Read the Docs build information
Build id: 934051
Project: institute-for-disease-modeling-pycomps
Version: latest
Commit: 03fc1fba88b2ee7abcf64537fd63d2414690d50c
Date: 2022-05-02T22:51:59.716834Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-05-02T22:52:01.568329Z, end-time: 2022-05-02T22:52:04.404963Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/pyCOMPS.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-05-02T22:52:04.604224Z, end-time: 2022-05-02T22:52:04.740014Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 03fc1fb Merge pull request #43 from InstituteforDiseaseModeling/add_utilities

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git clean -d -f -f


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python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-05-02T22:52:10.661615Z, end-time: 2022-05-02T22:52:12.515587Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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[rtd-command-info] start-time: 2022-05-02T22:52:12.694115Z, end-time: 2022-05-02T22:52:20.558981Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0
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Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.8 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.9

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python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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[rtd-command-info] start-time: 2022-05-02T22:52:26.889810Z, end-time: 2022-05-02T22:52:27.845482Z, duration: 0, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating pyCOMPS.egg-info
writing pyCOMPS.egg-info/PKG-INFO
writing dependency_links to pyCOMPS.egg-info/dependency_links.txt
writing entry points to pyCOMPS.egg-info/entry_points.txt
writing requirements to pyCOMPS.egg-info/requires.txt
writing top-level names to pyCOMPS.egg-info/top_level.txt
writing manifest file 'pyCOMPS.egg-info/SOURCES.txt'
reading manifest file 'pyCOMPS.egg-info/SOURCES.txt'
adding license file 'LICENSE.txt'
writing manifest file 'pyCOMPS.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/COMPS
copying COMPS/CredentialPrompt.py -> build/lib/COMPS
copying COMPS/AuthManager.py -> build/lib/COMPS
copying COMPS/__main__.py -> build/lib/COMPS
copying COMPS/Client.py -> build/lib/COMPS
copying COMPS/__init__.py -> build/lib/COMPS
creating build/lib/COMPS/Data
copying COMPS/Data/AssetCollectionFile.py -> build/lib/COMPS/Data
copying COMPS/Data/Priority.py -> build/lib/COMPS/Data
copying COMPS/Data/WorkItemFile.py -> build/lib/COMPS/Data
copying COMPS/Data/BaseEntity.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetType.py -> build/lib/COMPS/Data
copying COMPS/Data/Configuration.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetFile.py -> build/lib/COMPS/Data
copying COMPS/Data/Simulation.py -> build/lib/COMPS/Data
copying COMPS/Data/Suite.py -> build/lib/COMPS/Data
copying COMPS/Data/OutputFileMetadata.py -> build/lib/COMPS/Data
copying COMPS/Data/SimulationFile.py -> build/lib/COMPS/Data
copying COMPS/Data/TaggableEntity.py -> build/lib/COMPS/Data
copying COMPS/Data/QueryCriteria.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetCollection.py -> build/lib/COMPS/Data
copying COMPS/Data/WorkItem.py -> build/lib/COMPS/Data
copying COMPS/Data/HpcJob.py -> build/lib/COMPS/Data
copying COMPS/Data/__init__.py -> build/lib/COMPS/Data
copying COMPS/Data/Experiment.py -> build/lib/COMPS/Data
copying COMPS/Data/CommissionableEntity.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetManager.py -> build/lib/COMPS/Data
copying COMPS/Data/SerializableEntity.py -> build/lib/COMPS/Data
creating build/lib/COMPS/utils
copying COMPS/utils/__example_utility_template__.py -> build/lib/COMPS/utils
copying COMPS/utils/get_output_files_for_experiment.py -> build/lib/COMPS/utils
copying COMPS/utils/main.py -> build/lib/COMPS/utils
copying COMPS/utils/__init__.py -> build/lib/COMPS/utils
creating build/lib/COMPS/Data/WorkItems
copying COMPS/Data/WorkItems/BuilderWorkItem.py -> build/lib/COMPS/Data/WorkItems
copying COMPS/Data/WorkItems/__init__.py -> build/lib/COMPS/Data/WorkItems
copying COMPS/logging.ini -> build/lib/COMPS
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/CredentialPrompt.py -> build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/AuthManager.py -> build/bdist.linux-x86_64/egg/COMPS
creating build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetCollectionFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/Priority.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/WorkItemFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/BaseEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetType.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/Configuration.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/Simulation.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/Suite.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/OutputFileMetadata.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/SimulationFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/TaggableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/QueryCriteria.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetCollection.py -> build/bdist.linux-x86_64/egg/COMPS/Data
creating build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems
copying build/lib/COMPS/Data/WorkItems/BuilderWorkItem.py -> build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems
copying build/lib/COMPS/Data/WorkItems/__init__.py -> build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems
copying build/lib/COMPS/Data/WorkItem.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/HpcJob.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/__init__.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/Experiment.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/CommissionableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetManager.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/SerializableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/__main__.py -> build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/Client.py -> build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/logging.ini -> build/bdist.linux-x86_64/egg/COMPS
creating build/bdist.linux-x86_64/egg/COMPS/utils
copying build/lib/COMPS/utils/__example_utility_template__.py -> build/bdist.linux-x86_64/egg/COMPS/utils
copying build/lib/COMPS/utils/get_output_files_for_experiment.py -> build/bdist.linux-x86_64/egg/COMPS/utils
copying build/lib/COMPS/utils/main.py -> build/bdist.linux-x86_64/egg/COMPS/utils
copying build/lib/COMPS/utils/__init__.py -> build/bdist.linux-x86_64/egg/COMPS/utils
copying build/lib/COMPS/__init__.py -> build/bdist.linux-x86_64/egg/COMPS
byte-compiling build/bdist.linux-x86_64/egg/COMPS/CredentialPrompt.py to CredentialPrompt.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/AuthManager.py to AuthManager.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollectionFile.py to AssetCollectionFile.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Priority.py to Priority.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItemFile.py to WorkItemFile.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/BaseEntity.py to BaseEntity.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetType.py to AssetType.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Configuration.py to Configuration.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetFile.py to AssetFile.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Simulation.py to Simulation.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Suite.py to Suite.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/OutputFileMetadata.py to OutputFileMetadata.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/SimulationFile.py to SimulationFile.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/TaggableEntity.py to TaggableEntity.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/QueryCriteria.py to QueryCriteria.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollection.py to AssetCollection.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems/BuilderWorkItem.py to BuilderWorkItem.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItem.py to WorkItem.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/HpcJob.py to HpcJob.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Experiment.py to Experiment.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/CommissionableEntity.py to CommissionableEntity.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetManager.py to AssetManager.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/SerializableEntity.py to SerializableEntity.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Client.py to Client.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/__example_utility_template__.py to __example_utility_template__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_files_for_experiment.py to get_output_files_for_experiment.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/main.py to main.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/__init__.py to __init__.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyCOMPS.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/pyCOMPS-2.5.1b1-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pyCOMPS-2.5.1b1-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/pyCOMPS-2.5.1b1-py3.7.egg
Extracting pyCOMPS-2.5.1b1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Adding pyCOMPS 2.5.1b1 to easy-install.pth file
Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/pyCOMPS-2.5.1b1-py3.7.egg
Processing dependencies for pyCOMPS==2.5.1b1
Searching for xdg>=4.0.1
Reading https://pypi.org/simple/xdg/
Downloading https://files.pythonhosted.org/packages/ea/09/4a0f30aada49e142b94bbb232c023abcbc6ced7e2a9776533fb14977e9db/xdg-5.1.1-py3-none-any.whl#sha256=865a7b56ed1d4cd2fce2ead1eddf97360843619757f473cd90b75f1817ca541d
Best match: xdg 5.1.1
Processing xdg-5.1.1-py3-none-any.whl
Installing xdg-5.1.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Adding xdg 5.1.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/xdg-5.1.1-py3.7.egg
Searching for future==0.18.2
Best match: future 0.18.2
Adding future 0.18.2 to easy-install.pth file
Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin
Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Searching for pytz==2022.1
Best match: pytz 2022.1
Adding pytz 2022.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Searching for requests==2.27.1
Best match: requests 2.27.1
Adding requests 2.27.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Searching for certifi==2021.10.8
Best match: certifi 2021.10.8
Adding certifi 2021.10.8 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Searching for charset-normalizer==2.0.12
Best match: charset-normalizer 2.0.12
Adding charset-normalizer 2.0.12 to easy-install.pth file
Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Searching for urllib3==1.26.9
Best match: urllib3 1.26.9
Adding urllib3 1.26.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Searching for idna==3.3
Best match: idna 3.3
Adding idna 3.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for pyCOMPS==2.5.1b1

[rtd-command-info] start-time: 2022-05-02T22:52:29.223299Z, end-time: 2022-05-02T22:52:29.285983Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Sphinx Demo documentation build configuration file, created by
# sphinx-quickstart on Fri Aug 26 16:52:16 2016.
#
# 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 subprocess
import sys
import sphinx_rtd_theme
import configparser
from datetime import datetime

if sys.platform in ["linux", "darwin"]:
    subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
else:
    subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))


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

# If your documentation needs a minimal Sphinx version, state it here.
#
# 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.mathjax',
    'sphinx.ext.githubpages',
    'sphinx.ext.autodoc',
    'sphinxcontrib.napoleon',
    'sphinx.ext.todo',
    'plantweb.directive',
    'sphinxcontrib.programoutput',
    'sphinx_copybutton',
    'sphinx.ext.intersphinx',
    'sphinxext.remoteliteralinclude'
]


plantuml = 'plantweb'

autodoc_default_options = {
    'member-order': 'bysource',
    'members': None,
    'exclude-members': '__all__'
}

napoleon_google_docstring = True

# Add any paths that contain templates here, relative to this directory.
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'

# The encoding of source files.
#
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'pyCOMPS'
copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved'
author = u'Institute for Disease Modeling'

# 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 = u'1.0'
# The full version, including alpha/beta/rc tags.
# release = u'1.0'

# 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

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
# today = ''
#
# Else, today_fmt is used as the format for a strftime call.
#
# today_fmt = '%B %d, %Y'

# 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']

# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#
# 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

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False

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

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

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

# RST epilog is added to the end of every topic. Useful for replace
# directives to use across the docset.

rst_epilog = "\n.. include:: /variables.txt"


# -- 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 = '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 = {
# }

# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# The name for this set of Sphinx documents.
# "<project> v<release> documentation" by default.
#
# html_title = u'Sphinx Demo v1.0'

# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
html_logo = "images/IDM_white.png"

# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
html_favicon = "images/favicon.ico"

# 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_context = {
    'css_files': [
        '_static/theme_overrides.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 = []

# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
# html_last_updated_fmt = None

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#
# html_additional_pages = {}

# If false, no module index is generated.
#
# html_domain_indices = True

# If false, no index is generated.
#
# html_use_index = True

# If true, the index is split into individual pages for each letter.
#
# html_split_index = False

# If true, links to the reST sources are added to the pages.
#
html_show_sourcelink = False

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
html_show_sphinx = False

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is 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 = 'www.idmod.org/docs'

# This is the file name suffix for HTML files (e.g. ".xhtml").
# 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', 'zh'
#
# html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
# 'zh' user can custom change `jieba` dictionary path.
#
# 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'

# Output file base name for HTML help builder.
htmlhelp_basename = 'pyCOMPS'



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

latex_elements = {
     # 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 = [
    (master_doc, 'pycomps-docs.tex', u'pyCOMPS',
     u'Institute for Disease Modeling', 'manual'),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#
# latex_use_parts = False

# If true, show page references after internal links.
#
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
#
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
#
# latex_appendices = []

# It false, will not define \strong, \code,     itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True

# If false, no module index is generated.
#
# 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 = [
    (master_doc, 'pycomps-docs', u'pyCOMPS',
     [author], 1)
]

# If true, show URL addresses after external links.
#
man_show_urls = True


# -- 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 = [
    (master_doc, 'pycomps-docs', u'pyCOMPS',
     author, 'Institute for Disease Modeling', 'How to use pyCOMPS for running simulations.',
     'Miscellaneous'),
]

# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []

# If false, no module index is generated.
#
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
# intersphinx_mapping = {'https://docs.python.org/': None}

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
                       'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None),
                       'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None),
                       'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None),
                       'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None)
                       }



###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/pycomps/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/pycomps/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-pycomps',
    'name': u'pyCOMPS',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://docs.idmod.org/projects/pycomps/en/latest/',
    'analytics_code': 'UA-87656833-3',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'pyCOMPS',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-87656833-3',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '03fc1fba',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-pycomps/builds/934051/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-05-02T22:52:29.456826Z, end-time: 2022-05-02T22:52:35.632534Z, duration: 6, exit-code: 0
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v3.3.1
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 47 source files that are out of date
updating environment: [new config] 47 added, 0 changed, 0 removed
reading sources... [  2%] COMPS.AuthManager
reading sources... [  4%] COMPS.Client
reading sources... [  6%] COMPS.CredentialPrompt
reading sources... [  8%] COMPS.Data
reading sources... [ 10%] COMPS.Data.AssetCollection
reading sources... [ 12%] COMPS.Data.AssetCollectionFile
reading sources... [ 14%] COMPS.Data.AssetFile
reading sources... [ 17%] COMPS.Data.AssetManager
reading sources... [ 19%] COMPS.Data.AssetType
reading sources... [ 21%] COMPS.Data.BaseEntity
reading sources... [ 23%] COMPS.Data.CommissionableEntity
reading sources... [ 25%] COMPS.Data.Configuration
reading sources... [ 27%] COMPS.Data.Experiment
reading sources... [ 29%] COMPS.Data.HpcJob
reading sources... [ 31%] COMPS.Data.OutputFileMetadata
reading sources... [ 34%] COMPS.Data.Priority
reading sources... [ 36%] COMPS.Data.QueryCriteria
reading sources... [ 38%] COMPS.Data.SerializableEntity
reading sources... [ 40%] COMPS.Data.Simulation
reading sources... [ 42%] COMPS.Data.SimulationFile
reading sources... [ 44%] COMPS.Data.Suite
reading sources... [ 46%] COMPS.Data.TaggableEntity
reading sources... [ 48%] COMPS.Data.WorkItem
reading sources... [ 51%] COMPS.Data.WorkItemFile
reading sources... [ 53%] COMPS.Data.WorkItems
reading sources... [ 55%] COMPS.Data.WorkItems.BuilderWorkItem
reading sources... [ 57%] COMPS.utils
reading sources... [ 59%] COMPS.utils.get_output_files_for_experiment
reading sources... [ 61%] COMPS.utils.main
reading sources... [ 63%] architecture
reading sources... [ 65%] create-climateinput
reading sources... [ 68%] create-simulations
reading sources... [ 70%] create-workitems-simulations
reading sources... [ 72%] glossary
reading sources... [ 74%] howto-cleanup
reading sources... [ 76%] howto-create-climateinput
reading sources... [ 78%] howto-create-simulations
reading sources... [ 80%] howto-dashboard
reading sources... [ 82%] howto-example-campaign
reading sources... [ 85%] howto-example-config
reading sources... [ 87%] howto-multichart-view
reading sources... [ 89%] howto-weather-view
reading sources... [ 91%] index
reading sources... [ 93%] manage-workitems-simulations
reading sources... [ 95%] modules
reading sources... [ 97%] overview-comps
reading sources... [100%] overview-terminology

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  2%] COMPS.AuthManager
writing output... [  4%] COMPS.Client
writing output... [  6%] COMPS.CredentialPrompt
writing output... [  8%] COMPS.Data
writing output... [ 10%] COMPS.Data.AssetCollection
writing output... [ 12%] COMPS.Data.AssetCollectionFile
writing output... [ 14%] COMPS.Data.AssetFile
writing output... [ 17%] COMPS.Data.AssetManager
writing output... [ 19%] COMPS.Data.AssetType
writing output... [ 21%] COMPS.Data.BaseEntity
writing output... [ 23%] COMPS.Data.CommissionableEntity
writing output... [ 25%] COMPS.Data.Configuration
writing output... [ 27%] COMPS.Data.Experiment
writing output... [ 29%] COMPS.Data.HpcJob
writing output... [ 31%] COMPS.Data.OutputFileMetadata
writing output... [ 34%] COMPS.Data.Priority
writing output... [ 36%] COMPS.Data.QueryCriteria
writing output... [ 38%] COMPS.Data.SerializableEntity
writing output... [ 40%] COMPS.Data.Simulation
writing output... [ 42%] COMPS.Data.SimulationFile
writing output... [ 44%] COMPS.Data.Suite
writing output... [ 46%] COMPS.Data.TaggableEntity
writing output... [ 48%] COMPS.Data.WorkItem
writing output... [ 51%] COMPS.Data.WorkItemFile
writing output... [ 53%] COMPS.Data.WorkItems
writing output... [ 55%] COMPS.Data.WorkItems.BuilderWorkItem
writing output... [ 57%] COMPS.utils
writing output... [ 59%] COMPS.utils.get_output_files_for_experiment
writing output... [ 61%] COMPS.utils.main
writing output... [ 63%] architecture
writing output... [ 65%] create-climateinput
writing output... [ 68%] create-simulations
writing output... [ 70%] create-workitems-simulations
writing output... [ 72%] glossary
writing output... [ 74%] howto-cleanup
writing output... [ 76%] howto-create-climateinput
writing output... [ 78%] howto-create-simulations
writing output... [ 80%] howto-dashboard
writing output... [ 82%] howto-example-campaign
writing output... [ 85%] howto-example-config
writing output... [ 87%] howto-multichart-view
writing output... [ 89%] howto-weather-view
writing output... [ 91%] index
writing output... [ 93%] manage-workitems-simulations
writing output... [ 95%] modules
writing output... [ 97%] overview-comps
writing output... [100%] overview-terminology

generating indices... genindex py-modindex done
writing additional pages... search opensearch done
copying images... [  6%] _build/html/_images/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg
copying images... [ 12%] images/input-search-vietnam.png
copying images... [ 18%] images/input-search-vietnam-select.png
copying images... [ 25%] images/input-search-vietnam-selected.png
copying images... [ 31%] images/climate-submit.png
copying images... [ 37%] images/create-input-files-generate.png
copying images... [ 43%] images/dashboard-simsperstate.png
copying images... [ 50%] images/chart-select.png
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$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
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$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2022-05-02T22:52:44.888127Z, end-time: 2022-05-02T22:52:50.081749Z, duration: 5, exit-code: 0
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Chapter 5.

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Chapter 6.

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Chapter 7.
[47] [48]

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[49]
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Chapter 5.

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Chapter 1.
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Chapter 3.
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ut-search-vietnam-selected.png> <./climate-submit.png>] [11 <./create-input-fil
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g>] [15 <./chart-multi.png> <./chart-ychannel.png>] [16 <./weather-animation-cl
imateproject.png> <./weather-animation-play.png>] [17 <./weather-animation-temp
erature-time.png> <./weather-animation-chart.png>] [18]
Chapter 5.

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Chapter 6.

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