Optimise imports and perform some PEP8 fixes.

setup.py

@@ -1,19 +1,18 @@
-from setuptools import setup, find_packages
-from setuptools.command.install import install
-import os
 import io
+import os
+
+from setuptools import setup, find_packages
 
 SETUP_DIR = os.path.dirname(os.path.abspath(__file__))
 
-# List all of your Python package dependencies in the
-# requirements.txt file
 
 def readfile(filename, split=False):
     with io.open(filename, encoding="utf-8") as stream:
         if split:
             return stream.read().split("\n")
         return stream.read()
 
+
 readme = readfile("README.rst", split=True)[3:]  # skip title
 # For requirements not hosted on PyPi place listings
 # into the 'requirements.txt' file.
@@ -46,4 +45,4 @@ def readfile(filename, split=False):
     include_package_data=True,
     zip_safe=False,
     install_requires=requires,
-    )
+)

src/scaffoldmaker/__init__.py

@@ -1,2 +0,0 @@
-__import__('pkg_resources').declare_namespace(__name__)
-

src/scaffoldmaker/annotation/annotationgroup.py

@@ -2,14 +2,15 @@
 Describes subdomains of a scaffold with attached names and terms.
 """
 
+from opencmiss.utils.zinc.general import ChangeManager
 from opencmiss.zinc.field import Field, FieldGroup
 from opencmiss.zinc.result import RESULT_OK
-from opencmiss.utils.zinc.general import ChangeManager
 from scaffoldmaker.utils.zinc_utils import group_get_highest_dimension, \
     identifier_ranges_from_string, identifier_ranges_to_string, \
     mesh_group_add_identifier_ranges, mesh_group_to_identifier_ranges, \
     nodeset_group_add_identifier_ranges, nodeset_group_to_identifier_ranges
 
+
 class AnnotationGroup(object):
     '''
     Describes subdomains of a scaffold with attached names and terms.

src/scaffoldmaker/meshtypes/meshtype_1d_bifurcationtree1.py

@@ -3,11 +3,12 @@
 """
 
 from __future__ import division
-from math import cos, radians, sin, sqrt
+from math import cos, radians, sin
+
 from opencmiss.maths.vectorops import add, cross, magnitude, mult, normalize, sub
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFiniteElement
-from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.utils.zinc.general import ChangeManager
+from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base

src/scaffoldmaker/meshtypes/meshtype_1d_path1.py

@@ -3,16 +3,15 @@
 """
 
 from __future__ import division
-import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup
 from opencmiss.utils.zinc.general import ChangeManager
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
-from scaffoldmaker.utils.interpolation import DerivativeScalingMode, smoothCubicHermiteDerivativesLine, smoothCubicHermiteCrossDerivativesLine
 from scaffoldmaker.utils import vector
-from opencmiss.zinc.result import RESULT_OK
+from scaffoldmaker.utils.interpolation import smoothCubicHermiteCrossDerivativesLine
 
 
 class MeshType_1d_path1(Scaffold_base):

src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py

@@ -3,13 +3,14 @@
 """
 
 from __future__ import division
-import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
+
 class MeshType_2d_plate1(Scaffold_base):
     '''
     classdocs

src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py

@@ -6,14 +6,17 @@
 """
 
 from __future__ import division
+
 import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
 
+
 class MeshType_2d_platehole1(Scaffold_base):
     '''
     classdocs

src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py

@@ -3,13 +3,16 @@
 """
 
 from __future__ import division
+
 import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
+
 class MeshType_2d_sphere1(Scaffold_base):
     '''
     classdocs

src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py

@@ -3,13 +3,16 @@
 """
 
 from __future__ import division
+
 import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 
+
 class MeshType_2d_tube1(Scaffold_base):
     '''
     classdocs

src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcation1.py

@@ -3,7 +3,9 @@
 """
 
 from __future__ import division
+
 import math
+
 from opencmiss.maths.vectorops import cross, mult, normalize, sub
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.field import Field

src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcationtree1.py

@@ -4,16 +4,14 @@
 
 from __future__ import division
 import math
-from opencmiss.maths.vectorops import cross, mult, normalize, sub
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.meshtype_1d_bifurcationtree1 import MeshType_1d_bifurcationtree1
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.scaffoldpackage import ScaffoldPackage
-from scaffoldmaker.utils.bifurcation import get_curve_circle_points, \
-    make_tube_bifurcation_points, make_tube_bifurcation_elements_2d
-from scaffoldmaker.utils.geometry import createCirclePoints
+from scaffoldmaker.utils.bifurcation import get_curve_circle_points
 from scaffoldmaker.utils.interpolation import getCubicHermiteArcLength
 
 

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -3,8 +3,10 @@
 """
 
 from __future__ import division
-import math
+
 import copy
+import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element
 from opencmiss.zinc.field import Field
@@ -14,11 +16,11 @@
 from scaffoldmaker.meshtypes.meshtype_3d_ostium1 import MeshType_3d_ostium1, generateOstiumMesh
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.scaffoldpackage import ScaffoldPackage
+from scaffoldmaker.utils import interpolation as interp
+from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.annulusmesh import createAnnulusMesh3d
 from scaffoldmaker.utils.eftfactory_bicubichermitelinear import eftfactory_bicubichermitelinear
-from scaffoldmaker.utils import interpolation as interp
 from scaffoldmaker.utils.interpolation import getCubicHermiteBasis, smoothCubicHermiteDerivativesLine
-from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
 from scaffoldmaker.utils.tracksurface import TrackSurface, TrackSurfacePosition, calculate_surface_axes
 

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

@@ -6,6 +6,11 @@
 
 import copy
 import math
+
+from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
+from opencmiss.zinc.element import Element
+from opencmiss.zinc.field import Field
+from opencmiss.zinc.node import Node
 from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm
 from scaffoldmaker.annotation.bladder_terms import get_bladder_term
 from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion
@@ -21,10 +26,6 @@
 from scaffoldmaker.utils.interpolation import smoothCubicHermiteDerivativesLine
 from scaffoldmaker.utils.tracksurface import TrackSurface, TrackSurfacePosition, calculate_surface_axes
 from scaffoldmaker.utils.zinc_utils import exnodeStringFromNodeValues, mesh_destroy_elements_and_nodes_by_identifiers
-from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
-from opencmiss.zinc.element import Element
-from opencmiss.zinc.field import Field
-from opencmiss.zinc.node import Node
 
 
 class MeshType_3d_bladderurethra1(Scaffold_base):

src/scaffoldmaker/meshtypes/meshtype_3d_box1.py

@@ -3,15 +3,16 @@
 """
 
 from __future__ import division
-import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
-from opencmiss.zinc.element import Element, Elementbasis
+from opencmiss.zinc.element import Element
 from opencmiss.zinc.field import Field
 from opencmiss.zinc.node import Node
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
 
+
 class MeshType_3d_box1(Scaffold_base):
     '''
     classdocs

src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py

@@ -6,7 +6,9 @@
 """
 
 from __future__ import division
+
 import math
+
 from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates
 from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate
 from opencmiss.zinc.field import Field
@@ -15,6 +17,7 @@
 from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite
 from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative
 
+
 class MeshType_3d_boxhole1(Scaffold_base):
     '''
     classdocs