Read the Docs build information
Build id: 1112011
Project: institute-for-disease-modeling-emodpy-hiv
Version: latest
Commit: eca862ca9ddf0c52f251bd162c955816d06c9910
Date: 2022-09-25T15:53:04.208176Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-09-25T15:53:06.287576Z, end-time: 2022-09-25T15:53:07.998708Z, 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' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-09-25T15:53:08.202117Z, end-time: 2022-09-25T15:53:08.318462Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

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

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at eca862c Bump version: 1.0.6 → 1.0.7

[rtd-command-info] start-time: 2022-09-25T15:53:08.543013Z, end-time: 2022-09-25T15:53:08.606849Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-09-25T15:53:09.645478Z, end-time: 2022-09-25T15:53:15.168819Z, 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/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-09-25T15:53:15.358120Z, end-time: 2022-09-25T15:53:17.889699Z, duration: 2, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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/latest/lib/python3.7/site-packages (22.2.2)
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    Uninstalling setuptools-65.4.0:
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Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-09-25T15:53:18.073411Z, end-time: 2022-09-25T15:53:29.963056Z, duration: 11, 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 sphinx-rtd-theme readthedocs-sphinx-ext<2.2
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Building wheels for collected packages: mock
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=3bc5decfa343e0a620faffd4a9983f26b2d3616f5a7c5813b37804a48f308d55
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Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.9.24 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 importlib-metadata-4.12.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.2.1 readthedocs-sphinx-ext-2.1.9 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.2.0.post0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.3.0 urllib3-1.26.12 zipp-3.8.1

[rtd-command-info] start-time: 2022-09-25T15:53:30.211489Z, end-time: 2022-09-25T15:54:08.242941Z, duration: 38, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting emodpy~=1.15
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Collecting emod-hiv==1.0.1
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Collecting emod-malaria==0.0.17
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Collecting numpy
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Collecting idmtools-platform-comps~=1.6
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Collecting emod-api~=1.24
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Collecting pyCOMPS~=2.6
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Collecting astor
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Collecting idmtools~=1.6
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Collecting matplotlib
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Collecting keyring
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Collecting idmtools-models~=1.6
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Collecting astunparse
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Collecting click~=7.1
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Collecting bs4
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Collecting geographiclib
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Collecting shapely
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Collecting parse
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Collecting sklearn
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Collecting lz4
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Collecting pandas
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Collecting prodict
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Collecting pyyaml
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Collecting scipy
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Collecting pyproj
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Collecting graphviz
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Collecting diskcache~=5.2.1
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Collecting pipreqs<0.5,>=0.4.10
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Collecting pluggy~=0.13.1
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Collecting coloredlogs~=15.0
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Collecting pygit2<1.6.0,>=1.4.0
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Collecting backoff<1.11,>=1.10.0
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Collecting pyyaml
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Collecting more-itertools~=8.8.0
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Collecting tqdm<5,>=4.52.0
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Collecting packaging<21.0,>=20.4
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Collecting tabulate<0.9,>=0.8.9
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Collecting pytest-lazy-fixture~=0.6.3
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ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
sphinx 5.2.0.post0 requires packaging>=21.0, but you have packaging 20.9 which is incompatible.
Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 attrs-22.1.0 backoff-1.10.0 beautifulsoup4-4.11.1 bs4-0.0.1 cached-property-1.5.2 cffi-1.15.1 click-7.1.2 coloredlogs-15.0.1 cryptography-38.0.1 cycler-0.11.0 diskcache-5.2.1 docopt-0.6.2 emod-api-1.27.1 emod-hiv-1.0.1 emod-malaria-0.0.17 emodpy-1.20.0 fonttools-4.37.3 future-0.18.2 geographiclib-2.0 graphviz-0.20.1 humanfriendly-10.0 idmtools-1.6.7 idmtools-models-1.6.7 idmtools-platform-comps-1.6.7 iniconfig-1.1.1 jaraco.classes-3.2.2 jeepney-0.8.0 jinja2-3.0.3 joblib-1.2.0 keyring-23.9.3 kiwisolver-1.4.4 lz4-4.0.2 matplotlib-3.5.3 more-itertools-8.8.0 natsort-8.1.0 numpy-1.21.6 packaging-20.9 pandas-1.3.5 parse-1.19.0 pillow-9.2.0 pipreqs-0.4.11 pluggy-0.13.1 prodict-0.8.18 py-1.11.0 pyCOMPS-2.8.0 pycparser-2.21 pygit2-1.5.0 pyproj-3.2.1 pytest-7.1.3 pytest-lazy-fixture-0.6.3 python-dateutil-2.8.2 pyyaml-5.4.1 scikit-learn-1.0.2 scipy-1.7.3 shapely-1.8.4 six-1.16.0 sklearn-0.0 soupsieve-2.3.2.post1 tabulate-0.8.10 threadpoolctl-3.1.0 tomli-2.0.1 tqdm-4.64.1 xdg-5.1.1 yarg-0.1.9

