From 63ab143e7c7c3994d6b9b1fde0e5290d4b23f311 Mon Sep 17 00:00:00 2001
From: James Hensman <james.hensman@gmail.com>
Date: Thu, 12 Dec 2013 14:18:18 +0000
Subject: [PATCH] some tifying in the models classes

---
 GPy/likelihoods/bernoulli.py            |  8 ++++++--
 GPy/models/gp_classification.py         | 19 ++++---------------
 GPy/models/gp_multioutput_regression.py |  1 -
 GPy/models/gp_regression.py             |  1 +
 GPy/models/gradient_checker.py          |  6 ++----
 GPy/models/mrd.py                       |  6 ++----
 6 files changed, 15 insertions(+), 26 deletions(-)

diff --git a/GPy/likelihoods/bernoulli.py b/GPy/likelihoods/bernoulli.py
index 774eaf17..062528ca 100644
--- a/GPy/likelihoods/bernoulli.py
+++ b/GPy/likelihoods/bernoulli.py
@@ -22,8 +22,12 @@ class Bernoulli(Likelihood):
     .. See also::
         likelihood.py, for the parent class
     """
-    def __init__(self, gp_link=None, analytical_mean=False, analytical_variance=False):
-        super(Bernoulli, self).__init__(gp_link, analytical_mean, analytical_variance)
+    def __init__(self, gp_link=None):
+        if gp_link is None:
+            gp_link = link_functions.Probit()
+
+        super(Bernoulli, self).__init__(gp_link, 'Bernoulli')
+
         if isinstance(gp_link , (link_functions.Heaviside, link_functions.Probit)):
             self.log_concave = True
 
diff --git a/GPy/models/gp_classification.py b/GPy/models/gp_classification.py
index fce51cfa..634fd4e5 100644
--- a/GPy/models/gp_classification.py
+++ b/GPy/models/gp_classification.py
@@ -1,7 +1,7 @@
 # Copyright (c) 2013, Ricardo Andrade
+# Copyright (c) 2013, the GPy Authors (see AUTHORS.txt)
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
 
-
 import numpy as np
 from ..core import GP
 from .. import likelihoods
@@ -15,27 +15,16 @@ class GPClassification(GP):
 
     :param X: input observations
     :param Y: observed values, can be None if likelihood is not None
-    :param likelihood: a GPy likelihood, defaults to Binomial with probit link_function
     :param kernel: a GPy kernel, defaults to rbf
-    :param normalize_X:  whether to normalize the input data before computing (predictions will be in original scales)
-    :type normalize_X: False|True
-    :param normalize_Y:  whether to normalize the input data before computing (predictions will be in original scales)
-    :type normalize_Y: False|True
 
     .. Note:: Multiple independent outputs are allowed using columns of Y
 
     """
 
-    def __init__(self,X,Y=None,likelihood=None,kernel=None,normalize_X=False,normalize_Y=False):
+    def __init__(self, X, Y, kernel=None):
         if kernel is None:
             kernel = kern.rbf(X.shape[1])
 
-        if likelihood is None:
-            noise_model = likelihoods.binomial()
-            likelihood = likelihoods.EP(Y, noise_model)
-        elif Y is not None:
-            if not all(Y.flatten() == likelihood.data.flatten()):
-                raise Warning, 'likelihood.data and Y are different.'
+        likelihood = likelihoods.Bernoulli()
 
-        GP.__init__(self, X, likelihood, kernel, normalize_X=normalize_X)
-        self.ensure_default_constraints()
+        GP.__init__(self, X=X, Y=Y,  kernel=kernel, likelihood=likelihood, name='gp_classification')
diff --git a/GPy/models/gp_multioutput_regression.py b/GPy/models/gp_multioutput_regression.py
index f6ceac9d..2286ff95 100644
--- a/GPy/models/gp_multioutput_regression.py
+++ b/GPy/models/gp_multioutput_regression.py
@@ -1,7 +1,6 @@
 # Copyright (c) 2013, Ricardo Andrade
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
 
-
 import numpy as np
 from ..core import GP
 from .. import likelihoods
diff --git a/GPy/models/gp_regression.py b/GPy/models/gp_regression.py
index a833d11b..8be93d70 100644
--- a/GPy/models/gp_regression.py
+++ b/GPy/models/gp_regression.py
@@ -22,6 +22,7 @@ class GPRegression(GP):
     """
 
     def __init__(self, X, Y, kernel=None):
+
         if kernel is None:
             kernel = kern.rbf(X.shape[1])
 
diff --git a/GPy/models/gradient_checker.py b/GPy/models/gradient_checker.py
index 5afcd7c4..775334ac 100644
--- a/GPy/models/gradient_checker.py
+++ b/GPy/models/gradient_checker.py
@@ -1,8 +1,6 @@
-'''
-Created on 17 Jul 2013
+# ## Copyright (c) 2012, GPy authors (see AUTHORS.txt).
+# Licensed under the BSD 3-clause license (see LICENSE.txt)
 
-@author: maxz
-'''
 from GPy.core.model import Model
 import itertools
 import numpy
diff --git a/GPy/models/mrd.py b/GPy/models/mrd.py
index 2b9ef805..4ef9bf47 100644
--- a/GPy/models/mrd.py
+++ b/GPy/models/mrd.py
@@ -1,8 +1,6 @@
-'''
-Created on 10 Apr 2013
+# ## Copyright (c) 2013, GPy authors (see AUTHORS.txt).
+# Licensed under the BSD 3-clause license (see LICENSE.txt)
 
-@author: Max Zwiessele
-'''
 from GPy.core import Model
 from GPy.core import SparseGP
 from GPy.util.linalg import PCA