Read the Docs build information
Build id: 621385
Project: institute-for-disease-modeling-emodpy-hiv
Version: stable
Commit: a4bdb683c8444c33b37df064aa06251e823d1659
Date: 2021-04-27T23:43:23.128967Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-04-27T23:43:24.721774Z, end-time: 2021-04-27T23:43:26.170292Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emodpy-hiv.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2021-04-27T23:43:26.316902Z, end-time: 2021-04-27T23:43:26.394866Z, duration: 0, exit-code: 0
git checkout --force a4bdb683c8444c33b37df064aa06251e823d1659
Note: checking out 'a4bdb683c8444c33b37df064aa06251e823d1659'.

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 a4bdb68 Adding script and test for coverage

[rtd-command-info] start-time: 2021-04-27T23:43:26.518795Z, end-time: 2021-04-27T23:43:26.588541Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-04-27T23:43:27.717725Z, end-time: 2021-04-27T23:43:33.039963Z, duration: 5, 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-emodpy-hiv/envs/stable/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-04-27T23:43:33.177264Z, end-time: 2021-04-27T23:43:35.108907Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages (21.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages (56.0.0)

[rtd-command-info] start-time: 2021-04-27T23:43:35.220326Z, end-time: 2021-04-27T23:43:47.945302Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting mock==1.0.1
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages (from sphinx) (56.0.0)
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=ab446c1d74e7d3866a37218f63043983cc597f428bd20fe2826661f483b6f2c0
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Successfully built mock future
Installing collected packages: urllib3, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.16 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 snowballstemmer-2.1.0 sphinx-3.5.4 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 urllib3-1.26.4

[rtd-command-info] start-time: 2021-04-27T23:43:48.062369Z, end-time: 2021-04-27T23:44:20.281457Z, duration: 32, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Collecting emodpy~=1.10.2
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[rtd-command-info] start-time: 2021-04-27T23:44:21.020240Z, end-time: 2021-04-27T23:44:21.089482Z, duration: 0, exit-code: 0
cat examples/demo_scenario/conf.py
def config_reports( conf ):
    custom_event_list_for_later = [
      "ViralSuppressionYes",
      "ViralSuppressionNo",
      "DelayUntilBooster1",
      "ReceivedBooster",
      "Vaccinated",
      "ReceivedPrEP"
    ]
    conf.parameters.Report_Event_Recorder_Events = [
      "NewInfectionEvent",
      "Start_Treatment",
      "Started_ART"
    ]
    conf.parameters.Report_HIV_ART = 1
    #conf.parameters.Report_HIV_ART_Start_Year = 2004
    #conf.parameters.Report_HIV_ART_Stop_Year = 10000
    conf.parameters.Report_HIV_ByAgeAndGender = 1
    conf.parameters.Report_HIV_ByAgeAndGender_Add_Relationships = 1
    conf.parameters.Report_HIV_ByAgeAndGender_Add_Transmitters = 1
    conf.parameters.Report_HIV_ByAgeAndGender_Collect_Age_Bins_Data = [
      0,
      5,
      10,
      15,
      20,
      25,
      30,
      35,
      40,
      45,
      50,
      55,
      60,
      100
    ]
    conf.parameters.Report_HIV_ByAgeAndGender_Collect_Circumcision_Data = 1
    conf.parameters.Report_HIV_ByAgeAndGender_Collect_Gender_Data = 1
    conf.parameters.Report_HIV_ByAgeAndGender_Collect_HIV_Data = 1
    #conf.parameters.Report_HIV_ByAgeAndGender_Collect_IP_Data = [ "ARTstate" ]
    conf.parameters.Report_HIV_ByAgeAndGender_Collect_Intervention_Data = []
    conf.parameters.Report_HIV_ByAgeAndGender_Collect_On_Art_Data = 1
    rhbaagecl_events_for_later = [
      "Program_VMMC",
      "Non_Program_MMC"
    ]
    conf.parameters.Report_HIV_ByAgeAndGender_Event_Counter_List = [ "NewInfectionEvent" ]
    conf.parameters.Report_HIV_ByAgeAndGender_Has_Intervention_With_Name = "Traditional_MC"
    conf.parameters.Report_HIV_ByAgeAndGender_Start_Year = 1980
    conf.parameters.Report_HIV_ByAgeAndGender_Stop_Year = 2199
    conf.parameters.Report_HIV_Event_Channels_List = [
      "NewInfectionEvent"
    ]
    conf.parameters.Report_HIV_Infection = 1
    conf.parameters.Report_HIV_Mortality = 1
    conf.parameters.Report_HIV_Period = 365
    conf.parameters.Report_Relationship_Start = 1
    conf.parameters.Report_Transmission = 1
    conf.parameters.Report_HIV_Infection_Start_Year = 1980
    conf.parameters.Report_HIV_Infection_Stop_Year = 2050
   
