fix: dev: cython import errors

This commit fixes issues observed in Windows where some
cython modules are successfully imported, and some are not.
This causes the global config cython.working to be inconsistent,
which causes import errors when unavailable cython modules
are tried to be imported (example
https://github.com/SheffieldML/GPy/issues/266). This commit uses
a separate flag for each module to fix the issue.

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)

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)

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)

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

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