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

GPy/core/parameterization/lists_and_dicts.py

@@ -57,6 +57,7 @@ class ObservablesList(object):
 
     def __repr__(self):
         return self._poc.__repr__()
+    
 
     def add(self, priority, observable, callble):
         if observable is not None:

GPy/core/parameterization/param.py

@@ -57,9 +57,9 @@ class Param(OptimizationHandlable, ObsAr):
 
     def build_pydot(self,G):
         import pydot
-        node = pydot.Node(id(self), shape='record', label=self.name)
+        node = pydot.Node(id(self), shape='trapezium', label=self.name)#, fontcolor='white', color='white')
         G.add_node(node)
-        for o in self.observers.keys():
+        for _, o, _ in self.observers:
             label = o.name if hasattr(o, 'name') else str(o)
             observed_node = pydot.Node(id(o), label=label)
             G.add_node(observed_node)

GPy/core/parameterization/parameter_core.py

@@ -599,14 +599,13 @@ class OptimizationHandlable(Constrainable):
         return p
 
     def _set_params_transformed(self, p):
-        if p is self.param_array:
+        if not(p is self.param_array):
-            p = p.copy()
+            if self.has_parent() and self.constraints[__fixed__].size != 0:
-        if self.has_parent() and self.constraints[__fixed__].size != 0:
+                fixes = np.ones(self.size).astype(bool)
-            fixes = np.ones(self.size).astype(bool)
+                fixes[self.constraints[__fixed__]] = FIXED
-            fixes[self.constraints[__fixed__]] = FIXED
+                self.param_array.flat[fixes] = p
-            self.param_array.flat[fixes] = p
+            elif self._has_fixes(): self.param_array.flat[self._fixes_] = p
-        elif self._has_fixes(): self.param_array.flat[self._fixes_] = p
+            else: self.param_array.flat = p
-        else: self.param_array.flat = p
         self.untransform()
         self._trigger_params_changed()
 
@@ -621,7 +620,7 @@ class OptimizationHandlable(Constrainable):
     def num_params(self):
         """
         Return the number of parameters of this parameter_handle.
-        Param objects will allways return 0.
+        Param objects will always return 0.
         """
         raise NotImplemented, "Abstract, please implement in respective classes"
 
@@ -742,14 +741,15 @@ class Parameterizable(OptimizationHandlable):
             self.__visited = True
             for c in self._parameters_:
                 c.traverse(visit, *args, **kwargs)
+            self.__visited = False
 
     def traverse_parents(self, visit, *args, **kwargs):
         """
         Traverse the hierarchy upwards, visiting all parents and their children.
         See "visitor pattern" in literature. This is implemented in pre-order fashion.
-
+    
         Example:
-
+    
         parents = []
         self.traverse_parents(parents.append)
         print parents

GPy/core/parameterization/parameterized.py

@@ -82,15 +82,15 @@ class Parameterized(Parameterizable):
         import pydot  # @UnresolvedImport
         iamroot = False
         if G is None:
-            G = pydot.Dot(graph_type='digraph')
+            G = pydot.Dot(graph_type='digraph', bgcolor=None)
             iamroot=True
-        node = pydot.Node(id(self), shape='record', label=self.name)
+        node = pydot.Node(id(self), shape='box', label=self.name)#, color='white')
         G.add_node(node)
         for child in self._parameters_:
             child_node = child.build_pydot(G)
-            G.add_edge(pydot.Edge(node, child_node))
+            G.add_edge(pydot.Edge(node, child_node))#, color='white'))
 
-        for o in self.observers.keys():
+        for _, o, _ in self.observers:
             label = o.name if hasattr(o, 'name') else str(o)
             observed_node = pydot.Node(id(o), label=label)
             G.add_node(observed_node)