tidied code to meet flake8 recommendations

.travis.yml

@@ -16,7 +16,7 @@ install:
 
 script:
     - pytest --cov=./
-
+    - flake8
 
 after_success:
     - codecov

orientation/calc_angles.py

@@ -1,5 +1,6 @@
 import numpy as np
 
+
 def get_com(universe, selection):
 
     ''' Return the centre of mass of a selection string '''
@@ -13,60 +14,64 @@ def get_principal_axes(universe, selection):
 
     # Methodology taken from Beckstein
     # https://stackoverflow.com/questions/49239475/
-    # how-to-use-mdanalysis-to-principal-axes-and-moment-of-inertia-with-a-group-of-at/49268247#49268247
+    # how-to-use-mdanalysis-to-principal-axes-and-
+    # moment-of-inertia-with-a-group-of-at/49268247#49268247
 
     # select alpha carbons only
     CA = universe.select_atoms(selection)
 
     # calculate moment of inertia, and sort eigenvectors
-    I = CA.moment_of_inertia()
+    # PCB renamed I to Inertia (ambiguous variable name)
+    Inertia = CA.moment_of_inertia()
 
     # UT = CA.principal_axes()
     # U = UT.T
 
-    values, evecs = np.linalg.eigh(I)
+    values, evecs = np.linalg.eigh(Inertia)
     indices = np.argsort(values)
     U = evecs[:, indices]
 
-    ## Below is for testing ##
-    # Lambda = U.T.dot(I.dot(U))
+    # Below is for testing ##
+    # Lambda = U.T.dot(Inertia.dot(U))
     #
     # print(Lambda)
     # print(np.allclose(Lambda - np.diag(np.diagonal(Lambda)), 0))
 
-    #print("")
-    #print(U)
+    # print("")
+    # print(U)
 
     return U
 
 
 def dir_cosine(v1, v2):
 
-    ''' 
+    '''
     Given two vectors (v1 and v2) work out the direction cosine between
-    them. For more information see: https://en.wikipedia.org/wiki/Direction_cosine)
+     them. For more information see:
+     https://en.wikipedia.org/wiki/Direction_cosine)
     '''
 
-    direction_cosine = np.dot(v1, v2) / (np.linalg.norm(v1) * np.linalg.norm(v2))
+    direction_cosine = np.dot(v1, v2) / (np.linalg.norm(v1) *
+                                         np.linalg.norm(v2))
 
     return direction_cosine
 
 
 def make_direction_cosine_matrix(ref, axes_set):
 
     '''
-    Given a set of two axes (ref_option and axes_set) work out the direction cosine matrix
-    between them.
+    Given a set of two axes (ref_option and axes_set)
+     work out the direction cosine matrix between them.
     '''
     # Gather the individual vectors of our reference basis
     ex = ref[0, :]
     ey = ref[1, :]
     ez = ref[2, :]
 
     # principal axes calculated at this instance
-    u = axes_set[0, :] # 1st princpal axis (PA)
-    v = axes_set[1, :] # 2nd princpal axis (PA)
-    w = axes_set[2, :] # 3rd princpal axis (PA)
+    u = axes_set[0, :]  # 1st princpal axis (PA)
+    v = axes_set[1, :]  # 2nd princpal axis (PA)
+    w = axes_set[2, :]  # 3rd princpal axis (PA)
 
     # Work out the dot prod b/w the 1st PA and the unit vectors
     u_alpha = dir_cosine(u, ex)
@@ -83,9 +88,8 @@ def make_direction_cosine_matrix(ref, axes_set):
     w_beta = dir_cosine(w, ey)
     w_gamma = dir_cosine(w, ez)
 
-    # make all of the above into a 3 X 3 matrix and return it 
+    # make all of the above into a 3 X 3 matrix and return it
     c_matrix = np.asarray([[u_alpha, u_beta, u_gamma],
                           [v_alpha, v_beta, v_gamma],
-                          [w_alpha, w_beta, w_gamma]])                       
-
+                          [w_alpha, w_beta, w_gamma]])
     return c_matrix