Added debuggin, and interestingly likelihood rst.. shouldnt make a difference:

doc/GPy.examples.rst

@@ -33,6 +33,14 @@ examples Package
     :undoc-members:
     :show-inheritance:
 
+:mod:`poisson` Module
+---------------------
+
+.. automodule:: GPy.examples.poisson
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 :mod:`regression` Module
 ------------------------
 
@@ -57,6 +65,14 @@ examples Package
     :undoc-members:
     :show-inheritance:
 
+:mod:`sparse_ep_fix` Module
+---------------------------
+
+.. automodule:: GPy.examples.sparse_ep_fix
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 :mod:`uncertain_input_GP_regression_demo` Module
 ------------------------------------------------
 

doc/GPy.inference.rst

@@ -1,22 +1,6 @@
 inference Package
 =================
 
-:mod:`Expectation_Propagation` Module
--------------------------------------
-
-.. automodule:: GPy.inference.Expectation_Propagation
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`likelihoods` Module
--------------------------
-
-.. automodule:: GPy.inference.likelihoods
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 :mod:`optimization` Module
 --------------------------
 

doc/GPy.likelihoods.rst

@@ -0,0 +1,43 @@
+likelihoods Package
+===================
+
+:mod:`likelihoods` Package
+--------------------------
+
+.. automodule:: GPy.likelihoods
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`EP` Module
+----------------
+
+.. automodule:: GPy.likelihoods.EP
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`Gaussian` Module
+----------------------
+
+.. automodule:: GPy.likelihoods.Gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`likelihood` Module
+------------------------
+
+.. automodule:: GPy.likelihoods.likelihood
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`likelihood_functions` Module
+----------------------------------
+
+.. automodule:: GPy.likelihoods.likelihood_functions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

doc/GPy.models.rst

@@ -17,18 +17,18 @@ models Package
     :undoc-members:
     :show-inheritance:
 
-:mod:`GPLVM` Module
--------------------
+:mod:`GP` Module
+----------------
 
-.. automodule:: GPy.models.GPLVM
+.. automodule:: GPy.models.GP
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`GP_EP` Module
+:mod:`GPLVM` Module
 -------------------
 
-.. automodule:: GPy.models.GP_EP
+.. automodule:: GPy.models.GPLVM
     :members:
     :undoc-members:
     :show-inheritance:
@@ -41,10 +41,10 @@ models Package
     :undoc-members:
     :show-inheritance:
 
-:mod:`generalized_FITC` Module
-------------------------------
+:mod:`sparse_GP` Module
+-----------------------
 
-.. automodule:: GPy.models.generalized_FITC
+.. automodule:: GPy.models.sparse_GP
     :members:
     :undoc-members:
     :show-inheritance:

doc/GPy.rst

@@ -18,6 +18,7 @@ Subpackages
     GPy.examples
     GPy.inference
     GPy.kern
+    GPy.likelihoods
     GPy.models
     GPy.util
 

doc/conf.py

@@ -119,13 +119,26 @@ for mod_name in MOCK_MODULES:
 # ----------------------- READTHEDOCS ------------------
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 
+on_rtd = True
 if on_rtd:
     #sys.path.insert(0, os.getcwd() + "/../GPy")
     #sys.path.append(os.getcwd() + "/../GPy")
     print "I am here"
-    print(os.system("pwd"))
-    print(os.system("ls ../"))
-    os.system("sphinx-apidoc -f -o . ../GPy")
+    #print(os.system("pwd"))
+    #print(os.system("ls ../"))
+    #os.system("sphinx-apidoc -f -o . ../GPy")
+
+    import subprocess
+
+    proc = subprocess.Popen("pwd", stdout=subprocess.PIPE, shell=True)
+    (out, err) = proc.communicate()
+    print "program output:", out
+    proc = subprocess.Popen("ls ../", stdout=subprocess.PIPE, shell=True)
+    (out, err) = proc.communicate()
+    print "program output:", out
+    proc = subprocess.Popen("sphinx-apidoc -f -o . ../GPy", stdout=subprocess.PIPE, shell=True)
+    (out, err) = proc.communicate()
+    print "program output:", out
     #os.system("cd ..")
     #os.system("cd ./docs")