From 17ba95a110d61e980eec9b8bdc597f98f48e7ea8 Mon Sep 17 00:00:00 2001 From: James McMurray Date: Wed, 18 Sep 2013 14:11:59 +0100 Subject: [PATCH 1/6] Updated readme with instructions for compiling documentation, running unit tests --- README.md | 46 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 09bc78f5..1f08cbdb 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,54 @@ GPy === -A Gaussian processes framework in python +A Gaussian processes framework in Python. * [Online documentation](https://gpy.readthedocs.org/en/latest/) * [Unit tests (Travis-CI)](https://travis-ci.org/SheffieldML/GPy) Continuous integration status: ![CI status](https://travis-ci.org/SheffieldML/GPy.png) + + +Compiling documentation: +======================== + +The documentation is stored in doc/ and is compiled with the Sphinx Python documentation generator, and is written in the reStructuredText format. + +The Sphinx documentation is available here: http://sphinx-doc.org/latest/contents.html + + +Installing dependencies: +------------------------ + +To compile the documentation, first ensure that Sphinx is installed. On Debian-based systems, this can be achieved as follows: + + sudo apt-get install python-pip + sudo pip install sphinx + +A LaTeX distribution is also required to compile the equations. Note that the extra packages are necessary to install the unicode packages. To compile the equations to PNG format for use in HTML pages, the package *dvipng* must be installed. IPython is also required. On Debian-based systems, this can be achieved as follows: + + sudo apt-get install texlive texlive-latex-extra texlive-base texlive-recommended + sudo apt-get install dvipng + sudo apt-get install ipython + + +Compiling documentation: +------------------------ + +The documentation can be compiled as follows: + + cd doc + make html + +The HTML files are then stored in doc/_build/ + + +Running unit tests: +=================== + +Ensure nose is installed via pip: + pip install nose + +Run nosetests from the root directory of the repository: + nosetests -v \ No newline at end of file From 2e65b21e2367e55843c988066d31486dee760a77 Mon Sep 17 00:00:00 2001 From: James McMurray Date: Wed, 18 Sep 2013 14:15:02 +0100 Subject: [PATCH 2/6] Fixed readme --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1f08cbdb..0ff3d890 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,10 @@ Running unit tests: =================== Ensure nose is installed via pip: + pip install nose Run nosetests from the root directory of the repository: - nosetests -v \ No newline at end of file + + nosetests -v + From 6897cf34b5a904b1f1c1c2e22ddc46c8691224ea Mon Sep 17 00:00:00 2001 From: James McMurray Date: Wed, 18 Sep 2013 15:43:23 +0100 Subject: [PATCH 3/6] Changes to fix autodoc - need to test with ReadTheDocs still --- doc/conf.py | 4 ++-- setup.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index b6dad7fd..42def116 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -83,6 +83,7 @@ print "finished importing" ############################################################################# class Mock(object): + __all__ = [] def __init__(self, *args, **kwargs): pass @@ -105,8 +106,7 @@ class Mock(object): print "Mocking" MOCK_MODULES = ['sympy', 'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', - 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser', - 'matplotlib.pyplot' + 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser' ] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() diff --git a/setup.py b/setup.py index 90645e71..9ccf3990 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ setup(name = 'GPy', license = "BSD 3-clause", keywords = "machine-learning gaussian-processes kernels", url = "http://sheffieldml.github.com/GPy/", - packages = ['GPy', 'GPy.core', 'GPy.kern', 'GPy.util', 'GPy.models', 'GPy.inference', 'GPy.examples', 'GPy.likelihoods', 'GPy.testing'], + packages = ['GPy', 'GPy.core', 'GPy.kern', 'GPy.util', 'GPy.models', 'GPy.inference', 'GPy.examples', 'GPy.likelihoods', 'GPy.testing', 'GPy.util.latent_space_visualizations', 'GPy.util.latent_space_visualizations.controllers', 'GPy.likelihoods.noise_models', 'GPy.kern.parts', 'GPy.mappings'], package_dir={'GPy': 'GPy'}, package_data = {'GPy': ['GPy/examples']}, py_modules = ['GPy.