conf.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# liEensemble documentation build configuration file, created by
# sphinx-quickstart on Fri Aug 18 11:52:31 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

# 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.
#
import os
import sys
from datetime import datetime

exec(open("../libensemble/version.py").read())


if sys.version_info >= (3, 3):
    from unittest.mock import MagicMock
else:
    from mock import MagicMock


class Mock(MagicMock):
    @classmethod
    def __getattr__(cls, name):
        return MagicMock()


MOCK_MODULES = [
    "argparse",
    "dfols",
    "math",
    "mpi4py",
    "mpmath",
    "nlopt",
    "numpy",
    "numpy.lib",
    "numpy.lib.recfunctions",
    "numpy.linalg",
    "PETSc",
    "petsc4py",
    "psutil",
    "scipy",
    "scipy.io",
    "scipy.sparse",
    "scipy.spatial",
    "scipy.spatial.distance",
    "scipy.stats",
    "surmise.calibration",
    "surmise.emulation",
    "Tasmanian",
]

sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

# from libensemble import *
# from libensemble.alloc_funcs import *
# from libensemble.gen_funcs import *
# from libensemble.sim_funcs import *


# sys.path.insert(0, os.path.abspath('.'))
sys.path.append(os.path.abspath("../libensemble"))
##sys.path.append(os.path.abspath('../libensemble'))
sys.path.append(os.path.abspath("../libensemble/alloc_funcs"))
sys.path.append(os.path.abspath("../libensemble/gen_funcs"))
sys.path.append(os.path.abspath("../libensemble/sim_funcs"))
sys.path.append(os.path.abspath("../libensemble/comms"))
sys.path.append(os.path.abspath("../libensemble/utils"))
sys.path.append(os.path.abspath("../libensemble/tools"))
sys.path.append(os.path.abspath("../libensemble/executors"))
sys.path.append(os.path.abspath("../libensemble/executors/balsam_executors"))
sys.path.append(os.path.abspath("../libensemble/resources"))
# print(sys.path)

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
needs_sphinx = "3.3"

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    "sphinxcontrib.bibtex",
    "sphinx.ext.autodoc",
    "sphinx.ext.napoleon",
    # 'sphinx.ext.autosectionlabel',
    "sphinx.ext.intersphinx",
    "sphinx.ext.imgconverter",
    "sphinx.ext.mathjax",
]
bibtex_bibfiles = ["references.bib"]
bibtex_default_style = "unsrt"
# autosectionlabel_prefix_document = True
# extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.imgconverter']
# breathe_projects = { "libEnsemble": "../code/src/xml/" }
# breathe_default_project = "libEnsemble"

##breathe_projects_source = {"libEnsemble" : ( "../code/src/", ["libE.py", "test.cpp"] )}
# breathe_projects_source = {"libEnsemble" : ( "../code/src/", ["test.cpp","test2.cpp"] )}

intersphinx_mapping = {
    "community": ("https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/", None)
}

autodoc_mock_imports = ["balsam"]
extlinks = {
    "duref": ("http://docutils.sourceforge.net/docs/ref/rst/" "restructuredtext.html#%s", ""),
    "durole": ("http://docutils.sourceforge.net/docs/ref/rst/" "roles.html#%s", ""),
    "dudir": ("http://docutils.sourceforge.net/docs/ref/rst/" "directives.html#%s", ""),
}

# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]

# Configure bibtex_bibfiles setting for sphinxcontrib-bibtex 2.0.0
bibtex_bibfiles = ["references.bib"]

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = ".rst"

# The master toctree document.
master_doc = "index"

# The latex toctree document.
latex_doc = "latex_index"

# General information about the project.
project = "libEnsemble"
copyright = str(datetime.now().year) + " Argonne National Laboratory"
author = "Jeffrey Larson, Stephen Hudson, Stefan M. Wild, David Bindel and John-Luke Navarro"
today_fmt = "%B %-d, %Y"

# 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.
version = __version__
# The full version, including alpha/beta/rc tags.
release = __version__

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = "sphinx"

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False


# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
# html_theme = 'alabaster'
# html_theme = 'default'
# html_theme = 'graphite'
# html_theme = 'sphinxdoc'
html_theme = "sphinx_rtd_theme"

html_logo = "./images/libE_logo_white.png"

# 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 = {
    "navigation_depth": 3,
    "collapse_navigation": False,
    "logo_only": True,
}

# 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 = []


def setup(app):
    app.add_css_file("my_theme.css")


# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# This is required for the alabaster theme
# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
# html_sidebars = {
#    '**': [
#        'about.html',
#        'navigation.html',
#        'relations.html',  # needs 'show_related': True theme option to display
#        'searchbox.html',
#        'donate.html',
#    ]
# }


# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = "libEnsembledoc"


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
    # Sonny, Lenny, or Bjornstrup
    "fncychap": "\\usepackage[Lenny]{fncychap}",
    "extraclassoptions": "openany",
    "preamble": r"""
    \protected\def\sphinxcrossref#1{\texttt{#1}}

    \newsavebox\mytempbox
    \definecolor{sphinxnoteBgColor}{RGB}{221,233,239}
    \renewenvironment{sphinxnote}[1]{%
    \begin{lrbox}{\mytempbox}%
    \begin{minipage}{\columnwidth}%
    \begin{sphinxlightbox}%
    \sphinxstrong{#1}}%
    {\end{sphinxlightbox}%
    \end{minipage}%
    \end{lrbox}%
    \colorbox{sphinxnoteBgColor}{\usebox{\mytempbox}}}
                """,
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',
    # 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_doc,
        "libEnsemble.tex",
        "libEnsemble User Manual",
        "Stephen Hudson, Jeffrey Larson, Stefan M. Wild, \\\\ \\hfill David Bindel, John-Luke Navarro",
        "manual",
    ),
]

latex_logo = "images/libE_logo.png"

# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [(latex_doc, "libEnsemble", "libEnsemble User Manual", [author], 1)]


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (
        latex_doc,
        "libEnsemble",
        "libEnsemble User Manual",
        author,
        "libEnsemble",
        "One line description of project.",
        "Miscellaneous",
    ),
]