Read the Docs build information
Build id: 630937
Project: institute-for-disease-modeling-emodpy-hiv
Version: latest
Commit: 629c8b925d73ef0d1c9a12ca0cdaee8d495f01b1
Date: 2021-05-11T16:40:52.224966Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-05-11T16:40:53.713585Z, end-time: 2021-05-11T16:40:55.300246Z, 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,192.30.255.112' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2021-05-11T16:40:55.469866Z, end-time: 2021-05-11T16:40:55.552467Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at 629c8b9 Bump version: 0.0.15 → 0.0.16

[rtd-command-info] start-time: 2021-05-11T16:40:55.671104Z, end-time: 2021-05-11T16:40:55.736872Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-05-11T16:40:56.674292Z, end-time: 2021-05-11T16:41:01.873238Z, 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: 2021-05-11T16:41:02.003716Z, end-time: 2021-05-11T16:41:03.966804Z, 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/latest/lib/python3.7/site-packages (21.1.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (56.2.0)

[rtd-command-info] start-time: 2021-05-11T16:41:04.091576Z, end-time: 2021-05-11T16:41:17.507216Z, duration: 13, 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
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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'
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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-2.9.0 alabaster-0.7.12 babel-2.9.1 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-4.0.1 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: 2021-05-11T16:41:17.628078Z, end-time: 2021-05-11T16:41:54.683055Z, duration: 37, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Collecting emodpy~=1.11.0
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[rtd-command-info] start-time: 2021-05-11T16:41:54.814654Z, end-time: 2021-05-11T16:42:11.816190Z, duration: 17, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Collecting pynacl>=1.4.0
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idmtools 1.6.3 requires pygit2<1.6.0,>=1.4.0, but you have pygit2 1.2.1 which is incompatible.

