Merge branch 'devel' of github.com:SheffieldML/GPy into devel

GPy/core/parameterized.py

@@ -187,7 +187,7 @@ class Parameterized(object):
 
     def constrain_negative(self, regexp):
         """ Set negative constraints. """
-        self.constrain(regexp, transformations.negative_exponent())
+        self.constrain(regexp, transformations.negative_logexp())
 
     def constrain_positive(self, regexp):
         """ Set positive constraints. """

GPy/core/transformations.py

@@ -36,6 +36,20 @@ class logexp(transformation):
     def __str__(self):
         return '(+ve)'
 
+class negative_logexp(transformation):
+    domain = NEGATIVE
+    def f(self, x):
+        return -np.log(1. + np.exp(x))
+    def finv(self, f):
+        return np.log(np.exp(-f) - 1.)
+    def gradfactor(self, f):
+        ef = np.exp(-f)
+        return -(ef - 1.) / ef
+    def initialize(self, f):
+        return -np.abs(f)
+    def __str__(self):
+        return '(-ve)'
+
 class logexp_clipped(transformation):
     max_bound = 1e100
     min_bound = 1e-10

GPy/kern/constructors.py

@@ -227,7 +227,7 @@ def periodic_Matern52(input_dim, variance=1., lengthscale=None, period=2 * np.pi
      :param n_freq: the number of frequencies considered for the periodic subspace
      :type n_freq: int
     """
-    part = parts.periodic_Matern52part(input_dim, variance, lengthscale, period, n_freq, lower, upper)
+    part = parts.periodic_Matern52.PeriodicMatern52(input_dim, variance, lengthscale, period, n_freq, lower, upper)
     return kern(input_dim, [part])
 
 def prod(k1,k2,tensor=False):