[rtd-command-info] start-time: 2022-09-25T15:54:08.494248Z, end-time: 2022-09-25T15:54:13.982842Z, duration: 5, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Collecting pockets>=0.3
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Installing collected packages: pockets, MarkupSafe, docutils, sphinxcontrib-napoleon, plantweb, Jinja2, sphinxext.remoteliteralinclude, sphinx, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton
  Attempting uninstall: MarkupSafe
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  Attempting uninstall: docutils
    Found existing installation: docutils 0.17.1
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  Attempting uninstall: Jinja2
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  Attempting uninstall: sphinx
    Found existing installation: Sphinx 5.2.0.post0
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  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 1.0.0
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ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
idmtools-platform-comps 1.6.7 requires jinja2~=3.0.1, but you have jinja2 2.11.3 which is incompatible.
idmtools-models 1.6.7 requires jinja2~=3.0.1, but you have jinja2 2.11.3 which is incompatible.
Successfully installed Jinja2-2.11.3 MarkupSafe-2.0.1 docutils-0.16 plantweb-1.2.1 pockets-0.9.1 sphinx-3.2.1 sphinx-copybutton-0.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0

[rtd-command-info] start-time: 2022-09-25T15:54:14.181888Z, end-time: 2022-09-25T15:54:15.527491Z, duration: 1, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating emodpy_hiv.egg-info
writing emodpy_hiv.egg-info/PKG-INFO
writing dependency_links to emodpy_hiv.egg-info/dependency_links.txt
writing requirements to emodpy_hiv.egg-info/requires.txt
writing top-level names to emodpy_hiv.egg-info/top_level.txt
writing manifest file 'emodpy_hiv.egg-info/SOURCES.txt'
reading manifest file 'emodpy_hiv.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'emodpy_hiv.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/emodpy_hiv
copying emodpy_hiv/__init__.py -> build/lib/emodpy_hiv
copying emodpy_hiv/utils.py -> build/lib/emodpy_hiv
copying emodpy_hiv/download.py -> build/lib/emodpy_hiv
creating build/lib/tests
copying tests/__init__.py -> build/lib/tests
creating build/lib/emodpy_hiv/demographics
copying emodpy_hiv/demographics/HIVDemographics.py -> build/lib/emodpy_hiv/demographics
copying emodpy_hiv/demographics/__init__.py -> build/lib/emodpy_hiv/demographics
copying emodpy_hiv/demographics/DemographicsTemplates.py -> build/lib/emodpy_hiv/demographics
creating build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/prep.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/art.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/random.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/drawblood.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/reftracker.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/outbreak.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/modcoinf.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/cascade_helpers.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/pmtct.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/delay.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/stipostdebut.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/malecirc.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/__init__.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/sigmoiddiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/utils.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artstagingbycd4diag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artdropout.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/rapiddiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/yearandsexdiag.py -> build/lib/emodpy_hiv/interventions
creating build/lib/tests/unittests
copying tests/unittests/test_import.py -> build/lib/tests/unittests
copying tests/unittests/test_demographics.py -> build/lib/tests/unittests
copying tests/unittests/__init__.py -> build/lib/tests/unittests
copying tests/unittests/check_coverage.py -> build/lib/tests/unittests
copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests
copying tests/unittests/test_intervention.py -> build/lib/tests/unittests
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/emodpy_hiv
creating build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/demographics/HIVDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
copying build/lib/emodpy_hiv/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
copying build/lib/emodpy_hiv/download.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