def config_non_schema_params( conf ):
    conf.parameters["Disable_IP_Whitelist"] = 1
    conf.parameters["Enable_Continuous_Log_Flushing"] = 0
    conf.parameters["logLevel_default"] = "WARNING"
    #conf.parameters.alpha__logLevel_Memory = "WARNING"
    #conf.parameters.logLevel_InfectionHIV = "ERROR"
    #conf.parameters.logLevel_Instrumentation = "ERROR"
    #conf.parameters.logLevel_Memory = "ERROR"
    #conf.parameters.logLevel_OutbreakIndividual = "ERROR"
    #conf.parameters.logLevel_Simulation = "ERROR"
    #conf.parameters.logLevel_SusceptibilityHIV = "ERROR"

def set_config ( conf ):
    # 'Useless' params (not actually used by HIV) -- will be gone after merging in multi-parent depends-on solution from G-O.
    conf.parameters.Acquisition_Blocking_Immunity_Decay_Rate = 1
    conf.parameters.Acquisition_Blocking_Immunity_Duration_Before_Decay = 2
    conf.parameters.Base_Incubation_Period = 0
    conf.parameters.Incubation_Period_Distribution = "FIXED_DURATION"
    conf.parameters.Mortality_Blocking_Immunity_Decay_Rate = 0
    conf.parameters.Mortality_Blocking_Immunity_Duration_Before_Decay = 27000
    conf.parameters.Transmission_Blocking_Immunity_Decay_Rate = 1
    conf.parameters.Transmission_Blocking_Immunity_Duration_Before_Decay = 2
    #conf.parameters.Base_Mortality = 0

    # HIV Science Params
    conf.parameters.Simulation_Type = "HIV_SIM"
    conf.parameters.Base_Infectivity = 0.002327836
    conf.parameters.CD4_Post_Infection_Weibull_Heterogeneity = 0
    conf.parameters.CD4_Post_Infection_Weibull_Scale = 540.55
    conf.parameters.Coital_Dilution_Factor_2_Partners = 0.75
    conf.parameters.Coital_Dilution_Factor_3_Partners = 0.6
    conf.parameters.Coital_Dilution_Factor_4_Plus_Partners = 0.45
    conf.parameters.Days_Between_Symptomatic_And_Death_Weibull_Heterogeneity = 0.5
    conf.parameters.Days_Between_Symptomatic_And_Death_Weibull_Scale = 618.341625
    conf.parameters.Enable_Maternal_Infection_Transmission = 1
    conf.parameters.HIV_Age_Max_for_Adult_Age_Dependent_Survival = 50
    conf.parameters.Male_To_Female_Relative_Infectivity_Ages = [ 0, 15, 25 ]
    conf.parameters.Male_To_Female_Relative_Infectivity_Multipliers = [ 4.684, 4.684, 2.962 ]
    conf.parameters.Maternal_Infection_Transmission_Probability = 0.3
    conf.parameters.Maternal_Transmission_ART_Multiplier = 0.03334
    conf.parameters.Min_Days_Between_Adding_Relationships = 0
    conf.parameters.PFA_Burnin_Duration_In_Days = 5475
    conf.parameters.STI_Coinfection_Acquisition_Multiplier = 5.5
    conf.parameters.STI_Coinfection_Transmission_Multiplier = 5.5
    conf.parameters.Sexual_Debut_Age_Female_Weibull_Heterogeneity = 0.299281948
    conf.parameters.Sexual_Debut_Age_Female_Weibull_Scale = 16.34494123
    conf.parameters.Sexual_Debut_Age_Male_Weibull_Heterogeneity = 0.053712118
    conf.parameters.Sexual_Debut_Age_Male_Weibull_Scale = 17.72188303

    # Simulation Setup
    conf.parameters.Base_Population_Scale_Factor = 0.05
    conf.parameters.Individual_Sampling_Type = "FIXED_SAMPLING"
    conf.parameters.Load_Balance_Filename = ""
    conf.parameters.Node_Grid_Size = 0.009 
    conf.parameters.Random_Number_Generator_Policy = "ONE_PER_NODE"
    conf.parameters.Random_Number_Generator_Type = "USE_AES_COUNTER"

    config_non_schema_params( conf )
    config_reports( conf )




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#          auto-created readthedocs.org specific configuration            #
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#
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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

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using_rtd_theme = (
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)
if using_rtd_theme:
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    html_style = None
    html_theme_options = {}
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if globals().get('websupport2_base_url', False):
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    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
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    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://institute-for-disease-modeling-emodpy-hiv.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/examples/demo_scenario/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'emodpy-hiv',
    'github_version': 'a4bdb683c8444c33b37df064aa06251e823d1659',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'a4bdb683c8444c33b37df064aa06251e823d1659',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'a4bdb683c8444c33b37df064aa06251e823d1659',
    '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': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'a4bdb683',
}

# 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 'tag' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-emodpy-hiv/builds/621385/'

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: 2021-04-27T23:44:21.195111Z, end-time: 2021-04-27T23:44:21.763760Z, duration: 0, exit-code: 2
python -m sphinx -T -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v3.5.4
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: [new config] 0 added, 0 changed, 0 removed

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages/sphinx/application.py", line 352, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 298, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 310, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/stable/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 421, in read
    self.env.doc2path(self.config.master_doc))
sphinx.errors.SphinxError: master file /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/checkouts/stable/examples/demo_scenario/index.rst not found

Sphinx error:
master file /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/checkouts/stable/examples/demo_scenario/index.rst not found