__init__'], From 474ef9b247acbb5ce50b3e64b853a4381da148fe Mon Sep 17 00:00:00 2001 From: James McMurray Date: Thu, 19 Sep 2013 14:36:33 +0100 Subject: [PATCH 4/6] Rebuilt documentation --- doc/GPy.core.rst | 69 ++--- doc/GPy.examples.rst | 41 +-- doc/GPy.inference.rst | 39 ++- doc/GPy.kern.parts.rst | 246 ++++++++++++++++++ doc/GPy.kern.rst | 55 ++-- doc/GPy.likelihoods.noise_models.rst | 70 +++++ doc/GPy.likelihoods.rst | 60 +++-- doc/GPy.mappings.rst | 38 +++ doc/GPy.models.rst | 97 ++++--- doc/GPy.rst | 18 +- doc/GPy.testing.rst | 83 +++--- ...atent_space_visualizations.controllers.rst | 30 +++ doc/GPy.util.latent_space_visualizations.rst | 17 ++ doc/GPy.util.rst | 84 +++--- 14 files changed, 721 insertions(+), 226 deletions(-) create mode 100644 doc/GPy.kern.parts.rst create mode 100644 doc/GPy.likelihoods.noise_models.rst create mode 100644 doc/GPy.mappings.rst create mode 100644 doc/GPy.util.latent_space_visualizations.controllers.rst create mode 100644 doc/GPy.util.latent_space_visualizations.rst diff --git a/doc/GPy.core.rst b/doc/GPy.core.rst index 0590450f..c4f1849d 100644 --- a/doc/GPy.core.rst +++ b/doc/GPy.core.rst @@ -1,91 +1,102 @@ -core Package -============ +GPy.core package +================ -:mod:`core` Package -------------------- +Submodules +---------- -.. automodule:: GPy.core - :members: - :undoc-members: - :show-inheritance: - -:mod:`domains` Module ---------------------- +GPy.core.domains module +----------------------- .. automodule:: GPy.core.domains :members: :undoc-members: :show-inheritance: -:mod:`fitc` Module ------------------- +GPy.core.fitc module +-------------------- .. automodule:: GPy.core.fitc :members: :undoc-members: :show-inheritance: -:mod:`gp` Module ----------------- +GPy.core.gp module +------------------ .. automodule:: GPy.core.gp :members: :undoc-members: :show-inheritance: -:mod:`gp_base` Module ---------------------- +GPy.core.gp_base module +----------------------- .. automodule:: GPy.core.gp_base :members: :undoc-members: :show-inheritance: -:mod:`model` Module -------------------- +GPy.core.mapping module +----------------------- + +.. automodule:: GPy.core.mapping + :members: + :undoc-members: + :show-inheritance: + +GPy.core.model module +--------------------- .. automodule:: GPy.core.model :members: :undoc-members: :show-inheritance: -:mod:`parameterized` Module ---------------------------- +GPy.core.parameterized module +----------------------------- .. automodule:: GPy.core.parameterized :members: :undoc-members: :show-inheritance: -:mod:`priors` Module --------------------- +GPy.core.priors module +---------------------- .. automodule:: GPy.core.priors :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp` Module ------------------------ +GPy.core.sparse_gp module +------------------------- .. automodule:: GPy.core.sparse_gp :members: :undoc-members: :show-inheritance: -:mod:`svigp` Module -------------------- +GPy.core.svigp module +--------------------- .. automodule:: GPy.core.svigp :members: :undoc-members: :show-inheritance: -:mod:`transformations` Module ------------------------------ +GPy.core.transformations module +------------------------------- .. automodule:: GPy.core.transformations :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.core + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.examples.rst b/doc/GPy.examples.rst index fedfd4b9..4fd3528f 100644 --- a/doc/GPy.examples.rst +++ b/doc/GPy.examples.rst @@ -1,51 +1,54 @@ -examples Package -================ +GPy.examples package +==================== -:mod:`examples` Package ------------------------ +Submodules +---------- -.. automodule:: GPy.examples - :members: - :undoc-members: - :show-inheritance: - -:mod:`classification` Module ----------------------------- +GPy.examples.classification module +---------------------------------- .. automodule:: GPy.examples.classification :members: :undoc-members: :show-inheritance: -:mod:`dimensionality_reduction` Module --------------------------------------- +GPy.examples.dimensionality_reduction module +-------------------------------------------- .. automodule:: GPy.examples.dimensionality_reduction :members: :undoc-members: :show-inheritance: -:mod:`regression` Module ------------------------- +GPy.examples.regression module +------------------------------ .. automodule:: GPy.examples.regression :members: :undoc-members: :show-inheritance: -:mod:`stochastic` Module ------------------------- +GPy.examples.stochastic module +------------------------------ .. automodule:: GPy.examples.stochastic :members: :undoc-members: :show-inheritance: -:mod:`tutorials` Module ------------------------ +GPy.examples.tutorials module +----------------------------- .. automodule:: GPy.examples.tutorials :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.examples + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.inference.rst b/doc/GPy.inference.rst index 6a1bef4a..28f42994 100644 --- a/doc/GPy.inference.rst +++ b/doc/GPy.inference.rst @@ -1,51 +1,62 @@ -inference Package -================= +GPy.inference package +===================== -:mod:`conjugate_gradient_descent` Module ----------------------------------------- +Submodules +---------- + +GPy.inference.conjugate_gradient_descent module +----------------------------------------------- .. automodule:: GPy.inference.conjugate_gradient_descent :members: :undoc-members: :show-inheritance: -:mod:`gradient_descent_update_rules` Module -------------------------------------------- +GPy.inference.gradient_descent_update_rules module +-------------------------------------------------- .. automodule:: GPy.inference.gradient_descent_update_rules :members: :undoc-members: :show-inheritance: -:mod:`optimization` Module --------------------------- +GPy.inference.optimization module +--------------------------------- .. automodule:: GPy.inference.optimization :members: :undoc-members: :show-inheritance: -:mod:`samplers` Module ----------------------- +GPy.inference.samplers module +----------------------------- .. automodule:: GPy.inference.samplers :members: :undoc-members: :show-inheritance: -:mod:`scg` Module ------------------ +GPy.inference.scg module +------------------------ .. automodule:: GPy.inference.scg :members: :undoc-members: :show-inheritance: -:mod:`sgd` Module ------------------ +GPy.inference.sgd module +------------------------ .. automodule:: GPy.inference.sgd :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.inference + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.kern.parts.rst b/doc/GPy.kern.parts.rst new file mode 100644 index 00000000..ec0661b4 --- /dev/null +++ b/doc/GPy.kern.parts.rst @@ -0,0 +1,246 @@ +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.kern.rst b/doc/GPy.kern.rst index 35d9ec00..b4b9d9aa 100644 --- a/doc/GPy.kern.rst +++ b/doc/GPy.kern.rst @@ -1,29 +1,5 @@ -kern Package -============ - -:mod:`kern` Package -------------------- - -.. automodule:: GPy.kern - :members: - :undoc-members: - :show-inheritance: - -:mod:`constructors` Module --------------------------- - -.. automodule:: GPy.kern.constructors - :members: - :undoc-members: - :show-inheritance: - -:mod:`kern` Module ------------------- - -.. automodule:: GPy.kern.kern - :members: - :undoc-members: - :show-inheritance: +GPy.kern package +================ Subpackages ----------- @@ -32,3 +8,30 @@ Subpackages GPy.kern.parts +Submodules +---------- + +GPy.kern.constructors module +---------------------------- + +.. automodule:: GPy.kern.constructors + :members: + :undoc-members: + :show-inheritance: + +GPy.kern.kern module +-------------------- + +.. automodule:: GPy.kern.kern + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: GPy.kern + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.likelihoods.noise_models.rst b/doc/GPy.likelihoods.noise_models.rst new file mode 100644 index 00000000..d1a4f451 --- /dev/null +++ b/doc/GPy.likelihoods.noise_models.rst @@ -0,0 +1,70 @@ +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.likelihoods.rst b/doc/GPy.likelihoods.rst index 9fec38f8..c3da2650 