diff --git a/GPy/kern/src/coregionalize.py b/GPy/kern/src/coregionalize.py
index 197d7ece..704d0370 100644
--- a/GPy/kern/src/coregionalize.py
+++ b/GPy/kern/src/coregionalize.py
@@ -6,11 +6,14 @@ import numpy as np
 from ...core.parameterization import Param
 from paramz.transformations import Logexp
 from ...util.config import config # for assesing whether to use cython
+
 try:
     from . import coregionalize_cython
-    config.set('cython', 'working', 'True')
+    cython_coregionalize_working = True
 except ImportError:
-    config.set('cython', 'working', 'False')
+    print('warning in coregionalize: failed to import cython module: falling back to numpy')
+    cython_coregionalize_working = False
+
 
 class Coregionalize(Kern):
     """
@@ -61,7 +64,7 @@ class Coregionalize(Kern):
         self.B = np.dot(self.W, self.W.T) + np.diag(self.kappa)
 
     def K(self, X, X2=None):
-        if config.getboolean('cython', 'working'):
+        if cython_coregionalize_working and config.getboolean('cython', 'working'):
             return self._K_cython(X, X2)
         else:
             return self._K_numpy(X, X2)
@@ -92,7 +95,7 @@ class Coregionalize(Kern):
             index2 = np.asarray(X2, dtype=np.int)
 
         #attempt to use cython for a nasty double indexing loop: fall back to numpy
-        if config.getboolean('cython', 'working'):
+        if cython_coregionalize_working and config.getboolean('cython', 'working'):
             dL_dK_small = self._gradient_reduce_cython(dL_dK, index, index2)
         else:
             dL_dK_small = self._gradient_reduce_numpy(dL_dK, index, index2)
diff --git a/GPy/kern/src/stationary.py b/GPy/kern/src/stationary.py
index 4e8ddb77..81681d60 100644
--- a/GPy/kern/src/stationary.py
+++ b/GPy/kern/src/stationary.py
@@ -14,9 +14,10 @@ from paramz.transformations import Logexp
 
 try:
     from . import stationary_cython
+    cython_stationary_working = True
 except ImportError:
     print('warning in stationary: failed to import cython module: falling back to numpy')
-    config.set('cython', 'working', 'false')
+    cython_stationary_working = False
 
 
 class Stationary(Kern):
@@ -196,7 +197,7 @@ class Stationary(Kern):
 
             tmp = dL_dr*self._inv_dist(X, X2)
             if X2 is None: X2 = X
-            if config.getboolean('cython', 'working'):
+            if cython_stationary_working and config.getboolean('cython', 'working'):
                 self.lengthscale.gradient = self._lengthscale_grads_cython(tmp, X, X2)
             else:
                 self.lengthscale.gradient = self._lengthscale_grads_pure(tmp, X, X2)
@@ -239,7 +240,7 @@ class Stationary(Kern):
         """
         Given the derivative of the objective wrt K (dL_dK), compute the derivative wrt X
         """
-        if config.getboolean('cython', 'working'):
+        if cython_stationary_working and config.getboolean('cython', 'working'):
             return self._gradients_X_cython(dL_dK, X, X2)
         else:
             return self._gradients_X_pure(dL_dK, X, X2)
diff --git a/GPy/testing/cython_tests.py b/GPy/testing/cython_tests.py
index c4bca5cd..c777aae0 100644
--- a/GPy/testing/cython_tests.py
+++ b/GPy/testing/cython_tests.py
@@ -2,21 +2,25 @@ import numpy as np
 import scipy as sp
 from GPy.util import choleskies
 import GPy
-from ..util.config import config
 import unittest
 
 try:
-    from ..util import linalg_cython
     from ..util import choleskies_cython
-    config.set('cython', 'working', 'True')
+    choleskies_cython_working = True
 except ImportError:
-    config.set('cython', 'working', 'False')
+    choleskies_cython_working = False
+
+try:
+    from ..kern.src import stationary_cython
+    stationary_cython_working = True
+except ImportError:
+    stationary_cython_working = False
 
