)
 simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
 
 message = "Number of simplices=" + repr(simplex_tree.num_simplices())
@@ -65,7 +77,10 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 # invert the persistence diagram
-invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))]
+invert_diag = [
+    (diag[pers][0], (1.0 - diag[pers][1][0], 1.0 - diag[pers][1][1]))
+    for pers in range(len(diag))
+]
 
 if args.no_diagram == False:
     pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band)