Added kern _src files using api-doc -P ../doc ../ to include private modules

This commit is contained in:
Alan Saul 2014-11-04 16:16:16 +00:00
parent 6f78a724fc
commit 8ed9f0735a
6 changed files with 490 additions and 10 deletions

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GPy.kern._src.psi_comp package
==============================
Submodules
----------
GPy.kern._src.psi_comp.linear_psi_comp module
---------------------------------------------
.. automodule:: GPy.kern._src.psi_comp.linear_psi_comp
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.psi_comp.rbf_psi_comp module
------------------------------------------
.. automodule:: GPy.kern._src.psi_comp.rbf_psi_comp
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.psi_comp.rbf_psi_gpucomp module
---------------------------------------------
.. automodule:: GPy.kern._src.psi_comp.rbf_psi_gpucomp
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.psi_comp.sslinear_psi_comp module
-----------------------------------------------
.. automodule:: GPy.kern._src.psi_comp.sslinear_psi_comp
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.psi_comp.ssrbf_psi_comp module
--------------------------------------------
.. automodule:: GPy.kern._src.psi_comp.ssrbf_psi_comp
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.psi_comp.ssrbf_psi_gpucomp module
-----------------------------------------------
.. automodule:: GPy.kern._src.psi_comp.ssrbf_psi_gpucomp
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.kern._src.psi_comp
:members:
:undoc-members:
:show-inheritance:

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GPy.kern._src package
=====================
Subpackages
-----------
.. toctree::
GPy.kern._src.psi_comp
Submodules
----------
GPy.kern._src.ODE_UY module
---------------------------
.. automodule:: GPy.kern._src.ODE_UY
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.ODE_UYC module
----------------------------
.. automodule:: GPy.kern._src.ODE_UYC
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.ODE_st module
---------------------------
.. automodule:: GPy.kern._src.ODE_st
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.ODE_t module
--------------------------
.. automodule:: GPy.kern._src.ODE_t
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.add module
------------------------
.. automodule:: GPy.kern._src.add
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.brownian module
-----------------------------
.. automodule:: GPy.kern._src.brownian
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.coregionalize module
----------------------------------
.. automodule:: GPy.kern._src.coregionalize
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.hierarchical module
---------------------------------
.. automodule:: GPy.kern._src.hierarchical
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.independent_outputs module
----------------------------------------
.. automodule:: GPy.kern._src.independent_outputs
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.kern module
-------------------------
.. automodule:: GPy.kern._src.kern
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.kernel_slice_operations module
--------------------------------------------
.. automodule:: GPy.kern._src.kernel_slice_operations
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.linear module
---------------------------
.. automodule:: GPy.kern._src.linear
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.mlp module
------------------------
.. automodule:: GPy.kern._src.mlp
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.periodic module
-----------------------------
.. automodule:: GPy.kern._src.periodic
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.poly module
-------------------------
.. automodule:: GPy.kern._src.poly
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.prod module
-------------------------
.. automodule:: GPy.kern._src.prod
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.rbf module
------------------------
.. automodule:: GPy.kern._src.rbf
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.splitKern module
------------------------------
.. automodule:: GPy.kern._src.splitKern
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.static module
---------------------------
.. automodule:: GPy.kern._src.static
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.stationary module
-------------------------------
.. automodule:: GPy.kern._src.stationary
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.symbolic module
-----------------------------
.. automodule:: GPy.kern._src.symbolic
:members:
:undoc-members:
:show-inheritance:
GPy.kern._src.trunclinear module
--------------------------------
.. automodule:: GPy.kern._src.trunclinear
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: GPy.kern._src
:members:
:undoc-members:
:show-inheritance:

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@ -1,6 +1,13 @@
GPy.kern package GPy.kern package
================ ================
Subpackages
-----------
.. toctree::
GPy.kern._src
Module contents Module contents
--------------- ---------------

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@ -60,14 +60,6 @@ GPy.likelihoods.mixed_noise module
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
GPy.likelihoods.ordinal module
------------------------------
.. automodule:: GPy.likelihoods.ordinal
:members:
:undoc-members:
:show-inheritance:
GPy.likelihoods.poisson module GPy.likelihoods.poisson module
------------------------------ ------------------------------

