silence warnings

docs/example2.py

@@ -130,7 +130,7 @@
 
     solver(b, u)
 
-    u_global = dmConst.augmentWithBoundaryData(u, g_interp)
+    u_global = u.augmentWithBoundaryData(g_interp)
 
     plt.figure().gca().set_title('Numerical solution, constant kernel')
     u_global.plot()

drivers/runNonlocal.py

@@ -7,7 +7,6 @@
 ###################################################################################
 
 from mpi4py import MPI
-import numpy as np
 from PyNucleus import driver, DIRICHLET, NEUMANN
 from PyNucleus.nl import (nonlocalPoissonProblem,
                           discretizedNonlocalProblem)

fem/PyNucleus_fem/factories.py

@@ -9,9 +9,7 @@
 from PyNucleus_base.factory import factory
 from . functions import (simpleAnisotropy, simpleAnisotropy2, inclusions, inclusionsHong,
                          motorPermeability)
-from . functions import (function,
-                         vectorFunction,
-                         _rhsFunSin1D, _solSin1D, _rhsFunSin2D, _cos1D, _cos2D, _rhsCos2D, _grad_cos2d_n,
+from . functions import (_rhsFunSin1D, _solSin1D, _rhsFunSin2D, _cos1D, _cos2D, _rhsCos2D, _grad_cos2d_n,
                          _rhsFunSin3D, _solSin2D, _solSin3D, Lambda, constant,
                          monomial,
                          complexLambda,

fem/PyNucleus_fem/mesh.py

@@ -17,7 +17,6 @@
 from . meshCy import (meshBase,
                       boundaryVertices,
                       boundaryEdges,
-                      boundaryFaces,
                       boundaryFacesWithOrientation,
                       boundaryVerticesFromBoundaryEdges,
                       boundaryEdgesFromBoundaryFaces,

multilevelSolver/PyNucleus_multilevelSolver/__init__.py

@@ -16,4 +16,3 @@
 
 solverFactory.register('mg', multigrid, isMultilevelSolver=True)
 solverFactory.register('complex_mg', Complexmultigrid, isMultilevelSolver=True)
-

multilevelSolver/PyNucleus_multilevelSolver/connectors.py

@@ -11,7 +11,6 @@
 from mpi4py import MPI
 import logging
 import numpy as np
-from copy import deepcopy
 from PyNucleus_base.myTypes import REAL, INDEX, TAG
 from PyNucleus_base import uninitialized
 from . levels import meshLevel, algebraicLevel

multilevelSolver/PyNucleus_multilevelSolver/geometricMG.py

@@ -8,7 +8,6 @@
 from __future__ import division
 import logging
 import numpy as np
-from PyNucleus_base.ip_norm import norm_serial as norm
 from PyNucleus_base.utilsFem import getLoggingTimer
 from PyNucleus_base import REAL, INDEX, uninitialized
 from PyNucleus_fem import P1_DoFMap

nl/PyNucleus_nl/discretizedProblems.py

@@ -22,7 +22,6 @@
 from PyNucleus_multilevelSolver import hierarchyManager
 from copy import copy
 from . helpers import paramsForFractionalHierarchy
-from . fractionalOrders import singleVariableUnsymmetricFractionalOrder
 from . kernelsCy import FRACTIONAL
 from . nonlocalProblems import (DIRICHLET,
                                 NEUMANN, HOMOGENEOUS_NEUMANN,

nl/PyNucleus_nl/nonlocalLaplacianBase.pyx

@@ -11,6 +11,7 @@ from libc.math cimport (sin, cos, sinh, cosh, tanh, sqrt, atan2,
                         log, ceil,
                         fabs as abs, M_PI as pi, pow,
                         tgamma as gamma)
+from scipy.special import factorial
 from PyNucleus_base.myTypes import INDEX, REAL, COMPLEX, ENCODE, BOOL
 from PyNucleus_base import uninitialized
 from PyNucleus_base.blas cimport mydot
@@ -58,7 +59,7 @@ cdef class PermutationIndexer:
 
         self.factorials = np.zeros((N), dtype=INDEX)
         for i in range(N):
-            self.factorials[i] = np.math.factorial(N-1-i)
+            self.factorials[i] = factorial(N-1-i, True)
         self.lehmer = np.zeros(N, dtype=INDEX)
 
     cdef INDEX_t rank(self, INDEX_t[::1] perm):

nl/PyNucleus_nl/nonlocalLaplacianBase_{SCALAR}.pxi

@@ -72,8 +72,8 @@ cdef class {SCALAR_label}double_local_matrix_t:
             REAL_t eps = 1e-10
             INDEX_t dim = self.DoFMap.mesh.manifold_dim
 
-        perms = uninitialized((np.math.factorial(dim+1), dim+1), dtype=INDEX)
-        surface_perms = uninitialized((np.math.factorial(dim), dim), dtype=INDEX)
+        perms = uninitialized((factorial(dim+1, True), dim+1), dtype=INDEX)
+        surface_perms = uninitialized((factorial(dim, True), dim), dtype=INDEX)
 
         from itertools import permutations
 

tests/test_kernels.py

@@ -142,6 +142,7 @@ def idfuncFractional(param):
 mesh1d = meshFactory('interval', a=-1, b=1, hTarget=1e-2)
 dm1d = dofmapFactory('P1', mesh1d, -1)
 
+
 @pytest.fixture(scope='module', params=[
     # 1d kernels
     (1, fractionalOrderFactory('const', 0.25), np.inf, True, None, 0),