[rtd-command-info] start-time: 2021-05-11T16:42:11.943320Z, end-time: 2021-05-11T16:42:13.650024Z, 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'
adding license file 'LICENSE' (matched pattern 'LICEN[CS]E*')
reading manifest file 'emodpy_hiv.egg-info/SOURCES.txt'
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
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/malecirc.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artstagingbycd4diag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/drawblood.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/outbreak.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/cascade_helpers.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/utils.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/art.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artdropout.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/prep.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/stipostdebut.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/sigmoiddiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/modcoinf.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/yearandsexdiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/random.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/reftracker.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/rapiddiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/__init__.py -> build/lib/emodpy_hiv/interventions
creating build/lib/tests/unittests
copying tests/unittests/test_demographics.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_import.py -> build/lib/tests/unittests
copying tests/unittests/test_intervention.py -> build/lib/tests/unittests
copying tests/unittests/__init__.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
creating 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/artstagingbycd4diag.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/outbreak.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/cascade_helpers.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/art.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/prep.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/sigmoiddiag.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/yearandsexdiag.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/reftracker.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/rapiddiag.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/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
creating build/bdist.linux-x86_64/egg/tests
creating 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/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_import.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
copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests
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/interventions/malecirc.py to malecirc.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/drawblood.py to drawblood.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/artstagingbycd4agnosticdiag.py to artstagingbycd4agnosticdiag.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/utils.py to utils.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/artdropout.py to artdropout.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/stipostdebut.py to stipostdebut.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/modcoinf.py to modcoinf.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/emodpy_hiv/interventions/random.py to random.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/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/rapiddiag.py to rapiddiag.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/__init__.py to __init__.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/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_import.py to test_import.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_intervention.py to test_intervention.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/__init__.py to __init__.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-0.0.16-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-0.0.16-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-0.0.16-py3.7.egg
Extracting emodpy_hiv-0.0.16-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 0.0.16 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-0.0.16-py3.7.egg
Processing dependencies for emodpy-hiv==0.0.16
Searching for pygit2<1.6.0,>=1.4.0
Reading https://pypi.org/simple/pygit2/
Downloading https://files.pythonhosted.org/packages/98/ed/41a09ca93374015958a18e37280d02c833238272ce3f2e28b10c6253477d/pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl#sha256=fda3f8dd30608475f24a531e6f968010662ed7b9d4e303525d945c8933d9528f
Best match: pygit2 1.5.0
Processing pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl
Installing pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Adding pygit2 1.5.0 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/pygit2-1.5.0-py3.7-linux-x86_64.egg
Searching for numpy==1.20.3
Best match: numpy 1.20.3
Adding numpy 1.20.3 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 pandas==1.1.5
Best match: pandas 1.1.5
Adding pandas 1.1.5 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 emodpy==1.11.0
Best match: emodpy 1.11.0
Adding emodpy 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 python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
Adding python-dateutil 2.8.1 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 pytz==2021.1
Best match: pytz 2021.1
Adding pytz 2021.1 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 scikit-learn==0.24.2
Best match: scikit-learn 0.24.2
Adding scikit-learn 0.24.2 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 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 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==1.10.8
Best match: emod-api 1.10.8
Adding emod-api 1.10.8 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 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 idmtools==1.6.3
Best match: idmtools 1.6.3
Adding idmtools 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 idmtools-models==1.6.3
Best match: idmtools-models 1.6.3
Adding idmtools-models 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 idmtools-platform-comps==1.6.3
Best match: idmtools-platform-comps 1.6.3
Adding idmtools-platform-comps 1.6.3 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 matplotlib==3.4.2
Best match: matplotlib 3.4.2
Adding matplotlib 3.4.2 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 keyring==23.0.1
Best match: keyring 23.0.1
Adding keyring 23.0.1 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 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 scipy==1.6.3
Best match: scipy 1.6.3
Adding scipy 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 threadpoolctl==2.1.0
Best match: threadpoolctl 2.1.0
Adding threadpoolctl 2.1.0 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==1.0.1
Best match: joblib 1.0.1
Adding joblib 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 beautifulsoup4==4.9.3
Best match: beautifulsoup4 4.9.3
Adding beautifulsoup4 4.9.3 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==1.7.1
Best match: Shapely 1.7.1
Adding Shapely 1.7.1 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==1.50
Best match: geographiclib 1.50
Adding geographiclib 1.50 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==3.0.1
Best match: pyproj 3.0.1
Adding pyproj 3.0.1 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==3.1.3
Best match: lz4 3.1.3
Adding lz4 3.1.3 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 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 wheel==0.36.2
Best match: wheel 0.36.2
Adding wheel 0.36.2 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 diskcache==5.1.0
Best match: diskcache 5.1.0
Adding diskcache 5.1.0 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 more-itertools==8.7.0
Best match: more-itertools 8.7.0
Adding more-itertools 8.7.0 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 pipreqs==0.4.10
Best match: pipreqs 0.4.10
Adding pipreqs 0.4.10 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 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 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 tabulate==0.8.9
Best match: tabulate 0.8.9
Adding tabulate 0.8.9 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 tqdm==4.60.0
Best match: tqdm 4.60.0
Adding tqdm 4.60.0 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 coloredlogs==15.0
Best match: coloredlogs 15.0
Adding coloredlogs 15.0 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 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 Jinja2==2.11.3
Best match: Jinja2 2.11.3
Adding Jinja2 2.11.3 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 pyCOMPS==2.4.1
Best match: pyCOMPS 2.4.1
Adding pyCOMPS 2.4.1 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 kiwisolver==1.3.1
Best match: kiwisolver 1.3.1
Adding kiwisolver 1.3.1 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==2.4.7
Best match: pyparsing 2.4.7
Adding pyparsing 2.4.7 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 cycler==0.10.0
Best match: cycler 0.10.0
Adding cycler 0.10.0 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 Pillow==8.2.0
Best match: Pillow 8.2.0
Adding Pillow 8.2.0 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 importlib-metadata==4.0.1
Best match: importlib-metadata 4.0.1
Adding importlib-metadata 4.0.1 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 jeepney==0.6.0
Best match: jeepney 0.6.0
Adding jeepney 0.6.0 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==3.3.1
Best match: SecretStorage 3.3.1
Adding SecretStorage 3.3.1 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==2.2.1
Best match: soupsieve 2.2.1
Adding soupsieve 2.2.1 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 certifi==2020.12.5
Best match: certifi 2020.12.5
Adding certifi 2020.12.5 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 cffi==1.14.5
Best match: cffi 1.14.5
Adding cffi 1.14.5 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 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 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 humanfriendly==9.1
Best match: humanfriendly 9.1
Adding humanfriendly 9.1 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 MarkupSafe==1.1.1
Best match: MarkupSafe 1.1.1
Adding MarkupSafe 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 xdg==5.0.2
Best match: xdg 5.0.2
Adding xdg 5.0.2 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 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==2.25.1
Best match: requests 2.25.1
Adding requests 2.25.1 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==3.10.0.0
Best match: typing-extensions 3.10.0.0
Adding typing-extensions 3.10.0.0 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 zipp==3.4.1
Best match: zipp 3.4.1
Adding zipp 3.4.1 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 cryptography==3.4.7
Best match: cryptography 3.4.7
Adding cryptography 3.4.7 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 pycparser==2.20
Best match: pycparser 2.20
Adding pycparser 2.20 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 chardet==4.0.0
Best match: chardet 4.0.0
Adding chardet 4.0.0 to easy-install.pth file
Installing chardetect 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 idna==2.10
Best match: idna 2.10
Adding idna 2.10 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for urllib3==1.26.4
Best match: urllib3 1.26.4
Adding urllib3 1.26.4 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
Finished processing dependencies for emodpy-hiv==0.0.16

[rtd-command-info] start-time: 2021-05-11T16:42:14.503301Z, end-time: 2021-05-11T16:42:14.566832Z, 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__)))


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

# 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'
]

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'
        ]
}
# 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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file should't rely on extra depencies.

import importlib
import sys
import os.path

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

from sphinx import version_info

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

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

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

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


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-emodpy-hiv',
    'name': u'emodpy-hiv',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://institute-for-disease-modeling-emodpy-hiv.readthedocs-hosted.com/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': '629c8b92',
}