100644 --- a/doc/GPy.likelihoods.rst +++ b/doc/GPy.likelihoods.rst @@ -1,51 +1,69 @@ -likelihoods Package -=================== +GPy.likelihoods package +======================= -:mod:`likelihoods` Package --------------------------- +Subpackages +----------- -.. automodule:: GPy.likelihoods - :members: - :undoc-members: - :show-inheritance: +.. toctree:: -:mod:`ep` Module ----------------- + GPy.likelihoods.noise_models + +Submodules +---------- + +GPy.likelihoods.ep module +------------------------- .. automodule:: GPy.likelihoods.ep :members: :undoc-members: :show-inheritance: -:mod:`gaussian` Module ----------------------- +GPy.likelihoods.ep_mixed_noise module +------------------------------------- + +.. automodule:: GPy.likelihoods.ep_mixed_noise + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.gaussian module +------------------------------- .. automodule:: GPy.likelihoods.gaussian :members: :undoc-members: :show-inheritance: -:mod:`likelihood` Module ------------------------- +GPy.likelihoods.gaussian_mixed_noise module +------------------------------------------- + +.. automodule:: GPy.likelihoods.gaussian_mixed_noise + :members: + :undoc-members: + :show-inheritance: + +GPy.likelihoods.likelihood module +--------------------------------- .. automodule:: GPy.likelihoods.likelihood :members: :undoc-members: :show-inheritance: -:mod:`likelihood_functions` Module ----------------------------------- +GPy.likelihoods.noise_model_constructors module +----------------------------------------------- -.. automodule:: GPy.likelihoods.likelihood_functions +.. automodule:: GPy.likelihoods.noise_model_constructors :members: :undoc-members: :show-inheritance: -:mod:`link_functions` Module ----------------------------- -.. automodule:: GPy.likelihoods.link_functions +Module contents +--------------- + +.. automodule:: GPy.likelihoods :members: :undoc-members: :show-inheritance: - diff --git a/doc/GPy.mappings.rst b/doc/GPy.mappings.rst new file mode 100644 index 00000000..c48cb06e --- /dev/null +++ b/doc/GPy.mappings.rst @@ -0,0 +1,38 @@ +GPy.mappings package +==================== + +Submodules +---------- + +GPy.mappings.kernel module +-------------------------- + +.. automodule:: GPy.mappings.kernel + :members: + :undoc-members: + :show-inheritance: + +GPy.mappings.linear module +-------------------------- + +.. automodule:: GPy.mappings.linear + :members: + :undoc-members: + :show-inheritance: + +GPy.mappings.mlp module +----------------------- + +.. automodule:: GPy.mappings.mlp + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: GPy.mappings + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.models.rst b/doc/GPy.models.rst index 4d227642..4440513e 100644 --- a/doc/GPy.models.rst +++ b/doc/GPy.models.rst @@ -1,99 +1,134 @@ -models Package -============== +GPy.models package +================== -:mod:`models` Package ---------------------- +Submodules +---------- -.. automodule:: GPy.models - :members: - :undoc-members: - :show-inheritance: - -:mod:`bayesian_gplvm` Module ----------------------------- +GPy.models.bayesian_gplvm module +-------------------------------- .. automodule:: GPy.models.bayesian_gplvm :members: :undoc-members: :show-inheritance: -:mod:`fitc_classification` Module ---------------------------------- +GPy.models.bcgplvm module +------------------------- + +.. automodule:: GPy.models.bcgplvm + :members: + :undoc-members: + :show-inheritance: + +GPy.models.fitc_classification module +------------------------------------- .. automodule:: GPy.models.fitc_classification :members: :undoc-members: :show-inheritance: -:mod:`gp_classification` Module -------------------------------- +GPy.models.gp_classification module +----------------------------------- .. automodule:: GPy.models.gp_classification :members: :undoc-members: :show-inheritance: -:mod:`gp_regression` Module ---------------------------- +GPy.models.gp_multioutput_regression module +------------------------------------------- + +.. automodule:: GPy.models.gp_multioutput_regression + :members: + :undoc-members: + :show-inheritance: + +GPy.models.gp_regression module +------------------------------- .. automodule:: GPy.models.gp_regression :members: :undoc-members: :show-inheritance: -:mod:`gplvm` Module -------------------- +GPy.models.gplvm module +----------------------- .. automodule:: GPy.models.gplvm :members: :undoc-members: :show-inheritance: -:mod:`mrd` Module ------------------ +GPy.models.gradient_checker module +---------------------------------- + +.. automodule:: GPy.models.gradient_checker + :members: + :undoc-members: + :show-inheritance: + +GPy.models.mrd module +--------------------- .. automodule:: GPy.models.mrd :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp_classification` Module --------------------------------------- +GPy.models.sparse_gp_classification module +------------------------------------------ .. automodule:: GPy.models.sparse_gp_classification :members: :undoc-members: :show-inheritance: -:mod:`sparse_gp_regression` Module ----------------------------------- +GPy.models.sparse_gp_multioutput_regression module +-------------------------------------------------- + +.. automodule:: GPy.models.sparse_gp_multioutput_regression + :members: + :undoc-members: + :show-inheritance: + +GPy.models.sparse_gp_regression module +-------------------------------------- .. automodule:: GPy.models.sparse_gp_regression :members: :undoc-members: :show-inheritance: -:mod:`sparse_gplvm` Module --------------------------- +GPy.models.sparse_gplvm module +------------------------------ .. automodule:: GPy.models.sparse_gplvm :members: :undoc-members: :show-inheritance: -:mod:`svigp_regression` Module ------------------------------- +GPy.models.svigp_regression module +---------------------------------- .. automodule:: GPy.models.svigp_regression :members: :undoc-members: :show-inheritance: -:mod:`warped_gp` Module ------------------------ +GPy.models.warped_gp module +--------------------------- .. automodule:: GPy.models.warped_gp :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.models + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.rst b/doc/GPy.rst index e56e48e1..60092e91 100644 --- a/doc/GPy.rst +++ b/doc/GPy.rst @@ -1,14 +1,6 @@ -GPy Package +GPy package =========== -:mod:`GPy` Package ------------------- - -.. automodule:: GPy.__init__ - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -19,7 +11,15 @@ Subpackages GPy.inference GPy.kern GPy.likelihoods + GPy.mappings GPy.models GPy.testing GPy.util +Module contents +--------------- + +.. automodule:: GPy + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.testing.rst b/doc/GPy.testing.rst index 6c461177..bd5258b7 100644 --- a/doc/GPy.testing.rst +++ b/doc/GPy.testing.rst @@ -1,107 +1,110 @@ -testing Package -=============== +GPy.testing package +=================== -:mod:`testing` Package ----------------------- +Submodules +---------- -.. automodule:: GPy.testing - :members: - :undoc-members: - :show-inheritance: - -:mod:`bgplvm_tests` Module --------------------------- +GPy.testing.bgplvm_tests module +------------------------------- .. automodule:: GPy.testing.bgplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`cgd_tests` Module ------------------------ +GPy.testing.cgd_tests module +---------------------------- .. automodule:: GPy.testing.cgd_tests :members: :undoc-members: :show-inheritance: -:mod:`checkgrad` Module ------------------------ - -.. automodule:: GPy.testing.checkgrad - :members: - :undoc-members: - :show-inheritance: - -:mod:`examples_tests` Module ----------------------------- +GPy.testing.examples_tests module +--------------------------------- .. automodule:: GPy.testing.examples_tests :members: :undoc-members: :show-inheritance: -:mod:`gplvm_tests` Module -------------------------- +GPy.testing.gplvm_tests module +------------------------------ .. automodule:: GPy.testing.gplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`kernel_tests` Module --------------------------- +GPy.testing.kernel_tests module +------------------------------- .. automodule:: GPy.testing.kernel_tests :members: :undoc-members: :show-inheritance: -:mod:`mrd_tests` Module ------------------------ +GPy.testing.mapping_tests