Read the Docs build information
Build id: 1664247
Project: institute-for-disease-modeling-emod-malaria
Version: latest
Commit: cd7b42519d875288c6470b5274bd2f1513ee1e68
Date: 2023-08-16T16:58:22.699369Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2023-08-16T16:58:31.029238Z, end-time: 2023-08-16T16:58:54.150356Z, duration: 23, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/EMOD-docs.git .
Cloning into '.'...
Warning: Permanently added 'github.com' (ED25519) to the list of known hosts.

[rtd-command-info] start-time: 2023-08-16T16:58:54.689916Z, end-time: 2023-08-16T16:58:54.970361Z, duration: 0, exit-code: 0
git checkout --force origin/malaria-ongoing
Note: switching to 'origin/malaria-ongoing'.

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 cd7b4251 Merge pull request #1810 from KElsaesser-IDM/1499-migration-filenames

[rtd-command-info] start-time: 2023-08-16T16:58:55.399772Z, end-time: 2023-08-16T16:58:55.463700Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-08-16T16:58:55.917959Z, end-time: 2023-08-16T16:58:55.976184Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Build documentation in the docs/ directory with Sphinx
sphinx:
  fail_on_warning: true

# Build documentation with MkDocs
#mkdocs:
#  configuration: mkdocs.yml

# Optionally build your docs in additional formats such as PDF
formats:
  - htmlzip

# Optionally set the version of Python and requirements required to build your docs
python:
  version: 3.7
  install:
    - requirements: requirements.txt
        
# Optionally rank topics in search results, between -10 (lower) and 10 (higher).
# 0 is normal rank, not no rank

search:
  ranking:
    install-overview.html: 3
    model-overview.html: 3
    faq.html: 2
    parameter-overview.html: 2
    dev*: -5

[rtd-command-info] start-time: 2023-08-16T16:58:58.585711Z, end-time: 2023-08-16T16:59:03.647804Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
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-emod-malaria/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-08-16T16:59:04.101043Z, end-time: 2023-08-16T16:59:05.314538Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/latest/lib/python3.7/site-packages (23.2.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/latest/lib/python3.7/site-packages (68.0.0)

[rtd-command-info] start-time: 2023-08-16T16:59:05.855481Z, end-time: 2023-08-16T16:59:13.192043Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow==5.4.1 mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=6c8a8ef9dc959c11dbed33190da4eafe56919a79805851524baf789cc0ca061a
  Stored in directory: /tmp/pip-ephem-wheel-cache-vsx3v5vt/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 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 urllib3-2.0.4

[rtd-command-info] start-time: 2023-08-16T16:59:13.796006Z, end-time: 2023-08-16T16:59:20.988586Z, duration: 7, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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[rtd-command-info] start-time: 2023-08-16T16:59:27.458957Z, end-time: 2023-08-16T16:59:27.526699Z, duration: 0, exit-code: 0
cat emod/malaria/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.
# 
# See all configuration options: 
#     https://www.sphinx-doc.org/en/master/usage/configuration.html

import os
import sys

# -- Shared Configuration -------------------------------------------------
sys.path.insert(0, os.path.abspath(f"{os.path.dirname(__file__)}/.."))
from conf import *


# -- Project Information --------------------------------------------------
# General information about the project.
project = 'Malaria Model'
key = "emod-malaria"

# Additional Metadata
short_title = 'EMOD for Malaria'
long_title = 'EMOD Modeling Software for Malaria'
description = 'How to use the IDM EMOD software for modeling malaria.'

# -- General configuration ------------------------------------------------
tags.add('malaria')


# -- Options for HTML output ----------------------------------------------
# A dictionary of values to pass into the template engine’s context for all pages. 
# Single values can also be put in this dictionary using the -A command-line option of sphinx-build.
html_context.update({
    'docset_title': short_title
})

# 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 = f'{opensearch_baseurl}/{key}'

# -- Options for HTML help output -----------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = short_title



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

# 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, f'{key}-docs.tex', long_title, author, 'manual'),
]


# -- 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, f'{key}-docs', long_title, [author], 1)
]


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

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, f'{key}-docs', long_title, author, author, description, 
    'Miscellaneous'),
]




###########################################################################
#          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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("2.21_a", "/en/2.21_a/"),
    ("2.20_a", "/en/2.20_a/"),
    ("2.18", "/en/2.18/"),
    ("2.14", "/en/2.14/"),
    ("2.13", "/en/2.13/"),
    ("2.10", "/en/2.10/"),
    ("search", "/en/search/"),
    ],
    'downloads': [ 
    ("html", "//docs.idmod.org/_/downloads/emod-malaria/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-emod-malaria',
    'name': u'EMOD Malaria',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': '',
    'analytics_code': 'G-SVDSQH04EM',
    'single_version': False,
    'conf_py_path': '/emod/malaria/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'EMOD-docs',
    'github_version': 'malaria-ongoing',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'malaria-ongoing',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'malaria-ongoing',
    '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': 'G-SVDSQH04EM',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'cd7b4251',
}

# 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():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
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-emod-malaria/builds/1664247/'

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'])