Read the Docs build information Build id: 858352 Project: institute-for-disease-modeling-emod-malaria Version: latest Commit: 50b53aead63633fc600231256b88f73a1e83a900 Date: 2022-02-17T23:23:27.916500Z State: finished Success: False [rtd-command-info] start-time: 2022-02-17T23:23:29.878081Z, end-time: 2022-02-17T23:23:48.512118Z, duration: 18, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/EMOD-docs.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-02-17T23:23:48.713801Z, end-time: 2022-02-17T23:23:49.191176Z, duration: 0, exit-code: 0 git checkout --force origin/malaria-ongoing Note: checking out '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 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 HEAD is now at 50b53aea Merge pull request #1451 from Bridenbecker/MiscUpdates2 [rtd-command-info] start-time: 2022-02-17T23:23:49.367823Z, end-time: 2022-02-17T23:23:49.438402Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-02-17T23:23:50.679736Z, end-time: 2022-02-17T23:23:55.011516Z, duration: 4, 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-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. 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(line 3)) (3.0.7) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pockets, numpy, docutils, sphinxcontrib-napoleon, sphinx, plantweb, sphinx-rtd-theme, numpydoc Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed docutils-0.16 numpy-1.19.5 numpydoc-1.0.0 plantweb-1.2.1 pockets-0.9.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3 [rtd-command-info] start-time: 2022-02-17T23:24:12.151452Z, end-time: 2022-02-17T23:24:12.215228Z, 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 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/master/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/"), ("2.21", "/en/2.21/"), ("2.20", "/en/2.20/"), ("2.18", "/en/2.18/"), ("2.14", "/en/2.14/"), ("2.13", "/en/2.13/"), ("2.10", "/en/2.10/"), ], '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': 'https://docs.idmod.org/projects/emod-malaria/en/latest/', 'analytics_code': 'UA-87656833-3', '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': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '50b53aea', } # 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-emod-malaria/builds/858352/' 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: 2022-02-17T23:24:12.411884Z, end-time: 2022-02-17T23:24:51.687761Z, duration: 39, exit-code: 1 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.2.1 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/emodpy-covid/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-measles/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-tbhiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-airborne/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-tuberculosis/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-sti/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-environmental/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-typhoid/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-vector/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... resolved configuration: {'PY3': True, 'SUFFIX': '.rst', '__file__': '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/checkouts/latest/emod/malaria/conf.py', 'author': 'Institute for Disease Modeling', 'chinese': False, 'context': {'MEDIA_URL': 'https://media.readthedocs.com/media/', 'PRODUCTION_DOMAIN': 'readthedocs.com', 'READTHEDOCS': True, 'STATIC_URL': 'https://assets.readthedocs.com/', 'ad_free': False, 'analytics_code': 'UA-87656833-3', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': 'malaria-ongoing', 'canonical_url': None, 'commit': '50b53aea', 'conf_py_path': '/emod/malaria/', 'current_version': 'latest', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'downloads': [('html', '//docs.idmod.org/_/downloads/emod-malaria/en/latest/htmlzip/')], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': 'malaria-ongoing', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': 'malaria-ongoing', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'name': 'EMOD Malaria', 'new_theme': True, 'programming_language': 'words', 'proxied_api_host': '/_', 'rtd_language': 'en', 'single_version': False, 'slug': 'institute-for-disease-modeling-emod-malaria', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': 'latest', 'versions': [('latest', '/en/latest/'), ('2.21', '/en/2.21/'), ('2.20', '/en/2.20/'), ('2.18', '/en/2.18/'), ('2.14', '/en/2.14/'), ('2.13', '/en/2.13/'), ('2.10', '/en/2.10/')]}, 