added b-helpers to pep8-tests again

Author: pancetta

pySDC/implementations/problem_classes/boussinesq_helpers/build2DFDMatrix.py

@@ -1,6 +1,3 @@
-import sys
-
-sys.path.append('../')
 import numpy as np
 import scipy.sparse as sp
 from pySDC.implementations.problem_classes.boussinesq_helpers.buildFDMatrix import getMatrix, getUpwindMatrix, \
@@ -19,13 +16,16 @@ def get2DUpwindMatrix(N, dx, order):
 #
 #
 def get2DMesh(N, x_b, z_b, bc_hor, bc_ver):
+
     assert np.size(N) == 2, 'N needs to be an array with two entries: N[0]=Nx and N[1]=Nz'
     assert np.size(
         x_b) == 2, 'x_b needs to be an array with two entries: x_b[0] = left boundary, x_b[1] = right boundary'
     assert np.size(
         z_b) == 2, 'z_b needs to be an array with two entries: z_b[0] = lower boundary, z_b[1] = upper boundary'
 
     h = np.zeros(2)
+    x = None
+    z = None
 
     if bc_hor[0] in ['periodic']:
         assert bc_hor[1] in ['periodic'], 'Periodic boundary conditions must be prescribed at both boundaries'

pySDC/implementations/problem_classes/boussinesq_helpers/buildBoussinesq2DMatrix.py

@@ -1,59 +1,60 @@
 import numpy as np
 import scipy.sparse as sp
 from pySDC.implementations.problem_classes.boussinesq_helpers.build2DFDMatrix import get2DMatrix, getBCHorizontal, \
-  getBCVertical, get2DUpwindMatrix
+    get2DUpwindMatrix
+
 
 def getBoussinesq2DUpwindMatrix(N, dx, u_adv, order):
+    Dx = get2DUpwindMatrix(N, dx, order)
+
+    # Note: In the equations it is u_t + u_adv* D_x u = ... so in order to comply with the form u_t = M u,
+    # add a minus sign in front of u_adv
+
+    Zero = np.zeros((N[0] * N[1], N[0] * N[1]))
+    M1 = sp.hstack((-u_adv * Dx, Zero, Zero, Zero), format="csr")
+    M2 = sp.hstack((Zero, -u_adv * Dx, Zero, Zero), format="csr")
+    M3 = sp.hstack((Zero, Zero, -u_adv * Dx, Zero), format="csr")
+    M4 = sp.hstack((Zero, Zero, Zero, -u_adv * Dx), format="csr")
+    M = sp.vstack((M1, M2, M3, M4), format="csr")
+
+    return sp.csc_matrix(M)
+
 
-  Dx   = get2DUpwindMatrix(N, dx, order)
-  
-  # Note: In the equations it is u_t + u_adv* D_x u = ... so in order to comply with the form u_t = M u,
-  # add a minus sign in front of u_adv
-  
-  Zero = np.zeros((N[0]*N[1], N[0]*N[1]))
-  M1 = sp.hstack((-u_adv*Dx,        Zero,      Zero,      Zero), format="csr")
-  M2 = sp.hstack((     Zero,   -u_adv*Dx,      Zero,      Zero), format="csr")
-  M3 = sp.hstack((     Zero,        Zero, -u_adv*Dx,      Zero), format="csr")
-  M4 = sp.hstack((     Zero,        Zero,      Zero, -u_adv*Dx), format="csr")
-  M  = sp.vstack((M1,M2,M3,M4), format="csr")
-  
-  return sp.csc_matrix(M)
-  
 def getBoussinesq2DMatrix(N, h, bc_hor, bc_ver, c_s, Nfreq, order):
+    Dx_u, Dz_u = get2DMatrix(N, h, bc_hor[0], bc_ver[0], order)
+    Dx_w, Dz_w = get2DMatrix(N, h, bc_hor[1], bc_ver[1], order)
+    # Dx_b, Dz_b = get2DMatrix(N, h, bc_hor[2], bc_ver[2], order)
+    Dx_p, Dz_p = get2DMatrix(N, h, bc_hor[3], bc_ver[3], order)
 
-  Dx_u, Dz_u = get2DMatrix(N, h, bc_hor[0], bc_ver[0], order)
-  Dx_w, Dz_w = get2DMatrix(N, h, bc_hor[1], bc_ver[1], order)
-  Dx_b, Dz_b = get2DMatrix(N, h, bc_hor[2], bc_ver[2], order)
-  Dx_p, Dz_p = get2DMatrix(N, h, bc_hor[3], bc_ver[3], order)
+    # Id_N = sp.eye(N[0] * N[1])
 
-  Id_N = sp.eye(N[0]*N[1])
+    Zero = np.zeros((N[0] * N[1], N[0] * N[1]))
+    Id_w = sp.eye(N[0] * N[1])
 
-  Zero = np.zeros((N[0]*N[1],N[0]*N[1]))
-  Id_w = sp.eye(N[0]*N[1])
+    # Note: Bring all terms to right hand side, therefore a couple of minus signs
+    # are needed
 