creating build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/prep.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/art.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/random.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/drawblood.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/reftracker.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/modcoinf.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/cascade_helpers.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/pmtct.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/delay.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/stipostdebut.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/malecirc.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/sigmoiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/artstagingbycd4diag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/artdropout.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/rapiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/yearandsexdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
creating build/bdist.linux-x86_64/egg/tests
copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests
creating build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_import.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_demographics.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/check_coverage.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/schema_path_file.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_intervention.py -> build/bdist.linux-x86_64/egg/tests/unittests
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/HIVDemographics.py to HIVDemographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/download.py to download.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/prep.py to prep.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/art.py to art.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/random.py to random.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/drawblood.py to drawblood.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/reftracker.py to reftracker.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/outbreak.py to outbreak.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/modcoinf.py to modcoinf.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/cascade_helpers.py to cascade_helpers.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/pmtct.py to pmtct.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/delay.py to delay.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/stipostdebut.py to stipostdebut.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/malecirc.py to malecirc.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py to artstagingbycd4agnosticdiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/sigmoiddiag.py to sigmoiddiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4diag.py to artstagingbycd4diag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artdropout.py to artdropout.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/rapiddiag.py to rapiddiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/yearandsexdiag.py to yearandsexdiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_import.py to test_import.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demographics.py to test_demographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/check_coverage.py to check_coverage.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/schema_path_file.py to schema_path_file.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_intervention.py to test_intervention.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
tests.unittests.__pycache__.schema_path_file.cpython-37: module references __file__
tests.unittests.__pycache__.test_demographics.cpython-37: module references __file__
tests.unittests.__pycache__.test_intervention.cpython-37: module references __file__
creating dist
creating 'dist/emodpy_hiv-1.0.7-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 emodpy_hiv-1.0.7-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages/emodpy_hiv-1.0.7-py3.7.egg
Extracting emodpy_hiv-1.0.7-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Adding emodpy-hiv 1.0.7 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages/emodpy_hiv-1.0.7-py3.7.egg
Processing dependencies for emodpy-hiv==1.0.7
Searching for jinja2~=3.0.1
Reading https://pypi.org/simple/jinja2/
Downloading https://files.pythonhosted.org/packages/20/9a/e5d9ec41927401e41aea8af6d16e78b5e612bca4699d417f646a9610a076/Jinja2-3.0.3-py3-none-any.whl#sha256=077ce6014f7b40d03b47d1f1ca4b0fc8328a692bd284016f806ed0eaca390ad8
Best match: Jinja2 3.0.3
Processing Jinja2-3.0.3-py3-none-any.whl
Installing Jinja2-3.0.3-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Adding Jinja2 3.0.3 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages/Jinja2-3.0.3-py3.7.egg
Searching for numpy==1.21.6
Best match: numpy 1.21.6
Adding numpy 1.21.6 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emod-malaria==0.0.17
Best match: emod-malaria 0.0.17