# 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/630937/'

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: 2021-05-11T16:42:14.680717Z, end-time: 2021-05-11T16:42:19.339644Z, duration: 4, exit-code: 0
python -m sphinx -T -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)
rm: cannot remove 'emodpy_hiv_index.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 27 source files that are out of date
updating environment: [new config] 27 added, 0 changed, 0 removed
reading sources... [  3%] emodpy_hiv
reading sources... [  7%] emodpy_hiv.demographics
reading sources... [ 11%] emodpy_hiv.demographics.DemographicsTemplates
reading sources... [ 14%] emodpy_hiv.demographics.HIVDemographics
reading sources... [ 18%] emodpy_hiv.interventions
reading sources... [ 22%] emodpy_hiv.interventions.art
reading sources... [ 25%] emodpy_hiv.interventions.artdropout
reading sources... [ 29%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag
reading sources... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag
reading sources... [ 37%] emodpy_hiv.interventions.cascade_helpers
reading sources... [ 40%] emodpy_hiv.interventions.delay
reading sources... [ 44%] emodpy_hiv.interventions.drawblood
reading sources... [ 48%] emodpy_hiv.interventions.malecirc
reading sources... [ 51%] emodpy_hiv.interventions.modcoinf
reading sources... [ 55%] emodpy_hiv.interventions.outbreak
reading sources... [ 59%] emodpy_hiv.interventions.pmtct
reading sources... [ 62%] emodpy_hiv.interventions.prep
reading sources... [ 66%] emodpy_hiv.interventions.random
reading sources... [ 70%] emodpy_hiv.interventions.rapiddiag
reading sources... [ 74%] emodpy_hiv.interventions.reftracker
reading sources... [ 77%] emodpy_hiv.interventions.sigmoiddiag
reading sources... [ 81%] emodpy_hiv.interventions.stipostdebut
reading sources... [ 85%] emodpy_hiv.interventions.utils
reading sources... [ 88%] emodpy_hiv.interventions.yearandsexdiag
reading sources... [ 92%] emodpy_hiv_index
reading sources... [ 96%] index
reading sources... [100%] installation

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  3%] emodpy_hiv
writing output... [  7%] emodpy_hiv.demographics
writing output... [ 11%] emodpy_hiv.demographics.DemographicsTemplates
writing output... [ 14%] emodpy_hiv.demographics.HIVDemographics
writing output... [ 18%] emodpy_hiv.interventions
writing output... [ 22%] emodpy_hiv.interventions.art
writing output... [ 25%] emodpy_hiv.interventions.artdropout
writing output... [ 29%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag
writing output... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag
writing output... [ 37%] emodpy_hiv.interventions.cascade_helpers
writing output... [ 40%] emodpy_hiv.interventions.delay
writing output... [ 44%] emodpy_hiv.interventions.drawblood
writing output... [ 48%] emodpy_hiv.interventions.malecirc
writing output... [ 51%] emodpy_hiv.interventions.modcoinf
writing output... [ 55%] emodpy_hiv.interventions.outbreak
writing output... [ 59%] emodpy_hiv.interventions.pmtct
writing output... [ 62%] emodpy_hiv.interventions.prep
writing output... [ 66%] emodpy_hiv.interventions.random
writing output... [ 70%] emodpy_hiv.interventions.rapiddiag
writing output... [ 74%] emodpy_hiv.interventions.reftracker
writing output... [ 77%] emodpy_hiv.interventions.sigmoiddiag
writing output... [ 81%] emodpy_hiv.interventions.stipostdebut
writing output... [ 85%] emodpy_hiv.interventions.utils
writing output... [ 88%] emodpy_hiv.interventions.yearandsexdiag
writing output... [ 92%] emodpy_hiv_index
writing output... [ 96%] index
writing output... [100%] installation

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: 2021-05-11T16:42:19.473513Z, end-time: 2021-05-11T16:42:20.886775Z, duration: 1, exit-code: 0
python -m sphinx -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
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 pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] emodpy_hiv_index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... installation emodpy_hiv_index 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 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: 2021-05-11T16:42:21.098158Z, end-time: 2021-05-11T16:42:22.440706Z, duration: 1, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
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 pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 0 added, 1 changed, 0 removed
reading sources... [100%] emodpy_hiv_index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing emodpy-hiv-docs.tex... index installation emodpy_hiv_index 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 
resolving references...
done
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add_cus_dep( "glo", "gls", 0, "makeglo" );
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Chapter 1.
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Chapter 2.
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[6]
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[7]
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[8]
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[9]
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[10]
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[11]
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[12]
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[13]
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[14]
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Latexmk: All targets (institute-for-disease-modeling-emodpy-hiv.pdf) are up-to-date

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mv -f /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/checkouts/latest/docs/_build/latex/institute-for-disease-modeling-emodpy-hiv.pdf /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/artifacts/latest/sphinx_pdf/institute-for-disease-modeling-emodpy-hiv.pdf