mirror of
https://github.com/SheffieldML/GPy.git
synced 2026-04-24 20:36:23 +02:00
Merge branch 'devel' of github.com:SheffieldML/GPy into devel
This commit is contained in:
Martin Bubel
commit
cbac99d894
4 changed files with 132 additions and 124 deletions
|
|
@ -2,6 +2,8 @@
|
|||
|
||||
## Unreleased
|
||||
|
||||
* remove python2-style print statements (#1056)
|
||||
|
||||
* update import in `.plotting.matplot_dep.defaults` due to change in matplotlib
|
||||
|
||||
* Correct dl_dm term in student t inference #1065
|
||||
|
|
|
|||
|
|
@ -23,11 +23,11 @@ infr = GPy.inference.latent_function_inference.VarDTC_minibatch(mpi_comm=comm)
|
|||
m = GPy.models.BayesianGPLVM(data.T,1,mpi_comm=comm)
|
||||
m.optimize(max_iters=10)
|
||||
if comm.rank==0:
|
||||
print float(m.objective_function())
|
||||
print(float(m.objective_function()))
|
||||
m.inference_method.mpi_comm=None
|
||||
m.mpi_comm=None
|
||||
m._trigger_params_changed()
|
||||
print float(m.objective_function())
|
||||
print(float(m.objective_function()))
|
||||
"""
|
||||
with open("mpi_test__.py", "w") as f:
|
||||
f.write(code)
|
||||
|
|
@ -59,11 +59,11 @@ data = np.vstack([x,y])
|
|||
m = GPy.models.SparseGPRegression(data[:1].T,data[1:2].T,mpi_comm=comm)
|
||||
m.optimize(max_iters=10)
|
||||
if comm.rank==0:
|
||||
print float(m.objective_function())
|
||||
print(float(m.objective_function()))
|
||||
m.inference_method.mpi_comm=None
|
||||
m.mpi_comm=None
|
||||
m._trigger_params_changed()
|
||||
print float(m.objective_function())
|
||||
print(float(m.objective_function()))
|
||||
"""
|
||||
with open("mpi_test__.py", "w") as f:
|
||||
f.write(code)
|
||||
|
|
|
|||
|
|
@ -1,21 +1,20 @@
|
|||
|
||||
import numpy as np
|
||||
import GPy
|
||||
from mpi4py import MPI
|
||||
|
||||
np.random.seed(123456)
|
||||
comm = MPI.COMM_WORLD
|
||||
N = 100
|
||||
x = np.linspace(-6., 6., N)
|
||||
x = np.linspace(-6.0, 6.0, N)
|
||||
y = np.sin(x) + np.random.randn(N) * 0.05
|
||||
comm.Bcast(y)
|
||||
data = np.vstack([x,y])
|
||||
#infr = GPy.inference.latent_function_inference.VarDTC_minibatch(mpi_comm=comm)
|
||||
m = GPy.models.SparseGPRegression(data[:1].T,data[1:2].T,mpi_comm=comm)
|
||||
data = np.vstack([x, y])
|
||||
# infr = GPy.inference.latent_function_inference.VarDTC_minibatch(mpi_comm=comm)
|
||||
m = GPy.models.SparseGPRegression(data[:1].T, data[1:2].T, mpi_comm=comm)
|
||||
m.optimize(max_iters=10)
|
||||
if comm.rank==0:
|
||||
print float(m.objective_function())
|
||||
m.inference_method.mpi_comm=None
|
||||
m.mpi_comm=None
|
||||
if comm.rank == 0:
|
||||
print(float(m.objective_function()))
|
||||
m.inference_method.mpi_comm = None
|
||||
m.mpi_comm = None
|
||||
m._trigger_params_changed()
|
||||
print float(m.objective_function())
|
||||
|
||||
print(float(m.objective_function()))
