Merge with James's changes

GPy/kern/parts/sympykern.py

@@ -11,6 +11,7 @@ import tempfile
 import pdb
 import ast
 from kernpart import Kernpart
+from ...util.config import config
 
 class spkern(Kernpart):
     """
@@ -110,8 +111,9 @@ class spkern(Kernpart):
             'headers':['"sympy_helpers.h"'],
             'sources':[os.path.join(current_dir,"parts/sympy_helpers.cpp")],
             'extra_compile_args':extra_compile_args,
-            'extra_link_args':['-lgomp'],
+            'extra_link_args':[],
             'verbose':True}
+        if config.getboolean('parallel', 'openmp'): self.weave_kwargs.append('-lgomp')
 
     def __add__(self,other):
         return spkern(self._sp_k+other._sp_k)
@@ -343,7 +345,7 @@ class spkern(Kernpart):
 
         # Code to use when only X is provided. 
         self._dK_dtheta_code_X = self._dK_dtheta_code.replace('Z[', 'X[')
-        self._dK_dX_code_X = self._dK_dX_code.replace('Z[', 'X[').replace('+= partial[', '+= 2*partial[')
+        self._dK_dX_code_X = self._dK_dX_code.replace('Z[', 'X[').replace('+= partial[', '+= 2*partial[') 
         self._dK_dtheta_code_X = self._dK_dtheta_code.replace('Z2(', 'X2(')
         self._dK_dX_code_X = self._dK_dX_code_X.replace('Z2(', 'X2(')
 

GPy/testing/kernel_tests.py

@@ -35,7 +35,7 @@ class KernelTests(unittest.TestCase):
 
     def test_eq_sympykernel(self):
         if SYMPY_AVAILABLE:
-            kern = GPy.kern.eq_sympy(5, 3, output_ind=4)
+            kern = GPy.kern.eq_sympy(5, 3)
             self.assertTrue(GPy.kern.kern_test(kern, verbose=verbose))
 
     def test_rbf_invkernel(self):

GPy/util/symbolic.py

@@ -237,52 +237,3 @@ class erfcx(Function):
     def eval(cls, arg):
         return erfc(arg)*exp(arg*arg)
 
-class sinc_grad(Function):
-    nargs = 1
-    
-    def fdiff(self, argindex=1):
-        if argindex==1:
-            # Strictly speaking this should be computed separately, as it won't work when x=0. See http://calculus.subwiki.org/wiki/Sinc_function
-            return ((2-x*x)*sin(self.args[0]) - 2*x*cos(x))/(x*x*x)
-        else:
-            raise ArgumentIndexError(self, argindex)
-
-    
-    @classmethod
-    def eval(cls, x):
-        if x.is_Number:
-            if x is S.NaN:
-                return S.NaN
-            elif x is S.Zero:
-                return S.Zero
-            else:
-                return (x*cos(x) - sin(x))/(x*x)
-            
-class sinc(Function):
-    
-    nargs = 1
-    
-    def fdiff(self, argindex=1):
-        if argindex==1:
-            return sinc_grad(self.args[0])
-        else:
-            raise ArgumentIndexError(self, argindex)
-
-    
-    @classmethod
-    def eval(cls, arg):
-        if arg.is_Number:
-            if arg is S.NaN:
-                return S.NaN
-            elif arg is S.Zero:
-                return S.One
-            else:
-                return sin(arg)/arg
-
-        if arg.func is asin:
-            x = arg.args[0]
-            return x / arg
-
-    def _eval_is_real(self):
-        return self.args[0].is_real
-