Fixed parameter bugs

GPy/core/parameterization/parameterized.py

@@ -449,6 +449,8 @@ class Parameterized(Constrainable, Pickleable, Observable):
         # if removing constraints before adding new is not wanted, just delete the above line!
         self.constraints.add(transform, rav_i)
         param = self._get_original(param)
+        #FIXME: Max, is this the right thing to do to handle fixed?
+        if not (transform == __fixed__):
             param._set_params(transform.initialize(param._get_params()), update=False)
         if warning and any(reconstrained):
             # if you want to print the whole params object, which was reconstrained use:

GPy/core/parameterization/transformations.py

@@ -162,7 +162,9 @@ class Logistic(Transformation):
     def initialize(self, f):
         if np.any(np.logical_or(f < self.lower, f > self.upper)):
             print "Warning: changing parameters to satisfy constraints"
-        return np.where(np.logical_or(f < self.lower, f > self.upper), self.f(f * 0.), f)
+        #return np.where(np.logical_or(f < self.lower, f > self.upper), self.f(f * 0.), f)
+        #FIXME: Max, zeros_like right?
+        return np.where(np.logical_or(f < self.lower, f > self.upper), self.f(np.zeros_like(f)), f)
     def __str__(self):
         return '{},{}'.format(self.lower, self.upper)