|
||||
|
|
|
|||
|
|
@ -19,33 +19,35 @@ import shlex
|
|||
# If extensions (or modules to document with autodoc) are in another directory,
|
||||
# add these directories to sys.path here. If the directory is relative to the
|
||||
# documentation root, use os.path.abspath to make it absolute, like shown here.
|
||||
#for p in os.walk('../../GPy'):
|
||||
# for p in os.walk('../../GPy'):
|
||||
# sys.path.append(p[0])
|
||||
sys.path.insert(0, os.path.abspath('../../'))
|
||||
sys.path.insert(0, os.path.abspath('../../GPy/'))
|
||||
sys.path.insert(0, os.path.abspath("../../"))
|
||||
sys.path.insert(0, os.path.abspath("../../GPy/"))
|
||||
|
||||
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
|
||||
on_rtd = os.environ.get("READTHEDOCS", None) == "True"
|
||||
|
||||
import sys
|
||||
from unittest.mock import MagicMock
|
||||
|
||||
|
||||
class Mock(MagicMock):
|
||||
@classmethod
|
||||
def __getattr__(cls, name):
|
||||
return MagicMock()
|
||||
|
||||
|
||||
MOCK_MODULES = [
|
||||
"GPy.util.linalg.linalg_cython",
|
||||
"GPy.util.linalg_cython",
|
||||
"sympy",
|
||||
'GPy.kern.stationary_cython',
|
||||
"GPy.kern.stationary_cython",
|
||||
"sympy.utilities",
|
||||
"sympy.utilities.lambdify",
|
||||
]
|
||||
|
||||
sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
|
||||
|
||||
#on_rtd = True
|
||||
# on_rtd = True
|
||||
if on_rtd:
|
||||
# sys.path.append(os.path.abspath('../GPy'))
|
||||
|
||||
|
|
@ -63,8 +65,10 @@ if on_rtd:
|
|||
print("$ pwd: ")
|
||||
print(out)
|
||||
|
||||
#Lets regenerate our rst files from the source, -P adds private modules (i.e kern._src)
|
||||
proc = subprocess.Popen("sphinx-apidoc -M -P -f -o . ../../GPy", stdout=subprocess.PIPE, shell=True)
|
||||
# Lets regenerate our rst files from the source, -P adds private modules (i.e kern._src)
|
||||
proc = subprocess.Popen(
|
||||
"sphinx-apidoc -M -P -f -o . ../../GPy", stdout=subprocess.PIPE, shell=True
|
||||
)
|
||||
(out, err) = proc.communicate()
|
||||
print("$ Apidoc:")
|
||||
print(out)
|
||||
|
|
@ -73,84 +77,88 @@ if on_rtd:
|
|||
# -- General configuration ------------------------------------------------
|
||||
|
||||
# If your documentation needs a minimal Sphinx version, state it here.
|
||||
#needs_sphinx = '1.0'