module +-------------------------------- + +.. automodule:: GPy.testing.mapping_tests + :members: + :undoc-members: + :show-inheritance: + +GPy.testing.mrd_tests module +---------------------------- .. automodule:: GPy.testing.mrd_tests :members: :undoc-members: :show-inheritance: -:mod:`prior_tests` Module -------------------------- +GPy.testing.prior_tests module +------------------------------ .. automodule:: GPy.testing.prior_tests :members: :undoc-members: :show-inheritance: -:mod:`psi_stat_expactation_tests` Module ----------------------------------------- +GPy.testing.psi_stat_expectation_tests module +--------------------------------------------- -.. automodule:: GPy.testing.psi_stat_expactation_tests +.. automodule:: GPy.testing.psi_stat_expectation_tests :members: :undoc-members: :show-inheritance: -:mod:`psi_stat_gradient_tests` Module -------------------------------------- +GPy.testing.psi_stat_gradient_tests module +------------------------------------------ .. automodule:: GPy.testing.psi_stat_gradient_tests :members: :undoc-members: :show-inheritance: -:mod:`sparse_gplvm_tests` Module --------------------------------- +GPy.testing.sparse_gplvm_tests module +------------------------------------- .. automodule:: GPy.testing.sparse_gplvm_tests :members: :undoc-members: :show-inheritance: -:mod:`unit_tests` Module ------------------------- +GPy.testing.unit_tests module +----------------------------- .. automodule:: GPy.testing.unit_tests :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.testing + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/GPy.util.latent_space_visualizations.controllers.rst b/doc/GPy.util.latent_space_visualizations.controllers.rst new file mode 100644 index 00000000..a88c1f5c --- /dev/null +++ b/doc/GPy.util.latent_space_visualizations.controllers.rst @@ -0,0 +1,30 @@ +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 new file mode 100644 index 00000000..d8cbd843 --- /dev/null +++ b/doc/GPy.util.latent_space_visualizations.rst @@ -0,0 +1,17 @@ +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/GPy.util.rst b/doc/GPy.util.rst index e66329b6..c86280a7 100644 --- a/doc/GPy.util.rst +++ b/doc/GPy.util.rst @@ -1,123 +1,133 @@ -util Package -============ +GPy.util package +================ -:mod:`util` Package -------------------- +Subpackages +----------- -.. automodule:: GPy.util - :members: - :undoc-members: - :show-inheritance: +.. toctree:: -:mod:`Tango` Module -------------------- + GPy.util.latent_space_visualizations + +Submodules +---------- + +GPy.util.Tango module +--------------------- .. automodule:: GPy.util.Tango :members: :undoc-members: :show-inheritance: -:mod:`classification` Module ----------------------------- +GPy.util.classification module +------------------------------ .. automodule:: GPy.util.classification :members: :undoc-members: :show-inheritance: -:mod:`datasets` Module ----------------------- +GPy.util.datasets module +------------------------ .. automodule:: GPy.util.datasets :members: :undoc-members: :show-inheritance: -:mod:`decorators` Module ------------------------- +GPy.util.decorators module +-------------------------- .. automodule:: GPy.util.decorators :members: :undoc-members: :show-inheritance: -:mod:`linalg` Module --------------------- +GPy.util.linalg module +---------------------- .. automodule:: GPy.util.linalg :members: :undoc-members: :show-inheritance: -:mod:`misc` Module ------------------- +GPy.util.misc module +-------------------- .. automodule:: GPy.util.misc :members: :undoc-members: :show-inheritance: -:mod:`mocap` Module -------------------- +GPy.util.mocap module +--------------------- .. automodule:: GPy.util.mocap :members: :undoc-members: :show-inheritance: -:mod:`pca` Module ------------------ +GPy.util.multioutput module +--------------------------- -.. automodule:: GPy.util.pca +.. automodule:: GPy.util.multioutput :members: :undoc-members: :show-inheritance: -:mod:`plot` Module ------------------- +GPy.util.plot module +-------------------- .. automodule:: GPy.util.plot :members: :undoc-members: :show-inheritance: -:mod:`plot_latent` Module -------------------------- +GPy.util.plot_latent module +--------------------------- .. automodule:: GPy.util.plot_latent :members: :undoc-members: :show-inheritance: -:mod:`squashers` Module ------------------------ +GPy.util.squashers module +------------------------- .. automodule:: GPy.util.squashers :members: :undoc-members: :show-inheritance: -:mod:`univariate_Gaussian` Module ---------------------------------- +GPy.util.univariate_Gaussian module +----------------------------------- .. automodule:: GPy.util.univariate_Gaussian :members: :undoc-members: :show-inheritance: -:mod:`visualize` Module ------------------------ +GPy.util.visualize module +------------------------- .. automodule:: GPy.util.visualize :members: :undoc-members: :show-inheritance: -:mod:`warping_functions` Module -------------------------------- +GPy.util.warping_functions module +--------------------------------- .. automodule:: GPy.util.warping_functions :members: :undoc-members: :show-inheritance: + +Module contents +--------------- + +.. automodule:: GPy.util + :members: + :undoc-members: + :show-inheritance: From 9a81c48500edf8f1babaf6b49541c454159fc9a2 Mon Sep 17 00:00:00 2001 From: James Hensman Date: Fri, 20 Sep 2013 11:02:35 +0100 Subject: [PATCH 5/6] added hetero back to the init --- GPy/kern/parts/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GPy/kern/parts/__init__.py b/GPy/kern/parts/__init__.py index 643483f5..22feeb98 100644 --- a/GPy/kern/parts/__init__.py +++ b/GPy/kern/parts/__init__.py @@ -5,7 +5,7 @@ import exponential import finite_dimensional import fixed import gibbs -#import hetero #hetero.py is not commited: omitting for now. JH. +import hetero import hierarchical import independent_outputs import linear From 7af2d62ee60d2e2bd62d2ac0ee1b0e7a1de9f5bf Mon Sep 17 00:00:00 2001 From: James Hensman Date: Fri, 20 Sep 2013 13:03:24 +0100 Subject: [PATCH 6/6] do_test_latents appears to be working now --- GPy/core/sparse_gp.py | 2 +- GPy/models/bayesian_gplvm.py | 12 ++++++++++-- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/GPy/core/sparse_gp.py b/GPy/core/sparse_gp.py index cb96b478..31d2c695 100644 --- a/GPy/core/sparse_gp.py +++ b/GPy/core/sparse_gp.py @@ -292,7 +292,7 @@ class SparseGP(GPBase): Kxx = self.kern.Kdiag(Xnew, which_parts=which_parts) var = Kxx - np.sum(Kx * np.dot(Kmmi_LmiBLmi, Kx), 0) else: - # assert which_p.Tarts=='all', "swithching out parts of variational kernels is not implemented" + # assert which_parts=='all', "swithching out parts of variational kernels is not implemented" Kx = self.kern.psi1(self.Z, Xnew, X_variance_new) # , which_parts=which_parts) TODO: which_parts mu = np.dot(Kx, self.Cpsi1V) if full_cov: diff --git a/GPy/models/bayesian_gplvm.py b/GPy/models/bayesian_gplvm.py index e514ad19..e094d915 100644 --- a/GPy/models/bayesian_gplvm.py +++ b/GPy/models/bayesian_gplvm.py @@ -8,7 +8,7 @@ from .. import kern import itertools from matplotlib.colors import colorConverter from GPy.inference.optimization import SCG -from GPy.util import plot_latent +from GPy.util import plot_latent, linalg from GPy.models.gplvm import GPLVM from GPy.util.plot_latent import most_significant_input_dimensions from matplotlib import pyplot @@ -140,12 +140,20 @@ class BayesianGPLVM(SparseGP, GPLVM): dpsi0 = -0.5 * self.input_dim * self.likelihood.precision dpsi2 = self.dL_dpsi2[0][None, :, :] # TODO: this may change if we ignore het. likelihoods V = self.likelihood.precision * Y + + #compute CPsi1V + if self.Cpsi1V is None: + psi1V = np.dot(self.psi1.T, self.likelihood.V) + tmp, _ = linalg.dtrtrs(self._Lm, np.asfortranarray(psi1V), lower=1, trans=0) + tmp, _ = linalg.dpotrs(self.LB, tmp, lower=1) + self.Cpsi1V, _ = linalg.dtrtrs(self._Lm, tmp, lower=1, trans=1) + dpsi1 = np.dot(self.Cpsi1V, V.T) start = np.zeros(self.input_dim * 2) for n, dpsi1_n in enumerate(dpsi1.T[:, :, None]): - args = (self.kern, self.Z, dpsi0, dpsi1_n, dpsi2) + args = (self.kern, self.Z, dpsi0, dpsi1_n.T, dpsi2) xopt, fopt, neval, status = SCG(f=latent_cost, gradf=latent_grad, x=start, optargs=args, display=False) mu, log_S = xopt.reshape(2, 1, -1)