Adding emod-malaria 0.0.17 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emod-hiv==1.0.1
Best match: emod-hiv 1.0.1
Adding emod-hiv 1.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emodpy==1.20.0
Best match: emodpy 1.20.0
Adding emodpy 1.20.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idmtools-platform-comps==1.6.7
Best match: idmtools-platform-comps 1.6.7
Adding idmtools-platform-comps 1.6.7 to easy-install.pth file
Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for click==7.1.2
Best match: click 7.1.2
Adding click 7.1.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pyCOMPS==2.8.0
Best match: pyCOMPS 2.8.0
Adding pyCOMPS 2.8.0 to easy-install.pth file
Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for astunparse==1.6.3
Best match: astunparse 1.6.3
Adding astunparse 1.6.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for astor==0.8.1
Best match: astor 0.8.1
Adding astor 0.8.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for keyring==23.9.3
Best match: keyring 23.9.3
Adding keyring 23.9.3 to easy-install.pth file
Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for bs4==0.0.1
Best match: bs4 0.0.1
Adding bs4 0.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emod-api==1.27.1
Best match: emod-api 1.27.1
Adding emod-api 1.27.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for matplotlib==3.5.3
Best match: matplotlib 3.5.3
Adding matplotlib 3.5.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idmtools-models==1.6.7
Best match: idmtools-models 1.6.7
Adding idmtools-models 1.6.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idmtools==1.6.7
Best match: idmtools 1.6.7
Adding idmtools 1.6.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pytest-lazy-fixture==0.6.3
Best match: pytest-lazy-fixture 0.6.3
Adding pytest-lazy-fixture 0.6.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for tqdm==4.64.1
Best match: tqdm 4.64.1
Adding tqdm 4.64.1 to easy-install.pth file
Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for natsort==8.1.0
Best match: natsort 8.1.0
Adding natsort 8.1.0 to easy-install.pth file
Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pytz==2022.2.1
Best match: pytz 2022.2.1
Adding pytz 2022.2.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
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-emodpy-hiv/envs/latest/bin
Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for requests==2.28.1
Best match: requests 2.28.1
Adding requests 2.28.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for xdg==5.1.1
Best match: xdg 5.1.1
Adding xdg 5.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for wheel==0.37.1
Best match: wheel 0.37.1
Adding wheel 0.37.1 to easy-install.pth file
Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for six==1.16.0
Best match: six 1.16.0
Adding six 1.16.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for SecretStorage==3.3.3
Best match: SecretStorage 3.3.3
Adding SecretStorage 3.3.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for importlib-metadata==4.12.0
Best match: importlib-metadata 4.12.0
Adding importlib-metadata 4.12.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for jeepney==0.8.0
Best match: jeepney 0.8.0
Adding jeepney 0.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for jaraco.classes==3.2.2
Best match: jaraco.classes 3.2.2
Adding jaraco.classes 3.2.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for beautifulsoup4==4.11.1
Best match: beautifulsoup4 4.11.1
Adding beautifulsoup4 4.11.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for geographiclib==2.0
Best match: geographiclib 2.0
Adding geographiclib 2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for prodict==0.8.18
Best match: prodict 0.8.18
Adding prodict 0.8.18 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pyproj==3.2.1
Best match: pyproj 3.2.1
Adding pyproj 3.2.1 to easy-install.pth file
Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for lz4==4.0.2
Best match: lz4 4.0.2
Adding lz4 4.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pandas==1.3.5
Best match: pandas 1.3.5
Adding pandas 1.3.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for sklearn==0.0
Best match: sklearn 0.0
Adding sklearn 0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for parse==1.19.0
Best match: parse 1.19.0
Adding parse 1.19.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.7.3
Best match: scipy 1.7.3
Adding scipy 1.7.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for Shapely==1.8.4
Best match: Shapely 1.8.4
Adding Shapely 1.8.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for PyYAML==5.4.1
Best match: PyYAML 5.4.1
Adding PyYAML 5.4.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for graphviz==0.20.1
Best match: graphviz 0.20.1
Adding graphviz 0.20.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pyparsing==3.0.9
Best match: pyparsing 3.0.9
Adding pyparsing 3.0.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cycler==0.11.0
Best match: cycler 0.11.0
Adding cycler 0.11.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for fonttools==4.37.3
Best match: fonttools 4.37.3
Adding fonttools 4.37.3 to easy-install.pth file
Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for python-dateutil==2.8.2
Best match: python-dateutil 2.8.2
Adding python-dateutil 2.8.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for packaging==20.9
Best match: packaging 20.9
Adding packaging 20.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for Pillow==9.2.0
Best match: Pillow 9.2.0
Adding Pillow 9.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for kiwisolver==1.4.4
Best match: kiwisolver 1.4.4
Adding kiwisolver 1.4.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for backoff==1.10.0
Best match: backoff 1.10.0
Adding backoff 1.10.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for more-itertools==8.8.0
Best match: more-itertools 8.8.0
Adding more-itertools 8.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for coloredlogs==15.0.1
Best match: coloredlogs 15.0.1
Adding coloredlogs 15.0.1 to easy-install.pth file
Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for diskcache==5.2.1
Best match: diskcache 5.2.1
Adding diskcache 5.2.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pygit2==1.5.0
Best match: pygit2 1.5.0
Adding pygit2 1.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for tabulate==0.8.10
Best match: tabulate 0.8.10
Adding tabulate 0.8.10 to easy-install.pth file
Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pipreqs==0.4.11
Best match: pipreqs 0.4.11
Adding pipreqs 0.4.11 to easy-install.pth file
Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pluggy==0.13.1
Best match: pluggy 0.13.1
Adding pluggy 0.13.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pytest==7.1.3
Best match: pytest 7.1.3
Adding pytest 7.1.3 to easy-install.pth file
Installing py.test script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing pytest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for MarkupSafe==2.0.1
Best match: MarkupSafe 2.0.1
Adding MarkupSafe 2.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for certifi==2022.9.24
Best match: certifi 2022.9.24
Adding certifi 2022.9.24 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idna==3.4
Best match: idna 3.4
Adding idna 3.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for charset-normalizer==2.1.1
Best match: charset-normalizer 2.1.1
Adding charset-normalizer 2.1.1 to easy-install.pth file
Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for urllib3==1.26.12
Best match: urllib3 1.26.12
Adding urllib3 1.26.12 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cryptography==38.0.1
Best match: cryptography 38.0.1
Adding cryptography 38.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for typing-extensions==4.3.0
Best match: typing-extensions 4.3.0
Adding typing-extensions 4.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for zipp==3.8.1
Best match: zipp 3.8.1
Adding zipp 3.8.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for soupsieve==2.3.2.post1
Best match: soupsieve 2.3.2.post1
Adding soupsieve 2.3.2.post1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for scikit-learn==1.0.2
Best match: scikit-learn 1.0.2
Adding scikit-learn 1.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for humanfriendly==10.0
Best match: humanfriendly 10.0
Adding humanfriendly 10.0 to easy-install.pth file
Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cached-property==1.5.2
Best match: cached-property 1.5.2
Adding cached-property 1.5.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cffi==1.15.1
Best match: cffi 1.15.1
Adding cffi 1.15.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for docopt==0.6.2
Best match: docopt 0.6.2
Adding docopt 0.6.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for yarg==0.1.9
Best match: yarg 0.1.9
Adding yarg 0.1.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for iniconfig==1.1.1
Best match: iniconfig 1.1.1
Adding iniconfig 1.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for tomli==2.0.1
Best match: tomli 2.0.1
Adding tomli 2.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for py==1.11.0
Best match: py 1.11.0
Adding py 1.11.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for attrs==22.1.0
Best match: attrs 22.1.0
Adding attrs 22.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for joblib==1.2.0
Best match: joblib 1.2.0
Adding joblib 1.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for threadpoolctl==3.1.0
Best match: threadpoolctl 3.1.0
Adding threadpoolctl 3.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pycparser==2.21
Best match: pycparser 2.21
Adding pycparser 2.21 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for emodpy-hiv==1.0.7

