copy docs badges from readme to docs index

README.rst

@@ -21,10 +21,6 @@ SimPEG
     :target: https://travis-ci.org/simpeg/simpeg
     :alt: Travis CI build status
 
-.. image:: https://img.shields.io/coveralls/simpeg/simpeg.svg
-    :target: https://coveralls.io/r/simpeg/simpeg?branch=master
-    :alt: Coverage status
-
 .. image:: http://img.shields.io/badge/GITTER-JOIN_CHAT-brightgreen.svg?style=flat-square
     :alt: gitter chat room at https://gitter.im/simpeg/simpeg
     :target: https://gitter.im/simpeg/simpeg
@@ -32,6 +28,13 @@ SimPEG
 .. image:: https://codecov.io/gh/simpeg/simpeg/branch/master/graph/badge.svg
     :target: https://codecov.io/gh/simpeg/simpeg
 
+.. image:: https://www.quantifiedcode.com/api/v1/project/933aa3decf444538aa432c8817169b6d/badge.svg
+    :target: https://www.quantifiedcode.com/app/project/933aa3decf444538aa432c8817169b6d
+    :alt: Code issues
+
+.. image:: https://api.codacy.com/project/badge/Grade/4fc959a5294a418fa21fc7bc3b3aa078
+    :target: https://www.codacy.com/app/lindseyheagy/simpeg?utm_source=github.com&utm_medium=referral&utm_content=simpeg/simpeg&utm_campaign=Badge_Grade
+    :alt: codacy
 
 Simulation and Parameter Estimation in Geophysics  -  A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
 

SimPEG/DCIP/DCIPUtils.py

@@ -476,7 +476,7 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
     fid.write('! ' + surveyType + ' FORMAT\n')
 
     if iptype!=0:
-        fid.write('IPTYPE=%i\n'%iptype)
+        fid.write('IPTYPE={0:d}\n'.format(iptype))
 
     else:
         fid.write('! ' + stype + ' FORMAT\n')
@@ -512,7 +512,7 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
 
                 if surveyType == 'SURFACE':
 
-                    fid.writelines("%f " % ii for ii in mkvc(tx[0,:]))
+                    fid.writelines("{0:f} ".format(ii) for ii in mkvc(tx[0,:]))
                     M = M[:,0]
                     N = N[:,0]
 
@@ -521,7 +521,7 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
                     # Flip sign for z-elevation to depth
                     tx[2::2,:] = -tx[2::2,:]
 
-                    fid.writelines("%e " % ii for ii in mkvc(tx[::2,:]))
+                    fid.writelines("{0:e} ".format(ii) for ii in mkvc(tx[::2,:]))
                     M = M[:,0::2]
                     N = N[:,0::2]
 
@@ -529,22 +529,22 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
                     M[:,1::2] = -M[:,1::2]
                     N[:,1::2] = -N[:,1::2]
 
-                fid.write('%i\n'% nD)
+                fid.write('{0:d}\n'.format(nD))
                 np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%f',delimiter=' ',newline='\n')
 
         if dim=='3D':
 
             if surveyType == 'SURFACE':
 
-                fid.writelines("%e " % ii for ii in mkvc(tx[0:2,:]))
+                fid.writelines("{0:e} ".format(ii) for ii in mkvc(tx[0:2,:]))
                 M = M[:,0:2]
                 N = N[:,0:2]
 
             if surveyType == 'GENERAL':
 
-                fid.writelines("%e " % ii for ii in mkvc(tx[0:3,:]))
+                fid.writelines("{0:e} ".format(ii) for ii in mkvc(tx[0:3,:]))
 
-            fid.write('%i\n'% nD)
+            fid.write('{0:d}\n'.format(nD))
             np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
             fid.write('\n')
 

SimPEG/Directives.py

@@ -15,7 +15,7 @@ class InversionDirective(object):
     @inversion.setter
     def inversion(self, i):
         if getattr(self,'_inversion',None) is not None:
-            print 'Warning: InversionDirective %s has switched to a new inversion.' % self.__name__
+            print 'Warning: InversionDirective {0!s} has switched to a new inversion.'.format(self.__name__)
         self._inversion = i
 
     @property
@@ -47,7 +47,7 @@ class DirectiveList(object):
     def __init__(self, *directives, **kwargs):
         self.dList = []
         for d in directives:
-            assert isinstance(d, InversionDirective), 'All directives must be InversionDirectives not %s' % d.__name__
+            assert isinstance(d, InversionDirective), 'All directives must be InversionDirectives not {0!s}'.format(d.__name__)
             self.dList.append(d)
         Utils.setKwargs(self, **kwargs)
 
@@ -68,7 +68,7 @@ class DirectiveList(object):
     def inversion(self, i):
         if self.inversion is i: return
         if getattr(self,'_inversion',None) is not None:
-            print 'Warning: %s has switched to a new inversion.' % self.__name__
+            print 'Warning: {0!s} has switched to a new inversion.'.format(self.__name__)
         for d in self.dList:
             d.inversion = i
         self._inversion = i
@@ -79,7 +79,7 @@ class DirectiveList(object):
             return
 
         directives = ['initialize', 'endIter', 'finish']
-        assert ruleType in directives, 'Directive type must be in ["%s"]' % '", "'.join(directives)
+        assert ruleType in directives, 'Directive type must be in ["{0!s}"]'.format('", "'.join(directives))
         for r in self.dList:
             getattr(r, ruleType)()
 
@@ -141,7 +141,7 @@ class BetaSchedule(InversionDirective):
 
     def endIter(self):
         if self.opt.iter > 0 and self.opt.iter % self.coolingRate == 0:
-            if self.debug: print 'BetaSchedule is cooling Beta. Iteration: %d' % self.opt.iter
+            if self.debug: print 'BetaSchedule is cooling Beta. Iteration: {0:d}'.format(self.opt.iter)
             self.invProb.beta /= self.coolingFactor
 
 
@@ -181,7 +181,7 @@ class SaveEveryIteration(InversionDirective):
     def fileName(self):
         if getattr(self, '_fileName', None) is None:
             from datetime import datetime
-            self._fileName = '%s-%s'%(self.name, datetime.now().strftime('%Y-%m-%d-%H-%M'))
+            self._fileName = '{0!s}-{1!s}'.format(self.name, datetime.now().strftime('%Y-%m-%d-%H-%M'))
         return self._fileName
     @fileName.setter
     def fileName(self, value):
@@ -192,31 +192,31 @@ class SaveModelEveryIteration(SaveEveryIteration):
     """SaveModelEveryIteration"""
 
     def initialize(self):
-        print "SimPEG.SaveModelEveryIteration will save your models as: '###-%s.npy'"%self.fileName
+        print "SimPEG.SaveModelEveryIteration will save your models as: '###-{0!s}.npy'".format(self.fileName)
 
     def endIter(self):
-        np.save('%03d-%s' % (self.opt.iter, self.fileName), self.opt.xc)
+        np.save('{0:03d}-{1!s}'.format(self.opt.iter, self.fileName), self.opt.xc)
 
 
 class SaveOutputEveryIteration(SaveEveryIteration):
     """SaveModelEveryIteration"""
 
     def initialize(self):
-        print "SimPEG.SaveOutputEveryIteration will save your inversion progress as: '###-%s.txt'"%self.fileName
+        print "SimPEG.SaveOutputEveryIteration will save your inversion progress as: '###-{0!s}.txt'".format(self.fileName)
         f = open(self.fileName+'.txt', 'w')
         f.write("  #     beta     phi_d     phi_m       f\n")
         f.close()
 
     def endIter(self):
         f = open(self.fileName+'.txt', 'a')
-        f.write(' %3d %1.4e %1.4e %1.4e %1.4e\n'%(self.opt.iter, self.invProb.beta, self.invProb.phi_d, self.invProb.phi_m, self.opt.f))
+        f.write(' {0:3d} {1:1.4e} {2:1.4e} {3:1.4e} {4:1.4e}\n'.format(self.opt.iter, self.invProb.beta, self.invProb.phi_d, self.invProb.phi_m, self.opt.f))
         f.close()
 
 class SaveOutputDictEveryIteration(SaveEveryIteration):
     """SaveOutputDictEveryIteration"""
 
     def initialize(self):
-        print "SimPEG.SaveOutputDictEveryIteration will save your inversion progress as dictionary: '###-%s.npz'"%self.fileName
+        print "SimPEG.SaveOutputDictEveryIteration will save your inversion progress as dictionary: '###-{0!s}.npz'".format(self.fileName)
 
     def endIter(self):
         # Save the data.
@@ -328,7 +328,7 @@ class Update_IRLS(InversionDirective):
 
         # Beta Schedule
         if self.opt.iter > 0 and self.opt.iter % self.coolingRate == 0:
-            if self.debug: print 'BetaSchedule is cooling Beta. Iteration: %d' % self.opt.iter
+            if self.debug: print 'BetaSchedule is cooling Beta. Iteration: {0:d}'.format(self.opt.iter)
             self.invProb.beta /= self.coolingFactor
 
 
@@ -340,11 +340,11 @@ class Update_IRLS(InversionDirective):
             phim_new = self.reg.eval(self.invProb.curModel)
             self.f_change = np.abs(self.f_old - phim_new) / self.f_old
 
-            print "Regularization decrease: %6.3e" % (self.f_change)
+            print "Regularization decrease: {0:6.3e}".format((self.f_change))
 
             # Check for maximum number of IRLS cycles
             if self.IRLSiter == self.maxIRLSiter:
-                print "Reach maximum number of IRLS cycles: %i" % self.maxIRLSiter
+                print "Reach maximum number of IRLS cycles: {0:d}".format(self.maxIRLSiter)
                 self.opt.stopNextIteration = True
                 return
 

SimPEG/EM/FDEM/FieldsFDEM.py

@@ -42,7 +42,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: total electric field
         """
         if getattr(self, '_ePrimary', None) is None or getattr(self, '_eSecondary', None) is None:
-            raise NotImplementedError ('Getting e from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting e from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         return self._ePrimary(solution,srcList) + self._eSecondary(solution,srcList)
 
@@ -56,7 +56,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: total magnetic flux density
         """
         if getattr(self, '_bPrimary', None) is None or getattr(self, '_bSecondary', None) is None:
-            raise NotImplementedError ('Getting b from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting b from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         return self._bPrimary(solution, srcList) + self._bSecondary(solution, srcList)
 
@@ -70,7 +70,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: total magnetic field
         """
         if getattr(self, '_hPrimary', None) is None or getattr(self, '_hSecondary', None) is None:
-            raise NotImplementedError ('Getting h from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting h from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         return self._hPrimary(solution, srcList) + self._hSecondary(solution, srcList)
 
@@ -84,7 +84,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: total current density
         """
         if getattr(self, '_jPrimary', None) is None or getattr(self, '_jSecondary', None) is None:
-            raise NotImplementedError ('Getting j from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting j from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         return self._jPrimary(solution, srcList) + self._jSecondary(solution, srcList)
 
@@ -100,7 +100,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_eDeriv_u', None) is None or getattr(self, '_eDeriv_m', None) is None:
-            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting eDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
@@ -118,7 +118,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_bDeriv_u', None) is None or getattr(self, '_bDeriv_m', None) is None:
-            raise NotImplementedError ('Getting bDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting bDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._bDeriv_u(src, v, adjoint), self._bDeriv_m(src, v, adjoint)
@@ -136,7 +136,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_hDeriv_u', None) is None or getattr(self, '_hDeriv_m', None) is None:
-            raise NotImplementedError ('Getting hDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting hDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._hDeriv_u(src, v, adjoint), self._hDeriv_m(src, v, adjoint)
@@ -154,7 +154,7 @@ class FieldsFDEM(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_jDeriv_u', None) is None or getattr(self, '_jDeriv_m', None) is None:
-            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting jDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._jDeriv_u(src, v, adjoint), self._jDeriv_m(src, v, adjoint)

SimPEG/EM/FDEM/RxFDEM.py

@@ -11,8 +11,8 @@ class BaseRx(SimPEG.Survey.BaseRx):
     """
 
     def __init__(self, locs, orientation=None, component=None):
-        assert(orientation in ['x','y','z']), "Orientation %s not known. Orientation must be in 'x', 'y', 'z'. Arbitrary orientations have not yet been implemented."%orientation
+        assert(orientation in ['x','y','z']), "Orientation {0!s} not known. Orientation must be in 'x', 'y', 'z'. Arbitrary orientations have not yet been implemented.".format(orientation)
-        assert(component in ['real', 'imag']), "'component' must be 'real' or 'imag', not %s"%component
+        assert(component in ['real', 'imag']), "'component' must be 'real' or 'imag', not {0!s}".format(component)
 
         self.projComp = orientation
         self.component = component

SimPEG/EM/Static/DC/FieldsDC.py

@@ -9,7 +9,7 @@ class Fields(SimPEG.Problem.Fields):
 
     def _phiDeriv(self, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_phiDeriv_u', None) is None or getattr(self, '_phiDeriv_m', None) is None:
-            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting phiDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._phiDeriv_u(src, v, adjoint=adjoint), self._phiDeriv_m(src, v, adjoint=adjoint)
@@ -18,7 +18,7 @@ class Fields(SimPEG.Problem.Fields):
 
     def _eDeriv(self, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_eDeriv_u', None) is None or getattr(self, '_eDeriv_m', None) is None:
-            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting eDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
@@ -26,7 +26,7 @@ class Fields(SimPEG.Problem.Fields):
 
     def _jDeriv(self, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_jDeriv_u', None) is None or getattr(self, '_jDeriv_m', None) is None:
-            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting jDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._jDeriv_u(src, v, adjoint), self._jDeriv_m(src, v, adjoint)

SimPEG/EM/Static/DC/FieldsDC_2D.py

@@ -32,7 +32,7 @@ class Fields_ky(SimPEG.Problem.TimeFields):
 
     def _phiDeriv(self,kyInd, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_phiDeriv_u', None) is None or getattr(self, '_phiDeriv_m', None) is None:
-            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting phiDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._phiDeriv_u(kyInd, src, v, adjoint=adjoint), self._phiDeriv_m(kyInd, src, v, adjoint=adjoint)
@@ -41,7 +41,7 @@ class Fields_ky(SimPEG.Problem.TimeFields):
 
     def _eDeriv(self,kyInd, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_eDeriv_u', None) is None or getattr(self, '_eDeriv_m', None) is None:
-            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting eDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._eDeriv_u(kyInd, src, v, adjoint), self._eDeriv_m(kyInd, src, v, adjoint)
@@ -49,7 +49,7 @@ class Fields_ky(SimPEG.Problem.TimeFields):
 
     def _jDeriv(self,kyInd, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_jDeriv_u', None) is None or getattr(self, '_jDeriv_m', None) is None:
-            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting jDerivs from {0!s} is not implemented'.format(self.knownFields.keys()[0]))
 
         if adjoint:
             return self._jDeriv_u(kyInd, src, v, adjoint), self._jDeriv_m(kyInd, src, v, adjoint)

SimPEG/EM/Static/DC/ProblemDC.py

@@ -46,7 +46,7 @@ class BaseDCProblem(BaseEMProblem):
             du_dm_v = self.Ainv * ( - dA_dm_v + dRHS_dm_v )
 
             for rx in src.rxList:
-                df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                df_dmFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                 df_dm_v = df_dmFun(src, du_dm_v, v, adjoint=False)
                 Jv[src, rx] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
         return Utils.mkvc(Jv)
@@ -69,7 +69,7 @@ class BaseDCProblem(BaseEMProblem):
             u_src = f[src, self._solutionType]
             for rx in src.rxList:
                 PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
-                df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                df_duTFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                 df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
 
                 ATinvdf_duT = self.Ainv * df_duT

SimPEG/EM/Static/DC/ProblemDC_2D.py

@@ -60,7 +60,7 @@ class BaseDCProblem_2D(BaseEMProblem):
                 dRHS_dm_v = self.getRHSDeriv(ky, src, v)
                 du_dm_v = self.Ainv[iky] * ( - dA_dm_v + dRHS_dm_v )
                 for rx in src.rxList:
-                    df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                    df_dmFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                     df_dm_v = df_dmFun(iky, src, du_dm_v, v, adjoint=False)
                     # Trapezoidal intergration
                     Jv1_temp = 1./np.pi*rx.evalDeriv(ky, src, self.mesh, f, df_dm_v)
@@ -101,7 +101,7 @@ class BaseDCProblem_2D(BaseEMProblem):
                     ky = self.kys[iky]
                     AT = self.getA(ky)
                     PTv = rx.evalDeriv(ky, src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
-                    df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                    df_duTFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                     df_duT, df_dmT = df_duTFun(iky, src, None, PTv, adjoint=True)
 
                     ATinvdf_duT = self.Ainv[iky] * df_duT

SimPEG/EM/Static/IP/ProblemIP.py

@@ -56,7 +56,7 @@ class BaseIPProblem(BaseEMProblem):
             du_dm_v = self.Ainv * ( - dA_dm_v + dRHS_dm_v )
 
             for rx in src.rxList:
-                df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                df_dmFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                 df_dm_v = df_dmFun(src, du_dm_v, v, adjoint=False)
                 Jv[src, rx] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
         # Conductivity (d u / d log sigma)
@@ -83,7 +83,7 @@ class BaseIPProblem(BaseEMProblem):
             u_src = f[src, self._solutionType]
             for rx in src.rxList:
                 PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
-                df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                df_duTFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                 df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
                 ATinvdf_duT = self.Ainv * df_duT
                 dA_dmT = self.getADeriv(u_src, ATinvdf_duT, adjoint=True)

SimPEG/EM/Static/SIP/ProblemSIP.py

@@ -83,7 +83,7 @@ class BaseSIPProblem(BaseEMProblem):
                 for rx in src.rxList:
                     timeindex = rx.getTimeP(self.survey.times)
                     if timeindex[tind]:
-                        df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                        df_dmFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                         df_dm_v = df_dmFun(src, du_dm_v, v, adjoint=False)
                         Jv[src, rx, t] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
 
@@ -122,7 +122,7 @@ class BaseSIPProblem(BaseEMProblem):
                 for rx in src.rxList:
                     timeindex = rx.getTimeP(self.survey.times)
                     if timeindex[tind]:
-                        df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                        df_dmFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                         df_dm_v0 = df_dmFun(src, du_dm_v0, v0, adjoint=False)
                         df_dm_v1 = df_dmFun(src, du_dm_v1, v1, adjoint=False)
                         Jv[src, rx, t] = rx.evalDeriv(src, self.mesh, f, df_dm_v0)
@@ -153,7 +153,7 @@ class BaseSIPProblem(BaseEMProblem):
                     timeindex = rx.getTimeP(self.survey.times)
                     if timeindex[tind]:
                         PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx, t], adjoint=True) # wrt f, need possibility wrt m
-                        df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
+                        df_duTFun = getattr(f, '_{0!s}Deriv'.format(rx.projField), None)
                         df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
                         ATinvdf_duT = self.Ainv * df_duT
                         dA_dmT = self.getADeriv(u_src, ATinvdf_duT, adjoint=True)

SimPEG/EM/TDEM/BaseTDEM.py

@@ -47,7 +47,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
         self.waveformType = "GENERAL"
 
     def fields(self, m):
-        if self.verbose: print '%s\nCalculating fields(m)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print '{0!s}\nCalculating fields(m)\n{1!s}'.format('*'*50, '*'*50)
         self.curModel = m
         # Create a fields storage object
         F = self._FieldsForward_pair(self.mesh, self.survey)
@@ -55,7 +55,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
             # Set the initial conditions
             F[src,:,0] = src.getInitialFields(self.mesh)
         F = self.forward(m, self.getRHS, F=F)
-        if self.verbose: print '%s\nDone calculating fields(m)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print '{0!s}\nDone calculating fields(m)\n{1!s}'.format('*'*50, '*'*50)
         return F
 
     def forward(self, m, RHS, F=None):
@@ -70,11 +70,11 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
                 if Ainv is not None:
                     Ainv.clean()
                 A = self.getA(tInd)
-                if self.verbose: print 'Factoring...   (dt = %e)'%dt
+                if self.verbose: print 'Factoring...   (dt = {0:e})'.format(dt)
                 Ainv = self.Solver(A, **self.solverOpts)
                 if self.verbose: print 'Done'
             rhs = RHS(tInd, F)
-            if self.verbose: print '    Solving...   (tInd = %d)'%tInd
+            if self.verbose: print '    Solving...   (tInd = {0:d})'.format(tInd)
             sol = Ainv * rhs
             if self.verbose: print '    Done...'
             if sol.ndim == 1:
@@ -95,11 +95,11 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
                 if Ainv is not None:
                     Ainv.clean()
                 A = self.getA(tInd)
-                if self.verbose: print 'Factoring (Adjoint)...   (dt = %e)'%dt
+                if self.verbose: print 'Factoring (Adjoint)...   (dt = {0:e})'.format(dt)
                 Ainv = self.Solver(A, **self.solverOpts)
                 if self.verbose: print 'Done'
             rhs = RHS(tInd, F)
-            if self.verbose: print '    Solving (Adjoint)...   (tInd = %d)'%tInd
+            if self.verbose: print '    Solving (Adjoint)...   (tInd = {0:d})'.format(tInd)
             sol = Ainv * rhs
             if self.verbose: print '    Done...'
             if sol.ndim == 1:
@@ -123,14 +123,14 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
             * Compute \\\(\\\\vec{w} = -\\\mathbf{Q} \\\\vec{y}\\\)
 
