Read the Docs build information
Build id: 497066
Project: institute-for-disease-modeling-pycomps
Version: latest
Commit: b25b7d660f48f8fd32612036d60d883c6721c7ba
Date: 2020-12-03T19:12:34.623690Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-12-03T19:12:36.245174Z, end-time: 2020-12-03T19:12:37.518639Z, duration: 1, 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' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2020-12-03T19:12:37.971119Z, end-time: 2020-12-03T19:12:38.028778Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out '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 performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at b25b7d6 Update version to 2.4.1

[rtd-command-info] start-time: 2020-12-03T19:12:38.129950Z, end-time: 2020-12-03T19:12:38.178652Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-12-03T19:12:39.392537Z, end-time: 2020-12-03T19:12:43.166203Z, duration: 3, exit-code: 0
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: 2020-12-03T19:12:43.329334Z, end-time: 2020-12-03T19:12:44.840751Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages (20.3.1)

[rtd-command-info] start-time: 2020-12-03T19:12:45.126314Z, end-time: 2020-12-03T19:12:54.099535Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
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Building wheels for collected packages: mock, future
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Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
  Attempting uninstall: setuptools
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Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.9.0 certifi-2020.11.8 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.7 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2

[rtd-command-info] start-time: 2020-12-03T19:12:54.298250Z, end-time: 2020-12-03T19:13:00.170034Z, duration: 5, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Building wheels for collected packages: docopt, wrapt
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Installing collected packages: urllib3, wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, requests, pycparser, sphinx, pyjwt, pockets, docopt, deprecated, cffi, cached-property, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, PyGithub, pygit2, py-make, plantweb
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Successfully installed PyGithub-1.54 cached-property-1.5.2 cffi-1.14.4 deprecated-1.2.10 docopt-0.6.2 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.20 pygit2-1.2.1 pyjwt-1.7.1 requests-2.24.0 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.16 sphinxcontrib-qthelp-1.0.3 urllib3-1.25.11 wrapt-1.12.1

[rtd-command-info] start-time: 2020-12-03T19:13:00.303102Z, end-time: 2020-12-03T19:13:01.020844Z, 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 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'
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/Client.py -> build/lib/COMPS
copying COMPS/AuthManager.py -> build/lib/COMPS
copying COMPS/CredentialPrompt.py -> build/lib/COMPS
copying COMPS/__init__.py -> build/lib/COMPS
creating build/lib/COMPS/Data
copying COMPS/Data/CommissionableEntity.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetFile.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetManager.py -> build/lib/COMPS/Data
copying COMPS/Data/QueryCriteria.py -> build/lib/COMPS/Data
copying COMPS/Data/Priority.py -> build/lib/COMPS/Data
copying COMPS/Data/__init__.py -> build/lib/COMPS/Data
copying COMPS/Data/Configuration.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetType.py -> build/lib/COMPS/Data
copying COMPS/Data/WorkItem.py -> build/lib/COMPS/Data
copying COMPS/Data/Simulation.py -> build/lib/COMPS/Data
copying COMPS/Data/HpcJob.py -> build/lib/COMPS/Data
copying COMPS/Data/Suite.py -> build/lib/COMPS/Data
copying COMPS/Data/TaggableEntity.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/SerializableEntity.py -> build/lib/COMPS/Data
copying COMPS/Data/Experiment.py -> build/lib/COMPS/Data
copying COMPS/Data/SimulationFile.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetCollectionFile.py -> build/lib/COMPS/Data
copying COMPS/Data/OutputFileMetadata.py -> build/lib/COMPS/Data
copying COMPS/Data/AssetCollection.py -> build/lib/COMPS/Data
creating build/lib/COMPS/Data/WorkItems
copying COMPS/Data/WorkItems/__init__.py -> build/lib/COMPS/Data/WorkItems
copying COMPS/Data/WorkItems/BuilderWorkItem.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/Client.py -> build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/AuthManager.py -> build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/CredentialPrompt.py -> build/bdist.linux-x86_64/egg/COMPS
copying build/lib/COMPS/__init__.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/Data
copying build/lib/COMPS/Data/CommissionableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetFile.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/__init__.py -> 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/AssetManager.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/Priority.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/Configuration.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/WorkItem.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/HpcJob.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/TaggableEntity.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/SerializableEntity.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/SimulationFile.py -> 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/OutputFileMetadata.py -> build/bdist.linux-x86_64/egg/COMPS/Data
copying build/lib/COMPS/Data/AssetCollection.py -> build/bdist.linux-x86_64/egg/COMPS/Data
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/AuthManager.py to AuthManager.cpython-37.pyc
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/__init__.py to __init__.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/AssetFile.py to AssetFile.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/WorkItems/BuilderWorkItem.py to BuilderWorkItem.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/QueryCriteria.py to QueryCriteria.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/__init__.py to __init__.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/AssetType.py to AssetType.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/Simulation.py to Simulation.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/Suite.py to Suite.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/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/SerializableEntity.py to SerializableEntity.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/SimulationFile.py to SimulationFile.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/OutputFileMetadata.py to OutputFileMetadata.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollection.py to AssetCollection.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/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-2.4.1-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-2.4.1-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/pyCOMPS-2.4.1-py3.7.egg
Extracting pyCOMPS-2.4.1-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 2.4.1 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/pyCOMPS-2.4.1-py3.7.egg
Processing dependencies for pyCOMPS==2.4.1
Searching for xdg>=4.0.1
Reading https://pypi.org/simple/xdg/
Downloading https://files.pythonhosted.org/packages/be/eb/a4669d56ce4934d88a163e4b0d3cbc96606c073100bd6031f7972679877b/xdg-5.0.1-py3-none-any.whl#sha256=9ddd6649bee9148f952305603a08474e3ef37c909eb19dfcb9737d54ebcc407e
Best match: xdg 5.0.1
Processing xdg-5.0.1-py3-none-any.whl
Installing xdg-5.0.1-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 5.0.1 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-5.0.1-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==2020.4
Best match: pytz 2020.4
Adding pytz 2020.4 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==2.24.0
Best match: requests 2.24.0
Adding requests 2.24.0 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==2.10
Best match: idna 2.10
Adding idna 2.10 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 urllib3==1.25.11
Best match: urllib3 1.25.11
Adding urllib3 1.25.11 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 chardet==3.0.4
Best match: chardet 3.0.4
Adding chardet 3.0.4 to easy-install.pth file
Installing chardetect 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 certifi==2020.11.8
Best match: certifi 2020.11.8
Adding certifi 2020.11.8 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
Finished processing dependencies for pyCOMPS==2.4.1

