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

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This commit is contained in:
Neil Lawrence 2014-11-03 14:43:43 +00:00
commit fb385355bd
11 changed files with 74 additions and 374 deletions
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2
GPy/inference/latent_function_inference/var_dtc.py
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@ -167,7 +167,7 @@ class VarDTC(LatentFunctionInference):
woodbury_vector = Cpsi1Vf # == Cpsi1V woodbury_vector = Cpsi1Vf # == Cpsi1V
else: else:
print 'foobar' print 'foobar'
stop import ipdb; ipdb.set_trace()
psi1V = np.dot(Y.T*beta, psi1).T psi1V = np.dot(Y.T*beta, psi1).T
tmp, _ = dtrtrs(Lm, psi1V, lower=1, trans=0) tmp, _ = dtrtrs(Lm, psi1V, lower=1, trans=0)
tmp, _ = dpotrs(LB, tmp, lower=1) tmp, _ = dpotrs(LB, tmp, lower=1)

11
GPy/util/parallel.py
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@ -4,11 +4,10 @@ The module of tools for parallelization (MPI)
try: try:
from mpi4py import MPI from mpi4py import MPI
def get_id_within_node(comm=MPI.COMM_WORLD):
rank = comm.rank
nodename = MPI.Get_processor_name()
nodelist = comm.allgather(nodename)
return len([i for i in nodelist[:rank] if i==nodename])
except: except:
pass pass
def get_id_within_node(comm=MPI.COMM_WORLD):
rank = comm.rank
nodename = MPI.Get_processor_name()
nodelist = comm.allgather(nodename)
return len([i for i in nodelist[:rank] if i==nodename])

8
doc/GPy.inference.latent_function_inference.rst
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@ -44,6 +44,14 @@ GPy.inference.latent_function_inference.fitc module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.inference.latent_function_inference.inferenceX module
---------------------------------------------------------
.. automodule:: GPy.inference.latent_function_inference.inferenceX
:members:
:undoc-members:
:show-inheritance:
GPy.inference.latent_function_inference.laplace module GPy.inference.latent_function_inference.laplace module
------------------------------------------------------ ------------------------------------------------------

30
doc/GPy.inference.mcmc.rst Normal file
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@ -0,0 +1,30 @@
GPy.inference.mcmc package
==========================
Submodules
----------
GPy.inference.mcmc.hmc module
-----------------------------
.. automodule:: GPy.inference.mcmc.hmc
:members:
:undoc-members:
:show-inheritance:
GPy.inference.mcmc.samplers module
----------------------------------
.. automodule:: GPy.inference.mcmc.samplers
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.inference.mcmc
:members:
:undoc-members:
:show-inheritance:

246
doc/GPy.kern.parts.rst
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@ -1,246 +0,0 @@
GPy.kern.parts package
======================
Submodules
----------
GPy.kern.parts.Brownian module
------------------------------
.. automodule:: GPy.kern.parts.Brownian
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.Matern32 module
------------------------------
.. automodule:: GPy.kern.parts.Matern32
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.Matern52 module
------------------------------
.. automodule:: GPy.kern.parts.Matern52
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.bias module
--------------------------
.. automodule:: GPy.kern.parts.bias
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.coregionalize module
-----------------------------------
.. automodule:: GPy.kern.parts.coregionalize
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.exponential module
---------------------------------
.. automodule:: GPy.kern.parts.exponential
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.finite_dimensional module
----------------------------------------
.. automodule:: GPy.kern.parts.finite_dimensional
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.fixed module
---------------------------
.. automodule:: GPy.kern.parts.fixed
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.gibbs module
---------------------------
.. automodule:: GPy.kern.parts.gibbs
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.hetero module
----------------------------
.. automodule:: GPy.kern.parts.hetero
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.hierarchical module
----------------------------------
.. automodule:: GPy.kern.parts.hierarchical
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.independent_outputs module
-----------------------------------------
.. automodule:: GPy.kern.parts.independent_outputs
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.kernpart module
------------------------------
.. automodule:: GPy.kern.parts.kernpart
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.linear module
----------------------------
.. automodule:: GPy.kern.parts.linear
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.mlp module
-------------------------
.. automodule:: GPy.kern.parts.mlp
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.periodic_Matern32 module
---------------------------------------
.. automodule:: GPy.kern.parts.periodic_Matern32
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.periodic_Matern52 module
---------------------------------------
.. automodule:: GPy.kern.parts.periodic_Matern52
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.periodic_exponential module
------------------------------------------
.. automodule:: GPy.kern.parts.periodic_exponential
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.poly module
--------------------------
.. automodule:: GPy.kern.parts.poly
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.prod module
--------------------------
.. automodule:: GPy.kern.parts.prod
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.prod_orthogonal module
-------------------------------------
.. automodule:: GPy.kern.parts.prod_orthogonal
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.rational_quadratic module
----------------------------------------
.. automodule:: GPy.kern.parts.rational_quadratic
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.rbf module
-------------------------
.. automodule:: GPy.kern.parts.rbf
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.rbf_inv module
-----------------------------
.. automodule:: GPy.kern.parts.rbf_inv
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.rbfcos module
----------------------------
.. automodule:: GPy.kern.parts.rbfcos
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.spline module
----------------------------
.. automodule:: GPy.kern.parts.spline
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.symmetric module
-------------------------------
.. automodule:: GPy.kern.parts.symmetric
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.sympykern module
-------------------------------
.. automodule:: GPy.kern.parts.sympykern
:members:
:undoc-members:
:show-inheritance:
GPy.kern.parts.white module
---------------------------
.. automodule:: GPy.kern.parts.white
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.kern.parts
:members:
:undoc-members:
:show-inheritance:

70
doc/GPy.likelihoods.noise_models.rst
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@ -1,70 +0,0 @@
GPy.likelihoods.noise_models package
====================================
Submodules
----------
GPy.likelihoods.noise_models.binomial_noise module
--------------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.binomial_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.noise_models.exponential_noise module
-----------------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.exponential_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.noise_models.gamma_noise module
-----------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.gamma_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.noise_models.gaussian_noise module
--------------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.gaussian_noise
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.noise_models.gp_transformations module
------------------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.gp_transformations
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.noise_models.noise_distributions module
-------------------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.noise_distributions
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.noise_models.poisson_noise module
-------------------------------------------------
.. automodule:: GPy.likelihoods.noise_models.poisson_noise
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.likelihoods.noise_models
:members:
:undoc-members:
:show-inheritance:

16
doc/GPy.models.rst
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@ -12,6 +12,14 @@ GPy.models.bayesian_gplvm module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.bayesian_gplvm_minibatch module
------------------------------------------
.. automodule:: GPy.models.bayesian_gplvm_minibatch
:members:
:undoc-members:
:show-inheritance:
GPy.models.bcgplvm module GPy.models.bcgplvm module
------------------------- -------------------------
@ -116,6 +124,14 @@ GPy.models.sparse_gp_coregionalized_regression module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.models.sparse_gp_minibatch module
-------------------------------------
.. automodule:: GPy.models.sparse_gp_minibatch
:members:
:undoc-members:
:show-inheritance:
GPy.models.sparse_gp_multioutput_regression module GPy.models.sparse_gp_multioutput_regression module
-------------------------------------------------- --------------------------------------------------

8
doc/GPy.testing.rst
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@ -28,6 +28,14 @@ GPy.testing.index_operations_tests module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.testing.inference_tests module
----------------------------------
.. automodule:: GPy.testing.inference_tests
:members:
:undoc-members:
:show-inheritance:
GPy.testing.kernel_tests module GPy.testing.kernel_tests module
------------------------------- -------------------------------

30
doc/GPy.util.latent_space_visualizations.controllers.rst
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@ -1,30 +0,0 @@
GPy.util.latent_space_visualizations.controllers package
========================================================
Submodules
----------
GPy.util.latent_space_visualizations.controllers.axis_event_controller module
-----------------------------------------------------------------------------
.. automodule:: GPy.util.latent_space_visualizations.controllers.axis_event_controller
:members:
:undoc-members:
:show-inheritance:
GPy.util.latent_space_visualizations.controllers.imshow_controller module
-------------------------------------------------------------------------
.. automodule:: GPy.util.latent_space_visualizations.controllers.imshow_controller
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.util.latent_space_visualizations.controllers
:members:
:undoc-members:
:show-inheritance:

17
doc/GPy.util.latent_space_visualizations.rst
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@ -1,17 +0,0 @@
GPy.util.latent_space_visualizations package
============================================
Subpackages
-----------
.. toctree::
GPy.util.latent_space_visualizations.controllers
Module contents
---------------
.. automodule:: GPy.util.latent_space_visualizations
:members:
:undoc-members:
:show-inheritance:

10
doc/conf.py
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@ -11,6 +11,9 @@
# All configuration values have a default; values that are commented out # All configuration values have a default; values that are commented out
# serve to show the default. # serve to show the default.
autodoc_default_flags = ['members', 'show-inheritance', 'private-members', 'special-members']
autodoc_member_order = "source"
import sys import sys
import os import os
@ -114,7 +117,7 @@ for mod_name in MOCK_MODULES:
# ----------------------- READTHEDOCS ------------------ # ----------------------- READTHEDOCS ------------------
on_rtd = os.environ.get('READTHEDOCS', None) == 'True' on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
on_rtd = True #on_rtd = True
if on_rtd: if on_rtd:
sys.path.append(os.path.abspath('../GPy')) sys.path.append(os.path.abspath('../GPy'))
@ -126,7 +129,8 @@ if on_rtd:
proc = subprocess.Popen("ls ../", stdout=subprocess.PIPE, shell=True) proc = subprocess.Popen("ls ../", stdout=subprocess.PIPE, shell=True)
(out, err) = proc.communicate() (out, err) = proc.communicate()
print "program output:", out print "program output:", out
proc = subprocess.Popen("sphinx-apidoc -f -o . ../GPy", stdout=subprocess.PIPE, shell=True) #proc = subprocess.Popen("sphinx-apidoc -f -o . ../GPy", stdout=subprocess.PIPE, shell=True)
proc = subprocess.Popen("make html", stdout=subprocess.PIPE, shell=True)
(out, err) = proc.communicate() (out, err) = proc.communicate()
print "program output:", out print "program output:", out
#proc = subprocess.Popen("whereis numpy", stdout=subprocess.PIPE, shell=True) #proc = subprocess.Popen("whereis numpy", stdout=subprocess.PIPE, shell=True)
@ -397,5 +401,3 @@ epub_copyright = u'2013, Author'
# Allow duplicate toc entries. # Allow duplicate toc entries.
#epub_tocdup = True #epub_tocdup = True
autodoc_member_order = "source"