         """
-        if self.verbose: print '%s\nCalculating J(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print '{0!s}\nCalculating J(v)\n{1!s}'.format('*'*50, '*'*50)
         self.curModel = m
         if f is None:
             f = self.fields(m)
         p = self.Gvec(m, v, f)
         y = self.solveAh(m, p)
         Jv = self.survey.evalDeriv(f, v=y)
-        if self.verbose: print '%s\nDone calculating J(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print '{0!s}\nDone calculating J(v)\n{1!s}'.format('*'*50, '*'*50)
         return - mkvc(Jv)
 
     def Jtvec(self, m, v, f=None):
@@ -148,7 +148,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
             * Compute \\\(\\\\vec{w} = -\\\mathbf{G}^\\\\top y\\\)
 
         """
-        if self.verbose: print '%s\nCalculating J^T(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print '{0!s}\nCalculating J^T(v)\n{1!s}'.format('*'*50, '*'*50)
         self.curModel = m
         if f is None:
             f = self.fields(m)
@@ -159,6 +159,6 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
         p = self.survey.evalDeriv(f, v=v, adjoint=True)
         y = self.solveAht(m, p)
         w = self.Gtvec(m, y, f)
-        if self.verbose: print '%s\nDone calculating J^T(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print '{0!s}\nDone calculating J^T(v)\n{1!s}'.format('*'*50, '*'*50)
         return - mkvc(w)
 

SimPEG/EM/Utils/testingUtils.py

@@ -58,7 +58,7 @@ def getFDEMProblem(fdemType, comp, SrcList, freq, useMu=False, verbose=False):
                 Src.append(EM.FDEM.Src.RawVec([rx0], freq, mesh.getEdgeInnerProduct()*S_m, S_e))
 
     if verbose:
-        print '  Fetching %s problem' % (fdemType)
+        print '  Fetching {0!s} problem'.format((fdemType))
 
     if fdemType == 'e':
         survey = EM.FDEM.Survey(Src)
@@ -94,7 +94,7 @@ def crossCheckTest(SrcList, fdemType1, fdemType2, comp, addrandoms = False, useM
 
     prb1 = getFDEMProblem(fdemType1, comp, SrcList, freq, useMu, verbose)
     mesh = prb1.mesh
-    print 'Cross Checking Forward: %s, %s formulations - %s' % (fdemType1, fdemType2, comp)
+    print 'Cross Checking Forward: {0!s}, {1!s} formulations - {2!s}'.format(fdemType1, fdemType2, comp)
 
     logsig = np.log(np.ones(mesh.nC)*CONDUCTIVITY)
     mu = np.ones(mesh.nC)*MU

SimPEG/Examples/EM_Schenkel_Morrison_Casing.py

@@ -110,7 +110,7 @@ def run(plotIt=True):
     # Mesh
     mesh = Mesh.CylMesh([hx,1.,hz], [0.,0.,-np.sum(hz[:npadzu+ncz-nza])])
 
-    print 'Mesh Extent xmax: %f,: zmin: %f, zmax: %f'%(mesh.vectorCCx.max(), mesh.vectorCCz.min(), mesh.vectorCCz.max())
+    print 'Mesh Extent xmax: {0:f},: zmin: {1:f}, zmax: {2:f}'.format(mesh.vectorCCx.max(), mesh.vectorCCz.min(), mesh.vectorCCz.max())
     print 'Number of cells', mesh.nC
 
     if plotIt is True:

SimPEG/Examples/Mesh_Operators_CahnHilliard.py

@@ -98,7 +98,7 @@ def run(plotIt=True, n=60):
             ii = int(ii)
             out = M.plotImage(PHIS[ii][1],ax=ax)
             ax.axis('off')
-            ax.set_title('Elapsed Time: %4.1f'%PHIS[ii][0])
+            ax.set_title('Elapsed Time: {0:4.1f}'.format(PHIS[ii][0]))
         plt.show()
 
 if __name__ == '__main__':

SimPEG/Examples/Mesh_QuadTree_FaceDiv.py

@@ -29,15 +29,15 @@ def run(plotIt=True, n=60):
         axes[0].set_ylim([-1,17])
 
         for ii, loc in zip(range(M.nC),M.gridCC):
-            axes[0].text(loc[0]+0.2,loc[1],'%d'%ii, color='r')
+            axes[0].text(loc[0]+0.2,loc[1],'{0:d}'.format(ii), color='r')
 
         axes[0].plot(M.gridFx[:,0],M.gridFx[:,1], 'g>')
         for ii, loc in zip(range(M.nFx),M.gridFx):
-            axes[0].text(loc[0]+0.2,loc[1],'%d'%ii, color='g')
+            axes[0].text(loc[0]+0.2,loc[1],'{0:d}'.format(ii), color='g')
 
         axes[0].plot(M.gridFy[:,0],M.gridFy[:,1], 'm^')
         for ii, loc in zip(range(M.nFy),M.gridFy):
-            axes[0].text(loc[0]+0.2,loc[1]+0.2,'%d'%(ii+M.nFx), color='m')
+            axes[0].text(loc[0]+0.2,loc[1]+0.2,'{0:d}'.format((ii+M.nFx)), color='m')
 
         axes[1].spy(M.faceDiv)
         axes[1].set_title('Face Divergence')

SimPEG/Examples/__init__.py

@@ -59,7 +59,7 @@ if __name__ == '__main__':
         if line == "##### AUTOIMPORTS #####\n":
             inimports = not inimports
             if inimports:
-                out += '\n'.join(["import %s"%_ for _ in exfiles])
+                out += '\n'.join(["import {0!s}".format(_) for _ in exfiles])
                 out += '\n\n__examples__ = ["' + '", "'.join(exfiles)+ '"]\n'
                 out += '\n##### AUTOIMPORTS #####\n'
     f.close()
@@ -76,11 +76,11 @@ if __name__ == '__main__':
 
         docstr = runFunction.__doc__
         if docstr is None:
-            doc = '%s\n%s'%(name.replace('_',' '),'='*len(name))
+            doc = '{0!s}\n{1!s}'.format(name.replace('_',' '), '='*len(name))
         else:
             doc = '\n'.join([_[8:].rstrip() for _ in docstr.split('\n')])
 
-        out = """.. _examples_%s:
+        out = """.. _examples_{0!s}:
 
 .. --------------------------------- ..
 ..                                   ..
@@ -90,21 +90,21 @@ if __name__ == '__main__':
 ..                                   ..
 .. --------------------------------- ..
 
-%s
+{1!s}
 
 .. plot::
 
     from SimPEG import Examples
-    Examples.%s.run()
+    Examples.{2!s}.run()
 
-.. literalinclude:: ../../../SimPEG/Examples/%s.py
+.. literalinclude:: ../../../SimPEG/Examples/{3!s}.py
     :language: python
     :linenos:
-"""%(name,doc,name,name)
+""".format(name, doc, name, name)
 
         rst = os.path.sep.join((filePath.split(os.path.sep)[:-3] + ['docs', 'content', 'examples', name + '.rst']))
 
-        print 'Creating: %s.rst'%name
+        print 'Creating: {0!s}.rst'.format(name)
         f = open(rst, 'w')
         f.write(out)
         f.close()

SimPEG/FLOW/Richards/Empirical.py

@@ -116,7 +116,7 @@ class RichardsMap(object):
         ax.semilogx(self.k(h, m), h)
 
     def _assertMatchesPair(self, pair):
-        assert isinstance(self, pair), "Mapping object must be an instance of a %s class."%(pair.__name__)
+        assert isinstance(self, pair), "Mapping object must be an instance of a {0!s} class.".format((pair.__name__))
 
 
 

SimPEG/FLOW/Richards/RichardsProblem.py

@@ -140,7 +140,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
         for ii, dt in enumerate(self.timeSteps):
             bc = self.getBoundaryConditions(ii, u[ii])
             u[ii+1] = self.rootFinder.root(lambda hn1m, return_g=True: self.getResidual(m, u[ii], hn1m, dt, bc, return_g=return_g), u[ii])
-            if self.debug: print "Solving Fields (%4d/%d - %3.1f%% Done) %d Iterations, %4.2f seconds"%(ii+1, self.nT, 100.0*(ii+1)/self.nT, self.rootFinder.iter, time.time() - tic)
+            if self.debug: print "Solving Fields ({0:4d}/{1:d} - {2:3.1f}% Done) {3:d} Iterations, {4:4.2f} seconds".format(ii+1, self.nT, 100.0*(ii+1)/self.nT, self.rootFinder.iter, time.time() - tic)
         return u
 
     @Utils.timeIt

SimPEG/Fields.py

@@ -37,7 +37,7 @@ class Fields(object):
         for f in self.knownFields:
             loc =self.knownFields[f]
             sz += np.array(self._storageShape(loc)).prod()*8.0/(1024**2)
-        return "%e MB"%sz
+        return "{0:e} MB".format(sz)
 
     def _storageShape(self, loc):
         nSrc = self.survey.nSrc
@@ -84,12 +84,12 @@ class Fields(object):
             return
         if accessType=='set' and name not in self.knownFields:
             if name in self.aliasFields:
-                raise KeyError("Invalid field name (%s) for setter, you can't set an aliased property"%name)
+                raise KeyError("Invalid field name ({0!s}) for setter, you can't set an aliased property".format(name))
             else:
-                raise KeyError('Invalid field name (%s) for setter'%name)
+                raise KeyError('Invalid field name ({0!s}) for setter'.format(name))
 
         elif accessType=='get' and (name not in self.knownFields and name not in self.aliasFields):
-            raise KeyError('Invalid field name (%s) for getter'%name)
+            raise KeyError('Invalid field name ({0!s}) for getter'.format(name))
         return name
 
     def _indexAndNameFromKey(self, key, accessType):

SimPEG/Maps.py

@@ -101,7 +101,7 @@ class IdentityMap(object):
             :return: passed the test?
 
         """
-        print 'Testing %s' % str(self)
+        print 'Testing {0!s}'.format(str(self))
         if m is None:
             m = abs(np.random.rand(self.nP))
         if 'plotIt' not in kwargs:
@@ -111,21 +111,21 @@ class IdentityMap(object):
     def _assertMatchesPair(self, pair):
         assert (isinstance(self, pair) or
             isinstance(self, ComboMap) and isinstance(self.maps[0], pair)
-            ), "Mapping object must be an instance of a %s class."%(pair.__name__)
+            ), "Mapping object must be an instance of a {0!s} class.".format((pair.__name__))
 
     def __mul__(self, val):
         if isinstance(val, IdentityMap):
             if not (self.shape[1] == '*' or val.shape[0] == '*') and not self.shape[1] == val.shape[0]:
-                raise ValueError('Dimension mismatch in %s and %s.' % (str(self), str(val)))
+                raise ValueError('Dimension mismatch in {0!s} and {1!s}.'.format(str(self), str(val)))
             return ComboMap([self, val])
         elif isinstance(val, np.ndarray):
             if not self.shape[1] == '*' and not self.shape[1] == val.shape[0]:
-                raise ValueError('Dimension mismatch in %s and np.ndarray%s.' % (str(self), str(val.shape)))
+                raise ValueError('Dimension mismatch in {0!s} and np.ndarray{1!s}.'.format(str(self), str(val.shape)))
             return self._transform(val)
         raise Exception('Unrecognized data type to multiply. Try a map or a numpy.ndarray!')
 
     def __str__(self):
-        return "%s(%s,%s)" % (self.__class__.__name__, self.shape[0], self.shape[1])
+        return "{0!s}({1!s},{2!s})".format(self.__class__.__name__, self.shape[0], self.shape[1])
 
 
 class ComboMap(IdentityMap):
@@ -140,7 +140,7 @@ class ComboMap(IdentityMap):
             if ii > 0 and not (self.shape[1] == '*' or m.shape[0] == '*') and not self.shape[1] == m.shape[0]:
                 prev = self.maps[-1]
                 errArgs = (prev.__class__.__name__, prev.shape[0], prev.shape[1], m.__class__.__name__, m.shape[0], m.shape[1])
-                raise ValueError('Dimension mismatch in map[%s] (%s, %s) and map[%s] (%s, %s).' % errArgs)
+                raise ValueError('Dimension mismatch in map[{0!s}] ({1!s}, {2!s}) and map[{3!s}] ({4!s}, {5!s}).'.format(*errArgs))
 
             if isinstance(m, ComboMap):
                 self.maps += m.maps
@@ -173,7 +173,7 @@ class ComboMap(IdentityMap):
         return deriv
 
     def __str__(self):
-        return 'ComboMap[%s](%s,%s)' % (' * '.join([m.__str__() for m in self.maps]), self.shape[0], self.shape[1])
+        return 'ComboMap[{0!s}]({1!s},{2!s})'.format(' * '.join([m.__str__() for m in self.maps]), self.shape[0], self.shape[1])
 
 
 class ExpMap(IdentityMap):

SimPEG/Mesh/BaseMesh.py

@@ -522,7 +522,7 @@ class BaseRectangularMesh(BaseMesh):
         assert xType in outType, 'You cannot change type of components.'
         if type(x) == list:
             for i, xi in enumerate(x):
-                assert isinstance(x, np.ndarray), "x[%i] must be a numpy array" % i
+                assert isinstance(x, np.ndarray), "x[{0:d}] must be a numpy array".format(i)
                 assert xi.size == x[0].size, "Number of elements in list must not change."
 
             x_array = np.ones((x.size, len(x)))

SimPEG/Mesh/CurvilinearMesh.py

@@ -4,14 +4,28 @@ from DiffOperators import DiffOperators
 from InnerProducts import InnerProducts
 from View import CurvView
 
+
 # Some helper functions.
-length2D = lambda x: (x[:, 0]**2 + x[:, 1]**2)**0.5
+def length2D(x):
-length3D = lambda x: (x[:, 0]**2 + x[:, 1]**2 + x[:, 2]**2)**0.5
+    return (x[:, 0]**2 + x[:, 1]**2)**0.5
-normalize2D = lambda x: x/np.kron(np.ones((1, 2)), Utils.mkvc(length2D(x), 2))
-normalize3D = lambda x: x/np.kron(np.ones((1, 3)), Utils.mkvc(length3D(x), 2))
 
 
-class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvView):
+def length3D(x):
+    return (x[:, 0]**2 + x[:, 1]**2 + x[:, 2]**2)**0.5
+
+
+def normalize2D(x):
+    return x/np.kron(np.ones((1, 2)), Utils.mkvc(length2D(x), 2))
+
+
+def normalize3D(x):
+    return x/np.kron(np.ones((1, 3)), Utils.mkvc(length3D(x), 2))
+
+
+# Curvi Mesh
+
+class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts,
+                      CurvView):
     """
     CurvilinearMesh is a mesh class that deals with curvilinear meshes.
 
@@ -31,12 +45,16 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
     _meshType = 'Curv'
 
     def __init__(self, nodes):
-        assert type(nodes) == list, "'nodes' variable must be a list of np.ndarray"
+        assert type(nodes) == list, ("'nodes' variable must be a list of "
+                                     "np.ndarray")
         assert len(nodes) > 1, "len(node) must be greater than 1"
 
         for i, nodes_i in enumerate(nodes):
-            assert isinstance(nodes_i, np.ndarray), ("nodes[%i] is not a numpy array." % i)
+            assert isinstance(nodes_i, np.ndarray), ("nodes[{0:d}] is not a"
-            assert nodes_i.shape == nodes[0].shape, ("nodes[%i] is not the same shape as nodes[0]" % i)
+                                                     "numpy array.".format(i))
+            assert nodes_i.shape == nodes[0].shape, ("nodes[{0:d}] is not the "
+                                                     "same shape as nodes[0]"
+                                                     .format(i))
 
         assert len(nodes[0].shape) == len(nodes), "Dimension mismatch"
         assert len(nodes[0].shape) > 1, "Not worth using Curv for a 1D mesh."
@@ -48,80 +66,79 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
         for i, node_i in enumerate(nodes):
             self._gridN[:, i] = Utils.mkvc(node_i.astype(float))
 
-    def gridCC():
+    @property
-        doc = "Cell-centered grid."
+    def gridCC(self):
-
+        """
-        def fget(self):
+        Cell-centered grid
-            if self._gridCC is None:
+        """
-                self._gridCC = np.concatenate([self.aveN2CC*self.gridN[:,i] for i in range(self.dim)]).reshape((-1,self.dim), order='F')
+        if getattr(self, '_gridCC', None) is None:
+            self._gridCC = np.concatenate([self.aveN2CC*self.gridN[:, i]
+                                           for i in range(self.dim)]).reshape(
+                                           (-1, self.dim), order='F')
         return self._gridCC
-        return locals()
-    _gridCC = None  # Store grid by default
-    gridCC = property(**gridCC())
 
-    def gridN():
+    @property
-        doc = "Nodal grid."
+    def gridN(self):
-
+        """
-        def fget(self):
+        Nodal grid.
-            if self._gridN is None:
+        """
+        if getattr(self, '_gridN', None) is None:
             raise Exception("Someone deleted this. I blame you.")
         return self._gridN
-        return locals()
-    _gridN = None  # Store grid by default
-    gridN = property(**gridN())
 
-    def gridFx():
+    @property
-        doc = "Face staggered grid in the x direction."
+    def gridFx(self):
+        """
+        Face staggered grid in the x direction.
+        """
 
-        def fget(self):
+        if getattr(self, '_gridFx', None) is None:
-            if self._gridFx is None:
             N = self.r(self.gridN, 'N', 'N', 'M')
             if self.dim == 2:
                 XY = [Utils.mkvc(0.5 * (n[:, :-1] + n[:, 1:])) for n in N]
                 self._gridFx = np.c_[XY[0], XY[1]]
             elif self.dim == 3:
-                    XYZ = [Utils.mkvc(0.25 * (n[:, :-1, :-1] + n[:, :-1, 1:] + n[:, 1:, :-1] + n[:, 1:, 1:])) for n in N]
+                XYZ = [Utils.mkvc(0.25 * (n[:, :-1, :-1] + n[:, :-1, 1:] +
+                       n[:, 1:, :-1] + n[:, 1:, 1:])) for n in N]
                 self._gridFx = np.c_[XYZ[0], XYZ[1], XYZ[2]]
         return self._gridFx
-        return locals()
-    _gridFx = None  # Store grid by default
-    gridFx = property(**gridFx())
 
-    def gridFy():
+    @property
-        doc = "Face staggered grid in the y direction."
+    def gridFy(self):
+        """
+        Face staggered grid in the y direction.
+        """
 
-        def fget(self):
+        if getattr(self, '_gridFy', None) is None:
-            if self._gridFy is None:
             N = self.r(self.gridN, 'N', 'N', 'M')
             if self.dim == 2:
                 XY = [Utils.mkvc(0.5 * (n[:-1, :] + n[1:, :])) for n in N]
                 self._gridFy = np.c_[XY[0], XY[1]]
             elif self.dim == 3:
-                    XYZ = [Utils.mkvc(0.25 * (n[:-1, :, :-1] + n[:-1, :, 1:] + n[1:, :, :-1] + n[1:, :, 1:])) for n in N]
+                XYZ = [Utils.mkvc(0.25 * (n[:-1, :, :-1] + n[:-1, :, 1:] +
+                       n[1:, :, :-1] + n[1:, :, 1:])) for n in N]
                 self._gridFy = np.c_[XYZ[0], XYZ[1], XYZ[2]]
         return self._gridFy
-        return locals()
-    _gridFy = None  # Store grid by default
-    gridFy = property(**gridFy())
 
-    def gridFz():
+    @property
-        doc = "Face staggered grid in the z direction."
+    def gridFz(self):
+        """
+        Face staggered grid in the y direction.
+        """
 
-        def fget(self):
+        if getattr(self, '_gridFz', None) is None:
-            if self._gridFz is None and self.dim == 3:
             N = self.r(self.gridN, 'N', 'N', 'M')
-                XYZ = [Utils.mkvc(0.25 * (n[:-1, :-1, :] + n[:-1, 1:, :] + n[1:, :-1, :] + n[1:, 1:, :])) for n in N]
+            XYZ = [Utils.mkvc(0.25 * (n[:-1, :-1, :] + n[:-1, 1:, :] +
+                   n[1:, :-1, :] + n[1:, 1:, :])) for n in N]
             self._gridFz = np.c_[XYZ[0], XYZ[1], XYZ[2]]
         return self._gridFz
-        return locals()
-    _gridFz = None  # Store grid by default
-    gridFz = property(**gridFz())
 
-    def gridEx():
+    @property
-        doc = "Edge staggered grid in the x direction."
+    def gridEx(self):
-
+        """
-        def fget(self):
+        Edge staggered grid in the x direction.
-            if self._gridEx is None:
+        """
+        if getattr(self, '_gridEx', None) is None:
             N = self.r(self.gridN, 'N', 'N', 'M')
             if self.dim == 2:
                 XY = [Utils.mkvc(0.5 * (n[:-1, :] + n[1:, :])) for n in N]
@@ -130,15 +147,13 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
                 XYZ = [Utils.mkvc(0.5 * (n[:-1, :, :] + n[1:, :, :])) for n in N]
                 self._gridEx = np.c_[XYZ[0], XYZ[1], XYZ[2]]
         return self._gridEx
-        return locals()
-    _gridEx = None  # Store grid by default
-    gridEx = property(**gridEx())
 
-    def gridEy():
+    @property
-        doc = "Edge staggered grid in the y direction."
+    def gridEy(self):
-
+        """
-        def fget(self):
+        Edge staggered grid in the y direction.
-            if self._gridEy is None:
+        """
+        if getattr(self, '_gridEy', None) is None:
             N = self.r(self.gridN, 'N', 'N', 'M')
             if self.dim == 2:
                 XY = [Utils.mkvc(0.5 * (n[:, :-1] + n[:, 1:])) for n in N]
@@ -147,22 +162,17 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
                 XYZ = [Utils.mkvc(0.5 * (n[:, :-1, :] + n[:, 1:, :])) for n in N]
                 self._gridEy = np.c_[XYZ[0], XYZ[1], XYZ[2]]
         return self._gridEy
-        return locals()
-    _gridEy = None  # Store grid by default
-    gridEy = property(**gridEy())
 
-    def gridEz():
+    @property
-        doc = "Edge staggered grid in the z direction."
+    def gridEz(self):
-
+        """
-        def fget(self):
+        Edge staggered grid in the z direction.
-            if self._gridEz is None and self.dim == 3:
+        """
+        if getattr(self, '_gridEz', None) is None and self.dim == 3:
             N = self.r(self.gridN, 'N', 'N', 'M')
             XYZ = [Utils.mkvc(0.5 * (n[:, :, :-1] + n[:, :, 1:])) for n in N]
             self._gridEz = np.c_[XYZ[0], XYZ[1], XYZ[2]]
         return self._gridEz
-        return locals()
-    _gridEz = None  # Store grid by default
-    gridEz = property(**gridEz())
 
     # --------------- Geometries ---------------------
     #
@@ -194,19 +204,25 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
     #            | /              | /
     #            D -------------- C
     #       node(i+1,j,k)      node(i+1,j+1,k)
-    def vol():
-        doc = "Construct cell volumes of the 3D model as 1d array."
 
