diff --git a/GPy/inference/latent_function_inference/var_dtc.py b/GPy/inference/latent_function_inference/var_dtc.py index 0459132a..cfc2bb47 100644 --- a/GPy/inference/latent_function_inference/var_dtc.py +++ b/GPy/inference/latent_function_inference/var_dtc.py @@ -167,7 +167,7 @@ class VarDTC(LatentFunctionInference): woodbury_vector = Cpsi1Vf # == Cpsi1V else: print 'foobar' - stop + import ipdb; ipdb.set_trace() psi1V = np.dot(Y.T*beta, psi1).T tmp, _ = dtrtrs(Lm, psi1V, lower=1, trans=0) tmp, _ = dpotrs(LB, tmp, lower=1) diff --git a/GPy/util/parallel.py b/GPy/util/parallel.py index fd8791d4..bc847c95 100644 --- a/GPy/util/parallel.py +++ b/GPy/util/parallel.py @@ -4,11 +4,10 @@ The module of tools for parallelization (MPI) try: 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: 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]) diff --git a/doc/GPy.inference.latent_function_inference.rst b/doc/GPy.inference.latent_function_inference.rst index c47da33a..98d16705 100644 --- a/doc/GPy.inference.latent_function_inference.rst +++ b/doc/GPy.inference.latent_function_inference.rst @@ -44,6 +44,14 @@ GPy.inference.latent_function_inference.fitc module :undoc-members: :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 ------------------------------------------------------ diff --git a/doc/GPy.inference.mcmc.rst b/doc/GPy.inference.mcmc.rst new file mode 100644 index 00000000..273658b7 --- /dev/null +++ b/doc/GPy.inference.mcmc.rst @@ -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: diff --git a/doc/GPy.kern.parts.rst b/doc/GPy.kern.parts.rst deleted file mode 100644 index ec0661b4..00000000 --- a/doc/GPy.kern.parts.rst +++ /dev/null @@ -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: diff --git a/doc/GPy.likelihoods.noise_models.rst b/doc/GPy.likelihoods.noise_models.rst deleted file mode 100644 index d1a4f451..00000000 --- a/doc/GPy.likelihoods.noise_models.rst +++ /dev/null @@ -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: diff --git a/doc/GPy.models.rst b/doc/GPy.models.rst index 5ee7e3a9..cb043afa 100644 --- a/doc/GPy.models.rst +++ b/doc/GPy.models.rst @@ -12,6 +12,14 @@ GPy.models.bayesian_gplvm module :undoc-members: :show-inheritance: +GPy.models.bayesian_gplvm_minibatch module +------------------------------------------ + +.. automodule:: GPy.models.bayesian_gplvm_minibatch + :members: + :undoc-members: + :show-inheritance: + GPy.models.bcgplvm module ------------------------- @@ -116,6 +124,14 @@ GPy.models.sparse_gp_coregionalized_regression module :undoc-members: :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 -------------------------------------------------- diff --git a/doc/GPy.testing.rst b/doc/GPy.testing.rst index 2d1132d7..45bb307f 100644 --- a/doc/GPy.testing.rst +++ b/doc/GPy.testing.rst @@ -28,6 +28,14 @@ GPy.testing.index_operations_tests module :undoc-members: :show-inheritance: +GPy.testing.inference_tests module +---------------------------------- + +.. automodule:: GPy.testing.inference_tests + :members: + :undoc-members: + :show-inheritance: + GPy.testing.kernel_tests module ------------------------------- diff --git a/doc/GPy.util.latent_space_visualizations.controllers.rst b/doc/GPy.util.latent_space_visualizations.controllers.rst deleted file mode 100644 index a88c1f5c..00000000 --- a/doc/GPy.util.latent_space_visualizations.controllers.rst +++ /dev/null @@ -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: diff --git a/doc/GPy.util.latent_space_visualizations.rst b/doc/GPy.util.latent_space_visualizations.rst deleted file mode 100644 index d8cbd843..00000000 --- a/doc/GPy.util.latent_space_visualizations.rst +++ /dev/null @@ -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: diff --git a/doc/conf.py b/doc/conf.py index 7b71a897..f051c986 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -11,6 +11,9 @@ # All configuration values have a default; values that are commented out # serve to show the default. +autodoc_default_flags = ['members', 'show-inheritance', 'private-members', 'special-members'] +autodoc_member_order = "source" + import sys import os @@ -114,7 +117,7 @@ for mod_name in MOCK_MODULES: # ----------------------- READTHEDOCS ------------------ on_rtd = os.environ.get('READTHEDOCS', None) == 'True' -on_rtd = True +#on_rtd = True if on_rtd: sys.path.append(os.path.abspath('../GPy')) @@ -126,7 +129,8 @@ if on_rtd: 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) + #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() print "program output:", out #proc = subprocess.Popen("whereis numpy", stdout=subprocess.PIPE, shell=True) @@ -397,5 +401,3 @@ epub_copyright = u'2013, Author' # Allow duplicate toc entries. #epub_tocdup = True - -autodoc_member_order = "source"