'copyright': '1999 - 2022, Bill & Melinda Gates Foundation. All rights ' 'reserved.', 'datetime': , 'description': 'How to use the IDM EMOD software for modeling malaria.', 'exclude_patterns': ['_build', 'Thumbs.db', '.DS_Store', '_build'], 'extensions': ['readthedocs_ext.readthedocs', 'sphinx.ext.mathjax', 'sphinx.ext.intersphinx'], 'html_baseurl': 'https://docs.idmod.org/projects/emod-malaria/en/latest/', 'html_context': {'MEDIA_URL': 'https://media.readthedocs.com/media/', 'PRODUCTION_DOMAIN': 'readthedocs.com', 'READTHEDOCS': True, 'STATIC_URL': 'https://assets.readthedocs.com/', 'ad_free': False, 'analytics_code': 'UA-87656833-3', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': 'malaria-ongoing', 'canonical_url': None, 'commit': '50b53aea', 'conf_py_path': '/emod/malaria/', 'current_version': 'latest', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'docset_title': 'EMOD for Malaria', 'downloads': [('html', '//docs.idmod.org/_/downloads/emod-malaria/en/latest/htmlzip/')], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': 'malaria-ongoing', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': 'malaria-ongoing', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'idm_docs_home': 'https://docs.idmod.org', 'name': 'EMOD Malaria', 'new_theme': True, 'programming_language': 'words', 'proxied_api_host': '/_', 'rtd_language': 'en', 'single_version': False, 'slug': 'institute-for-disease-modeling-emod-malaria', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': 'latest', 'versions': [('latest', '/en/latest/'), ('2.21', '/en/2.21/'), ('2.20', '/en/2.20/'), ('2.18', '/en/2.18/'), ('2.14', '/en/2.14/'), ('2.13', '/en/2.13/'), ('2.10', '/en/2.10/')]}, 'html_favicon': '../images/favicon.ico', 'html_logo': '../images/IDM_white.png', 'html_show_sourcelink': False, 'html_show_sphinx': False, 'html_static_path': ['../_static'], 'html_theme': 'sphinx_rtd_theme', 'html_theme_path': ['/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/latest/lib/python3.7/site-packages'], 'html_use_opensearch': 'docs.idmod.org/projects/emod-malaria', 'htmlhelp_basename': 'EMOD for Malaria', 'importlib': , 'intersphinx_mapping': {'emod-airborne': ('emod-airborne', ('https://docs.idmod.org/projects/emod-airborne/en/latest/', (None,))), 'emod-environmental': ('emod-environmental', ('https://docs.idmod.org/projects/emod-environmental/en/latest/', (None,))), 'emod-generic': ('emod-generic', ('https://docs.idmod.org/projects/emod-generic/en/latest/', (None,))), 'emod-hiv': ('emod-hiv', ('https://docs.idmod.org/projects/emod-hiv/en/latest/', (None,))), 'emod-malaria': ('emod-malaria', ('https://docs.idmod.org/projects/emod-malaria/en/latest/', (None,))), 'emod-sti': ('emod-sti', ('https://docs.idmod.org/projects/emod-sti/en/latest/', (None,))), 'emod-tbhiv': ('emod-tbhiv', ('https://docs.idmod.org/projects/emod-tuberculosis/en/latest/', (None,))), 'emod-typhoid': ('emod-typhoid', ('https://docs.idmod.org/projects/emod-typhoid/en/latest/', (None,))), 'emod-vector': ('emod-vector', ('https://docs.idmod.org/projects/emod-vector/en/latest/', (None,))), 'emod_api': ('emod_api', ('https://docs.idmod.org/projects/emod-api/en/latest/', (None,))), 'emodpy': ('emodpy', ('https://docs.idmod.org/projects/emodpy/en/latest/', (None,))), 'emodpy_covid': ('emodpy_covid', ('https://docs.idmod.org/projects/emodpy-covid/en/latest/', (None,))), 'emodpy_generic': ('emodpy_generic', ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', (None,))), 'emodpy_malaria': ('emodpy_malaria', ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', (None,))), 'emodpy_measles': ('emodpy_measles', ('https://docs.idmod.org/projects/emodpy-measles/en/latest/', (None,))), 'emodpy_tbhiv': ('emodpy_tbhiv', ('https://docs.idmod.org/projects/emodpy-tbhiv/en/latest/', (None,))), 'idmtools': ('idmtools', ('https://docs.idmod.org/projects/idmtools/en/latest/', (None,))), 'pycomps': ('pycomps', ('https://docs.idmod.org/projects/pycomps/en/latest/', (None,))), 'python': ('python', ('https://docs.python.org/3', (None,)))}, 'japanese': False, 'key': 'emod-malaria', 'language': 'en', 'language_user': None, 'latex_documents': [('index', 'emod-malaria-docs.tex', 'EMOD Modeling Software for Malaria', 'Institute for Disease Modeling', 'manual')], 'latex_elements': {}, 'latex_elements_user': {}, 'latex_engine_user': None, 'latex_use_xindy': False, 'log_config': , 'long_title': 'EMOD Modeling Software for Malaria', 'man_pages': [('index', 'emod-malaria-docs', 'EMOD Modeling Software for Malaria', ['Institute for Disease Modeling'], 