-        def fget(self):
+    @property
-            if(self._vol is None):
+    def vol(self):
+        """
+        Construct cell volumes of the 3D model as 1d array
+        """
+
+        if getattr(self, '_vol', None) is None:
             if self.dim == 2:
                 A, B, C, D = Utils.indexCube('ABCD', self.vnC+1)
-                    normal, area = Utils.faceInfo(np.c_[self.gridN, np.zeros((self.nN, 1))], A, B, C, D)
+                normal, area = Utils.faceInfo(np.c_[self.gridN, np.zeros(
+                                              (self.nN, 1))], A, B, C, D)
                 self._vol = area
             elif self.dim == 3:
                 # Each polyhedron can be decomposed into 5 tetrahedrons
-                    # However, this presents a choice so we may as well divide in two ways and average.
+                # However, this presents a choice so we may as well divide in
-                    A, B, C, D, E, F, G, H = Utils.indexCube('ABCDEFGH', self.vnC+1)
+                # two ways and average.
+                A, B, C, D, E, F, G, H = Utils.indexCube('ABCDEFGH', self.vnC +
+                                                         1)
 
                 vol1 = (Utils.volTetra(self.gridN, A, B, D, E) +  # cutted edge top
                         Utils.volTetra(self.gridN, B, E, F, G) +  # cutted edge top
@@ -222,50 +238,60 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
 
                 self._vol = (vol1 + vol2)/2
         return self._vol
-        return locals()
-    _vol = None
-    vol = property(**vol())
 
-    def area():
+    @property
-        doc = "Face areas."
+    def area(self):
-
+        if (getattr(self, '_area', None) is None or
-        def fget(self):
+            getattr(self, '_normals', None) is None):
-            if(self._area is None or self._normals is None):
             # Compute areas of cell faces
             if(self.dim == 2):
                 xy = self.gridN
-                    A, B = Utils.indexCube('AB', self.vnC+1, np.array([self.nNx, self.nCy]))
+                A, B = Utils.indexCube('AB', self.vnC+1, np.array([self.nNx,
+                                       self.nCy]))
                 edge1 = xy[B, :] - xy[A, :]
                 normal1 = np.c_[edge1[:, 1], -edge1[:, 0]]
                 area1 = length2D(edge1)
-                    A, D = Utils.indexCube('AD', self.vnC+1, np.array([self.nCx, self.nNy]))
+                A, D = Utils.indexCube('AD', self.vnC+1, np.array([self.nCx,
-                    # Note that we are doing A-D to make sure the normal points the right way.
+                                       self.nNy]))
-                    # Think about it. Look at the picture. Normal points towards C iff you do this.
+                # Note that we are doing A-D to make sure the normal points the
+                # right way.
+                # Think about it. Look at the picture. Normal points towards C
+                # iff you do this.
                 edge2 = xy[A, :] - xy[D, :]
                 normal2 = np.c_[edge2[:, 1], -edge2[:, 0]]
                 area2 = length2D(edge2)
                 self._area = np.r_[Utils.mkvc(area1), Utils.mkvc(area2)]
                 self._normals = [normalize2D(normal1), normalize2D(normal2)]
+
             elif(self.dim == 3):
 
-                    A, E, F, B = Utils.indexCube('AEFB', self.vnC+1, np.array([self.nNx, self.nCy, self.nCz]))
+                A, E, F, B = Utils.indexCube('AEFB', self.vnC+1, np.array(
-                    normal1, area1 = Utils.faceInfo(self.gridN, A, E, F, B, average=False, normalizeNormals=False)
+                                             [self.nNx, self.nCy, self.nCz]))
+                normal1, area1 = Utils.faceInfo(self.gridN, A, E, F, B,
+                                                average=False,
+                                                normalizeNormals=False)
 
-                    A, D, H, E = Utils.indexCube('ADHE', self.vnC+1, np.array([self.nCx, self.nNy, self.nCz]))
+                A, D, H, E = Utils.indexCube('ADHE', self.vnC+1, np.array(
-                    normal2, area2 = Utils.faceInfo(self.gridN, A, D, H, E, average=False, normalizeNormals=False)
+                                             [self.nCx, self.nNy, self.nCz]))
+                normal2, area2 = Utils.faceInfo(self.gridN, A, D, H, E,
+                                                average=False,
+                                                normalizeNormals=False)
 
-                    A, B, C, D = Utils.indexCube('ABCD', self.vnC+1, np.array([self.nCx, self.nCy, self.nNz]))
+                A, B, C, D = Utils.indexCube('ABCD', self.vnC+1, np.array(
-                    normal3, area3 = Utils.faceInfo(self.gridN, A, B, C, D, average=False, normalizeNormals=False)
+                                             [self.nCx, self.nCy, self.nNz]))
+                normal3, area3 = Utils.faceInfo(self.gridN, A, B, C, D,
+                                                average=False,
+                                                normalizeNormals=False)
 
-                    self._area = np.r_[Utils.mkvc(area1), Utils.mkvc(area2), Utils.mkvc(area3)]
+                self._area = np.r_[Utils.mkvc(area1), Utils.mkvc(area2),
+                                   Utils.mkvc(area3)]
                 self._normals = [normal1, normal2, normal3]
         return self._area
-        return locals()
-    _area = None
-    area = property(**area())
 
-    def normals():
+    @property
-        doc = """Face normals: calling this will average
+    def normals(self):
+        """
+        Face normals: calling this will average
         the computed normals so that there is one
         per face. This is especially relevant in
         3D, as there are up to 4 different normals
@@ -276,8 +302,7 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
             NyX, NyY, NyZ = M.r(M.normals, 'F', 'Fy', 'M')
         """
 
-        def fget(self):
+        if getattr(self, '_normals', None) is None:
-            if(self._normals is None):
             self.area  # calling .area will create the face normals
         if self.dim == 2:
             return normalize2D(np.r_[self._normals[0], self._normals[1]])
@@ -286,48 +311,55 @@ class CurvilinearMesh(BaseRectangularMesh, DiffOperators, InnerProducts, CurvVie
             normal2 = (self._normals[1][0] + self._normals[1][1] + self._normals[1][2] + self._normals[1][3])/4
             normal3 = (self._normals[2][0] + self._normals[2][1] + self._normals[2][2] + self._normals[2][3])/4
             return normalize3D(np.r_[normal1, normal2, normal3])
-        return locals()
-    _normals = None
-    normals = property(**normals())
 
-    def edge():
+    @property
-        doc = "Edge legnths."
+    def edge(self):
-
+        """
-        def fget(self):
+        Edge lengths
-            if(self._edge is None or self._tangents is None):
+        """
+        if getattr(self, '_edge', None) is None:
             if(self.dim == 2):
                 xy = self.gridN
-                    A, D = Utils.indexCube('AD', self.vnC+1, np.array([self.nCx, self.nNy]))
+                A, D = Utils.indexCube('AD', self.vnC+1, np.array([self.nCx,
+                                                                  self.nNy]))
                 edge1 = xy[D, :] - xy[A, :]
-                    A, B = Utils.indexCube('AB', self.vnC+1, np.array([self.nNx, self.nCy]))
+                A, B = Utils.indexCube('AB', self.vnC+1, np.array([self.nNx,
+                                                                   self.nCy]))
                 edge2 = xy[B, :] - xy[A, :]
-                    self._edge = np.r_[Utils.mkvc(length2D(edge1)), Utils.mkvc(length2D(edge2))]
+                self._edge = np.r_[Utils.mkvc(length2D(edge1)),
-                    self._tangents = np.r_[edge1, edge2]/np.c_[self._edge, self._edge]
+                                   Utils.mkvc(length2D(edge2))]
+                self._tangents = np.r_[edge1, edge2]/np.c_[self._edge,
+                                                           self._edge]
             elif(self.dim == 3):
                 xyz = self.gridN
-                    A, D = Utils.indexCube('AD', self.vnC+1, np.array([self.nCx, self.nNy, self.nNz]))
+                A, D = Utils.indexCube('AD', self.vnC+1, np.array([self.nCx,
+                                                                   self.nNy,
+                                                                   self.nNz]))
                 edge1 = xyz[D, :] - xyz[A, :]
-                    A, B = Utils.indexCube('AB', self.vnC+1, np.array([self.nNx, self.nCy, self.nNz]))
+                A, B = Utils.indexCube('AB', self.vnC+1, np.array([self.nNx,
+                                                                   self.nCy,
+                                                                   self.nNz]))
                 edge2 = xyz[B, :] - xyz[A, :]
-                    A, E = Utils.indexCube('AE', self.vnC+1, np.array([self.nNx, self.nNy, self.nCz]))
+                A, E = Utils.indexCube('AE', self.vnC+1, np.array([self.nNx,
+                                                                   self.nNy,
+                                                                   self.nCz]))
                 edge3 = xyz[E, :] - xyz[A, :]
-                    self._edge = np.r_[Utils.mkvc(length3D(edge1)), Utils.mkvc(length3D(edge2)), Utils.mkvc(length3D(edge3))]
+                self._edge = np.r_[Utils.mkvc(length3D(edge1)),
-                    self._tangents = np.r_[edge1, edge2, edge3]/np.c_[self._edge, self._edge, self._edge]
+                                   Utils.mkvc(length3D(edge2)),
+                                   Utils.mkvc(length3D(edge3))]
+                self._tangents = (np.r_[edge1, edge2, edge3] /
+                                  np.c_[self._edge, self._edge, self._edge])
+            return self._edge
         return self._edge
-        return locals()
-    _edge = None
-    edge = property(**edge())
 
-    def tangents():
+    @property
-        doc = "Edge tangents."
+    def tangents(self):
-
+        """
-        def fget(self):
+        Edge tangents
-            if(self._tangents is None):
+        """
+        if getattr(self, '_tangents', None) is None:
             self.edge  # calling .edge will create the tangents
         return self._tangents
-        return locals()
-    _tangents = None
-    tangents = property(**tangents())
 
 
 

SimPEG/Mesh/DiffOperators.py

@@ -18,13 +18,15 @@ def checkBC(bc):
 
     for bc_i in bc:
         assert type(bc_i) is str, "each bc must be a string"
-        assert bc_i in ['dirichlet', 'neumann'], "each bc must be either, 'dirichlet' or 'neumann'"
+        assert bc_i in ['dirichlet', 'neumann'], ("each bc must be either,"
+                                                  "'dirichlet' or 'neumann'")
     return bc
 
 
 def ddxCellGrad(n, bc):
     """
-        Create 1D derivative operator from cell-centers to nodes this means we go from n to n+1
+        Create 1D derivative operator from cell-centers to nodes this means we
+        go from n to n+1
 
         For Cell-Centered **Dirichlet**, use a ghost point::
 
@@ -52,7 +54,8 @@ def ddxCellGrad(n, bc):
     """
     bc = checkBC(bc)
 
-    D = sp.spdiags((np.ones((n+1, 1))*[-1, 1]).T, [-1, 0], n+1, n, format="csr")
+    D = sp.spdiags((np.ones((n+1, 1))*[-1, 1]).T, [-1, 0], n+1, n,
+                   format="csr")
     # Set the first side
     if(bc[0] == 'dirichlet'):
         D[0, 0] = 2
@@ -65,10 +68,11 @@ def ddxCellGrad(n, bc):
         D[-1, -1] = 0
     return D
 
+
 def ddxCellGradBC(n, bc):
     """
-
+        Create 1D derivative operator from cell-centers to nodes this means we
-        Create 1D derivative operator from cell-centers to nodes this means we go from n to n+1
+        go from n to n+1
 
         For Cell-Centered **Dirichlet**, use a ghost point::
 
@@ -121,14 +125,16 @@ class DiffOperators(object):
         Class creates the differential operators that you need!
     """
     def __init__(self):
-        raise Exception('DiffOperators is a base class providing differential operators on meshes and cannot run on its own. Inherit to your favorite Mesh class.')
+        raise Exception('DiffOperators is a base class providing differential'
+                        'operators on meshes and cannot run on its own.'
+                        'Inherit to your favorite Mesh class.')
 
-    def faceDiv():
+    @property
-        doc = "Construct divergence operator (face-stg to cell-centres)."
+    def faceDiv(self):
-
+        """
-        def fget(self):
+        Construct divergence operator (face-stg to cell-centres).
-            if(self._faceDiv is None):
+        """
-                # The number of cell centers in each direction
+        if getattr(self, '_faceDiv', None) is None:
             n = self.vnC
             # Compute faceDivergence operator on faces
             if(self.dim == 1):
@@ -146,17 +152,15 @@ class DiffOperators(object):
             S = self.area
             V = self.vol
             self._faceDiv = sdiag(1/V)*D*sdiag(S)
-
         return self._faceDiv
-        return locals()
-    _faceDiv = None
-    faceDiv = property(**faceDiv())
 
-    def faceDivx():
+    @property
-        doc = "Construct divergence operator in the x component (face-stg to cell-centres)."
+    def faceDivx(self):
-
+        """
-        def fget(self):
+        Construct divergence operator in the x component (face-stg to
-            if(self._faceDivx is None):
+        cell-centres).
+        """
+        if getattr(self, '_faceDivx', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
             # Compute faceDivergence operator on faces
@@ -172,16 +176,12 @@ class DiffOperators(object):
             self._faceDivx = sdiag(1/V)*D1*sdiag(S)
 
         return self._faceDivx
-        return locals()
-    _faceDivx = None
-    faceDivx = property(**faceDivx())
 
-    def faceDivy():
+    @property
-        doc = "Construct divergence operator in the y component (face-stg to cell-centres)."
+    def faceDivy(self):
-
+        if(self.dim < 2):
-        def fget(self):
+            return None
-            if(self.dim < 2): return None
+        if getattr(self, '_faceDivy', None) is None:
-            if(self._faceDivy is None):
             # The number of cell centers in each direction
             n = self.vnC
             # Compute faceDivergence operator on faces
@@ -193,18 +193,17 @@ class DiffOperators(object):
             S = self.r(self.area, 'F', 'Fy', 'V')
             V = self.vol
             self._faceDivy = sdiag(1/V)*D2*sdiag(S)
-
         return self._faceDivy
-        return locals()
-    _faceDivy = None
-    faceDivy = property(**faceDivy())
 
-    def faceDivz():
+    @property
-        doc = "Construct divergence operator in the z component (face-stg to cell-centres)."
+    def faceDivz(self):
-
+        """
-        def fget(self):
+        Construct divergence operator in the z component (face-stg to
-            if(self.dim < 3): return None
+        cell-centres).
-            if(self._faceDivz is None):
+        """
+        if(self.dim < 3):
+            return None
+        if getattr(self, '_faceDivz', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
             # Compute faceDivergence operator on faces
@@ -213,17 +212,14 @@ class DiffOperators(object):
             S = self.r(self.area, 'F', 'Fz', 'V')
             V = self.vol
             self._faceDivz = sdiag(1/V)*D3*sdiag(S)
-
         return self._faceDivz
-        return locals()
-    _faceDivz = None
-    faceDivz = property(**faceDivz())
 
-    def nodalGrad():
+    @property
-        doc = "Construct gradient operator (nodes to edges)."
+    def nodalGrad(self):
-
+        """
-        def fget(self):
+        Construct gradient operator (nodes to edges).
-            if(self._nodalGrad is None):
+        """
+        if getattr(self, '_nodalGrad', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
             # Compute divergence operator on faces
@@ -242,15 +238,13 @@ class DiffOperators(object):
             L = self.edge
             self._nodalGrad = sdiag(1/L)*G
         return self._nodalGrad
-        return locals()
-    _nodalGrad = None
-    nodalGrad = property(**nodalGrad())
 
-    def nodalLaplacian():
+    @property
-        doc = "Construct laplacian operator (nodes to edges)."
+    def nodalLaplacian(self):
-
+        """
-        def fget(self):
+        Construct laplacian operator (nodes to edges).
-            if(self._nodalLaplacian is None):
+        """
+        if getattr(self, '_nodalLaplacian', None) is None:
             print 'Warning: Laplacian has not been tested rigorously.'
             # The number of cell centers in each direction
             n = self.vnC
@@ -274,22 +268,23 @@ class DiffOperators(object):
                 L = L1 + L2 + L3
             self._nodalLaplacian = L
         return self._nodalLaplacian
-        return locals()
-    _nodalLaplacian = None
-    nodalLaplacian = property(**nodalLaplacian())
 
     def setCellGradBC(self, BC):
         """
-        Function that sets the boundary conditions for cell-centred derivative operators.
+        Function that sets the boundary conditions for cell-centred derivative
+        operators.
 