-  # Note: Bring all terms to right hand side, therefore a couple of minus signs
-  # are needed
+    M1 = sp.hstack((Zero, Zero, Zero, -Dx_p), format="csr")
+    M2 = sp.hstack((Zero, Zero, Id_w, -Dz_p), format="csr")
+    M3 = sp.hstack((Zero, -Nfreq ** 2 * Id_w, Zero, Zero), format="csr")
+    M4 = sp.hstack((-c_s ** 2 * Dx_u, -c_s ** 2 * Dz_w, Zero, Zero), format="csr")
+    M = sp.vstack((M1, M2, M3, M4), format="csr")
 
-  M1 = sp.hstack((        Zero,          Zero,  Zero, -Dx_p), format="csr")
-  M2 = sp.hstack((        Zero,          Zero,  Id_w, -Dz_p), format="csr")
-  M3 = sp.hstack((        Zero, -Nfreq**2*Id_w,  Zero, Zero), format="csr")
-  M4 = sp.hstack((-c_s**2*Dx_u,   -c_s**2*Dz_w,  Zero, Zero), format="csr")
-  M  = sp.vstack((M1,M2,M3,M4), format="csr")
+    Id = sp.eye(4 * N[0] * N[1])
 
-  Id = sp.eye(4*N[0]*N[1])
+    return sp.csc_matrix(Id), sp.csc_matrix(M)
 
-  return sp.csc_matrix(Id), sp.csc_matrix(M)
 
 def getBoussinesqBCHorizontal(value, N, dx, bc_hor):
-  
-  bu_left, bu_right = getBCHorizontal( value[0], N, dx, bc_hor[0] )
-  bw_left, bw_right = getBCHorizontal( value[1], N, dx, bc_hor[1] )
-  bb_left, bb_right = getBCHorizontal( value[2], N, dx, bc_hor[2] )
-  bp_left, bp_right = getBCHorizontal( value[3], N, dx, bc_hor[3] )
-  
-  b_left  = np.concatenate(( bp_left,  bp_left,  bu_left + bw_left))
-  b_right = np.concatenate(( bp_right, bp_right, bu_right + bw_right))
-  return b_left, b_right
+    bu_left, bu_right = getBCHorizontal(value[0], N, dx, bc_hor[0])
+    bw_left, bw_right = getBCHorizontal(value[1], N, dx, bc_hor[1])
+    # bb_left, bb_right = getBCHorizontal(value[2], N, dx, bc_hor[2])
+    bp_left, bp_right = getBCHorizontal(value[3], N, dx, bc_hor[3])
+
+    b_left = np.concatenate((bp_left, bp_left, bu_left + bw_left))
+    b_right = np.concatenate((bp_right, bp_right, bu_right + bw_right))
+    return b_left, b_right
+
 
 def getBoussinesqBCVertical():
-  return 0.0
+    return 0.0

pySDC/implementations/problem_classes/boussinesq_helpers/buildFDMatrix.py

@@ -124,7 +124,8 @@ def getMatrix(N, dx, bc_left, bc_right, order):
             A[N - 1, :] = np.zeros(N)
             A[N - 1, N - 2] = -6.0
 
-    A = coeff * (1.0 / dx) * A
+    A *= coeff * (1.0 / dx)
+
     return sp.csc_matrix(A)
 
 
@@ -138,11 +139,13 @@ def getBCLeft(value, N, dx, type, order):
         coeff = 1.0 / 2.0
     elif order == 4:
         coeff = 1.0 / 12.0
+    else:
+        raise NotImplementedError('wrong order, got %s' % order)
 
     b = np.zeros(N)
     if type in ['dirichlet']:
         if order == 2:
-            b[0] = -value;
+            b[0] = -value
         elif order == 4:
             b[0] = -6.0 * value
             b[1] = 1.0 * value
@@ -167,6 +170,8 @@ def getBCRight(value, N, dx, type, order):
         coeff = 1.0 / 2.0
     elif order == 4:
         coeff = 1.0 / 12.0
+    else:
+        raise NotImplementedError('wrong order, got %s' % order)
 
     b = np.zeros(N)
     if type in ['dirichlet']:

pySDC/implementations/problem_classes/boussinesq_helpers/helper_classes.py

@@ -21,4 +21,4 @@ def __init__(self):
 
     def __call__(self, residuals):
         self.counter += 1
-        self.residual = residuals
+        self.residual = residuals

tests/test_pep8.py

@@ -12,9 +12,8 @@ def check_files(dir):
     style.options.max_line_length = 120
     python_files = []
     for root, _, files in os.walk(dir):
-        if root != 'pySDC/implementations/problem_classes/boussinesq_helpers':
-            python_files += [os.path.join(root, f) for f in files if f.endswith('.py')]
-    # python_files = [os.path.join(dir, f) for f in os.listdir(dir) if f.endswith('.py') and f != '__init__.py']
+        # if root != 'pySDC/implementations/problem_classes/boussinesq_helpers':
+        python_files += [os.path.join(root, f) for f in files if f.endswith('.py')]
     print(python_files)
 
     for file in python_files: