Pass flake8

Author: ddomingof

src/diffupy/kernels.py

@@ -27,6 +27,7 @@
 
 def commute_time_kernel(graph: nx.Graph, normalized: bool = False) -> Matrix:
     """Compute the commute-time kernel, which is the expected time of going back and forth between a couple of nodes.
+
     If the network is connected, then the commuted time kernel will be totally dense, therefore reflecting global
     properties of the network. For further details, see [Yen, 2007]. This kernel can be computed using both the
     unnormalised and normalised graph Laplacian.
@@ -44,7 +45,7 @@ def commute_time_kernel(graph: nx.Graph, normalized: bool = False) -> Matrix:
 
 
 def diffusion_kernel(graph: nx.Graph, sigma2: float = 1, normalized: bool = True) -> Matrix:
-    """Computes the classical diffusion kernel that involves matrix exponentiation.
+    """Compute the classical diffusion kernel that involves matrix exponentiation.
 
     It has a "bandwidth" parameter sigma^2 that controls the extent of the spreading.
     Quoting [Smola, 2003]:

src/diffupy/matrix.py

@@ -73,7 +73,7 @@ def __str__(self):
         return f"\nmatrix {self.name} \n  {s} \n "
 
     def __iter__(self, **kargs):
-        """Helper method for the matrix class."""
+        """Help method for the matrix class."""
         self.i = -1
         self.j = 0
 
@@ -85,7 +85,7 @@ def __iter__(self, **kargs):
         return self
 
     def __next__(self):
-        """Helper method for the matrix class."""
+        """Help method for the matrix class."""
         if self.i >= len(self.rows_labels) - 1 and self.j >= len(self.cols_labels) - 1:
             self.get_labels = True
             self.get_indices = False
@@ -443,6 +443,7 @@ class LaplacianMatrix(Matrix):
     """Laplacian matrix class"""
 
     def __init__(self, graph, normalized=False, name=''):
+        """Initialize object."""
         l_mat = get_laplacian(graph, normalized)
 
         Matrix.__init__(self, mat=l_mat, quadratic=True, name=name, graph=graph)

src/diffupy/validate_input.py

@@ -15,7 +15,6 @@
 
 def _validate_method(method: str) -> None:
     """Ensures that 'method' is a valid character."""
-
     if not isinstance(method, str):
         raise ValueError(f"The supplied 'method' must be a string. The given argument is a {type(method)}")
 
@@ -28,7 +27,6 @@ def _validate_method(method: str) -> None:
 
 def _validate_scores(scores: Matrix) -> None:
     """Check scores sanity: Ensures that scores are suitable for diffusion."""
-
     #  Check labels list
     if not scores.cols_labels:
         raise ValueError("Scores must be a named list but supplied list contains no names.")
@@ -76,7 +74,6 @@ def _validate_scores(scores: Matrix) -> None:
 
 def _validate_graph(graph: nx.Graph) -> None:
     """Check graph sanity: Ensures that 'graph' is a valid NetworkX Graph object."""
-
     if graph in [None, 'NA', 'Nan']:
         raise ValueError("'graph' missing")