         Examples::
+            # Neumann in all directions
+            BC = 'neumann'
 
-            BC = 'neumann'                                            # Neumann in all directions
+            # 3D, Dirichlet in y Neumann else
-            BC = ['neumann', 'dirichlet', 'neumann']                  # 3D, Dirichlet in y Neumann else
+            BC = ['neumann', 'dirichlet', 'neumann']
-            BC = [['neumann', 'dirichlet'], 'dirichlet', 'dirichlet'] # 3D, Neumann in x on bottom of domain,
-                                                                      #     Dirichlet else
 
+            # 3D, Neumann in x on bottom of domain,  Dirichlet else
+            BC = [['neumann', 'dirichlet'], 'dirichlet', 'dirichlet']
         """
+
         if(type(BC) is str):
             BC = [BC]*self.dim
         if(type(BC) is list):
@@ -323,26 +318,24 @@ class DiffOperators(object):
             G = sp.vstack((G1, G2, G3), format="csr")
         return G
 
-    def cellGrad():
+    @property
-        doc = "The cell centered Gradient, takes you to cell faces."
+    def cellGrad(self):
-
+        """
-        def fget(self):
+        The cell centered Gradient, takes you to cell faces.
-            if(self._cellGrad is None):
+        """
+        if getattr(self, '_cellGrad', None) is None:
             G = self._cellGradStencil()
-                # Compute areas of cell faces & volumes
+            S = self.area  # Compute areas of cell faces & volumes
-                S = self.area
             V = self.aveCC2F*self.vol  # Average volume between adjacent cells
             self._cellGrad = sdiag(S/V)*G
         return self._cellGrad
-        return locals()
-    _cellGrad = None
-    cellGrad = property(**cellGrad())
 
-    def cellGradBC():
+    @property
-        doc = "The cell centered Gradient boundary condition matrix"
+    def cellGradBC(self):
-
+        """
-        def fget(self):
+        The cell centered Gradient boundary condition matrix
-            if(self._cellGradBC is None):
+        """
+        if getattr(self, '_cellGradBC', None) is None:
             BC = self.setCellGradBC(self._cellGradBC_list)
             n = self.vnC
             if(self.dim == 1):
@@ -361,9 +354,33 @@ class DiffOperators(object):
             V = self.aveCC2F*self.vol  # Average volume between adjacent cells
             self._cellGradBC = sdiag(S/V)*G
         return self._cellGradBC
-        return locals()
+
-    _cellGradBC = None
+    # def cellGradBC():
-    cellGradBC = property(**cellGradBC())
+    #     doc = "The cell centered Gradient boundary condition matrix"
+
+    #     def fget(self):
+    #         if(self._cellGradBC is None):
+    #             BC = self.setCellGradBC(self._cellGradBC_list)
+    #             n = self.vnC
+    #             if(self.dim == 1):
+    #                 G = ddxCellGradBC(n[0], BC[0])
+    #             elif(self.dim == 2):
+    #                 G1 = sp.kron(speye(n[1]), ddxCellGradBC(n[0], BC[0]))
+    #                 G2 = sp.kron(ddxCellGradBC(n[1], BC[1]), speye(n[0]))
+    #                 G = sp.block_diag((G1, G2), format="csr")
+    #             elif(self.dim == 3):
+    #                 G1 = kron3(speye(n[2]), speye(n[1]), ddxCellGradBC(n[0], BC[0]))
+    #                 G2 = kron3(speye(n[2]), ddxCellGradBC(n[1], BC[1]), speye(n[0]))
+    #                 G3 = kron3(ddxCellGradBC(n[2], BC[2]), speye(n[1]), speye(n[0]))
+    #                 G = sp.block_diag((G1, G2, G3), format="csr")
+    #             # Compute areas of cell faces & volumes
+    #             S = self.area
+    #             V = self.aveCC2F*self.vol  # Average volume between adjacent cells
+    #             self._cellGradBC = sdiag(S/V)*G
+    #         return self._cellGradBC
+    #     return locals()
+    # _cellGradBC = None
+    # cellGradBC = property(**cellGradBC())
 
     def _cellGradxStencil(self):
         BC = ['neumann', 'neumann']
@@ -376,11 +393,12 @@ class DiffOperators(object):
             G1 = kron3(speye(n[2]), speye(n[1]), ddxCellGrad(n[0], BC))
         return G1
 
-
+    @property
-    def cellGradx():
+    def cellGradx(self):
-        doc = "Cell centered Gradient in the x dimension. Has neumann boundary conditions."
+        """
-
+        Cell centered Gradient in the x dimension. Has neumann boundary
-        def fget(self):
+        conditions.
+        """
         if getattr(self, '_cellGradx', None) is None:
             G1 = self._cellGradxStencil()
             # Compute areas of cell faces & volumes
@@ -388,8 +406,6 @@ class DiffOperators(object):
             L = self.r(self.area/V, 'F','Fx', 'V')
             self._cellGradx = sdiag(L)*G1
         return self._cellGradx
-        return locals()
-    cellGradx = property(**cellGradx())
 
     def _cellGradyStencil(self):
         if self.dim < 2: return None
@@ -401,10 +417,10 @@ class DiffOperators(object):
             G2 = kron3(speye(n[2]), ddxCellGrad(n[1], BC), speye(n[0]))
         return G2
 
-    def cellGrady():
+    @property
-        doc = "Cell centered Gradient in the x dimension. Has neumann boundary conditions."
+    def cellGrady(self):
-        def fget(self):
+        if self.dim < 2:
-            if self.dim < 2: return None
+            return None
         if getattr(self, '_cellGrady', None) is None:
             G2 = self._cellGradyStencil()
             # Compute areas of cell faces & volumes
@@ -412,8 +428,6 @@ class DiffOperators(object):
             L = self.r(self.area/V, 'F', 'Fy', 'V')
             self._cellGrady = sdiag(L)*G2
         return self._cellGrady
-        return locals()
-    cellGrady = property(**cellGrady())
 
     def _cellGradzStencil(self):
         if self.dim < 3: return None
@@ -422,10 +436,14 @@ class DiffOperators(object):
         G3 = kron3(ddxCellGrad(n[2], BC), speye(n[1]), speye(n[0]))
         return G3
 
-    def cellGradz():
+    @property
-        doc = "Cell centered Gradient in the x dimension. Has neumann boundary conditions."
+    def cellGradz(self):
-        def fget(self):
+        """
-            if self.dim < 3: return None
+        Cell centered Gradient in the x dimension. Has neumann boundary
+        conditions.
+        """
+        if self.dim < 3:
+            return None
         if getattr(self, '_cellGradz', None) is None:
             G3 = self._cellGradzStencil()
             # Compute areas of cell faces & volumes
@@ -433,23 +451,18 @@ class DiffOperators(object):
             L = self.r(self.area/V, 'F', 'Fz', 'V')
             self._cellGradz = sdiag(L)*G3
         return self._cellGradz
-        return locals()
-    cellGradz = property(**cellGradz())
 
-    def edgeCurl():
+    @property
-        doc = "Construct the 3D curl operator."
+    def edgeCurl(self):
-
+        """
-        def fget(self):
+        Construct the 3D curl operator.
-            if(self._edgeCurl is None):
+        """
+        if getattr(self, '_edgeCurl', None) is None:
             assert self.dim > 1, "Edge Curl only programed for 2 or 3D."
-                # The number of cell centers in each direction
-                n = self.vnC
 
-                # Compute lengths of cell edges
+            n = self.vnC  # The number of cell centers in each direction
-                L = self.edge
+            L = self.edge  # Compute lengths of cell edges
-
+            S = self.area # Compute areas of cell faces
-                # Compute areas of cell faces
-                S = self.area
 
             # Compute divergence operator on faces
             if self.dim == 2:
@@ -477,11 +490,7 @@ class DiffOperators(object):
                                sp.hstack((-D21, D12, O3))), format="csr")
 
                 self._edgeCurl = sdiag(1/S)*(C*sdiag(L))
-
         return self._edgeCurl
-        return locals()
-    _edgeCurl = None
-    edgeCurl = property(**edgeCurl())
 
     def getBCProjWF(self, BC, discretization='CC'):
         """
@@ -489,16 +498,19 @@ class DiffOperators(object):
         The weak form boundary condition projection matrices.
 
         Examples::
+            # Neumann in all directions
+            BC = 'neumann'
 
-            BC = 'neumann'                                            # Neumann in all directions
+            # 3D, Dirichlet in y Neumann else
-            BC = ['neumann', 'dirichlet', 'neumann']                  # 3D, Dirichlet in y Neumann else
+            BC = ['neumann', 'dirichlet', 'neumann']
-            BC = [['neumann', 'dirichlet'], 'dirichlet', 'dirichlet'] # 3D, Neumann in x on bottom of domain,
-                                                                      #     Dirichlet else
 
+            # 3D, Neumann in x on bottom of domain, Dirichlet else
+            BC = [['neumann', 'dirichlet'], 'dirichlet', 'dirichlet']
         """
 
         if discretization is not 'CC':
-            raise NotImplementedError('Boundary conditions only implemented for CC discretization.')
+            raise NotImplementedError('Boundary conditions only implemented'
+                                      'for CC discretization.')
 
         if(type(BC) is str):
             BC = [BC for _ in self.vnC]  # Repeat the str self.dim times
@@ -510,7 +522,6 @@ class DiffOperators(object):
         for i, bc_i in enumerate(BC):
             BC[i] = checkBC(bc_i)
 
-
         def projDirichlet(n, bc):
             bc = checkBC(bc)
             ij = ([0, n], [0, 1])
@@ -550,6 +561,7 @@ class DiffOperators(object):
             Pin = projNeumannIn(n[0], BC[0])
 
             Pout = projNeumannOut(n[0], BC[0])
+
         elif(self.dim == 2):
             Pbc1 = sp.kron(speye(n[1]), projDirichlet(n[0], BC[0]))
             Pbc2 = sp.kron(projDirichlet(n[1], BC[1]), speye(n[0]))
@@ -564,12 +576,14 @@ class DiffOperators(object):
             P1 = sp.kron(speye(n[1]), projNeumannOut(n[0], BC[0]))
             P2 = sp.kron(projNeumannOut(n[1], BC[1]), speye(n[0]))
             Pout = sp.block_diag((P1, P2), format="csr")
+
         elif(self.dim == 3):
             Pbc1 = kron3(speye(n[2]), speye(n[1]), projDirichlet(n[0], BC[0]))
             Pbc2 = kron3(speye(n[2]), projDirichlet(n[1], BC[1]), speye(n[0]))
             Pbc3 = kron3(projDirichlet(n[2], BC[2]), speye(n[1]), speye(n[0]))
             Pbc = sp.block_diag((Pbc1, Pbc2, Pbc3), format="csr")
-            indF = np.r_[(indF[0] | indF[1]), (indF[2] | indF[3]), (indF[4] | indF[5])]
+            indF = np.r_[(indF[0] | indF[1]), (indF[2] | indF[3]), (indF[4] |
+                          indF[5])]
             Pbc = Pbc*sdiag(self.area[indF])
 
             P1 = kron3(speye(n[2]), speye(n[1]), projNeumannIn(n[0], BC[0]))
@@ -586,15 +600,13 @@ class DiffOperators(object):
 
     def getBCProjWF_simple(self, discretization='CC'):
         """
-
         The weak form boundary condition projection matrices
         when mixed boundary condition is used
-
-
         """
 
         if discretization is not 'CC':
-            raise NotImplementedError('Boundary conditions only implemented for CC discretization.')
+            raise NotImplementedError('Boundary conditions only implemented'
+                                      'for CC discretization.')
 
         def projBC(n):
             ij = ([0, n], [0, 1])
@@ -613,9 +625,11 @@ class DiffOperators(object):
                 vals[1] = 1
             return sp.csr_matrix((vals, ij), shape=(n+1, 2))
 
-        BC = [['dirichlet','dirichlet'],['dirichlet','dirichlet'],['dirichlet','dirichlet']]
+        BC = [['dirichlet', 'dirichlet'], ['dirichlet', 'dirichlet'],
+              ['dirichlet', 'dirichlet']]
         n = self.vnC
         indF = self.faceBoundaryInd
+
         if(self.dim == 1):
             Pbc = projDirichlet(n[0], BC[0])
             B = projBC(n[0])
@@ -653,9 +667,11 @@ class DiffOperators(object):
         if(self.dim == 1):
             return self.aveFx2CC
         elif(self.dim == 2):
-            return (0.5)*sp.hstack((self.aveFx2CC, self.aveFy2CC), format="csr")
+            return (0.5)*sp.hstack((self.aveFx2CC, self.aveFy2CC),
+                                    format="csr")
         elif(self.dim == 3):
-            return (1./3.)*sp.hstack((self.aveFx2CC, self.aveFy2CC, self.aveFz2CC), format="csr")
+            return (1./3.)*sp.hstack((self.aveFx2CC, self.aveFy2CC,
+                                      self.aveFz2CC), format="csr")
 
     @property
     def aveF2CCV(self):
@@ -665,11 +681,16 @@ class DiffOperators(object):
         elif(self.dim == 2):
             return sp.block_diag((self.aveFx2CC, self.aveFy2CC), format="csr")
         elif(self.dim == 3):
-            return sp.block_diag((self.aveFx2CC, self.aveFy2CC, self.aveFz2CC), format="csr")
+            return sp.block_diag((self.aveFx2CC, self.aveFy2CC, self.aveFz2CC),
+                                 format="csr")
 
     @property
     def aveFx2CC(self):
-        "Construct the averaging operator on cell faces in the x direction to cell centers."
+        """
+        Construct the averaging operator on cell faces in the x direction to
+        cell centers.
+        """
+
         if getattr(self, '_aveFx2CC', None) is None:
             n = self.vnC
             if(self.dim == 1):
@@ -682,8 +703,12 @@ class DiffOperators(object):
 
     @property
     def aveFy2CC(self):
-        "Construct the averaging operator on cell faces in the y direction to cell centers."
+        """
-        if self.dim < 2: return None
+        Construct the averaging operator on cell faces in the y direction to
+        cell centers.
+        """
+        if self.dim < 2:
+            return None
         if getattr(self, '_aveFy2CC', None) is None:
             n = self.vnC
             if(self.dim == 2):
@@ -694,7 +719,10 @@ class DiffOperators(object):
 
     @property
     def aveFz2CC(self):
-        "Construct the averaging operator on cell faces in the z direction to cell centers."
+        """
+        Construct the averaging operator on cell faces in the z direction to
+        cell centers.
+        """
         if self.dim < 3: return None
         if getattr(self, '_aveFz2CC', None) is None:
             n = self.vnC
@@ -711,12 +739,18 @@ class DiffOperators(object):
             if(self.dim == 1):
                 self._aveCC2F = avExtrap(n[0])
             elif(self.dim == 2):
-                self._aveCC2F = sp.vstack((sp.kron(speye(n[1]), avExtrap(n[0])),
+                self._aveCC2F = sp.vstack((sp.kron(speye(n[1]),
-                                           sp.kron(avExtrap(n[1]), speye(n[0]))), format="csr")
+                                           avExtrap(n[0])),
+                                           sp.kron(avExtrap(n[1]),
+                                           speye(n[0]))), format="csr")
             elif(self.dim == 3):
-                self._aveCC2F = sp.vstack((kron3(speye(n[2]), speye(n[1]), avExtrap(n[0])),
+                self._aveCC2F = sp.vstack((kron3(speye(n[2]), speye(n[1]),
-                                           kron3(speye(n[2]), avExtrap(n[1]), speye(n[0])),
+                                                 avExtrap(n[0])),
-                                           kron3(avExtrap(n[2]), speye(n[1]), speye(n[0]))), format="csr")
+                                           kron3(speye(n[2]), avExtrap(n[1]),
+                                                 speye(n[0])),
+                                           kron3(avExtrap(n[2]), speye(n[1]),
+                                                 speye(n[0]))),
+                                          format="csr")
         return self._aveCC2F
 
     @property
@@ -727,7 +761,8 @@ class DiffOperators(object):
         elif(self.dim == 2):
             return 0.5*sp.hstack((self.aveEx2CC, self.aveEy2CC), format="csr")
         elif(self.dim == 3):
-            return (1./3)*sp.hstack((self.aveEx2CC, self.aveEy2CC, self.aveEz2CC), format="csr")
+            return (1./3)*sp.hstack((self.aveEx2CC, self.aveEy2CC,
+                                     self.aveEz2CC), format="csr")
 
     @property
     def aveE2CCV(self):
@@ -737,11 +772,15 @@ class DiffOperators(object):
         elif(self.dim == 2):
             return sp.block_diag((self.aveEx2CC, self.aveEy2CC), format="csr")
         elif(self.dim == 3):
-            return sp.block_diag((self.aveEx2CC, self.aveEy2CC, self.aveEz2CC), format="csr")
+            return sp.block_diag((self.aveEx2CC, self.aveEy2CC, self.aveEz2CC),
+                                 format="csr")
 
     @property
     def aveEx2CC(self):
-        "Construct the averaging operator on cell edges in the x direction to cell centers."
+        """
+        Construct the averaging operator on cell edges in the x direction to
+        cell centers.
+        """
         if getattr(self, '_aveEx2CC', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
@@ -755,8 +794,12 @@ class DiffOperators(object):
 
     @property
     def aveEy2CC(self):
-        "Construct the averaging operator on cell edges in the y direction to cell centers."
+        """
-        if self.dim < 2: return None
+        Construct the averaging operator on cell edges in the y direction to
+        cell centers.
+        """
+        if self.dim < 2:
+            return None
         if getattr(self, '_aveEy2CC', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
@@ -768,8 +811,12 @@ class DiffOperators(object):
 
     @property
     def aveEz2CC(self):
-        "Construct the averaging operator on cell edges in the z direction to cell centers."
+        """
-        if self.dim < 3: return None
+        Construct the averaging operator on cell edges in the z direction to
+        cell centers.
+        """
+        if self.dim < 3:
+            return None
         if getattr(self, '_aveEz2CC', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
@@ -793,7 +840,10 @@ class DiffOperators(object):
 
     @property
     def aveN2E(self):
-        "Construct the averaging operator on cell nodes to cell edges, keeping each dimension separate."
+        """
+        Construct the averaging operator on cell nodes to cell edges, keeping
+        each dimension separate.
+        """
 
         if getattr(self, '_aveN2E', None) is None:
             # The number of cell centers in each direction
@@ -802,16 +852,24 @@ class DiffOperators(object):
                 self._aveN2E = av(n[0])
             elif(self.dim == 2):
                 self._aveN2E = sp.vstack((sp.kron(speye(n[1]+1), av(n[0])),
-                                          sp.kron(av(n[1]), speye(n[0]+1))), format="csr")
+                                          sp.kron(av(n[1]), speye(n[0]+1))),
+                                         format="csr")
             elif(self.dim == 3):
-                self._aveN2E = sp.vstack((kron3(speye(n[2]+1), speye(n[1]+1), av(n[0])),
+                self._aveN2E = sp.vstack((kron3(speye(n[2]+1), speye(n[1]+1),
-                                          kron3(speye(n[2]+1), av(n[1]), speye(n[0]+1)),
+                                                av(n[0])),
-                                          kron3(av(n[2]), speye(n[1]+1), speye(n[0]+1))), format="csr")
+                                          kron3(speye(n[2]+1), av(n[1]),
+                                                speye(n[0]+1)),
+                                          kron3(av(n[2]), speye(n[1]+1),
+                                                speye(n[0]+1))),
+                                         format="csr")
         return self._aveN2E
 
     @property
     def aveN2F(self):
-        "Construct the averaging operator on cell nodes to cell faces, keeping each dimension separate."
+        """
+        Construct the averaging operator on cell nodes to cell faces, keeping
+        each dimension separate.
+        """
         if getattr(self, '_aveN2F', None) is None:
             # The number of cell centers in each direction
             n = self.vnC
@@ -819,9 +877,14 @@ class DiffOperators(object):
                 self._aveN2F = av(n[0])
             elif(self.dim == 2):
                 self._aveN2F = sp.vstack((sp.kron(av(n[1]), speye(n[0]+1)),
-                                          sp.kron(speye(n[1]+1), av(n[0]))), format="csr")
+                                          sp.kron(speye(n[1]+1), av(n[0]))),
+                                         format="csr")
             elif(self.dim == 3):
-                self._aveN2F = sp.vstack((kron3(av(n[2]), av(n[1]), speye(n[0]+1)),
+                self._aveN2F = sp.vstack((kron3(av(n[2]), av(n[1]),
-                                          kron3(av(n[2]), speye(n[1]+1), av(n[0])),
+                                                speye(n[0]+1)),
-                                          kron3(speye(n[2]+1), av(n[1]), av(n[0]))), format="csr")
+                                          kron3(av(n[2]), speye(n[1]+1),
+                                                av(n[0])),
+                                          kron3(speye(n[2]+1), av(n[1]),
+                                                av(n[0]))),
+                                         format="csr")
         return self._aveN2F

SimPEG/Mesh/InnerProducts.py

@@ -421,7 +421,7 @@ class InnerProducts(object):
     def _getEdgePx(M):
         """Returns a function for creating projection matrices"""
         def Px(xEdge):
-            assert xEdge == 'eX0', 'xEdge = %s, not eX0' % xEdge
+            assert xEdge == 'eX0', 'xEdge = {0!s}, not eX0'.format(xEdge)
             return sp.identity(M.nC)
         return Px
 

SimPEG/Mesh/MeshIO.py

@@ -198,11 +198,11 @@ class TensorMeshIO(object):
         """
         assert mesh.dim == 3
         s = ''
-        s += '%i %i %i\n' %tuple(mesh.vnC)
+        s += '{0:d} {1:d} {2:d}\n'.format(*tuple(mesh.vnC))
         origin = mesh.x0 + np.array([0,0,mesh.hz.sum()]) # Have to it in the same operation or use mesh.x0.copy(), otherwise the mesh.x0 is updated.
         origin.dtype = float
 
-        s += '%.2f %.2f %.2f\n' %tuple(origin)
+        s += '{0:.2f} {1:.2f} {2:.2f}\n'.format(*tuple(origin))
         s += ('%.2f '*mesh.nCx+'\n')%tuple(mesh.hx)
         s += ('%.2f '*mesh.nCy+'\n')%tuple(mesh.hy)
         s += ('%.2f '*mesh.nCz+'\n')%tuple(mesh.hz[::-1])

SimPEG/Mesh/TensorMesh.py

@@ -23,8 +23,8 @@ class BaseTensorMesh(BaseMesh):
                 h_i = self._unitDimensions[i] * np.ones(int(h_i))/int(h_i)
             elif type(h_i) is list:
                 h_i = Utils.meshTensor(h_i)
-            assert isinstance(h_i, np.ndarray), ("h[%i] is not a numpy array." % i)
+            assert isinstance(h_i, np.ndarray), ("h[{0:d}] is not a numpy array.".format(i))
-            assert len(h_i.shape) == 1, ("h[%i] must be a 1D numpy array." % i)
+            assert len(h_i.shape) == 1, ("h[{0:d}] must be a 1D numpy array.".format(i))
             h[i] = h_i[:] # make a copy.
 
         x0 = np.zeros(len(h))
@@ -41,7 +41,7 @@ class BaseTensorMesh(BaseMesh):
                 elif x_i == 'N':
                     x0[i] = -h_i.sum()
                 else:
-                    raise Exception("x0[%i] must be a scalar or '0' to be zero, 'C' to center, or 'N' to be negative." % i)
+                    raise Exception("x0[{0:d}] must be a scalar or '0' to be zero, 'C' to center, or 'N' to be negative.".format(i))
 
         if isinstance(self, BaseRectangularMesh):
             BaseRectangularMesh.__init__(self, np.array([x.size for x in h]), x0)
@@ -239,7 +239,7 @@ class BaseTensorMesh(BaseMesh):
             'CCVz'  -> z-component of vector field defined on cell centers
         """
         if self._meshType == 'CYL' and self.isSymmetric and locType in ['Ex','Ez','Fy']:
-            raise Exception('Symmetric CylMesh does not support %s interpolation, as this variable does not exist.' % locType)
+            raise Exception('Symmetric CylMesh does not support {0!s} interpolation, as this variable does not exist.'.format(locType))
 
         loc = Utils.asArray_N_x_Dim(loc, self.dim)
 

SimPEG/Mesh/TreeMesh.py

@@ -177,7 +177,7 @@ class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
         return l
 
     def __str__(self):
-        outStr = '  ---- %sTreeMesh ----  '%('Oc' if self.dim == 3 else 'Quad')
+        outStr = '  ---- {0!s}TreeMesh ----  '.format(('Oc' if self.dim == 3 else 'Quad'))
         def printH(hx, outStr=''):
             i = -1
             while True:
@@ -213,7 +213,7 @@ class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
             outStr += printH(self.hy, outStr='\n   hy:')
             outStr += printH(self.hz, outStr='\n   hz:')
         outStr += '\n  nC: {0:d}'.format(self.nC)
-        outStr += '\n  Fill: %2.2f%%'%(self.fill*100)
+        outStr += '\n  Fill: {0:2.2f}%'.format((self.fill*100))
         return outStr
 
     @property
@@ -2210,7 +2210,7 @@ class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
 
         ax.set_xlabel('y' if normal == 'X' else 'x')
         ax.set_ylabel('y' if normal == 'Z' else 'z')
-        ax.set_title('Slice %d, %s = %4.2f' % (ind,normal,indLoc))
+        ax.set_title('Slice {0:d}, {1!s} = {2:4.2f}'.format(ind, normal, indLoc))
 
         if grid:
             _ = antiNormalInd
@@ -2240,7 +2240,7 @@ class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
             if key < 0 : #Handle negative indices
                 key += len( self )
             if key >= len( self ) :
-                raise IndexError, "The index (%d) is out of range."%key
+                raise IndexError, "The index ({0:d}) is out of range.".format(key)
 
             self._numberCells() # no-op if numbered
             index   = self._i2cc[key]

SimPEG/Mesh/View.py

@@ -171,7 +171,7 @@ class TensorView(object):
                         iz = ix + iy*nX
                         if iz < self.nCz:
                             ax.text((ix+1)*(self.vectorNx[-1]-self.x0[0])-pad,(iy)*(self.vectorNy[-1]-self.x0[1])+pad,
-                                     '#%i'%iz,color=annotationColor,verticalalignment='bottom',horizontalalignment='right',size='x-large')
+                                     '#{0:.0f}'.format(iz),color=annotationColor,verticalalignment='bottom',horizontalalignment='right',size='x-large')
 
         ax.set_title(vType)
         if showIt: plt.show()
@@ -221,10 +221,10 @@ class TensorView(object):
         vTypeOpts = ['CC', 'CCv','N','F','E','Fx','Fy','Fz','E','Ex','Ey','Ez']
 
         # Some user error checking
-        assert vType in vTypeOpts, "vType must be in ['%s']" % "','".join(vTypeOpts)
+        assert vType in vTypeOpts, "vType must be in ['{0!s}']".format("','".join(vTypeOpts))
         assert self.dim == 3, 'Must be a 3D mesh. Use plotImage.'
-        assert view in viewOpts, "view must be in ['%s']" % "','".join(viewOpts)
+        assert view in viewOpts, "view must be in ['{0!s}']".format("','".join(viewOpts))
-        assert normal in normalOpts, "normal must be in ['%s']" % "','".join(normalOpts)
+        assert normal in normalOpts, "normal must be in ['{0!s}']".format("','".join(normalOpts))
         assert type(grid) is bool, 'grid must be a boolean'
 
         szSliceDim = getattr(self, 'nC'+normal.lower()) #: Size of the sliced dimension
@@ -295,7 +295,7 @@ class TensorView(object):
 
         ax.set_xlabel('y' if normal == 'X' else 'x')
         ax.set_ylabel('y' if normal == 'Z' else 'z')
-        ax.set_title('Slice %d' % ind)
+        ax.set_title('Slice {0:.0f}'.format(ind))
         return out
 
 
@@ -316,11 +316,11 @@ class TensorView(object):
         vTypeOptsV = ['CCv','F','E']
         vTypeOpts = vTypeOptsCC + vTypeOptsV
         if view == 'vec':
-            assert vType in vTypeOptsV, "vType must be in ['%s'] when view='vec'" % "','".join(vTypeOptsV)
+            assert vType in vTypeOptsV, "vType must be in ['{0!s}'] when view='vec'".format("','".join(vTypeOptsV))
-        assert vType in vTypeOpts, "vType must be in ['%s']" % "','".join(vTypeOpts)
+        assert vType in vTypeOpts, "vType must be in ['{0!s}']".format("','".join(vTypeOpts))
 
         viewOpts = ['real','imag','abs','vec']
-        assert view in viewOpts, "view must be in ['%s']" % "','".join(viewOpts)
+        assert view in viewOpts, "view must be in ['{0!s}']".format("','".join(viewOpts))
 
 
         if ax is None:

SimPEG/Optimization.py

@@ -121,7 +121,7 @@ class Minimize(object):
     @callback.setter
     def callback(self, value):
         if self.callback is not None:
-            print 'The callback on the %s Optimization was replaced.' % self.__name__
+            print 'The callback on the {0!s} Optimization was replaced.'.format(self.__name__)
         self._callback = value
 
 
@@ -855,7 +855,7 @@ class NewtonRoot(object):
             if self.comments and self.doLS: print '\tLinesearch:\n'
             # Enter Linesearch
             while True and self.doLS:
-                if self.comments: print '\t\tResid: %e\n'%norm(rt)
+                if self.comments: print '\t\tResid: {0:e}\n'.format(norm(rt))
                 if norm(rt) <= norm(r) or norm(rt) < self.tol:
                     break
 
@@ -873,7 +873,7 @@ class NewtonRoot(object):
             if norm(rt) < self.tol:
                 break
             if self.iter > self.maxIter:
-                print 'NewtonRoot stopped by maxIters (%d). norm: %4.4e' % (self.maxIter, norm(rt))
+                print 'NewtonRoot stopped by maxIters ({0:d}). norm: {1:4.4e}'.format(self.maxIter, norm(rt))
                 break
 
         return x

SimPEG/Problem.py

@@ -49,7 +49,7 @@ class BaseProblem(object):
 
     def pair(self, d):
         """Bind a survey to this problem instance using pointers."""
-        assert isinstance(d, self.surveyPair), "Data object must be an instance of a %s class."%(self.surveyPair.__name__)
+        assert isinstance(d, self.surveyPair), "Data object must be an instance of a {0!s} class.".format((self.surveyPair.__name__))
         if d.ispaired:
             raise Exception("The survey object is already paired to a problem. Use survey.unpair()")
         self._survey = d

SimPEG/PropMaps.py

@@ -19,85 +19,85 @@ class Property(object):
         return getattr(self, '_propertyLink', None)
     @propertyLink.setter
     def propertyLink(self, value):
-        assert type(value) is tuple and len(value) == 2 and type(value[0]) is str and issubclass(value[1], Maps.IdentityMap), 'Use format: ("%s", Maps.ReciprocalMap)'%self.name
+        assert type(value) is tuple and len(value) == 2 and type(value[0]) is str and issubclass(value[1], Maps.IdentityMap), 'Use format: ("{0!s}", Maps.ReciprocalMap)'.format(self.name)
         self._propertyLink = value
 
     def _getMapProperty(self):
         prop = self
         def fget(self):
-            return getattr(self, '_%sMap'%prop.name, None)
+            return getattr(self, '_{0!s}Map'.format(prop.name), None)
         def fset(self, val):
             if prop.propertyLink is not None:
                 linkName, linkMap = prop.propertyLink
-                assert getattr(self, '%sMap'%linkName, None) is None, 'Cannot set both sides of a linked property.'
+                assert getattr(self, '{0!s}Map'.format(linkName), None) is None, 'Cannot set both sides of a linked property.'
             # TODO: Check if the mapping can be correct
-            setattr(self, '_%sMap'%prop.name, val)
+            setattr(self, '_{0!s}Map'.format(prop.name), val)
         return property(fget=fget, fset=fset, doc=prop.doc)
 
     def _getIndexProperty(self):
         prop = self
         def fget(self):
-            return getattr(self, '_%sIndex'%prop.name, slice(None))
+            return getattr(self, '_{0!s}Index'.format(prop.name), slice(None))
         def fset(self, val):
-            setattr(self, '_%sIndex'%prop.name, val)
+            setattr(self, '_{0!s}Index'.format(prop.name), val)
         return property(fget=fget, fset=fset, doc=prop.doc)
 
     def _getProperty(self):
         prop = self
         def fget(self):
-            mapping = getattr(self, '%sMap'%prop.name)
+            mapping = getattr(self, '{0!s}Map'.format(prop.name))
             if mapping is None and prop.propertyLink is None:
                 return prop.defaultVal
 
             if mapping is None and prop.propertyLink is not None:
                 linkName, linkMapClass = prop.propertyLink
                 linkMap = linkMapClass(None)
-                if getattr(self, '%sMap'%linkName, None) is None:
+                if getattr(self, '{0!s}Map'.format(linkName), None) is None:
                     return prop.defaultVal
-                m = getattr(self, '%s'%linkName)
+                m = getattr(self, '{0!s}'.format(linkName))
                 return linkMap * m
 
-            m = getattr(self, '%sModel'%prop.name)
+            m = getattr(self, '{0!s}Model'.format(prop.name))
             return mapping * m
         return property(fget=fget)
 
     def _getModelDerivProperty(self):
         prop = self
         def fget(self):
-            mapping = getattr(self, '%sMap'%prop.name)
+            mapping = getattr(self, '{0!s}Map'.format(prop.name))
             if mapping is None and prop.propertyLink is None:
                 return None
 
             if mapping is None and prop.propertyLink is not None:
                 linkName, linkMapClass = prop.propertyLink
-                linkedMap = getattr(self, '%sMap'%linkName)
+                linkedMap = getattr(self, '{0!s}Map'.format(linkName))
                 if linkedMap is None:
                     return None
                 linkMap = linkMapClass(None) * linkedMap
-                m = getattr(self, '%sModel'%linkName)
+                m = getattr(self, '{0!s}Model'.format(linkName))
                 return linkMap.deriv( m )
 
-            m = getattr(self, '%sModel'%prop.name)
+            m = getattr(self, '{0!s}Model'.format(prop.name))
             return mapping.deriv( m )
         return property(fget=fget)
 
     def _getModelProperty(self):
         prop = self
         def fget(self):
-            mapping = getattr(self, '%sMap'%prop.name)
+            mapping = getattr(self, '{0!s}Map'.format(prop.name))
             if mapping is None:
                 return None
-            index = getattr(self.propMap, '%sIndex'%prop.name)
+            index = getattr(self.propMap, '{0!s}Index'.format(prop.name))
             return self.vector[index]
         return property(fget=fget)
 
     def _getModelProjProperty(self):
         prop = self
         def fget(self):
-            mapping = getattr(self, '%sMap'%prop.name)
+            mapping = getattr(self, '{0!s}Map'.format(prop.name))
             if mapping is None:
                 return None
-            inds = getattr(self.propMap, '%sIndex'%prop.name)
+            inds = getattr(self.propMap, '{0!s}Index'.format(prop.name))
             if type(inds) is slice:
                 inds = range(*inds.indices(self.nP))
             nI, nP = len(inds),self.nP
@@ -107,7 +107,7 @@ class Property(object):
     def _getModelMapProperty(self):
         prop = self
         def fget(self):
-            return getattr(self.propMap, '_%sMap'%prop.name, None)
+            return getattr(self.propMap, '_{0!s}Map'.format(prop.name), None)
         return property(fget=fget)
 
 
@@ -123,7 +123,7 @@ class PropModel(object):
         inds = []
         if getattr(self, '_nP', None) is None:
             for name in self.propMap._properties:
-                index = getattr(self.propMap, '%sIndex'%name, None)
+                index = getattr(self.propMap, '{0!s}Index'.format(name), None)
                 if index is not None:
                     if type(index) is slice:
                         inds += range(*index.indices(len(self.vector)))
@@ -163,9 +163,9 @@ class _PropMapMetaClass(type):
             if prop.defaultInvProp:
                 defaultInvProps += [p]
             if prop.propertyLink is not None:
-                assert prop.propertyLink[0] in _properties, "You can only link to things that exist: '%s' is trying to link to '%s'"%(prop.name, prop.propertyLink[0])
+                assert prop.propertyLink[0] in _properties, "You can only link to things that exist: '{0!s}' is trying to link to '{1!s}'".format(prop.name, prop.propertyLink[0])
         if len(defaultInvProps) > 1:
-            raise Exception('You have more than one default inversion property: %s' % defaultInvProps)
+            raise Exception('You have more than one default inversion property: {0!s}'.format(defaultInvProps))
 
         newClass = super(_PropMapMetaClass, cls).__new__(cls, name, bases, attrs)
 
@@ -223,7 +223,7 @@ class PropMap(object):
                 type(m[0]) is str and
                 m[0] in self._properties and
                 isinstance(m[1], Maps.IdentityMap)
-                for m in maps]), "Use signature: [%s]" % (', '.join(["('%s', %sMap)"%(p,p) for p in self._properties]))
+                for m in maps]), "Use signature: [{0!s}]".format((', '.join(["('{0!s}', {1!s}Map)".format(p, p) for p in self._properties])))
         if slices is None:
             slices = dict()
         else:
@@ -236,8 +236,8 @@ class PropMap(object):
 
         nP = 0
         for name, mapping in maps:
-            setattr(self, '%sMap'%name, mapping)
+            setattr(self, '{0!s}Map'.format(name), mapping)
-            setattr(self, '%sIndex'%name, slices.get(name, slice(nP, nP + mapping.nP)))
+            setattr(self, '{0!s}Index'.format(name), slices.get(name, slice(nP, nP + mapping.nP)))
             nP += mapping.nP
         self.nP = nP
 
@@ -250,12 +250,12 @@ class PropMap(object):
 
     def clearMaps(self):
         for name in self._properties:
-            setattr(self, '%sMap'%name, None)
+            setattr(self, '{0!s}Map'.format(name), None)
-            setattr(self, '%sIndex'%name, None)
+            setattr(self, '{0!s}Index'.format(name), None)
 
     def __call__(self, vec):
         return self.PropModel(self, vec)
 
     def __contains__(self, val):
-        activeMaps = [name for name in self._properties if getattr(self, '%sMap'%name) is not None]
+        activeMaps = [name for name in self._properties if getattr(self, '{0!s}Map'.format(name)) is not None]
         return val in activeMaps

SimPEG/Survey.py

@@ -26,7 +26,7 @@ class BaseRx(object):
     def rxType(self, value):
         known = self.knownRxTypes
         if known is not None:
-            assert value in known, "rxType must be in ['%s']" % ("', '".join(known))
+            assert value in known, "rxType must be in ['{0!s}']".format(("', '".join(known)))
         self._rxType = value
 
     @property
@@ -125,7 +125,7 @@ class BaseSrc(object):
     def __init__(self, rxList, **kwargs):
         assert type(rxList) is list, 'rxList must be a list'
         for rx in rxList:
-            assert isinstance(rx, self.rxPair), 'rxList must be a %s'%self.rxPair.__name__
+            assert isinstance(rx, self.rxPair), 'rxList must be a {0!s}'.format(self.rxPair.__name__)
         assert len(set(rxList)) == len(rxList), 'The rxList must be unique'
         self.uid = str(uuid.uuid4())
         self.rxList = rxList
@@ -227,7 +227,7 @@ class BaseSurvey(object):
     @srcList.setter
     def srcList(self, value):
         assert type(value) is list, 'srcList must be a list'
-        assert np.all([isinstance(src, self.srcPair) for src in value]), 'All sources must be instances of %s' % self.srcPair.__name__
+        assert np.all([isinstance(src, self.srcPair) for src in value]), 'All sources must be instances of {0!s}'.format(self.srcPair.__name__)
         assert len(set(value)) == len(value), 'The srcList must be unique'
         self._srcList = value
         self._sourceOrder = dict()
@@ -238,10 +238,10 @@ class BaseSurvey(object):
             sources = [sources]
         for src in sources:
             if getattr(src,'uid',None) is None:
-                raise KeyError('Source does not have a uid: %s'%str(src))
+                raise KeyError('Source does not have a uid: {0!s}'.format(str(src)))
         inds = map(lambda src: self._sourceOrder.get(src.uid, None), sources)
         if None in inds:
-            raise KeyError('Some of the sources specified are not in this survey. %s'%str(inds))
+            raise KeyError('Some of the sources specified are not in this survey. {0!s}'.format(str(inds)))
         return inds
 
     @property
@@ -263,7 +263,7 @@ class BaseSurvey(object):
     def pair(self, p):
         """Bind a problem to this survey instance using pointers"""
         assert hasattr(p, 'surveyPair'), "Problem must have an attribute 'surveyPair'."
-        assert isinstance(self, p.surveyPair), "Problem requires survey object must be an instance of a %s class."%(p.surveyPair.__name__)
+        assert isinstance(self, p.surveyPair), "Problem requires survey object must be an instance of a {0!s} class.".format((p.surveyPair.__name__))
         if p.ispaired:
             raise Exception("The problem object is already paired to a survey. Use prob.unpair()")
         self._prob = p

SimPEG/Tests.py

@@ -4,7 +4,6 @@ from SimPEG.Utils import mkvc, sdiag, diagEst
 from SimPEG import Utils
 from SimPEG.Mesh import TensorMesh, CurvilinearMesh, CylMesh
 from SimPEG.Mesh.TreeMesh import TreeMesh as Tree
-import numpy as np
 import scipy.sparse as sp
 import unittest
 import inspect
@@ -200,10 +199,10 @@ class OrderTest(unittest.TestCase):
                     print '_____________________________________________'
                     print '   h  |    error    | e(i-1)/e(i) |  order'
                     print '~~~~~~|~~~~~~~~~~~~~|~~~~~~~~~~~~~|~~~~~~~~~~'
-                    print '%4i  |  %8.2e   |' % (nc, err)
+                    print '{0:4d}  |  {1:8.2e}   |'.format(nc, err)
                 else:
                     order.append(np.log(err/err_old)/np.log(max_h/max_h_old))
-                    print '%4i  |  %8.2e   |   %6.4f    |  %6.4f' % (nc, err, err_old/err, order[-1])
+                    print '{0:4d}  |  {1:8.2e}   |   {2:6.4f}    |  {3:6.4f}'.format(nc, err, err_old/err, order[-1])
                 err_old = err
                 max_h_old = max_h
             print '---------------------------------------------'
@@ -258,8 +257,8 @@ def checkDerivative(fctn, x0, num=7, plotIt=True, dx=None, expectedOrder=2, tole
             Tests.checkDerivative(simplePass, np.random.randn(5))
     """
 
-    print "%s checkDerivative %s" % ('='*20, '='*20)
+    print "{0!s} checkDerivative {1!s}".format('='*20, '='*20)
-    print "iter    h         |ft-f0|   |ft-f0-h*J0*dx|  Order\n%s" % ('-'*57)
+    print "iter    h         |ft-f0|   |ft-f0-h*J0*dx|  Order\n{0!s}".format(('-'*57))
 
     f0, J0 = fctn(x0)
 
@@ -290,7 +289,7 @@ def checkDerivative(fctn, x0, num=7, plotIt=True, dx=None, expectedOrder=2, tole
 
         order0 = np.log10(E0[:-1]/E0[1:])
         order1 = np.log10(E1[:-1]/E1[1:])
-        print " %d   %1.2e    %1.3e     %1.3e      %1.3f" % (i, h[i], E0[i], E1[i], np.nan if i == 0 else order1[i-1])
+        print " {0:d}   {1:1.2e}    {2:1.3e}     {3:1.3e}      {4:1.3f}".format(i, h[i], E0[i], E1[i], np.nan if i == 0 else order1[i-1])
 