[rtd-command-info] start-time: 2022-09-25T15:54:17.572008Z, end-time: 2022-09-25T15:54:17.650622Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Sphinx Demo docs 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
# docs root, use os.path.abspath to make it absolute, like shown here.
#
import os
import subprocess
import sys
import sphinx_rtd_theme
import configparser
from datetime import datetime

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

# Rename "emodpy-hiv" to "API reference"
filename = 'modules.rst' # This must match the Makefile
with open(filename) as f: # Read existing file
    lines = f.readlines()
lines[0] = "API reference\n" # Blast away the existing heading and replace with this
lines[1] = "=============\n" # Ensure the heading is the right length
with open(filename, "w") as f: # Write new file
    f.writelines(lines)


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

tags.add('emodpyhiv')

# If your docs needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.mathjax',
    'sphinx.ext.githubpages',
    'sphinx.ext.autodoc',
    'sphinxcontrib.napoleon',
    'sphinx.ext.todo',
    'plantweb.directive',
    'sphinxcontrib.programoutput',
    'sphinx.ext.intersphinx',
    'sphinxext.remoteliteralinclude',
    'sphinx_copybutton'
]

plantuml = 'plantweb'

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

autodoc_mock_imports = []

napoleon_google_docstring = True
# napoleon_numpy_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'emodpy-hiv'
copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.'
author = u'Institute for Disease Modeling'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
#current_path = os.path.dirname(__file__)
#version_path = os.path.join(current_path, '..', '.bumpversion.cfg')
#config = configparser.ConfigParser()
#config.read(version_path)

#version = config['bumpversion']['current_version']
# The full version, including alpha/beta/rc tags.
# release = u'1.0'

# The language for content autogenerated by Sphinx. Refer to docs
# 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 docs 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
# docs.
# #
# 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> docs" 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',
        '_static/copy_button.css'
        ]
}

html_js_files = ['show_block_by_os.js']

# 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 docs.
#
# 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 = 'emodpy-hiv'

# -- 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, 'emodpy-hiv-docs.tex', u'emodpy-hiv',
     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, 'emodpy-hiv-docs', u'emodpy-hiv',
     [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, 'emodpy-hiv-docs', u'emodpy-hiv',
     author, 'Institute for Disease Modeling', 'How to use emodpy for HIV 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 = {'python': ('https://docs.python.org/3', None),
                       'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None),
                       'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None),
                       'emodpy_generic': ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', None),
                       'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None),
                       'calibra': ('https://docs.idmod.org/projects/idmtools_calibra/en/latest/', None),
                       'emod-hiv': ('https://docs.idmod.org/projects/emod-hiv/en/latest/', None),
                       'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None),
                       'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None)
                       }







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


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

import importlib
import sys
import os.path

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

from sphinx import version_info

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

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

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

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


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("v1.0.2", "/en/v1.0.2/"),
    ("v1.0.1", "/en/v1.0.1/"),
    ("v0.0.41", "/en/v0.0.41/"),
    ("v0.0.38", "/en/v0.0.38/"),
    ("v0.0.37", "/en/v0.0.37/"),
    ("v0.0.35", "/en/v0.0.35/"),
    ("v0.0.22", "/en/v0.0.22/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/emodpy-hiv/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/emodpy-hiv/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-emodpy-hiv',
    'name': u'emodpy-hiv',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://docs.idmod.org/projects/emodpy-hiv/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': 'emodpy-hiv',
    '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': 'eca862ca',
}