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@ -11,8 +11,29 @@
# 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_default_flags = ['members', 'show-inheritance', 'private-members', 'special-members']
autodoc_member_order = "source" #autodoc_default_flags = ['private-members', 'special-members']
#autodoc_default_flags = 'private-members'
#autodoc_member_order = "source"
#def autodoc_skip_member(app, what, name, obj, skip, options):
#exclusions = ('__weakref__', # special-members
#'__doc__', '__module__', '__dict__', # undoc-members
#)
#exclude = name in exclusions
#inclusions = ('_src')
#include = name in inclusions
#if include:
#print app, what, name, obj, skip, options
#return False
#return skip or exclude
#def setup(app):
##app.connect('autodoc-process-docstring', cut_lines(2))
##app.connect('autodoc_default_flags', autodoc_default_flags)
##app.connect('autodoc_member_order', autodoc_member_order)
#app.connect('autodoc-skip-member', autodoc_skip_member)
import sys import sys
import os import os
@ -114,6 +135,7 @@ MOCK_MODULES = ['sympy',
for mod_name in MOCK_MODULES: for mod_name in MOCK_MODULES:
sys.modules[mod_name] = Mock() sys.modules[mod_name] = Mock()
# ----------------------- READTHEDOCS ------------------ # ----------------------- READTHEDOCS ------------------
on_rtd = os.environ.get('READTHEDOCS', None) == 'True' on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