|
||||
# needs_sphinx = '1.0'
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be
|
||||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
|
||||
# ones.
|
||||
extensions = [
|
||||
'sphinx.ext.autodoc',
|
||||
"sphinx.ext.autodoc",
|
||||
#'sphinx.ext.coverage',
|
||||
'sphinx.ext.mathjax',
|
||||
'sphinx.ext.viewcode',
|
||||
'sphinx.ext.graphviz',
|
||||
'sphinx.ext.inheritance_diagram',
|
||||
"sphinx.ext.mathjax",
|
||||
"sphinx.ext.viewcode",
|
||||
"sphinx.ext.graphviz",
|
||||
"sphinx.ext.inheritance_diagram",
|
||||
]
|
||||
|
||||
#---sphinx.ext.inheritance_diagram config
|
||||
# ---sphinx.ext.inheritance_diagram config
|
||||
inheritance_graph_attrs = dict(rankdir="LR", dpi=1200)
|
||||
|
||||
#----- Autodoc
|
||||
#import sys
|
||||
#try:
|
||||
# ----- Autodoc
|
||||
# import sys
|
||||
# try:
|
||||
# from unittest.mock import MagicMock
|
||||
#except:
|
||||
# except:
|
||||
# from mock import Mock as MagicMock
|
||||
#
|
||||
#class Mock(MagicMock):
|
||||
# class Mock(MagicMock):
|
||||
# @classmethod
|
||||
# def __getattr__(cls, name):
|
||||
# return Mock()
|
||||
#
|
||||
#
|
||||
#sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
|
||||
# sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
|
||||
#
|
||||
import sphinx_rtd_theme
|
||||
|
||||
autodoc_default_flags = ['members',
|
||||
#'undoc-members',
|
||||
#'private-members',
|
||||
#'special-members',
|
||||
#'inherited-members',
|
||||
'show-inheritance']
|
||||
autodoc_default_flags = [
|
||||
"members",
|
||||
#'undoc-members',
|
||||
#'private-members',
|
||||
#'special-members',
|
||||
#'inherited-members',
|
||||
"show-inheritance",
|
||||
]
|
||||
|
||||
autodoc_member_order = 'groupwise'
|
||||
autodoc_member_order = "groupwise"
|
||||
add_function_parentheses = False
|
||||
add_module_names = False
|
||||
#modindex_common_prefix = ['GPy']
|
||||
# modindex_common_prefix = ['GPy']
|
||||
show_authors = True
|
||||
|
||||
# ------ Sphinx
|
||||
# Add any paths that contain templates here, relative to this directory.
|
||||
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]#templates_path = ['_templates']
|
||||
html_theme_path = [
|
||||
sphinx_rtd_theme.get_html_theme_path()
|
||||
] # templates_path = ['_templates']
|
||||
|
||||
# The suffix(es) of source filenames.
|
||||
# You can specify multiple suffix as a list of string:
|
||||
# source_suffix = ['.rst', '.md']
|
||||
source_suffix = '.rst'
|
||||
source_suffix = ".rst"
|
||||
|
||||
# The encoding of source files.
|
||||
#source_encoding = 'utf-8-sig'
|
||||
# source_encoding = 'utf-8-sig'
|
||||
|
||||
# The master toctree document.
|
||||
master_doc = 'index'
|
||||
master_doc = "index"
|
||||
|
||||
# General information about the project.
|
||||
project = u'GPy'
|
||||
#author = u'`Humans <https://github.com/SheffieldML/GPy/graphs/contributors>`_'
|
||||
author = 'GPy Authors, see https://github.com/SheffieldML/GPy/graphs/contributors'
|
||||
copyright = u'2020, '+author
|
||||
project = "GPy"
|
||||
# author = u'`Humans <https://github.com/SheffieldML/GPy/graphs/contributors>`_'
|
||||
author = "GPy Authors, see https://github.com/SheffieldML/GPy/graphs/contributors"
|
||||
copyright = "2020, " + author
|
||||
|
||||
# The version info for the project you're documenting, acts as replacement for
|
||||
# |version| and |release|, also used in various other places throughout the
|
||||
# built documents.
|
||||
#
|
||||
# The short X.Y version.
|
||||
with open('../../GPy/__version__.py', 'r') as f:
|
||||
with open("../../GPy/__version__.py", "r") as f:
|
||||
version = f.read()
|
||||
release = version
|
||||
|
||||
print version
|
||||
print(version)