# 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-emodpy-hiv/builds/1112011/'

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: 2022-09-25T15:54:17.872996Z, end-time: 2022-09-25T15:54:23.061489Z, duration: 5, exit-code: 0
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v3.2.1
rm: cannot remove 'modules.rst': No such file or directory
make: [generate-api] Error 1 (ignored)
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-generic/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/idmtools_calibra/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-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 30 source files that are out of date
updating environment: [new config] 30 added, 0 changed, 0 removed
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writing output... [ 36%] emodpy_hiv.interventions.cascade_helpers
writing output... [ 40%] emodpy_hiv.interventions.delay
writing output... [ 43%] emodpy_hiv.interventions.drawblood
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writing output... [ 50%] emodpy_hiv.interventions.modcoinf
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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: 2022-09-25T15:54:23.286004Z, end-time: 2022-09-25T15:54:27.122784Z, duration: 3, exit-code: 0
python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
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-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv...
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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-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: [new config] 30 added, 0 changed, 0 removed
reading sources... [  3%] emodpy_hiv
reading sources... [  6%] emodpy_hiv.demographics
reading sources... [ 10%] emodpy_hiv.demographics.DemographicsTemplates
reading sources... [ 13%] emodpy_hiv.demographics.HIVDemographics
reading sources... [ 16%] emodpy_hiv.download
reading sources... [ 20%] emodpy_hiv.interventions
reading sources... [ 23%] emodpy_hiv.interventions.art
reading sources... [ 26%] emodpy_hiv.interventions.artdropout
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reading sources... [ 40%] emodpy_hiv.interventions.delay
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reading sources... [ 93%] index
reading sources... [ 96%] installation
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looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... installation faq modules emodpy_hiv emodpy_hiv.demographics emodpy_hiv.demographics.DemographicsTemplates emodpy_hiv.demographics.HIVDemographics emodpy_hiv.interventions emodpy_hiv.interventions.art emodpy_hiv.interventions.artdropout emodpy_hiv.interventions.artstagingbycd4agnosticdiag emodpy_hiv.interventions.artstagingbycd4diag emodpy_hiv.interventions.cascade_helpers emodpy_hiv.interventions.delay emodpy_hiv.interventions.drawblood emodpy_hiv.interventions.malecirc emodpy_hiv.interventions.modcoinf emodpy_hiv.interventions.outbreak emodpy_hiv.interventions.pmtct emodpy_hiv.interventions.prep emodpy_hiv.interventions.random emodpy_hiv.interventions.rapiddiag emodpy_hiv.interventions.reftracker emodpy_hiv.interventions.sigmoiddiag emodpy_hiv.interventions.stipostdebut emodpy_hiv.interventions.utils emodpy_hiv.interventions.yearandsexdiag emodpy_hiv.download emodpy_hiv.utils 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: 2022-09-25T15:54:27.371123Z, end-time: 2022-09-25T15:54:28.844593Z, duration: 1, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v3.2.1
loading translations [en]... done
making output directory... done
loading pickled environment... done
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updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing emodpy-hiv-docs.tex... index installation faq modules emodpy_hiv emodpy_hiv.demographics emodpy_hiv.demographics.DemographicsTemplates emodpy_hiv.demographics.HIVDemographics emodpy_hiv.interventions emodpy_hiv.interventions.art emodpy_hiv.interventions.artdropout emodpy_hiv.interventions.artstagingbycd4agnosticdiag emodpy_hiv.interventions.artstagingbycd4diag emodpy_hiv.interventions.cascade_helpers emodpy_hiv.interventions.delay emodpy_hiv.interventions.drawblood emodpy_hiv.interventions.malecirc emodpy_hiv.interventions.modcoinf emodpy_hiv.interventions.outbreak emodpy_hiv.interventions.pmtct emodpy_hiv.interventions.prep emodpy_hiv.interventions.random emodpy_hiv.interventions.rapiddiag emodpy_hiv.interventions.reftracker emodpy_hiv.interventions.sigmoiddiag emodpy_hiv.interventions.stipostdebut emodpy_hiv.interventions.utils emodpy_hiv.interventions.yearandsexdiag emodpy_hiv.download emodpy_hiv.utils 
resolving references...
done
writing... done
copying TeX support files... copying TeX support files...
done
build succeeded.

WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/checkouts/latest/docs/_build/latex/_static/searchtools.js
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).

[rtd-command-info] start-time: 2022-09-25T15:54:29.151153Z, end-time: 2022-09-25T15:54:29.235163Z, 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: 2022-09-25T15:54:29.465744Z, end-time: 2022-09-25T15:54:45.348081Z, duration: 15, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emodpy-hiv -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-emodpy-hiv"  "emodpy-hiv-docs.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
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LaTeX2e <2017-04-15>
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Chapter 1.
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Chapter 2.

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Chapter 3.

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Chapter 1.
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[]\T1/ptm/m/n/10 The HIV team has some de-mo-graphic pa-ram-e-ter de-faults set
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Chapter 3.

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[11]
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[12]
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[13]
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[14]
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[15]
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[16]
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[17]
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[18]
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[19]
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[20]
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[29]) (./institute-for-disease-modeling-emodpy-hiv.aux) )
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