[rtd-command-info] start-time: 2020-12-03T19:13:02.339898Z, end-time: 2020-12-03T19:13:02.411752Z, 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

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'
]


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 = u'2020, 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}




###########################################################################
#          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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

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': [
    ],
    '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': 'b25b7d66',
}




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")

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: 2020-12-03T19:13:02.528771Z, end-time: 2020-12-03T19:13:06.533708Z, duration: 4, exit-code: 0
python sphinx-build -T -E -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.2.1
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 29 source files that are out of date
updating environment: [new config] 29 added, 0 changed, 0 removed
reading sources... [  3%] COMPS.AuthManager
reading sources... [  6%] COMPS.Client
reading sources... [ 10%] COMPS.CredentialPrompt
reading sources... [ 13%] COMPS.Data
reading sources... [ 17%] COMPS.Data.AssetCollection
reading sources... [ 20%] COMPS.Data.AssetCollectionFile
reading sources... [ 24%] COMPS.Data.AssetFile
reading sources... [ 27%] COMPS.Data.AssetManager
reading sources... [ 31%] COMPS.Data.AssetType
reading sources... [ 34%] COMPS.Data.BaseEntity
reading sources... [ 37%] COMPS.Data.CommissionableEntity
reading sources... [ 41%] COMPS.Data.Configuration
reading sources... [ 44%] COMPS.Data.Experiment
reading sources... [ 48%] COMPS.Data.HpcJob
reading sources... [ 51%] COMPS.Data.OutputFileMetadata
reading sources... [ 55%] COMPS.Data.Priority
reading sources... [ 58%] COMPS.Data.QueryCriteria
reading sources... [ 62%] COMPS.Data.SerializableEntity
reading sources... [ 65%] COMPS.Data.Simulation
reading sources... [ 68%] COMPS.Data.SimulationFile
reading sources... [ 72%] COMPS.Data.Suite
reading sources... [ 75%] COMPS.Data.TaggableEntity
reading sources... [ 79%] COMPS.Data.WorkItem
reading sources... [ 82%] COMPS.Data.WorkItemFile
reading sources... [ 86%] COMPS.Data.WorkItems
reading sources... [ 89%] COMPS.Data.WorkItems.BuilderWorkItem
reading sources... [ 93%] glossary
reading sources... [ 96%] index
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  3%] COMPS.AuthManager
writing output... [  6%] COMPS.Client
writing output... [ 10%] COMPS.CredentialPrompt
writing output... [ 13%] COMPS.Data
writing output... [ 17%] COMPS.Data.AssetCollection
writing output... [ 20%] COMPS.Data.AssetCollectionFile
writing output... [ 24%] COMPS.Data.AssetFile
writing output... [ 27%] COMPS.Data.AssetManager
writing output... [ 31%] COMPS.Data.AssetType
writing output... [ 34%] COMPS.Data.BaseEntity
writing output... [ 37%] COMPS.Data.CommissionableEntity
writing output... [ 41%] COMPS.Data.Configuration
writing output... [ 44%] COMPS.Data.Experiment
writing output... [ 48%] COMPS.Data.HpcJob
writing output... [ 51%] COMPS.Data.OutputFileMetadata
writing output... [ 55%] COMPS.Data.Priority
writing output... [ 58%] COMPS.Data.QueryCriteria
writing output... [ 62%] COMPS.Data.SerializableEntity
writing output... [ 65%] COMPS.Data.Simulation
writing output... [ 68%] COMPS.Data.SimulationFile
writing output... [ 72%] COMPS.Data.Suite
writing output... [ 75%] COMPS.Data.TaggableEntity
writing output... [ 79%] COMPS.Data.WorkItem
writing output... [ 82%] COMPS.Data.WorkItemFile
writing output... [ 86%] COMPS.Data.WorkItems
writing output... [ 89%] COMPS.Data.WorkItems.BuilderWorkItem
writing output... [ 93%] glossary
writing output... [ 96%] index
writing output... [100%] modules

generating indices...  genindex py-modindexdone
writing additional pages...  search opensearchdone
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2020-12-03T19:13:06.727381Z, end-time: 2020-12-03T19:13:09.998357Z, duration: 3, exit-code: 0
python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v3.2.1
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: [new config] 29 added, 0 changed, 0 removed
reading sources... [  3%] COMPS.AuthManager
reading sources... [  6%] COMPS.Client
reading sources... [ 10%] COMPS.CredentialPrompt
reading sources... [ 13%] COMPS.Data
reading sources... [ 17%] COMPS.Data.AssetCollection
reading sources... [ 20%] COMPS.Data.AssetCollectionFile
reading sources... [ 24%] COMPS.Data.AssetFile
reading sources... [ 27%] COMPS.Data.AssetManager
reading sources... [ 31%] COMPS.Data.AssetType
reading sources... [ 34%] COMPS.Data.BaseEntity
reading sources... [ 37%] COMPS.Data.CommissionableEntity
reading sources... [ 41%] COMPS.Data.Configuration
reading sources... [ 44%] COMPS.Data.Experiment
reading sources... [ 48%] COMPS.Data.HpcJob
reading sources... [ 51%] COMPS.Data.OutputFileMetadata
reading sources... [ 55%] COMPS.Data.Priority
reading sources... [ 58%] COMPS.Data.QueryCriteria
reading sources... [ 62%] COMPS.Data.SerializableEntity
reading sources... [ 65%] COMPS.Data.Simulation
reading sources... [ 68%] COMPS.Data.SimulationFile
reading sources... [ 72%] COMPS.Data.Suite
reading sources... [ 75%] COMPS.Data.TaggableEntity
reading sources... [ 79%] COMPS.Data.WorkItem
reading sources... [ 82%] COMPS.Data.WorkItemFile
reading sources... [ 86%] COMPS.Data.WorkItems
reading sources... [ 89%] COMPS.Data.WorkItems.BuilderWorkItem
reading sources... [ 93%] glossary
reading sources... [ 96%] index
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... modules COMPS.Data COMPS.Data.WorkItems COMPS.Data.WorkItems.BuilderWorkItem COMPS.Data.AssetCollection COMPS.Data.AssetCollectionFile COMPS.Data.AssetFile COMPS.Data.AssetManager COMPS.Data.AssetType COMPS.Data.BaseEntity COMPS.Data.CommissionableEntity COMPS.Data.Configuration COMPS.Data.Experiment COMPS.Data.HpcJob COMPS.Data.OutputFileMetadata COMPS.Data.Priority COMPS.Data.QueryCriteria COMPS.Data.SerializableEntity COMPS.Data.Simulation COMPS.Data.SimulationFile COMPS.Data.Suite COMPS.Data.TaggableEntity COMPS.Data.WorkItem COMPS.Data.WorkItemFile COMPS.AuthManager COMPS.Client COMPS.CredentialPrompt glossary done
writing... done
writing additional files...  opensearchdone
copying static files... ... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2020-12-03T19:13:10.238216Z, end-time: 2020-12-03T19:13:13.458768Z, duration: 3, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v3.2.1
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: [new config] 29 added, 0 changed, 0 removed
reading sources... [  3%] COMPS.AuthManager
reading sources... [  6%] COMPS.Client
reading sources... [ 10%] COMPS.CredentialPrompt
reading sources... [ 13%] COMPS.Data
reading sources... [ 17%] COMPS.Data.AssetCollection
reading sources... [ 20%] COMPS.Data.AssetCollectionFile
reading sources... [ 24%] COMPS.Data.AssetFile
reading sources... [ 27%] COMPS.Data.AssetManager
reading sources... [ 31%] COMPS.Data.AssetType
reading sources... [ 34%] COMPS.Data.BaseEntity
reading sources... [ 37%] COMPS.Data.CommissionableEntity
reading sources... [ 41%] COMPS.Data.Configuration
reading sources... [ 44%] COMPS.Data.Experiment
reading sources... [ 48%] COMPS.Data.HpcJob
reading sources... [ 51%] COMPS.Data.OutputFileMetadata
reading sources... [ 55%] COMPS.Data.Priority
reading sources... [ 58%] COMPS.Data.QueryCriteria
reading sources... [ 62%] COMPS.Data.SerializableEntity
reading sources... [ 65%] COMPS.Data.Simulation
reading sources... [ 68%] COMPS.Data.SimulationFile
reading sources... [ 72%] COMPS.Data.Suite
reading sources... [ 75%] COMPS.Data.TaggableEntity
reading sources... [ 79%] COMPS.Data.WorkItem
reading sources... [ 82%] COMPS.Data.WorkItemFile
reading sources... [ 86%] COMPS.Data.WorkItems
reading sources... [ 89%] COMPS.Data.WorkItems.BuilderWorkItem
reading sources... [ 93%] glossary
reading sources... [ 96%] index
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing pycomps-docs.tex... index modules COMPS.Data COMPS.Data.WorkItems COMPS.Data.WorkItems.BuilderWorkItem COMPS.Data.AssetCollection COMPS.Data.AssetCollectionFile COMPS.Data.AssetFile COMPS.Data.AssetManager COMPS.Data.AssetType COMPS.Data.BaseEntity COMPS.Data.CommissionableEntity COMPS.Data.Configuration COMPS.Data.Experiment COMPS.Data.HpcJob COMPS.Data.OutputFileMetadata COMPS.Data.Priority COMPS.Data.QueryCriteria COMPS.Data.SerializableEntity COMPS.Data.Simulation COMPS.Data.SimulationFile COMPS.Data.Suite COMPS.Data.TaggableEntity COMPS.Data.WorkItem COMPS.Data.WorkItemFile COMPS.AuthManager COMPS.Client COMPS.CredentialPrompt glossary 
resolving references...
done
writing... done
copying TeX support files... copying TeX support files...
done
build succeeded.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).
WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/checkouts/latest/docs/_build/latex/_static/searchtools.js

[rtd-command-info] start-time: 2020-12-03T19:13:13.679050Z, end-time: 2020-12-03T19:13:13.734473Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2020-12-03T19:13:13.875338Z, end-time: 2020-12-03T19:13:15.570214Z, duration: 1, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-pycomps -interaction=nonstopmode
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, <GEN1> chunk 1.
Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, <GEN2> chunk 1.
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-pycomps"  "pycomps-docs.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./pycomps-docs.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
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(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
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(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
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(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
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(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
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(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
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(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
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(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
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(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
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(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
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(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
(./sphinxmessages.sty)
Writing index file institute-for-disease-modeling-pycomps.idx
(./institute-for-disease-modeling-pycomps.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
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nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1] [2]
Chapter 1.
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[27]

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[28]
Chapter 2.
[29] [30]

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ine 3271.


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lection' on page 31 undefined on input line 3276.


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missionableEntity' on page 31 undefined on input line 3282.


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ion' on page 31 undefined on input line 3283.


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tFileMetadata' on page 31 undefined on input line 3286.


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ge 31 undefined on input line 3287.


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ntity' on page 31 undefined on input line 3293.


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ge 31 undefined on input line 3294.


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e' on page 31 undefined on input line 3295.


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[31]
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 )
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Chapter 1.
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Chapter 1.
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