     # Ensure we are about precision
     order0 = order0[E0[1:] > eps]
@@ -302,10 +301,10 @@ def checkDerivative(fctn, x0, num=7, plotIt=True, dx=None, expectedOrder=2, tole
     passTest = belowTol or correctOrder
 
     if passTest:
-        print "%s PASS! %s" % ('='*25, '='*25)
+        print "{0!s} PASS! {1!s}".format('='*25, '='*25)
         print happiness[np.random.randint(len(happiness))]+'\n'
     else:
-        print "%s\n%s FAIL! %s\n%s" % ('*'*57, '<'*25, '>'*25, '*'*57)
+        print "{0!s}\n{1!s} FAIL! {2!s}\n{3!s}".format('*'*57, '<'*25, '>'*25, '*'*57)
         print sadness[np.random.randint(len(sadness))]+'\n'
 
 
@@ -314,7 +313,7 @@ def checkDerivative(fctn, x0, num=7, plotIt=True, dx=None, expectedOrder=2, tole
         ax = ax or plt.subplot(111)
         ax.loglog(h, E0, 'b')
         ax.loglog(h, E1, 'g--')
-        ax.set_title('Check Derivative - %s' % ('PASSED :)' if passTest else 'FAILED :('))
+        ax.set_title('Check Derivative - {0!s}'.format(('PASSED :)' if passTest else 'FAILED :(')))
         ax.set_xlabel('h')
         ax.set_ylabel('Error')
         leg = ax.legend(['$\mathcal{O}(h)$', '$\mathcal{O}(h^2)$'], loc='best',

SimPEG/Utils/SolverUtils.py

@@ -8,7 +8,7 @@ def _checkAccuracy(A, b, X, accuracyTol):
     if nrm_b > 0:
         nrm /= nrm_b
     if nrm > accuracyTol:
-        msg = '### SolverWarning ###: Accuracy on solve is above tolerance: %e > %e' % (nrm, accuracyTol)
+        msg = '### SolverWarning ###: Accuracy on solve is above tolerance: {0:e} > {1:e}'.format(nrm, accuracyTol)
         print msg
         warnings.warn(msg, RuntimeWarning)
 

SimPEG/Utils/codeutils.py

@@ -32,7 +32,7 @@ def memProfileWrapper(towrap, *funNames):
         if hasattr(towrap,f):
             attrs[f] = profile(getattr(towrap,f))
         else:
-            print '%s not found in %s Class' % (f, towrap.__name__)
+            print '{0!s} not found in {1!s} Class'.format(f, towrap.__name__)
 
     return type(towrap.__name__ + 'MemProfileWrap', (towrap,), attrs)
 
@@ -65,7 +65,7 @@ def setKwargs(obj, ignore=None,  **kwargs):
         if hasattr(obj, attr):
             setattr(obj, attr, kwargs[attr])
         else:
-            raise Exception('%s attr is not recognized' % attr)
+            raise Exception('{0!s} attr is not recognized'.format(attr))
 
     hook(obj,hook, silent=True)
     hook(obj,setKwargs, silent=True)
@@ -74,7 +74,7 @@ def printTitles(obj, printers, name='Print Titles', pad=''):
     titles = ''
     widths = 0
     for printer in printers:
-        titles += ('{:^%i}'%printer['width']).format(printer['title']) + ''
+        titles += ('{{:^{0:d}}}'.format(printer['width'])).format(printer['title']) + ''
         widths += printer['width']
     print pad + "{0} {1} {0}".format('='*((widths-1-len(name))/2), name)
     print pad + titles
@@ -83,7 +83,7 @@ def printTitles(obj, printers, name='Print Titles', pad=''):
 def printLine(obj, printers, pad=''):
     values = ''
     for printer in printers:
-        values += ('{:^%i}'%printer['width']).format(printer['format'] % printer['value'](obj))
+        values += ('{{:^{0:d}}}'.format(printer['width'])).format(printer['format'] % printer['value'](obj))
     print pad + values
 
 def checkStoppers(obj, stoppers):
@@ -104,12 +104,12 @@ def checkStoppers(obj, stoppers):
     return (len(optimal)>0 and all(optimal)) | (len(critical)>0 and any(critical))
 
 def printStoppers(obj, stoppers, pad='', stop='STOP!', done='DONE!'):
-    print pad + "%s%s%s" % ('-'*25,stop,'-'*25)
+    print pad + "{0!s}{1!s}{2!s}".format('-'*25, stop, '-'*25)
     for stopper in stoppers:
         l = stopper['left'](obj)
         r = stopper['right'](obj)
         print pad + stopper['str'] % (l<=r,l,r)
-    print pad + "%s%s%s" % ('-'*25,done,'-'*25)
+    print pad + "{0!s}{1!s}{2!s}".format('-'*25, done, '-'*25)
 
 def callHooks(match, mainFirst=False):
     """
@@ -144,14 +144,14 @@ def callHooks(match, mainFirst=False):
 
 
         extra = """
-            If you have things that also need to run in the method %s, you can create a method::
+            If you have things that also need to run in the method {0!s}, you can create a method::
 
-                def _%s*(self, ... ):
+                def _{1!s}*(self, ... ):
                     pass
 
-            Where the * can be any string. If present, _%s* will be called at the start of the default %s call.
+            Where the * can be any string. If present, _{2!s}* will be called at the start of the default {3!s} call.
             You may also completely overwrite this function.
-        """ % (match, match, match, match)
+        """.format(match, match, match, match)
         doc = wrapper.__doc__
         wrapper.__doc__ = ('' if doc is None else doc) + extra
         return wrapper
@@ -186,7 +186,7 @@ def asArray_N_x_Dim(pts, dim):
         elif len(pts.shape) == 1:
             pts = pts[:,np.newaxis]
 
-        assert pts.shape[1] == dim, "pts must be a column vector of shape (nPts, %d) not (%d, %d)" % ((dim,)+pts.shape)
+        assert pts.shape[1] == dim, "pts must be a column vector of shape (nPts, {0:d}) not ({1:d}, {2:d})".format(*((dim,)+pts.shape))
 
         return pts
 
@@ -207,17 +207,17 @@ def requires(var):
 
         .. note::
 
-            To use survey.%s(), SimPEG requires that a problem be bound to the survey.
+            To use survey.{0!s}(), SimPEG requires that a problem be bound to the survey.
             If a problem has not been bound, an Exception will be raised.
             To bind a problem to the Data object::
 
                 survey.pair(myProblem)
 
-            """ % f.__name__
+            """.format(f.__name__)
         else:
             extra = """
-                To use *%s* method, SimPEG requires that the %s be specified.
+                To use *{0!s}* method, SimPEG requires that the {1!s} be specified.
-            """ % (f.__name__, var)
+            """.format(f.__name__, var)
         @wraps(f)
         def requiresVarWrapper(self,*args,**kwargs):
             if getattr(self, var, None) is None:

SimPEG/Utils/curvutils.py

@@ -80,7 +80,7 @@ def indexCube(nodes, gridSize, n=None):
     # Make sure that we choose from the possible nodes.
     possibleNodes = 'ABCD' if gridSize.size == 2 else 'ABCDEFGH'
     for node in nodes:
-        assert node in possibleNodes, "Nodes must be chosen from: '%s'" % possibleNodes
+        assert node in possibleNodes, "Nodes must be chosen from: '{0!s}'".format(possibleNodes)
     dim = gridSize.size
     if n is None:
         n = gridSize - 1

SimPEG/Utils/matutils.py

@@ -278,7 +278,7 @@ class TensorType(object):
         else:
             raise Exception('Unexpected shape of tensor')
     def __str__(self):
-        return 'TensorType[%i]: %s' % (self._tt, self._tts)
+        return 'TensorType[{0:d}]: {1!s}'.format(self._tt, self._tts)
     def __eq__(self, v): return self._tt == v
     def __le__(self, v): return self._tt <= v
     def __ge__(self, v): return self._tt >= v

SimPEG/Utils/modelutils.py

@@ -26,7 +26,7 @@ def surface2ind_topo(mesh, topo, gridLoc='CC'):
             gridTopo = Ftopo(XY).reshape(mesh.vnN[:2], order='F')
 
             if mesh._meshType not in ['TENSOR', 'CYL', 'BASETENSOR']:
-                raise NotImplementedError('Nodal surface2ind_topo not implemented for %s mesh'%mesh._meshType)
+                raise NotImplementedError('Nodal surface2ind_topo not implemented for {0!s} mesh'.format(mesh._meshType))
 
             Nz = mesh.vectorNz[1:] # TODO: this will only work for tensor meshes
             actind = np.array([False]*mesh.nC).reshape(mesh.vnC, order='F')
@@ -47,7 +47,7 @@ def surface2ind_topo(mesh, topo, gridLoc='CC'):
 
             gridTopo = Ftopo(mesh.vectorNx)
             if mesh._meshType not in ['TENSOR', 'CYL', 'BASETENSOR']:
-                raise NotImplementedError('Nodal surface2ind_topo not implemented for %s mesh'%mesh._meshType)
+                raise NotImplementedError('Nodal surface2ind_topo not implemented for {0!s} mesh'.format(mesh._meshType))
 
             Ny = mesh.vectorNy[1:] # TODO: this will only work for tensor meshes
             actind = np.array([False]*mesh.nC).reshape(mesh.vnC, order='F')

docs/conf.py

@@ -266,7 +266,7 @@ def _supress_nonlocal_image_warn(self, msg, node):
     from docutils.utils import get_source_line
 
     if not msg.startswith('nonlocal image URI found:'):
-        self._warnfunc(msg, '%s:%s' % get_source_line(node))
+        self._warnfunc(msg, '{0!s}:{1!s}'.format(*get_source_line(node)))
 
 supress_nonlocal_image_warn()
 

docs/content/api_core/api_installing.rst

@@ -66,7 +66,7 @@ Numpy and Matlab
 Lessons in Python
 -----------------
 
-* `Software Carpentry <http://software-carpentry.org/v4/python/index.html>`_
+* `Software Carpentry <http://swcarpentry.github.io/python-novice-inflammation/>`_
 * `Introduction to NumPy and Matplotlib <http://www.youtube.com/watch?v=3Fp1zn5ao2M>`_
 
 Editing Python

docs/content/dc/index.rst

@@ -47,7 +47,16 @@ direct current (DC) resistivity and induced polarization (IP) geophysical proble
 DC resistivity survey
 =====================
 
-Electrical resistivity of subsurface materials is measured by causing an electrical current to flow in the earth between one pair of electrodes while the voltage across a second pair of electrodes is measured. The result is an "apparent" resistivity which is a value representing the weighted average resistivity over a volume of the earth. Variations in this measurement are caused by variations in the soil, rock, and pore fluid electrical resistivity. Surveys require contact with the ground, so they can be labour intensive. Results are sometimes interpreted directly, but more commonly, 1D, 2D or 3D models are estimated using inversion procedures (`GPG <http://www.eos.ubc.ca/courses/eosc350/content/>`_).
+Electrical resistivity of subsurface materials is measured by causing an
+electrical current to flow in the earth between one pair of electrodes while
+the voltage across a second pair of electrodes is measured. The result is an
+"apparent" resistivity which is a value representing the weighted average
+resistivity over a volume of the earth. Variations in this measurement are
+caused by variations in the soil, rock, and pore fluid electrical resistivity.
+Surveys require contact with the ground, so they can be labour intensive.
+Results are sometimes interpreted directly, but more commonly, 1D, 2D or 3D
+models are estimated using inversion procedures (`GPG
+<http://gpg.geosci.xyz>`_).
 
 
 Background

docs/index.rst

@@ -16,16 +16,24 @@ SimPEG Documentation
     :target: https://github.com/simpeg/simpeg/blob/master/LICENSE
     :alt: BSD 3 clause license.
 
-.. image:: https://img.shields.io/travis/simpeg/simpeg.svg
+.. image:: https://api.travis-ci.org/simpeg/simpeg.svg?branch=master
-    :target: https://travis-ci.org/simpeg/simpeg?branch=master
+    :target: https://travis-ci.org/simpeg/simpeg
     :alt: Travis CI build status
 
-.. image:: https://img.shields.io/coveralls/simpeg/simpeg.svg
+.. image:: http://img.shields.io/badge/GITTER-JOIN_CHAT-brightgreen.svg?style=flat-square
-    :target: https://coveralls.io/r/simpeg/simpeg?branch=master
+    :alt: gitter chat room at https://gitter.im/simpeg/simpeg
-    :alt: Coverage status
+    :target: https://gitter.im/simpeg/simpeg
 
 .. image:: https://codecov.io/gh/simpeg/simpeg/branch/master/graph/badge.svg
-    :target: https://codecov.io/gh/simpeg/simpeg
+    :target: https://codecov.io/gh/simpeg/simpeg
+
+.. image:: https://www.quantifiedcode.com/api/v1/project/933aa3decf444538aa432c8817169b6d/badge.svg
+    :target: https://www.quantifiedcode.com/app/project/933aa3decf444538aa432c8817169b6d
+    :alt: Code issues
+
+.. image:: https://api.codacy.com/project/badge/Grade/4fc959a5294a418fa21fc7bc3b3aa078
+    :target: https://www.codacy.com/app/lindseyheagy/simpeg?utm_source=github.com&utm_medium=referral&utm_content=simpeg/simpeg&utm_campaign=Badge_Grade
+    :alt: codacy
 
 
 Simulation and Parameter Estimation in Geophysics  -  A python package for simulation and gradient based parameter estimation in the context of geophysical applications.

docs/simpegdocs.py

@@ -54,7 +54,7 @@ class Images(webapp2.RequestHandler):
 class Redirect(webapp2.RequestHandler):
     def get(self):
         path = str(self.request.path).split(os.path.sep)[3:]
-        self.redirect(('/%s'%os.path.sep.join(path)), permanent=True)
+        self.redirect(('/{0!s}'.format(os.path.sep.join(path))), permanent=True)
 
 
 class MainPage(webapp2.RequestHandler):

tests/base/test_Fields.py

@@ -1,14 +1,16 @@
 import unittest
-from SimPEG import *
+from SimPEG import Mesh, Problem, Fields, Survey, Utils
+import numpy as np
 
 
 class FieldsTest(unittest.TestCase):
 
     def setUp(self):
-        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10,11,12]],[0,0,-30])
+        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10, 11, 12]],
+                               [0, 0, -30])
         x = np.linspace(5, 10, 3)
         XYZ = Utils.ndgrid(x, x, np.r_[0.])
-        srcLoc = np.r_[0,0,0.]
+        srcLoc = np.r_[0., 0., 0.]
         rxList0 = Survey.BaseRx(XYZ, 'exi')
         Src0 = Survey.BaseSrc([rxList0], loc=srcLoc)
         rxList1 = Survey.BaseRx(XYZ, 'bxi')
@@ -21,7 +23,10 @@ class FieldsTest(unittest.TestCase):
         srcList = [Src0, Src1, Src2, Src3, Src4]
         survey = Survey.BaseSurvey(srcList=srcList)
         self.D = Survey.Data(survey)
-        self.F = Problem.Fields(mesh, survey, knownFields={'phi':'CC','e':'E','b':'F'}, dtype={"phi":float,"e":complex,"b":complex})
+        self.F = Problem.Fields(mesh, survey, knownFields={'phi': 'CC',
+                                                           'e': 'E', 'b': 'F'},
+                                dtype={"phi": float, "e": complex,
+                                       "b": complex})
         self.Src0 = Src0
         self.Src1 = Src1
         self.mesh = mesh
@@ -38,16 +43,18 @@ class FieldsTest(unittest.TestCase):
         self.assertTrue('e' in F)
 
     def test_overlappingFields(self):
-        self.assertRaises(AssertionError, Problem.Fields, self.F.mesh, self.F.survey,
+        self.assertRaises(AssertionError, Problem.Fields, self.F.mesh,
-                            knownFields={'b':'F'},
+                          self.F.survey, knownFields={'b': 'F'},
                           aliasFields={'b': ['b', (lambda F, b, ind: b)]})
 
     def test_SetGet(self):
         F = self.F
         nSrc = F.survey.nSrc
-        e = np.random.rand(F.mesh.nE, nSrc) + np.random.rand(F.mesh.nE, nSrc)*1j
+        e = (np.random.rand(F.mesh.nE, nSrc) +
+             np.random.rand(F.mesh.nE, nSrc)*1j)
         F[:, 'e'] = e
-        b = np.random.rand(F.mesh.nF, nSrc) + np.random.rand(F.mesh.nF, nSrc)*1j
+        b = (np.random.rand(F.mesh.nF, nSrc) +
+             np.random.rand(F.mesh.nF, nSrc)*1j)
         F[:, 'b'] = b
 
         self.assertTrue(np.all(F[:, 'e'] == e))
@@ -86,12 +93,16 @@ class FieldsTest(unittest.TestCase):
     def test_assertions(self):
         freq = [self.Src0, self.Src1]
         bWrongSize = np.random.rand(self.F.mesh.nE, self.F.survey.nSrc)
+
         def fun(): self.F[freq, 'b'] = bWrongSize
         self.assertRaises(ValueError, fun)
+
         def fun(): self.F[-999.]
         self.assertRaises(KeyError, fun)
+
         def fun(): self.F['notRight']
         self.assertRaises(KeyError, fun)
+
         def fun(): self.F[freq, 'notThere']
         self.assertRaises(KeyError, fun)
 
@@ -99,7 +110,8 @@ class FieldsTest(unittest.TestCase):
 class FieldsTest_Alias(unittest.TestCase):
 
     def setUp(self):
-        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10,11,12]],[0,0,-30])
+        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10, 11, 12]],
+                               [0, 0, -30])
         x = np.linspace(5, 10, 3)
         XYZ = Utils.ndgrid(x, x, np.r_[0.])
         srcLoc = np.r_[0, 0, 0.]
@@ -114,7 +126,11 @@ class FieldsTest_Alias(unittest.TestCase):
         Src4 = Survey.BaseSrc([rxList0, rxList1, rxList2, rxList3], loc=srcLoc)
         srcList = [Src0, Src1, Src2, Src3, Src4]
         survey = Survey.BaseSurvey(srcList=srcList)
-        self.F = Problem.Fields(mesh, survey, knownFields={'e':'E'}, aliasFields={'b':['e','F',(lambda e, ind: self.F.mesh.edgeCurl * e)]})
+        self.F = Problem.Fields(mesh, survey, knownFields={'e': 'E'},
+                                aliasFields={'b': ['e', 'F',
+                                                   (lambda e, ind:
+                                                    self.F.mesh.edgeCurl *
+                                                    e)]})
         self.Src0 = Src0
         self.Src1 = Src1
         self.mesh = mesh
@@ -149,18 +165,20 @@ class FieldsTest_Alias(unittest.TestCase):
         def alias(e, ind):
             self.assertTrue(ind[0] is self.Src0)
             return self.F.mesh.edgeCurl * e
-        F = Problem.Fields(self.F.mesh, self.F.survey, knownFields={'e':'E'}, aliasFields={'b':['e','F',alias]})
+        F = Problem.Fields(self.F.mesh, self.F.survey, knownFields={'e': 'E'},
+                           aliasFields={'b': ['e', 'F', alias]})
         e = np.random.rand(F.mesh.nE, 1)
         F[self.Src0, 'e'] = e
         F[self.Src0, 'b']
 
