old_contents: """
  gen_mesh_bc.py
  
  Generate meshes and PML boundary conditions for QIBA digital phantoms.
  
  Mark Palmeri
  mlp6@duke.edu
  2015-03-17
  """
  
  import os
  
  FEMGIT = '/home/mlp6/git/fem'
  
  # all units are CGS
  focalDepths = [3.0, 5.0, 7.0]
  nodeSpacing = 0.025
  axialExtent = 1.5 # ratio of focal depth to extent the mesh in depth
  
  for fd in focalDepths:
  
      nodefile = 'nodesFoc%.fmm.dyn' % (fd*10)
      elemfile = 'elemsFoc%.fmm.dyn' % (fd*10)
  
      os.system('python %s/mesh/GenMesh.py '
                '--nodefile %s '
                '--elefile %s '
                '--xyz -1.0 0.0 0.0 2.5 -%.1f 0.0 '
                '--numElem 40 100 %.f' %
                (FEMGIT, nodefile, elemfile, fd*axialExtent,
                 fd*axialExtent/nodeSpacing)
                )
  
      os.system('python %s/mesh/bc.py '
                '--pml '
                '--nodefile %s '
                '--elefile %s '
                '--bcfile bcPMLfoc%.fmm.dyn' %
                (FEMGIT, nodefile, elemfile, fd*10)
                )
  
new_contents: """
  gen_mesh_bc.py
  
  Generate meshes and PML boundary conditions for QIBA digital phantoms.
  
  Mark Palmeri
  mlp6@duke.edu
  2015-03-17
  """
  
  import os
  
  FEMGIT = '/home/mlp6/git/fem'
  
  # all units are CGS
  focalDepths = [3.0, 5.0, 7.0]
  nodeSpacing = 0.025
  axialExtent = 1.5  # ratio of focal depth to extent the mesh in depth
  
  for fd in focalDepths:
  
      nodefile = 'nodesFoc%.fmm.dyn' % (fd*10)
      elemfile = 'elemsFoc%.fmm.dyn' % (fd*10)
  
      os.system('python %s/mesh/GenMesh.py '
                '--nodefile %s '
                '--elefile %s '
                '--xyz -1.0 0.0 0.0 2.5 -%.1f 0.0 '
                '--numElem 40 100 %.f' %
                (FEMGIT, nodefile, elemfile, fd*axialExtent,
                 fd*axialExtent/nodeSpacing)
                )
  
      os.system('python %s/mesh/bc.py '
                '--pml '
                '--nodefile %s '
                '--elefile %s '
                '--bcfile bcPMLfoc%.fmm.dyn' %
                (FEMGIT, nodefile, elemfile, fd*10)
                )
  
subject: refactor syntax (PEP8)