1)], 'man_show_urls': True, 'master_doc': 'index', 'opensearch_baseurl': 'docs.idmod.org/projects', 'os': , 'project': 'Malaria Model', 'project_language': 'en', 'pygments_style': 'sphinx', 'rst_epilog': '\n.. include:: /../reuse/variables.txt', 'setup': , 'short_title': 'EMOD for Malaria', 'source_suffix': '.rst', 'sphinx': , 'sphinx_rtd_theme': , 'string_types': , 'sys': , 'tags': , 'templates_path': ['../_templates'], 'texinfo_documents': [('index', 'emod-malaria-docs', 'EMOD Modeling Software for Malaria', 'Institute for Disease Modeling', 'Institute for Disease Modeling', 'How to use the IDM EMOD software for modeling ' 'malaria.', 'Miscellaneous')], 'todo_include_todos': False, 'using_rtd_theme': False, 'version': '2.21', 'version_info': (3, 2, 1, 'final', 0)} building [mo]: targets for 0 po files that are out of date building [html]: targets for 223 source files that are out of date updating environment: [new config] 223 added, 0 changed, 0 removed reading sources... 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[100%] whats-new /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/checkouts/latest/emod/malaria/parameter-campaign-targeting-config.rst:1: WARNING: Problem with "include" directive: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 10083: invalid start byte /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/checkouts/latest/emod/malaria/software-report-malaria-node-demographics-genetics.rst:97: WARNING: Error with CSV data in "csv-table" directive: ',' expected after '"' .. csv-table:: :header: Parameter, Data type, Description :widths: 15, 5, 40 NumIndividuals, integer, The number of individuals who meet the stratification values. NumInfected, integer, The number of infected individuals who meet the stratification values. NodeProp = , string, "For each possible Node Property, there is one column where the data in the column is the value of that particular property. If there are no Node Properties, then there are no columns." AvgInfectiousness, float, "The average infectiousness to mosquitos for the individuals of this row. Infectiousness is based on the number of mature gametocytes that the person has." AvgParasiteDensity, float, The average true parasite density for the individuals of this row. AvgGametocyteDensity, float, The average true gametocyte density for the individuals of this row. AvgVariantFractionPfEMP1Major, float, "For each individual, a count is made of the number of PfEMP1 Major antibodies the individual has and is divided by the total number of possible variants (Falciparum_PfEMP1_Variants). This is the average of this value for all the individuals represented in this row." AvgNumInfections, float, The average number of infections for the people of this row. AvgInfectionClearedDuration, float, The average duration to clear infections for the people of this row. NumInfectionsCleared, integer, The number of cleared infections for the people of this row. NumHasFever, integer, The number of people in the row that have a fever according to the diagnostic using the **Report_Detection_Threshold_Fever** parameter. NumHasClinicalSymptoms, integer, "If **Stratify_By_Has_Clinical_Symptoms** = 0, then this column is present with the number of people in the row that are considered to have 'clinical' symptoms. [barcodes], integer, "The number of human infections with the barcode that is the column header. If you used a wild card at a loci, it includes all the barcodes that match the other loci exactly but ignores differences at this loci. For example, A*T includes AAT, ACT, AGT, and ATT. There will be one column for each barcode." OtherBarcodes, integer, The number of human infections whose barcode is not counted by the other columns. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 0%] dev-architecture-campaigns writing output... [ 0%] dev-architecture-core writing output... [ 1%] dev-architecture-environment writing output... [ 1%] dev-architecture-overview writing output... [ 2%] dev-architecture-reporter writing output... [ 2%] dev-architecture-sim-controller writing output... [ 3%] dev-debugging-overview writing output... [ 3%] dev-install-build-emod writing output... [ 4%] dev-install-centos-docker writing output... [ 4%] dev-install-centos-docker-linux writing output... [ 4%] dev-install-centos-docker-win writing output... [ 5%] dev-install-centos-prerequisites writing output... [ 5%] dev-install-download-emod writing output... [ 6%] dev-install-overview writing output... 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