-
         def alias(e, ind):
             self.assertTrue(type(ind) is list)
             self.assertTrue(ind[0] is self.Src0)
             self.assertTrue(ind[1] is self.Src1)
             return self.F.mesh.edgeCurl * e
-        F = Problem.Fields(self.F.mesh, self.F.survey, knownFields={'e':'E'}, aliasFields={'b':['e','F',alias]})
+
+        F = Problem.Fields(self.F.mesh, self.F.survey, knownFields={'e': 'E'},
+                           aliasFields={'b': ['e', 'F', alias]})
         e = np.random.rand(F.mesh.nE, 2)
         F[[self.Src0, self.Src1], 'e'] = e
         F[[self.Src0, self.Src1], 'b']
@@ -169,7 +187,8 @@ class FieldsTest_Alias(unittest.TestCase):
 class FieldsTest_Time(unittest.TestCase):
 
     def setUp(self):
-        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10,11,12]],[0,0,-30])
+        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10, 11, 12]],
+                               [0, 0, -30])
         x = np.linspace(5, 10, 3)
         XYZ = Utils.ndgrid(x, x, np.r_[0.])
         srcLoc = np.r_[0, 0, 0.]
@@ -186,7 +205,9 @@ class FieldsTest_Time(unittest.TestCase):
         survey = Survey.BaseSurvey(srcList=srcList)
         prob = Problem.BaseTimeProblem(mesh, timeSteps=[(10., 3), (20., 2)])
         survey.pair(prob)
-        self.F = Problem.TimeFields(mesh, survey, knownFields={'phi':'CC','e':'E','b':'F'})
+        self.F = Problem.TimeFields(mesh, survey, knownFields={'phi': 'CC',
+                                                               'e': 'E',
+                                                               'b': 'F'})
         self.Src0 = Src0
         self.Src1 = Src1
         self.mesh = mesh
@@ -230,7 +251,8 @@ class FieldsTest_Time(unittest.TestCase):
 
         b = np.random.rand(F.mesh.nF, 1, nT)
         F[self.Src0, 'b', 0] = b[:, :, 0]
-        self.assertTrue(np.all(F[self.Src0, 'b', 0] == Utils.mkvc(b[:,0,0],2)))
+        self.assertTrue(np.all(F[self.Src0, 'b', 0] == Utils.mkvc(b[:, 0, 0],
+                                                                  2)))
 
         phi = np.random.rand(F.mesh.nC, 2, nT)
         F[[self.Src0, self.Src1], 'phi'] = phi
@@ -246,11 +268,14 @@ class FieldsTest_Time(unittest.TestCase):
         self.assertTrue(F[self.Src0, 'b'].shape == (F.mesh.nF, nT))
         self.assertTrue(np.all(F[self.Src0, 'b'] == b[:, 0, :]))
         self.assertTrue(np.all(F[self.Src1, 'b'] == b[:, 1, :]))
-        self.assertTrue(np.all(F[self.Src0,'b',1] == Utils.mkvc(b[:,0,1],2)))
+        self.assertTrue(np.all(F[self.Src0, 'b', 1] ==
-        self.assertTrue(np.all(F[self.Src1,'b',1] == Utils.mkvc(b[:,1,1],2)))
+                        Utils.mkvc(b[:, 0, 1], 2)))
-        self.assertTrue(np.all(F[self.Src0,'b',4] == Utils.mkvc(b[:,0,4],2)))
+        self.assertTrue(np.all(F[self.Src1, 'b', 1] ==
-        self.assertTrue(np.all(F[self.Src1,'b',4] == Utils.mkvc(b[:,1,4],2)))
+                        Utils.mkvc(b[:, 1, 1], 2)))
-
+        self.assertTrue(np.all(F[self.Src0, 'b', 4] ==
+                        Utils.mkvc(b[:, 0, 4], 2)))
+        self.assertTrue(np.all(F[self.Src1, 'b', 4] ==
+                        Utils.mkvc(b[:, 1, 4], 2)))
 
         b = np.random.rand(F.mesh.nF, 2, nT)
         F[[self.Src0, self.Src1], 'b', 0] = b[:, :, 0]
@@ -258,12 +283,16 @@ class FieldsTest_Time(unittest.TestCase):
     def test_assertions(self):
         freq = [self.Src0, self.Src1]
         bWrongSize = np.random.rand(self.F.mesh.nE, self.F.survey.nSrc)
+
         def fun(): self.F[freq, 'b'] = bWrongSize
         self.assertRaises(ValueError, fun)
+
         def fun(): self.F[-999.]
         self.assertRaises(KeyError, fun)
+
         def fun(): self.F['notRight']
         self.assertRaises(KeyError, fun)
+
         def fun(): self.F[freq, 'notThere']
         self.assertRaises(KeyError, fun)
 
@@ -271,7 +300,8 @@ class FieldsTest_Time(unittest.TestCase):
 class FieldsTest_Time_Aliased(unittest.TestCase):
 
     def setUp(self):
-        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10,11,12]],[0,0,-30])
+        mesh = Mesh.TensorMesh([np.ones(n)*5 for n in [10, 11, 12]],
+                               [0, 0, -30])
         x = np.linspace(5, 10, 3)
         XYZ = Utils.ndgrid(x, x, np.r_[0.])
         srcLoc = np.r_[0, 0, 0.]
@@ -288,9 +318,11 @@ class FieldsTest_Time_Aliased(unittest.TestCase):
         survey = Survey.BaseSurvey(srcList=srcList)
         prob = Problem.BaseTimeProblem(mesh, timeSteps=[(10., 3), (20., 2)])
         survey.pair(prob)
+
         def alias(b, srcInd, timeInd):
             return self.F.mesh.edgeCurl.T * b + timeInd
-        self.F = Problem.TimeFields(mesh, survey, knownFields={'b':'F'}, aliasFields={'e':['b','E',alias]})
+        self.F = Problem.TimeFields(mesh, survey, knownFields={'b': 'F'},
+                                    aliasFields={'e': ['b', 'E', alias]})
         self.Src0 = Src0
         self.Src1 = Src1
         self.mesh = mesh
@@ -307,7 +339,6 @@ class FieldsTest_Time_Aliased(unittest.TestCase):
         self.assertTrue('e' in F)
         self.assertTrue('b' in F)
 
-
     def test_simpleAlias(self):
         F = self.F
         nSrc = F.survey.nSrc
@@ -325,7 +356,8 @@ class FieldsTest_Time_Aliased(unittest.TestCase):
         self.assertTrue(np.all(F[self.Src0, 'e', :] == e[:, 0, :]))
         self.assertTrue(np.all(F[self.Src1, 'e', :] == e[:, 1, :]))
         for t in range(nT):
-            self.assertTrue(np.all(F[self.Src1, 'e', t] == Utils.mkvc(e[:,1,t],2) ))
+            self.assertTrue(np.all(F[self.Src1, 'e', t] ==
+                            Utils.mkvc(e[:, 1, t], 2)))
 
         b = np.random.rand(F.mesh.nF, nT)
         F[self.Src0, 'b', :] = b
@@ -341,34 +373,41 @@ class FieldsTest_Time_Aliased(unittest.TestCase):
     def test_aliasFunction(self):
         nT = self.F.survey.prob.nT + 1
         count = [0]
+
         def alias(e, srcInd, timeInd):
             count[0] += 1
             self.assertTrue(srcInd[0] is self.Src0)
             return self.F.mesh.edgeCurl * e
-        F = Problem.TimeFields(self.F.mesh, self.F.survey, knownFields={'e':'E'}, aliasFields={'b':['e','F',alias]})
+        F = Problem.TimeFields(self.F.mesh, self.F.survey,
+                               knownFields={'e': 'E'},
+                               aliasFields={'b': ['e', 'F', alias]})
         e = np.random.rand(F.mesh.nE, 1, nT)
         F[self.Src0, 'e', :] = e
         F[self.Src0, 'b', :]
-        self.assertTrue(count[0] == nT) # ensure that this is called for every time separately.
+        # ensure that this is called for every time separately.
+        self.assertTrue(count[0] == nT)
         e = np.random.rand(F.mesh.nE, 1, 1)
         F[self.Src0, 'e', 1] = e
         count[0] = 0
         F[self.Src0, 'b', 1]
         self.assertTrue(count[0] == 1)  # ensure that this is called only once.
 
-
         def alias(e, srcInd, timeInd):
             count[0] += 1
             self.assertTrue(type(srcInd) is list)
             self.assertTrue(srcInd[0] is self.Src0)
             self.assertTrue(srcInd[1] is self.Src1)
             return self.F.mesh.edgeCurl * e
-        F = Problem.TimeFields(self.F.mesh, self.F.survey, knownFields={'e':'E'}, aliasFields={'b':['e','F',alias]})
+        F = Problem.TimeFields(self.F.mesh, self.F.survey,
+                               knownFields={'e': 'E'},
+                               aliasFields={'b': ['e', 'F', alias]})
         e = np.random.rand(F.mesh.nE, 2, nT)
         F[[self.Src0, self.Src1], 'e', :] = e
         count[0] = 0
         F[[self.Src0, self.Src1], 'b', :]
-        self.assertTrue(count[0] == nT) # ensure that this is called for every time separately.
+
+        # ensure that this is called for every time separately.
+        self.assertTrue(count[0] == nT)
         e = np.random.rand(F.mesh.nE, 2, 1)
         F[[self.Src0, self.Src1], 'e', 1] = e
         count[0] = 0

tests/base/test_regularization.py

@@ -28,14 +28,14 @@ class RegularizationTests(unittest.TestCase):
 
                 for i, mesh in enumerate(self.meshlist):
 
-                    print 'Testing %iD'%mesh.dim
+                    print 'Testing {0:d}D'.format(mesh.dim)
 
                     mapping = r.mapPair(mesh)
                     reg = r(mesh, mapping=mapping)
                     m = np.random.rand(mapping.nP)
                     reg.mref = np.ones_like(m)*np.mean(m)
 
-                    print 'Check: phi_m (mref) = %f' %reg.eval(reg.mref)
+                    print 'Check: phi_m (mref) = {0:f}'.format(reg.eval(reg.mref))
                     passed = reg.eval(reg.mref) < TOL
                     self.assertTrue(passed)
 
@@ -56,7 +56,7 @@ class RegularizationTests(unittest.TestCase):
 
                 for i, mesh in enumerate(self.meshlist):
 
-                    print 'Testing Active Cells %iD'%(mesh.dim)
+                    print 'Testing Active Cells {0:d}D'.format((mesh.dim))
 
                     if mesh.dim == 1:
                         indActive = Utils.mkvc(mesh.gridCC <= 0.8)
@@ -70,7 +70,7 @@ class RegularizationTests(unittest.TestCase):
                         m = np.random.rand(mesh.nC)[indAct]
                         reg.mref = np.ones_like(m)*np.mean(m)
 
-                    print 'Check: phi_m (mref) = %f' %reg.eval(reg.mref)
+                    print 'Check: phi_m (mref) = {0:f}'.format(reg.eval(reg.mref))
                     passed = reg.eval(reg.mref) < TOL
                     self.assertTrue(passed)
 
@@ -87,7 +87,7 @@ class RegularizationTests(unittest.TestCase):
 
             for i, mesh in enumerate(self.meshlist):
 
-                print 'Testing %iD'%mesh.dim
+                print 'Testing {0:d}D'.format(mesh.dim)
 
                 # mapping = r.mapPair(mesh)
                 # reg = r(mesh, mapping=mapping)

tests/docs/test_docs.py

@@ -14,9 +14,9 @@ class Doc_Test(unittest.TestCase):
         html_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['html'])
 
         check = subprocess.call(["sphinx-build", "-nW", "-b", "html", "-d",
-            "%s"%(doctrees_path) ,
+            "{0!s}".format((doctrees_path)) ,
-            "%s"%(self.path_to_docs),
+            "{0!s}".format((self.path_to_docs)),
-            "%s"%(html_path)])
+            "{0!s}".format((html_path))])
         assert check == 0
 
     # def test_latex(self):
@@ -29,15 +29,15 @@ class Doc_Test(unittest.TestCase):
     #         "%s"%(latex_path)])
     #     assert check == 0
 
-    # def test_linkcheck(self):
+    def test_linkcheck(self):
-    #     doctrees_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['doctrees'])
+        doctrees_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['doctrees'])
-    #     link_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build'])
+        link_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build'])
 
-    #     check = subprocess.call(["sphinx-build", "-nW", "-b", "linkcheck", "-d",
+        check = subprocess.call(["sphinx-build", "-nW", "-b", "linkcheck", "-d",
-    #         "%s"%(doctrees_path),
+            "%s"%(doctrees_path),
-    #         "%s"%(self.path_to_docs),
+            "%s"%(self.path_to_docs),
-    #         "%s"%(link_path)])
+            "%s"%(link_path)])
-    #     assert check == 0
+        assert check == 0
 
 if __name__ == '__main__':
     unittest.main()

tests/em/fdem/inverse/adjoint/test_FDEM_adjointEB.py

@@ -21,7 +21,7 @@ SrcList = ['RawVec', 'MagDipole'] #or 'MAgDipole_Bfield', 'CircularLoop', 'RawVe
 
 def adjointTest(fdemType, comp):
     prb = getFDEMProblem(fdemType, comp, SrcList, freq)
-    print 'Adjoint %s formulation - %s' % (fdemType, comp)
+    print 'Adjoint {0!s} formulation - {1!s}'.format(fdemType, comp)
 
     m  = np.log(np.ones(prb.mapping.nP)*CONDUCTIVITY)
     mu = np.ones(prb.mesh.nC)*MU

tests/em/fdem/inverse/adjoint/test_FDEM_adjointHJ.py

@@ -21,7 +21,7 @@ SrcList = ['RawVec', 'MagDipole'] #or 'MAgDipole_Bfield', 'CircularLoop', 'RawVe
 
 def adjointTest(fdemType, comp):
     prb = getFDEMProblem(fdemType, comp, SrcList, freq)
-    print 'Adjoint %s formulation - %s' % (fdemType, comp)
+    print 'Adjoint {0!s} formulation - {1!s}'.format(fdemType, comp)
 
     m  = np.log(np.ones(prb.mapping.nP)*CONDUCTIVITY)
     mu = np.ones(prb.mesh.nC)*MU

tests/em/fdem/inverse/derivs/test_FDEM_derivs.py

@@ -26,7 +26,7 @@ SrcType = ['MagDipole', 'RawVec'] #or 'MAgDipole_Bfield', 'CircularLoop', 'RawVe
 def derivTest(fdemType, comp):
 
     prb = getFDEMProblem(fdemType, comp, SrcType, freq)
-    print '%s formulation - %s' % (fdemType, comp)
+    print '{0!s} formulation - {1!s}'.format(fdemType, comp)
     x0 = np.log(np.ones(prb.mapping.nP)*CONDUCTIVITY)
     mu = np.log(np.ones(prb.mesh.nC)*MU)
 

tests/em/tdem/test_TDEM_forward_Analytic.py

@@ -55,7 +55,7 @@ def halfSpaceProblemAnaDiff(meshType, sig_half=1e-2, rxOffset=50., bounds=None,
     if showIt == True:
         plt.loglog(rx.times[bz_calc>0], bz_calc[bz_calc>0], 'r', rx.times[bz_calc<0], -bz_calc[bz_calc<0], 'r--')
         plt.loglog(rx.times, abs(bz_ana), 'b*')
-        plt.title('sig_half = %e'%sig_half)
+        plt.title('sig_half = {0:e}'.format(sig_half))
         plt.show()
 
     return log10diff

tests/examples/test_examples.py

@@ -25,7 +25,7 @@ class compareInitFiles(unittest.TestCase):
 
 def get(test):
     def test_func(self):
-        print '\nTesting %s.run(plotIt=False)\n'%test
+        print '\nTesting {0!s}.run(plotIt=False)\n'.format(test)
         getattr(Examples, test).run(plotIt=False)
         self.assertTrue(True)
     return test_func

tests/flow/test_Richards.py

@@ -121,7 +121,7 @@ class RichardsTests1D(unittest.TestCase):
         tol = TOL*(10**int(np.log10(np.abs(zJv))))
         passed = np.abs(vJz - zJv) < tol
         print 'Richards Adjoint Test - PressureHead'
-        print '%4.4e === %4.4e, diff=%4.4e < %4.e'%(vJz, zJv,np.abs(vJz - zJv),tol)
+        print '{0:4.4e} === {1:4.4e}, diff={2:4.4e} < {3:4e}'.format(vJz, zJv, np.abs(vJz - zJv), tol)
         self.assertTrue(passed,True)
 
     def test_Sensitivity(self):
@@ -193,7 +193,7 @@ class RichardsTests2D(unittest.TestCase):
         tol = TOL*(10**int(np.log10(np.abs(zJv))))
         passed = np.abs(vJz - zJv) < tol
         print '2D: Richards Adjoint Test - PressureHead'
-        print '%4.4e === %4.4e, diff=%4.4e < %4.e'%(vJz, zJv,np.abs(vJz - zJv),tol)
+        print '{0:4.4e} === {1:4.4e}, diff={2:4.4e} < {3:4e}'.format(vJz, zJv, np.abs(vJz - zJv), tol)
         self.assertTrue(passed,True)
 
     def test_Sensitivity(self):
@@ -265,7 +265,7 @@ class RichardsTests3D(unittest.TestCase):
         tol = TOL*(10**int(np.log10(np.abs(zJv))))
         passed = np.abs(vJz - zJv) < tol
         print '3D: Richards Adjoint Test - PressureHead'
-        print '%4.4e === %4.4e, diff=%4.4e < %4.e'%(vJz, zJv,np.abs(vJz - zJv),tol)
+        print '{0:4.4e} === {1:4.4e}, diff={2:4.4e} < {3:4e}'.format(vJz, zJv, np.abs(vJz - zJv), tol)
         self.assertTrue(passed,True)
 
     def test_Sensitivity(self):

tests/mesh/test_CurvilinearMesh.py

@@ -10,7 +10,9 @@ class BasicCurvTests(unittest.TestCase):
         a = np.array([1, 1, 1])
         b = np.array([1, 2])
         c = np.array([1, 4])
-        gridIt = lambda h: [np.cumsum(np.r_[0, x]) for x in h]
+
+        def gridIt(h): return [np.cumsum(np.r_[0, x]) for x in h]
+
         X, Y = ndgrid(gridIt([a, b]), vector=False)
         self.TM2 = TensorMesh([a, b])
         self.Curv2 = CurvilinearMesh([X, Y])
@@ -19,7 +21,10 @@ class BasicCurvTests(unittest.TestCase):
         self.Curv3 = CurvilinearMesh([X, Y, Z])
 
     def test_area_3D(self):
-        test_area = np.array([1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 4, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2])
+        test_area = np.array([1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 4, 8, 8, 8, 8,
+                              1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4,
+                              4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1,
+                              1, 2, 2, 2])
         self.assertTrue(np.all(self.Curv3.area == test_area))
 
     def test_vol_3D(self):
@@ -33,54 +38,85 @@ class BasicCurvTests(unittest.TestCase):
         self.assertTrue(t1)
 
     def test_edge_3D(self):
-        test_edge = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4])
+        test_edge = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+                              1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2,
+                              2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 2,
+                              2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4,
+                              4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4])
         t1 = np.all(self.Curv3.edge == test_edge)
         self.assertTrue(t1)
 
     def test_edge_2D(self):
-        test_edge = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2])
+        test_edge = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2,
+                              2])
         t1 = np.all(self.Curv2.edge == test_edge)
         self.assertTrue(t1)
 
     def test_tangents(self):
         T = self.Curv2.tangents
-        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ex', 'V')[0] == np.ones(self.Curv2.nEx)))
+        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ex', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ex', 'V')[1] == np.zeros(self.Curv2.nEx)))
+                        np.ones(self.Curv2.nEx)))
-        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ey', 'V')[0] == np.zeros(self.Curv2.nEy)))
+        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ex', 'V')[1] ==
-        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ey', 'V')[1] == np.ones(self.Curv2.nEy)))
+                        np.zeros(self.Curv2.nEx)))
+        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ey', 'V')[0] ==
+                        np.zeros(self.Curv2.nEy)))
+        self.assertTrue(np.all(self.Curv2.r(T, 'E', 'Ey', 'V')[1] ==
+                        np.ones(self.Curv2.nEy)))
 
         T = self.Curv3.tangents
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ex', 'V')[0] == np.ones(self.Curv3.nEx)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ex', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ex', 'V')[1] == np.zeros(self.Curv3.nEx)))
+                        np.ones(self.Curv3.nEx)))
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ex', 'V')[2] == np.zeros(self.Curv3.nEx)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ex', 'V')[1] ==
+                        np.zeros(self.Curv3.nEx)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ex', 'V')[2] ==
+                        np.zeros(self.Curv3.nEx)))
 
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ey', 'V')[0] == np.zeros(self.Curv3.nEy)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ey', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ey', 'V')[1] == np.ones(self.Curv3.nEy)))
+                        np.zeros(self.Curv3.nEy)))
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ey', 'V')[2] == np.zeros(self.Curv3.nEy)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ey', 'V')[1] ==
+                        np.ones(self.Curv3.nEy)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ey', 'V')[2] ==
+                        np.zeros(self.Curv3.nEy)))
 
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ez', 'V')[0] == np.zeros(self.Curv3.nEz)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ez', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ez', 'V')[1] == np.zeros(self.Curv3.nEz)))
+                        np.zeros(self.Curv3.nEz)))
-        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ez', 'V')[2] == np.ones(self.Curv3.nEz)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ez', 'V')[1] ==
+                        np.zeros(self.Curv3.nEz)))
+        self.assertTrue(np.all(self.Curv3.r(T, 'E', 'Ez', 'V')[2] ==
+                        np.ones(self.Curv3.nEz)))
 
     def test_normals(self):
         N = self.Curv2.normals
-        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fx', 'V')[0] == np.ones(self.Curv2.nFx)))
+        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fx', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fx', 'V')[1] == np.zeros(self.Curv2.nFx)))
+                        np.ones(self.Curv2.nFx)))
-        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fy', 'V')[0] == np.zeros(self.Curv2.nFy)))
+        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fx', 'V')[1] ==
-        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fy', 'V')[1] == np.ones(self.Curv2.nFy)))
+                        np.zeros(self.Curv2.nFx)))
+        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fy', 'V')[0] ==
+                        np.zeros(self.Curv2.nFy)))
+        self.assertTrue(np.all(self.Curv2.r(N, 'F', 'Fy', 'V')[1] ==
+                        np.ones(self.Curv2.nFy)))
 
         N = self.Curv3.normals
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fx', 'V')[0] == np.ones(self.Curv3.nFx)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fx', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fx', 'V')[1] == np.zeros(self.Curv3.nFx)))
+                        np.ones(self.Curv3.nFx)))
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fx', 'V')[2] == np.zeros(self.Curv3.nFx)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fx', 'V')[1] ==
+                        np.zeros(self.Curv3.nFx)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fx', 'V')[2] ==
+                        np.zeros(self.Curv3.nFx)))
 
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fy', 'V')[0] == np.zeros(self.Curv3.nFy)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fy', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fy', 'V')[1] == np.ones(self.Curv3.nFy)))
+                        np.zeros(self.Curv3.nFy)))
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fy', 'V')[2] == np.zeros(self.Curv3.nFy)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fy', 'V')[1] ==
+                        np.ones(self.Curv3.nFy)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fy', 'V')[2] ==
+                        np.zeros(self.Curv3.nFy)))
 
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fz', 'V')[0] == np.zeros(self.Curv3.nFz)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fz', 'V')[0] ==
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fz', 'V')[1] == np.zeros(self.Curv3.nFz)))
+                        np.zeros(self.Curv3.nFz)))
-        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fz', 'V')[2] == np.ones(self.Curv3.nFz)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fz', 'V')[1] ==
+                        np.zeros(self.Curv3.nFz)))
+        self.assertTrue(np.all(self.Curv3.r(N, 'F', 'Fz', 'V')[2] ==
+                        np.ones(self.Curv3.nFz)))
 
     def test_grid(self):
         self.assertTrue(np.all(self.Curv2.gridCC == self.TM2.gridCC))

tests/mesh/test_Mixed_boundaryPoisson.py

@@ -2,12 +2,12 @@ import numpy as np
 import scipy.sparse as sp
 import unittest
 import matplotlib.pyplot as plt
-from SimPEG import *
+from SimPEG import Mesh, Tests, Utils, Solver
 
 MESHTYPES = ['uniformTensorMesh']
 
+
 def getxBCyBC_CC(mesh, alpha, beta, gamma):
-# def getxBCyBC(mesh, alpha, beta, gamma):
     """
     This is a subfunction generating mixed-boundary condition:
 
@@ -17,13 +17,15 @@ def getxBCyBC_CC(mesh, alpha, beta, gamma):
 
         \rho \vec{j} = -\nabla \phi \phi
 
-        \alpha \phi + \beta \frac{\partial \phi}{\partial r} = \gamma \ at \ r = \partial \Omega
+        \alpha \phi + \beta \frac{\partial \phi}{\partial r} = \gamma \ at \ r
+        = \partial \Omega
 
         xBC = f_1(\alpha, \beta, \gamma)
         yBC = f(\alpha, \beta, \gamma)
 
     Computes xBC and yBC for cell-centered discretizations
     """
+
     if mesh.dim == 1:  # 1D
         if (len(alpha) != 2 or len(beta) != 2 or len(gamma) != 2):
             raise Exception("Lenght of list, alpha should be 2")
@@ -65,8 +67,10 @@ def getxBCyBC_CC(mesh, alpha, beta, gamma):
         # h_xm, h_xp = mesh.gridCC[fCCxm,0], mesh.gridCC[fCCxp,0]
         # h_ym, h_yp = mesh.gridCC[fCCym,1], mesh.gridCC[fCCyp,1]
 
-        h_xm, h_xp = mesh.hx[0]*np.ones_like(alpha_xm), mesh.hx[-1]*np.ones_like(alpha_xp)
+        h_xm = mesh.hx[0]*np.ones_like(alpha_xm)
-        h_ym, h_yp = mesh.hy[0]*np.ones_like(alpha_ym), mesh.hy[-1]*np.ones_like(alpha_yp)
+        h_xp = mesh.hx[-1]*np.ones_like(alpha_xp)
+        h_ym = mesh.hy[0]*np.ones_like(alpha_ym)
+        h_yp = mesh.hy[-1]*np.ones_like(alpha_yp)
 
         a_xm = gamma_xm/(0.5*alpha_xm-beta_xm/h_xm)
         b_xm = (0.5*alpha_xm+beta_xm/h_xm)/(0.5*alpha_xm-beta_xm/h_xm)
@@ -87,8 +91,10 @@ def getxBCyBC_CC(mesh, alpha, beta, gamma):
         yBC_ym = 0.5*(1.-b_ym)
         yBC_yp = 0.5*(1.-1./b_yp)
 
-        sortindsfx = np.argsort(np.r_[np.arange(mesh.nFx)[fxm], np.arange(mesh.nFx)[fxp]])
+        sortindsfx = np.argsort(np.r_[np.arange(mesh.nFx)[fxm],
-        sortindsfy = np.argsort(np.r_[np.arange(mesh.nFy)[fym], np.arange(mesh.nFy)[fyp]])
+                                np.arange(mesh.nFx)[fxp]])
+        sortindsfy = np.argsort(np.r_[np.arange(mesh.nFy)[fym],
+                                np.arange(mesh.nFy)[fyp]])
 
         xBC_x = np.r_[xBC_xm, xBC_xp][sortindsfx]
         xBC_y = np.r_[xBC_ym, xBC_yp][sortindsfy]
@@ -116,9 +122,12 @@ def getxBCyBC_CC(mesh, alpha, beta, gamma):
         # h_ym, h_yp = mesh.gridCC[fCCym,1], mesh.gridCC[fCCyp,1]
         # h_zm, h_zp = mesh.gridCC[fCCzm,2], mesh.gridCC[fCCzp,2]
 
-        h_xm, h_xp = mesh.hx[0]*np.ones_like(alpha_xm), mesh.hx[-1]*np.ones_like(alpha_xp)
+        h_xm = mesh.hx[0]*np.ones_like(alpha_xm)
-        h_ym, h_yp = mesh.hy[0]*np.ones_like(alpha_ym), mesh.hy[-1]*np.ones_like(alpha_yp)
+        h_xp = mesh.hx[-1]*np.ones_like(alpha_xp)
-        h_zm, h_zp = mesh.hz[0]*np.ones_like(alpha_zm), mesh.hz[-1]*np.ones_like(alpha_zp)
+        h_ym = mesh.hy[0]*np.ones_like(alpha_ym)
+        h_yp = mesh.hy[-1]*np.ones_like(alpha_yp)
+        h_zm = mesh.hz[0]*np.ones_like(alpha_zm)
+        h_zp = mesh.hz[-1]*np.ones_like(alpha_zp)
 
         a_xm = gamma_xm/(0.5*alpha_xm-beta_xm/h_xm)
         b_xm = (0.5*alpha_xm+beta_xm/h_xm)/(0.5*alpha_xm-beta_xm/h_xm)
@@ -148,9 +157,12 @@ def getxBCyBC_CC(mesh, alpha, beta, gamma):
         yBC_zm = 0.5*(1.-b_zm)
         yBC_zp = 0.5*(1.-1./b_zp)
 
-        sortindsfx = np.argsort(np.r_[np.arange(mesh.nFx)[fxm], np.arange(mesh.nFx)[fxp]])
+        sortindsfx = np.argsort(np.r_[np.arange(mesh.nFx)[fxm],
-        sortindsfy = np.argsort(np.r_[np.arange(mesh.nFy)[fym], np.arange(mesh.nFy)[fyp]])
+                                np.arange(mesh.nFx)[fxp]])
-        sortindsfz = np.argsort(np.r_[np.arange(mesh.nFz)[fzm], np.arange(mesh.nFz)[fzp]])
+        sortindsfy = np.argsort(np.r_[np.arange(mesh.nFy)[fym],
+                                np.arange(mesh.nFy)[fyp]])
+        sortindsfz = np.argsort(np.r_[np.arange(mesh.nFz)[fzm],
+                                np.arange(mesh.nFz)[fzp]])
 
         xBC_x = np.r_[xBC_xm, xBC_xp][sortindsfx]
         xBC_y = np.r_[xBC_ym, xBC_yp][sortindsfy]
@@ -165,6 +177,7 @@ def getxBCyBC_CC(mesh, alpha, beta, gamma):
 
     return xBC, yBC
 
+
 class Test1D_InhomogeneousMixed(Tests.OrderTest):
     name = "1D - Mixed"
     meshTypes = MESHTYPES
@@ -174,10 +187,13 @@ class Test1D_InhomogeneousMixed(Tests.OrderTest):
 
     def getError(self):
         # Test function
-        phi_fun = lambda x: np.cos(np.pi*x)
+        def phi_fun(x): return np.cos(np.pi*x)
-        j_fun = lambda x: np.pi*np.sin(np.pi*x)
+
-        phi_deriv = lambda x: -j_fun(x)
+        def j_fun(x): return np.pi*np.sin(np.pi*x)
-        q_fun = lambda x: (np.pi**2)*np.cos(np.pi*x)
+
+        def phi_deriv(x): return -j_fun(x)
+
+        def q_fun(x): return (np.pi**2)*np.cos(np.pi*x)
 
         xc_ana = phi_fun(self.M.gridCC)
         q_ana = q_fun(self.M.gridCC)
@@ -199,7 +215,6 @@ class Test1D_InhomogeneousMixed(Tests.OrderTest):
         gamma = alpha*phi_bc + beta*phi_deriv_bc
         x_BC, y_BC = getxBCyBC_CC(self.M, alpha, beta, gamma)
 
-
         sigma = np.ones(self.M.nC)
         Mfrho = self.M.getFaceInnerProduct(1./sigma)
         MfrhoI = self.M.getFaceInnerProduct(1./sigma, invMat=True)
@@ -222,13 +237,13 @@ class Test1D_InhomogeneousMixed(Tests.OrderTest):
             NotImplementedError
         return err
 
-
     def test_order(self):
         print "==== Testing Mixed boudary conduction for CC-problem ===="
         self.name = "1D"
         self.myTest = 'xc'
         self.orderTest()
 
+
 class Test2D_InhomogeneousMixed(Tests.OrderTest):
     name = "2D - Mixed"
     meshTypes = MESHTYPES
@@ -238,12 +253,23 @@ class Test2D_InhomogeneousMixed(Tests.OrderTest):
 
     def getError(self):
         # Test function
-        phi_fun = lambda x: np.cos(np.pi*x[:,0])*np.cos(np.pi*x[:,1])
+        def phi_fun(x):
-        j_funX = lambda x: +np.pi*np.sin(np.pi*x[:,0])*np.cos(np.pi*x[:,1])
+            return np.cos(np.pi*x[:, 0])*np.cos(np.pi*x[:, 1])
-        j_funY = lambda x: +np.pi*np.cos(np.pi*x[:,0])*np.sin(np.pi*x[:,1])
+
-        phideriv_funX = lambda x: -j_funX(x)
+        def j_funX(x):
-        phideriv_funY = lambda x: -j_funY(x)
+            return +np.pi*np.sin(np.pi*x[:, 0])*np.cos(np.pi*x[:, 1])
-        q_fun = lambda x: +2*(np.pi**2)*phi_fun(x)
+
+        def j_funY(x):
+            return +np.pi*np.cos(np.pi*x[:, 0])*np.sin(np.pi*x[:, 1])
+
+        def phideriv_funX(x):
+            return -j_funX(x)
+
+        def phideriv_funY(x):
+            return -j_funY(x)
+
+        def q_fun(x):
+            return +2*(np.pi**2)*phi_fun(x)
 
         xc_ana = phi_fun(self.M.gridCC)
         q_ana = q_fun(self.M.gridCC)
@@ -259,18 +285,26 @@ class Test2D_InhomogeneousMixed(Tests.OrderTest):
         gBFyp = self.M.gridFy[fyp, :]
 
         # Setup Mixed B.C (alpha, beta, gamma)
-        alpha_xm, alpha_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
+        alpha_xm = np.ones_like(gBFxm[:, 0])
-        beta_xm, beta_xp =  np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
+        alpha_xp = np.ones_like(gBFxp[:, 0])
-        alpha_ym, alpha_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
+        beta_xm = np.ones_like(gBFxm[:, 0])
-        beta_ym, beta_yp =  np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
+        beta_xp = np.ones_like(gBFxp[:, 0])
+        alpha_ym = np.ones_like(gBFym[:, 1])
+        alpha_yp = np.ones_like(gBFyp[:, 1])
+        beta_ym = np.ones_like(gBFym[:, 1])
+        beta_yp = np.ones_like(gBFyp[:, 1])
 
         phi_bc_xm, phi_bc_xp = phi_fun(gBFxm), phi_fun(gBFxp)
         phi_bc_ym, phi_bc_yp = phi_fun(gBFym), phi_fun(gBFyp)
 
-        phiderivX_bc_xm, phiderivX_bc_xp = phideriv_funX(gBFxm), phideriv_funX(gBFxp)
+        phiderivX_bc_xm = phideriv_funX(gBFxm)
-        phiderivY_bc_ym, phiderivY_bc_yp = phideriv_funY(gBFym), phideriv_funY(gBFyp)
+        phiderivX_bc_xp = phideriv_funX(gBFxp)
+        phiderivY_bc_ym = phideriv_funY(gBFym)
+        phiderivY_bc_yp = phideriv_funY(gBFyp)
+
+        def gamma_fun(alpha, beta, phi, phi_deriv):
+            return alpha*phi + beta*phi_deriv
 
-        gamma_fun = lambda alpha, beta, phi, phi_deriv: alpha*phi + beta*phi_deriv
         gamma_xm = gamma_fun(alpha_xm, beta_xm, phi_bc_xm, phiderivX_bc_xm)
         gamma_xp = gamma_fun(alpha_xp, beta_xp, phi_bc_xp, phiderivX_bc_xp)
         gamma_ym = gamma_fun(alpha_ym, beta_ym, phi_bc_ym, phiderivY_bc_ym)
@@ -282,7 +316,6 @@ class Test2D_InhomogeneousMixed(Tests.OrderTest):
 
         x_BC, y_BC = getxBCyBC_CC(self.M, alpha, beta, gamma)
 
-
         sigma = np.ones(self.M.nC)
         Mfrho = self.M.getFaceInnerProduct(1./sigma)
         MfrhoI = self.M.getFaceInnerProduct(1./sigma, invMat=True)
@@ -303,13 +336,13 @@ class Test2D_InhomogeneousMixed(Tests.OrderTest):
             NotImplementedError
         return err
 
-
     def test_order(self):
         print "==== Testing Mixed boudary conduction for CC-problem ===="
         self.name = "2D"
         self.myTest = 'xc'
         self.orderTest()
 
+
 class Test3D_InhomogeneousMixed(Tests.OrderTest):
     name = "3D - Mixed"
     meshTypes = MESHTYPES
@@ -319,16 +352,29 @@ class Test3D_InhomogeneousMixed(Tests.OrderTest):
 
     def getError(self):
         # Test function
-        phi_fun = lambda x: np.cos(np.pi*x[:,0])*np.cos(np.pi*x[:,1])*np.cos(np.pi*x[:,2])
+        def phi_fun(x):
-        j_funX = lambda x: +np.pi*np.sin(np.pi*x[:,0])*np.cos(np.pi*x[:,1])*np.cos(np.pi*x[:,2])
+            return (np.cos(np.pi*x[:, 0])*np.cos(np.pi*x[:, 1]) *
-        j_funY = lambda x: +np.pi*np.cos(np.pi*x[:,0])*np.sin(np.pi*x[:,1])*np.cos(np.pi*x[:,2])
+                    np.cos(np.pi*x[:, 2]))
-        j_funZ = lambda x: +np.pi*np.cos(np.pi*x[:,0])*np.cos(np.pi*x[:,1])*np.sin(np.pi*x[:,2])
 
-        phideriv_funX = lambda x: -j_funX(x)
+        def j_funX(x):
-        phideriv_funY = lambda x: -j_funY(x)
+            return (np.pi*np.sin(np.pi*x[:, 0])*np.cos(np.pi*x[:, 1]) *
-        phideriv_funZ = lambda x: -j_funZ(x)
+                    np.cos(np.pi*x[:, 2]))
 
-        q_fun = lambda x: 3*(np.pi**2)*phi_fun(x)
+        def j_funY(x):
+            return (np.pi*np.cos(np.pi*x[:, 0])*np.sin(np.pi*x[:, 1]) *
+                    np.cos(np.pi*x[:, 2]))
+
+        def j_funZ(x):
+            return (np.pi*np.cos(np.pi*x[:, 0])*np.cos(np.pi*x[:, 1]) *
+                    np.sin(np.pi*x[:, 2]))
+
+        def phideriv_funX(x): return -j_funX(x)
+
+        def phideriv_funY(x): return -j_funY(x)
+
+        def phideriv_funZ(x): return -j_funZ(x)
+
+        def q_fun(x): return 3*(np.pi**2)*phi_fun(x)
 
         xc_ana = phi_fun(self.M.gridCC)
         q_ana = q_fun(self.M.gridCC)
@@ -346,23 +392,33 @@ class Test3D_InhomogeneousMixed(Tests.OrderTest):
         gBFzp = self.M.gridFz[fzp, :]
 
         # Setup Mixed B.C (alpha, beta, gamma)
-        alpha_xm, alpha_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
+        alpha_xm = np.ones_like(gBFxm[:, 0])
-        beta_xm, beta_xp =  np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
+        alpha_xp = np.ones_like(gBFxp[:, 0])
-        alpha_ym, alpha_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
+        beta_xm = np.ones_like(gBFxm[:, 0])
-        beta_ym, beta_yp =  np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
+        beta_xp = np.ones_like(gBFxp[:, 0])
-        alpha_zm, alpha_zp = np.ones_like(gBFzm[:,2]), np.ones_like(gBFzp[:,2])
+        alpha_ym = np.ones_like(gBFym[:, 1])
-        beta_zm, beta_zp =  np.ones_like(gBFzm[:,2]), np.ones_like(gBFzp[:,2])
+        alpha_yp = np.ones_like(gBFyp[:, 1])
-
+        beta_ym = np.ones_like(gBFym[:, 1])
+        beta_yp = np.ones_like(gBFyp[:, 1])
+        alpha_zm = np.ones_like(gBFzm[:, 2])
+        alpha_zp = np.ones_like(gBFzp[:, 2])
+        beta_zm = np.ones_like(gBFzm[:, 2])
+        beta_zp = np.ones_like(gBFzp[:, 2])
 
         phi_bc_xm, phi_bc_xp = phi_fun(gBFxm), phi_fun(gBFxp)
         phi_bc_ym, phi_bc_yp = phi_fun(gBFym), phi_fun(gBFyp)
         phi_bc_zm, phi_bc_zp = phi_fun(gBFzm), phi_fun(gBFzp)
 
-        phiderivX_bc_xm, phiderivX_bc_xp = phideriv_funX(gBFxm), phideriv_funX(gBFxp)
+        phiderivX_bc_xm = phideriv_funX(gBFxm)
-        phiderivY_bc_ym, phiderivY_bc_yp = phideriv_funY(gBFym), phideriv_funY(gBFyp)
+        phiderivX_bc_xp = phideriv_funX(gBFxp)
-        phiderivY_bc_zm, phiderivY_bc_zp = phideriv_funZ(gBFzm), phideriv_funZ(gBFzp)
+        phiderivY_bc_ym = phideriv_funY(gBFym)
+        phiderivY_bc_yp = phideriv_funY(gBFyp)
+        phiderivY_bc_zm = phideriv_funZ(gBFzm)
+        phiderivY_bc_zp = phideriv_funZ(gBFzp)
+
+        def gamma_fun(alpha, beta, phi, phi_deriv):
+            return alpha*phi + beta*phi_deriv
 
-        gamma_fun = lambda alpha, beta, phi, phi_deriv: alpha*phi + beta*phi_deriv
         gamma_xm = gamma_fun(alpha_xm, beta_xm, phi_bc_xm, phiderivX_bc_xm)
         gamma_xp = gamma_fun(alpha_xp, beta_xp, phi_bc_xp, phiderivX_bc_xp)
         gamma_ym = gamma_fun(alpha_ym, beta_ym, phi_bc_ym, phiderivY_bc_ym)
@@ -376,7 +432,6 @@ class Test3D_InhomogeneousMixed(Tests.OrderTest):
 
         x_BC, y_BC = getxBCyBC_CC(self.M, alpha, beta, gamma)
 
-
         sigma = np.ones(self.M.nC)
         Mfrho = self.M.getFaceInnerProduct(1./sigma)
         MfrhoI = self.M.getFaceInnerProduct(1./sigma, invMat=True)
@@ -398,14 +453,11 @@ class Test3D_InhomogeneousMixed(Tests.OrderTest):
             NotImplementedError
         return err
 
-
     def test_order(self):
         print "==== Testing Mixed boudary conduction for CC-problem ===="
         self.name = "3D"
         self.myTest = 'xc'
         self.orderTest()
 
-
-
 if __name__ == '__main__':
     unittest.main()

tests/mesh/test_interpolation.py

@@ -2,8 +2,6 @@ import numpy as np
 import unittest
 from SimPEG.Utils import mkvc
 from SimPEG import Mesh, Tests
-import unittest
-
 
 MESHTYPES = ['uniformTensorMesh', 'randomTensorMesh']
 TOLERANCES = [0.9, 0.5, 0.5]

tests/utils/test_Zero.py

@@ -52,7 +52,7 @@ class Tests(unittest.TestCase):
         assert o <= -1
         assert not (o > -1)
         assert o >= -1
-        assert -(-o)*o == -o
+        assert -1.*(-o)*o == -o
         o = Identity()
         assert +o == o
         assert -o == -o