 """
 These tests make sure that the pure python and cython codes work the same
 """
 
-@unittest.skipIf(not config.getboolean('cython', 'working'),"Cython modules have not been built on this machine")
+@unittest.skipIf(not choleskies_cython_working,"Cython cholesky module has not been built on this machine")
 class CythonTestChols(np.testing.TestCase):
     def setUp(self):
         self.flat = np.random.randn(45,5)
@@ -30,7 +34,7 @@ class CythonTestChols(np.testing.TestCase):
         A2 = choleskies._triang_to_flat_cython(self.triang)
         np.testing.assert_allclose(A1, A2)
 
-@unittest.skipIf(not config.getboolean('cython', 'working'),"Cython modules have not been built on this machine")
+@unittest.skipIf(not stationary_cython_working,"Cython stationary module has not been built on this machine")
 class test_stationary(np.testing.TestCase):
     def setUp(self):
         self.k = GPy.kern.RBF(10)
@@ -60,7 +64,7 @@ class test_stationary(np.testing.TestCase):
         g2 = self.k._lengthscale_grads_cython(self.dKxz, self.X, self.Z)
         np.testing.assert_allclose(g1, g2)
 
-@unittest.skipIf(not config.getboolean('cython', 'working'),"Cython modules have not been built on this machine")
+@unittest.skipIf(not choleskies_cython_working,"Cython cholesky module has not been built on this machine")
 class test_choleskies_backprop(np.testing.TestCase):
     def setUp(self):
         a =np.random.randn(10,12)
diff --git a/GPy/testing/kernel_tests.py b/GPy/testing/kernel_tests.py
index 053fce35..e5bc5683 100644
--- a/GPy/testing/kernel_tests.py
+++ b/GPy/testing/kernel_tests.py
@@ -14,10 +14,10 @@ from ..util.config import config
 verbose = 0
 
 try:
-    from ..util import linalg_cython
-    config.set('cython', 'working', 'True')
+    from ..util import choleskies_cython
+    cython_choleskies_working = True
 except ImportError:
-    config.set('cython', 'working', 'False')
+    cython_choleskies_working = False
 
 
 class Kern_check_model(GPy.core.Model):
@@ -618,7 +618,7 @@ class KernelTestsNonContinuous(unittest.TestCase):
         kern = GPy.kern.Coregionalize(1, output_dim=3, active_dims=[-1])
         self.assertTrue(check_kernel_gradient_functions(kern, X=self.X, X2=self.X2, verbose=verbose, fixed_X_dims=-1))
 
-@unittest.skipIf(not config.getboolean('cython', 'working'),"Cython modules have not been built on this machine")
+@unittest.skipIf(not cython_choleskies_working,"Cython choleskies module has not been built on this machine")
 class Coregionalize_cython_test(unittest.TestCase):
     """
     Make sure that the coregionalize kernel work with and without cython enabled
diff --git a/GPy/util/choleskies.py b/GPy/util/choleskies.py
index 2676b6e6..54a7ea74 100644
--- a/GPy/util/choleskies.py
+++ b/GPy/util/choleskies.py
@@ -4,11 +4,14 @@
 import numpy as np
 from . import linalg
 from .config import config
+
 try:
     from . import choleskies_cython
-    config.set('cython', 'working', 'True')
+    cython_choleskies_working = True
 except ImportError:
-    config.set('cython', 'working', 'False')
+    print('warning in choleskies: failed to import cython module: falling back to numpy')
+    cython_choleskies_working = False
+
 
 def safe_root(N):
     i = np.sqrt(N)
@@ -100,7 +103,7 @@ def indexes_to_fix_for_low_rank(rank, size):
     return np.setdiff1d(np.arange((size**2+size)/2), keep)
 
 
-if config.getboolean('cython', 'working'):
+if cython_choleskies_working and config.getboolean('cython', 'working'):
     triang_to_flat = _triang_to_flat_cython
     flat_to_triang = _flat_to_triang_cython
     backprop_gradient = choleskies_cython.backprop_gradient_par_c