|
||||
|
||||
# version = '0.8.8'
|
||||
# The full version, including alpha/beta/rc tags.
|
||||
|
|
@ -161,27 +169,29 @@ print version
|
|||
#
|
||||
# This is also used if you do content translation via gettext catalogs.
|
||||
# Usually you set "language" from the command line for these cases.
|
||||
language = 'python'
|
||||
language = "python"
|
||||
|
||||
# autodoc:
|
||||
autoclass_content = 'both'
|
||||
autodoc_default_flags = ['members',
|
||||
#'undoc-members',
|
||||
#'private-members',
|
||||
#'special-members',
|
||||
#'inherited-members',
|
||||
'show-inheritance']
|
||||
autodoc_member_order = 'groupwise'
|
||||
autoclass_content = "both"
|
||||
autodoc_default_flags = [
|
||||
"members",
|
||||
#'undoc-members',
|
||||
#'private-members',
|
||||
#'special-members',
|
||||
#'inherited-members',
|
||||
"show-inheritance",
|
||||
]
|
||||
autodoc_member_order = "groupwise"
|
||||
add_function_parentheses = False
|
||||
add_module_names = False
|
||||
modindex_common_prefix = ['paramz']
|
||||
modindex_common_prefix = ["paramz"]
|
||||
show_authors = True
|
||||
|
||||
# There are two options for replacing |today|: either, you set today to some
|
||||
# non-false value, then it is used:
|
||||
#today = ''
|
||||
# today = ''
|
||||
# Else, today_fmt is used as the format for a strftime call.
|
||||
#today_fmt = '%B %d, %Y'
|
||||
# today_fmt = '%B %d, %Y'
|
||||
|
||||
# List of patterns, relative to source directory, that match files and
|
||||
# directories to ignore when looking for source files.
|
||||
|
|
@ -189,27 +199,27 @@ exclude_patterns = []
|
|||
|
||||
# The reST default role (used for this markup: `text`) to use for all
|
||||
# documents.
|
||||
#default_role = None
|
||||
# default_role = None
|
||||
|
||||
# If true, '()' will be appended to :func: etc. cross-reference text.
|
||||
#add_function_parentheses = True
|
||||
# add_function_parentheses = True
|
||||
|
||||
# If true, the current module name will be prepended to all description
|
||||
# unit titles (such as .. function::).
|
||||
#add_module_names = True
|
||||
# add_module_names = True
|
||||
|
||||
# If true, sectionauthor and moduleauthor directives will be shown in the
|
||||
# output. They are ignored by default.
|
||||
#show_authors = False
|
||||
# show_authors = False
|
||||
|
||||
# The name of the Pygments (syntax highlighting) style to use.
|
||||
pygments_style = 'sphinx'
|
||||
pygments_style = "sphinx"
|
||||
|
||||
# A list of ignored prefixes for module index sorting.
|
||||
#modindex_common_prefix = []
|
||||
# modindex_common_prefix = []
|
||||
|
||||
# If true, keep warnings as "system message" paragraphs in the built documents.
|
||||
#keep_warnings = False
|
||||
# keep_warnings = False
|
||||
|
||||
# If true, `todo` and `todoList` produce output, else they produce nothing.
|
||||
todo_include_todos = False
|
||||
|
|
@ -219,62 +229,62 @@ todo_include_todos = False
|
|||
|
||||
# The theme to use for HTML and HTML Help pages. See the documentation for
|
||||
# a list of builtin themes.
|
||||
html_theme = 'sphinx_rtd_theme'
|
||||
html_theme = "sphinx_rtd_theme"
|
||||
|
||||
# Theme options are theme-specific and customize the look and feel of a theme
|
||||
# further. For a list of options available for each theme, see the
|
||||
# documentation.
|
||||
#html_theme_options = dict(sidebarwidth='20}
|
||||
# html_theme_options = dict(sidebarwidth='20}
|
||||
|
||||
# Add any paths that contain custom themes here, relative to this directory.
|
||||
#html_theme_path = []