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/home/alans/Work/GPy/GPy/__init__.py:docstring of GPy.load:1: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP:7: WARNING: Field list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP:10: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/core/gp.py:docstring of GPy.core.gp.GP.predictive_gradients:5: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/core/model.py:docstring of GPy.core.model.Model.optimize_restarts:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/doc/GPy.core.rst:65: WARNING: autodoc: failed to import module u'GPy.core.symbolic'; the following exception was raised:
Traceback (most recent call last):
File "/home/alans/anaconda/envs/GPy/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 335, in import_object
__import__(self.modname)
File "/home/alans/Work/GPy/GPy/core/symbolic.py", line 10, in <module>
from sympy.utilities.lambdify import lambdastr, _imp_namespace, _get_namespace
ImportError: No module named lambdify
/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Indexable.unset_priors:1: WARNING: Inline emphasis start-string without end-string.
/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Nameable.hierarchy_name:4: WARNING: Field list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Observable.notify_observers:5: SEVERE: Unexpected section title or transition.
^^^^^^^^^^^^^^^^
/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Observable.notify_observers:6: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Parameterizable.traverse:1: WARNING: Inline emphasis start-string without end-string.
/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py:docstring of GPy.core.parameterization.parameter_core.Parameterizable.traverse:1: WARNING: Inline strong start-string without end-string.
/home/alans/Work/GPy/GPy/core/parameterization/parameterized.py:docstring of GPy.core.parameterization.parameterized.Parameterized:18: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/core/parameterization/parameterized.py:docstring of GPy.core.parameterization.parameterized.Parameterized:20: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/core/parameterization/ties_and_remappings.py:docstring of GPy.core.parameterization.ties_and_remappings.Tie:18: SEVERE: Unexpected section title or transition.
================================
/home/alans/Work/GPy/doc/GPy.examples.rst:18: WARNING: autodoc: failed to import module u'GPy.examples.coreg_example'; the following exception was raised:
Traceback (most recent call last):
File "/home/alans/anaconda/envs/GPy/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 335, in import_object
__import__(self.modname)
File "/home/alans/Work/GPy/GPy/examples/coreg_example.py", line 44, in <module>
m = GPy.models.SparseGPCoregionalizedRegression(X_list=[X1], Y_list=[Y1], Z_list = [Z1], kernel=kern)
File "/home/alans/Work/GPy/GPy/core/parameterization/parameterized.py", line 19, in __call__
self = super(ParametersChangedMeta, self).__call__(*args, **kw)
File "/home/alans/Work/GPy/GPy/models/sparse_gp_coregionalized_regression.py", line 66, in __init__
self['.*inducing'][:,-1].fix()
File "/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py", line 444, in constrain_fixed
self.notify_observers(self, None if trigger_parent else -np.inf)
File "/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py", line 148, in notify_observers
[callble(self, which=which) for _, _, callble in self.observers]
File "/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py", line 1077, in _pass_through_notify_observers
self.notify_observers(which=which)
File "/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py", line 148, in notify_observers
[callble(self, which=which) for _, _, callble in self.observers]
File "/home/alans/Work/GPy/GPy/core/parameterization/parameter_core.py", line 1075, in _parameters_changed_notification
self.parameters_changed()
File "/home/alans/Work/GPy/GPy/core/sparse_gp.py", line 66, in parameters_changed
self.posterior, self._log_marginal_likelihood, self.grad_dict = self.inference_method.inference(self.kern, self.X, self.Z, self.likelihood, self.Y, self.Y_metadata)
File "/home/alans/Work/GPy/GPy/inference/latent_function_inference/var_dtc.py", line 170, in inference
import ipdb; ipdb.set_trace()
ImportError: No module named ipdb
/home/alans/Work/GPy/GPy/kern/_src/coregionalize.py:docstring of GPy.kern._src.coregionalize.Coregionalize:5: ERROR: Unexpected indentation.
/home/alans/Work/GPy/doc/GPy.kern._src.rst:73: WARNING: autodoc: failed to import module u'GPy.kern._src.hierarchical'; the following exception was raised:
Traceback (most recent call last):
File "/home/alans/anaconda/envs/GPy/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 335, in import_object
__import__(self.modname)
File "/home/alans/Work/GPy/GPy/kern/_src/hierarchical.py", line 4, in <module>
from kernpart import Kernpart
ImportError: No module named kernpart
/home/alans/Work/GPy/GPy/kern/_src/independent_outputs.py:docstring of GPy.kern._src.independent_outputs.IndependentOutputs:9: WARNING: Field list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:22: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/kern/_src/stationary.py:docstring of GPy.kern._src.stationary.Stationary:23: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/doc/GPy.kern._src.rst:177: WARNING: autodoc: failed to import module u'GPy.kern._src.symbolic'; the following exception was raised:
Traceback (most recent call last):
File "/home/alans/anaconda/envs/GPy/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 335, in import_object
__import__(self.modname)
File "/home/alans/Work/GPy/GPy/kern/_src/symbolic.py", line 5, in <module>
from ...core.symbolic import Symbolic_core
File "/home/alans/Work/GPy/GPy/core/symbolic.py", line 10, in <module>
from sympy.utilities.lambdify import lambdastr, _imp_namespace, _get_namespace
ImportError: No module named lambdify
/home/alans/Work/GPy/GPy/models/gp_kronecker_gaussian_regression.py:docstring of GPy.models.gp_kronecker_gaussian_regression.GPKroneckerGaussianRegression:13: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/models/gp_kronecker_gaussian_regression.py:docstring of GPy.models.gp_kronecker_gaussian_regression.GPKroneckerGaussianRegression:18: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/models/gp_var_gauss.py:docstring of GPy.models.gp_var_gauss.GPVariationalGaussianApproximation:9: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:32: WARNING: Field list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:32: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/alans/Work/GPy/GPy/models/mrd.py:docstring of GPy.models.mrd.MRD:34: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/models/sparse_gp_minibatch.py:docstring of GPy.models.sparse_gp_minibatch.SparseGPMiniBatch:2: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/plotting/matplot_dep/netpbmfile.py:docstring of GPy.plotting.matplot_dep.netpbmfile.imread:6: SEVERE: Unexpected section title.
Examples
--------
/home/alans/Work/GPy/GPy/plotting/matplot_dep/netpbmfile.py:docstring of GPy.plotting.matplot_dep.netpbmfile.imsave:4: SEVERE: Unexpected section title.
Examples
--------
/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_checkgrad:6: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_checkgrad:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/GPy/testing/likelihood_tests.py:docstring of GPy.testing.likelihood_tests.dparam_partial:9: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/util/datasets.py:docstring of GPy.util.datasets.hapmap3:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/doc/GPy.util.rst:2: SEVERE: Duplicate ID: "module-GPy.util.diag".
/home/alans/Work/GPy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imread:6: SEVERE: Unexpected section title.
Examples
--------
/home/alans/Work/GPy/GPy/util/netpbmfile.py:docstring of GPy.util.netpbmfile.imsave:4: SEVERE: Unexpected section title.
Examples
--------
/home/alans/Work/GPy/doc/GPy.util.rst:2: SEVERE: Duplicate ID: "module-GPy.util.subarray_and_sorting".
/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:8: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:11: SEVERE: Unexpected section title.
Examples:
=========
/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:19: ERROR: Unexpected indentation.
/home/alans/Work/GPy/GPy/util/subarray_and_sorting.py:docstring of GPy.util.subarray_and_sorting.common_subarrays:21: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/alans/Work/GPy/doc/installation.rst:22: ERROR: Unexpected indentation.
/home/alans/Work/GPy/doc/installation.rst:27: ERROR: Unexpected indentation.
/home/alans/Work/GPy/doc/tuto_creating_new_kernels.rst:58: WARNING: Inline literal start-string without end-string.
/home/alans/Work/GPy/doc/tuto_creating_new_models.rst:24: ERROR: Unknown target name: "parameterized".
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short.
Interacting with Parameters:
=======================
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:83: WARNING: Title underline too short.
Interacting with Parameters:
=======================
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:109: WARNING: Title underline too short.
Regular expressions
----------------
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:164: WARNING: Title underline too short.
Setting and fetching parameters `parameter_array`
------------------------------------------
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:164: WARNING: Title underline too short.
Setting and fetching parameters `parameter_array`
------------------------------------------
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:220: WARNING: Title underline too short.
Getting the model parameter's gradients
============================
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:220: WARNING: Title underline too short.
Getting the model parameter's gradients
============================
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short.
Adjusting the model's constraints
================================
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:236: WARNING: Title underline too short.
Adjusting the model's constraints
================================
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:287: WARNING: Title underline too short.
Available Constraints
==============
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:287: WARNING: Title underline too short.
Available Constraints
==============
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short.
Tying Parameters
============
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:299: WARNING: Title underline too short.
Tying Parameters
============
/home/alans/Work/GPy/doc/tuto_parameterized.rst:3: WARNING: Title overline too short.
*******************
Parameterization handling
*******************
/home/alans/Work/GPy/doc/tuto_parameterized.rst:10: WARNING: Title underline too short.
Parameter handles
==============
/home/alans/Work/GPy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short.
:py:class:`~GPy.core.parameterization.parameterized.Parameterized`
==========
/home/alans/Work/GPy/doc/tuto_parameterized.rst:16: WARNING: Title underline too short.
:py:class:`~GPy.core.parameterization.parameterized.Parameterized`
==========
/home/alans/Work/GPy/doc/tuto_parameterized.rst:21: WARNING: Title underline too short.
:py:class:`~GPy.core.parameterization.param.Param`
===========
/home/alans/Work/GPy/doc/tuto_parameterized.rst:21: WARNING: Title underline too short.
:py:class:`~GPy.core.parameterization.param.Param`
===========
/home/alans/Work/GPy/doc/kernel_implementation.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/modules.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/tuto_GP_regression.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/tuto_creating_new_kernels.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/tuto_creating_new_models.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/tuto_kernel_overview.rst:: WARNING: document isn't included in any toctree
/home/alans/Work/GPy/doc/tuto_parameterized.rst:: WARNING: document isn't included in any toctree
WARNING: dvipng command 'dvipng' cannot be run (needed for math display), check the pngmath_dvipng setting
/home/alans/Work/GPy/doc/tuto_interacting_with_models.rst:336: WARNING: undefined label: creating_new_kernels (if the link has no caption the label must precede a section header)
WARNING: html_static_path entry u'/home/alans/Work/GPy/doc/_static' does not exist