|
||||
# html_theme_path = []
|
||||
|
||||
# The name for this set of Sphinx documents. If None, it defaults to
|
||||
# "<project> v<release> documentation".
|
||||
#html_title = None
|
||||
# html_title = None
|
||||
|
||||
# A shorter title for the navigation bar. Default is the same as html_title.
|
||||
#html_short_title = None
|
||||
# html_short_title = None
|
||||
|
||||
# The name of an image file (relative to this directory) to place at the top
|
||||
# of the sidebar.
|
||||
#html_logo = None
|
||||
# html_logo = None
|
||||
|
||||
# The name of an image file (within the static path) to use as favicon of the
|
||||
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
|
||||
# pixels large.
|
||||
#html_favicon = None
|
||||
# html_favicon = None
|
||||
|
||||
# Add any paths that contain custom static files (such as style sheets) here,
|
||||
# relative to this directory. They are copied after the builtin static files,
|
||||
# so a file named "default.css" will overwrite the builtin "default.css".
|
||||
html_static_path = ['_static']
|
||||
html_static_path = ["_static"]
|
||||
|
||||
html_css_files = [
|
||||
'wide.css',
|
||||
"wide.css",
|
||||
]
|
||||
|
||||
# Add any extra paths that contain custom files (such as robots.txt or
|
||||
# .htaccess) here, relative to this directory. These files are copied
|
||||
# directly to the root of the documentation.
|
||||
#html_extra_path = []
|
||||
# html_extra_path = []
|
||||
|
||||
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
|
||||
# using the given strftime format.
|
||||
#html_last_updated_fmt = '%b %d, %Y'
|
||||
# html_last_updated_fmt = '%b %d, %Y'
|
||||
|
||||
# If true, SmartyPants will be used to convert quotes and dashes to
|
||||
# typographically correct entities.
|
||||
#html_use_smartypants = True
|
||||
# html_use_smartypants = True
|
||||
|
||||
# Custom sidebar templates, maps document names to template names.
|
||||
#html_sidebars = {
|
||||
# html_sidebars = {
|
||||
# '**': ['globaltoc.html', 'localtoc.html', 'sourcelink.html', 'searchbox.html'],
|
||||
# 'using/windows': ['windowssidebar.html', 'searchbox.html'],
|
||||
#}
|
||||
# }
|
||||
# Additional templates that should be rendered to pages, maps page names to
|
||||
# template names.
|
||||
#html_additional_pages = {}
|
||||
# html_additional_pages = {}
|
||||
|
||||
# If false, no module index is generated.
|
||||
html_domain_indices = False
|
||||
|
|
@ -289,92 +299,89 @@ html_split_index = True
|
|||
html_show_sourcelink = True
|
||||
|
||||
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
|
||||
#html_show_sphinx = True
|
||||
# html_show_sphinx = True
|
||||
|
||||
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
|
||||
#html_show_copyright = True
|
||||
# html_show_copyright = True
|
||||
|
||||
# If true, an OpenSearch description file will be output, and all pages will
|
||||
# contain a <link> tag referring to it. The value of this option must be the
|
||||
# base URL from which the finished HTML is served.
|
||||
#html_use_opensearch = ''
|
||||
# html_use_opensearch = ''
|
||||
|
||||
# This is the file name suffix for HTML files (e.g. ".xhtml").
|
||||
#html_file_suffix = None
|
||||
# html_file_suffix = None
|
||||
|
||||
# Language to be used for generating the HTML full-text search index.
|
||||
# Sphinx supports the following languages:
|
||||
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
|
||||
# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
|
||||
#html_search_language = 'en'
|
||||
# html_search_language = 'en'
|
||||
|
||||
# A dictionary with options for the search language support, empty by default.
|
||||
# Now only 'ja' uses this config value
|
||||
#html_search_options = {'type': 'default'}
|
||||
# html_search_options = {'type': 'default'}
|
||||
|
||||
# The name of a javascript file (relative to the configuration directory) that
|
||||
# implements a search results scorer. If empty, the default will be used.
|
||||
#html_search_scorer = 'scorer.js'
|
||||
# html_search_scorer = 'scorer.js'
|
||||
|
||||
# Output file base name for HTML help builder.
|
||||
htmlhelp_basename = 'GPydoc'
|
||||
htmlhelp_basename = "GPydoc"
|
||||
|
||||
# -- Options for LaTeX output ---------------------------------------------
|
||||
|
||||
latex_elements = {
|
||||
# The paper size ('letterpaper' or 'a4paper').
|
||||
'papersize': 'a4paper',
|
||||
|
||||
# The font size ('10pt', '11pt' or '12pt').
|
||||
#'pointsize': '10pt',
|
||||
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
#'preamble': '',
|
||||
|
||||
# Latex figure (float) alignment
|
||||
'figure_align': 'htbp',
|
||||
# The paper size ('letterpaper' or 'a4paper').
|
||||
"papersize": "a4paper",
|
||||
# The font size ('10pt', '11pt' or '12pt').
|
||||
#'pointsize': '10pt',
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
#'preamble': '',
|
||||
# Latex figure (float) alignment
|
||||
"figure_align": "htbp",
|
||||
}
|
||||
|
||||
# Grouping the document tree into LaTeX files. List of tuples
|
||||
# (source start file, target name, title,
|
||||
# author, documentclass [howto, manual, or own class]).
|
||||
#latex_documents = [
|
||||
# latex_documents = [
|
||||
# (master_doc, 'GPy.tex', u'GPy Documentation',
|
||||
# u'GPy Authors', 'manual'),
|
||||
#]
|
||||
# ]
|
||||
|
||||
# The name of an image file (relative to this directory) to place at the top of
|
||||
# the title page.
|
||||
#latex_logo = None
|
||||
# latex_logo = None
|
||||
|
||||
# For "manual" documents, if this is true, then toplevel headings are parts,
|
||||
# not chapters.
|
||||
#latex_use_parts = False
|
||||
# latex_use_parts = False
|
||||
|
||||
# If true, show page references after internal links.
|
||||
#latex_show_pagerefs = False
|
||||
# latex_show_pagerefs = False
|
||||
|
||||
# If true, show URL addresses after external links.
|
||||
#latex_show_urls = False
|
||||
# latex_show_urls = False
|
||||
|
||||
# Documents to append as an appendix to all manuals.
|
||||
#latex_appendices = []
|
||||
# latex_appendices = []
|
||||
|
||||
# If false, no module index is generated.
|
||||
#latex_domain_indices = True
|
||||
# latex_domain_indices = True
|
||||
|
||||
|
||||
# -- Options for manual page output ---------------------------------------
|
||||
|
||||
# One entry per manual page. List of tuples
|
||||
# (source start file, name, description, authors, manual section).
|
||||
#man_pages = [
|
||||
# man_pages = [
|
||||
# (master_doc, 'gpy', u'GPy Documentation',
|
||||
# [author], 1)
|
||||
#]
|
||||
# ]
|
||||
|
||||
# If true, show URL addresses after external links.
|
||||
#man_show_urls = False
|
||||
# man_show_urls = False
|
||||
|
||||
|
||||
# -- Options for Texinfo output -------------------------------------------
|
||||
|
|
@ -382,20 +389,20 @@ latex_elements = {
|
|||
# Grouping the document tree into Texinfo files. List of tuples
|
||||
# (source start file, target name, title, author,
|
||||
# dir menu entry, description, category)
|
||||
#texinfo_documents = [
|
||||
# texinfo_documents = [
|
||||
# (master_doc, 'GPy', u'GPy Documentation',
|
||||
# author, 'GPy', 'One line description of project.',
|
||||
# 'Miscellaneous'),
|
||||
#]
|
||||
# ]
|
||||
|
||||
# Documents to append as an appendix to all manuals.
|
||||
#texinfo_appendices = []
|
||||
# texinfo_appendices = []
|
||||
|
||||
# If false, no module index is generated.
|
||||
#texinfo_domain_indices = True
|
||||
# texinfo_domain_indices = True
|
||||
|
||||
# How to display URL addresses: 'footnote', 'no', or 'inline'.
|
||||
#texinfo_show_urls = 'footnote'
|
||||
# texinfo_show_urls = 'footnote'
|
||||
|
||||
# If true, do not generate a @detailmenu in the "Top" node's menu.
|
||||
#texinfo_no_detailmenu = False
|
||||
# texinfo_no_detailmenu = False
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue