Read the Docs build information
Build id: 604445
Project: institute-for-disease-modeling-emodpy-malaria
Version: latest
Commit: 5cdbba39dbafb2b1f9ec2f67b0b73e9446102ba3
Date: 2021-04-01T17:21:37.976227Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-04-01T17:22:17.907738Z, end-time: 2021-04-01T17:22:20.124528Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emodpy-malaria.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2021-04-01T17:22:20.271371Z, end-time: 2021-04-01T17:22:20.487283Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: checking out 'origin/main'.

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 5cdbba3 Bump version: 0.0.39 → 0.0.40

[rtd-command-info] start-time: 2021-04-01T17:22:20.601696Z, end-time: 2021-04-01T17:22:20.672966Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-04-01T17:22:21.758032Z, end-time: 2021-04-01T17:22:25.824446Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-04-01T17:22:25.948439Z, end-time: 2021-04-01T17:22:27.823248Z, 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/artifactory/api/pypi/idm-pypi-production/simple
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (21.0.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (54.2.0)

[rtd-command-info] start-time: 2021-04-01T17:22:27.943890Z, end-time: 2021-04-01T17:22:37.054169Z, duration: 9, 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<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
Collecting mock==1.0.1
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
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  Stored in directory: /tmp/pip-ephem-wheel-cache-o_e7pp4f/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.16 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4

[rtd-command-info] start-time: 2021-04-01T17:22:37.181560Z, end-time: 2021-04-01T17:22:58.401622Z, duration: 21, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
Collecting emodpy~=1.10.2
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Installing collected packages: zipp, typing-extensions, pycparser, yarg, python-dateutil, numpy, importlib-metadata, humanfriendly, docopt, cffi, cached-property, xdg, tqdm, tabulate, soupsieve, pyyaml, pygit2, pluggy, pipreqs, pillow, pandas, more-itertools, kiwisolver, jeepney, geographiclib, diskcache, cycler, cryptography, coloredlogs, backoff, shapely, SecretStorage, scipy, pyproj, pyCOMPS, matplotlib, lz4, idmtools, geopy, beautifulsoup4, keyring, idmtools-platform-comps, idmtools-models, emod-api, click, bs4, astunparse, astor, emodpy
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Successfully installed SecretStorage-3.3.1 astor-0.8.1 astunparse-1.6.3 backoff-1.10.0 beautifulsoup4-4.9.3 bs4-0.0.1 cached-property-1.5.2 cffi-1.14.5 click-7.1.2 coloredlogs-15.0 cryptography-3.4.7 cycler-0.10.0 diskcache-5.1.0 docopt-0.6.2 emod-api-1.8.8 emodpy-1.10.3 geographiclib-1.50 geopy-2.1.0 humanfriendly-9.1 idmtools-1.6.3 idmtools-models-1.6.3 idmtools-platform-comps-1.6.3 importlib-metadata-3.10.0 jeepney-0.6.0 keyring-23.0.1 kiwisolver-1.3.1 lz4-3.1.3 matplotlib-3.4.1 more-itertools-8.7.0 numpy-1.20.2 pandas-1.1.5 pillow-8.1.2 pipreqs-0.4.10 pluggy-0.13.1 pyCOMPS-2.4.1 pycparser-2.20 pygit2-1.5.0 pyproj-3.0.1 python-dateutil-2.8.1 pyyaml-5.4.1 scipy-1.6.2 shapely-1.7.1 soupsieve-2.2.1 tabulate-0.8.9 tqdm-4.59.0 typing-extensions-3.7.4.3 xdg-5.0.1 yarg-0.1.9 zipp-3.4.1

[rtd-command-info] start-time: 2021-04-01T17:22:58.526332Z, end-time: 2021-04-01T17:23:04.127197Z, duration: 5, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
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Building wheels for collected packages: wrapt
  Building wheel for wrapt (setup.py): started
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  Created wheel for wrapt: filename=wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl size=71026 sha256=fcba0254c2b079f4c42904fa1911144bc7553660bc5774610a6ceb4d14a3b89f
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Successfully built wrapt
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  Attempting uninstall: sphinx
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      Successfully uninstalled Sphinx-1.8.5
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
  Attempting uninstall: pygit2
    Found existing installation: pygit2 1.5.0
    Uninstalling pygit2-1.5.0:
      Successfully uninstalled pygit2-1.5.0
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 1.6.3 requires pygit2<1.6.0,>=1.4.0, but you have pygit2 1.2.1 which is incompatible.
Successfully installed PyGithub-1.54.1 deprecated-1.2.12 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pygit2-1.2.1 pyjwt-1.7.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxcontrib-qthelp-1.0.3 wrapt-1.12.1

[rtd-command-info] start-time: 2021-04-01T17:23:04.242665Z, end-time: 2021-04-01T17:23:05.571328Z, duration: 1, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating emodpy_malaria.egg-info
writing emodpy_malaria.egg-info/PKG-INFO
writing dependency_links to emodpy_malaria.egg-info/dependency_links.txt
writing requirements to emodpy_malaria.egg-info/requires.txt
writing top-level names to emodpy_malaria.egg-info/top_level.txt
writing manifest file 'emodpy_malaria.egg-info/SOURCES.txt'
reading manifest file 'emodpy_malaria.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'emodpy_malaria.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_malaria
copying emodpy_malaria/config.py -> build/lib/emodpy_malaria
copying emodpy_malaria/__init__.py -> build/lib/emodpy_malaria
creating build/lib/tests
copying tests/__init__.py -> build/lib/tests
creating build/lib/emodpy_malaria/demographics
copying emodpy_malaria/demographics/MalariaDemographics.py -> build/lib/emodpy_malaria/demographics
copying emodpy_malaria/demographics/__init__.py -> build/lib/emodpy_malaria/demographics
creating build/lib/emodpy_malaria/reporters
copying emodpy_malaria/reporters/builtin.py -> build/lib/emodpy_malaria/reporters
copying emodpy_malaria/reporters/__init__.py -> build/lib/emodpy_malaria/reporters
creating build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/diag_survey.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/irs.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/mosquitorelease.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/drug.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/spacespraying.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/common.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/udbednet.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/sugartrap.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/outdoorrestkill.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/bednet.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/treatment_seeking.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/ivermectin.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/drug_campaign.py -> build/lib/emodpy_malaria/interventions
copying emodpy_malaria/interventions/__init__.py -> build/lib/emodpy_malaria/interventions
creating build/lib/tests/unittests
copying tests/unittests/test_malaria_reporters.py -> build/lib/tests/unittests
copying tests/unittests/test_malaria_config.py -> build/lib/tests/unittests
copying tests/unittests/get_unittest_coverage.py -> build/lib/tests/unittests
copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests
copying tests/unittests/test_treatment_seeking.py -> build/lib/tests/unittests
copying tests/unittests/test_malaria_interventions_as_files.py -> build/lib/tests/unittests
copying tests/unittests/test_import.py -> build/lib/tests/unittests
copying tests/unittests/test_malaria_interventions.py -> build/lib/tests/unittests
copying tests/unittests/__init__.py -> build/lib/tests/unittests
copying emodpy_malaria/malaria_drug_params.csv -> build/lib/emodpy_malaria
copying emodpy_malaria/malaria_vs_params.csv -> build/lib/emodpy_malaria
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/emodpy_malaria
copying build/lib/emodpy_malaria/config.py -> build/bdist.linux-x86_64/egg/emodpy_malaria
creating build/bdist.linux-x86_64/egg/emodpy_malaria/demographics
copying build/lib/emodpy_malaria/demographics/MalariaDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/demographics
copying build/lib/emodpy_malaria/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/demographics
creating build/bdist.linux-x86_64/egg/emodpy_malaria/reporters
copying build/lib/emodpy_malaria/reporters/builtin.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/reporters
copying build/lib/emodpy_malaria/reporters/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/reporters
copying build/lib/emodpy_malaria/malaria_drug_params.csv -> build/bdist.linux-x86_64/egg/emodpy_malaria
creating build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/diag_survey.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/irs.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/mosquitorelease.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/drug.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/spacespraying.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/common.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/udbednet.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/sugartrap.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/outdoorrestkill.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/bednet.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/treatment_seeking.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/ivermectin.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/drug_campaign.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions
copying build/lib/emodpy_malaria/malaria_vs_params.csv -> build/bdist.linux-x86_64/egg/emodpy_malaria
copying build/lib/emodpy_malaria/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria
creating build/bdist.linux-x86_64/egg/tests
creating build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_malaria_reporters.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_malaria_config.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/get_unittest_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_treatment_seeking.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_malaria_interventions_as_files.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_malaria_interventions.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_malaria/config.py to config.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/MalariaDemographics.py to MalariaDemographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/builtin.py to builtin.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/diag_survey.py to diag_survey.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/irs.py to irs.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/mosquitorelease.py to mosquitorelease.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/drug.py to drug.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/spacespraying.py to spacespraying.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/common.py to common.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/udbednet.py to udbednet.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/sugartrap.py to sugartrap.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/outdoorrestkill.py to outdoorrestkill.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/bednet.py to bednet.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/treatment_seeking.py to treatment_seeking.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/ivermectin.py to ivermectin.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/drug_campaign.py to drug_campaign.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_reporters.py to test_malaria_reporters.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_config.py to test_malaria_config.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/get_unittest_coverage.py to get_unittest_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_treatment_seeking.py to test_treatment_seeking.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_interventions_as_files.py to test_malaria_interventions_as_files.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_malaria_interventions.py to test_malaria_interventions.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_malaria.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_malaria.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_malaria.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_malaria.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_malaria.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
emodpy_malaria.__pycache__.config.cpython-37: module references __file__
tests.unittests.__pycache__.schema_path_file.cpython-37: module references __file__
tests.unittests.__pycache__.test_malaria_config.cpython-37: module references __file__
tests.unittests.__pycache__.test_malaria_interventions.cpython-37: module references __file__
tests.unittests.__pycache__.test_malaria_reporters.cpython-37: module references __file__
tests.unittests.__pycache__.test_treatment_seeking.cpython-37: module references __file__
creating dist
creating 'dist/emodpy_malaria-0.0.40-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_malaria-0.0.40-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages/emodpy_malaria-0.0.40-py3.7.egg
Extracting emodpy_malaria-0.0.40-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages
Adding emodpy-malaria 0.0.40 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages/emodpy_malaria-0.0.40-py3.7.egg
Processing dependencies for emodpy-malaria==0.0.40
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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages/pygit2-1.5.0-py3.7-linux-x86_64.egg
Searching for emodpy==1.10.3
Best match: emodpy 1.10.3
Adding emodpy 1.10.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for emod-api==1.8.8
Best match: emod-api 1.8.8
Adding emod-api 1.8.8 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for matplotlib==3.4.1
Best match: matplotlib 3.4.1
Adding matplotlib 3.4.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for geopy==2.1.0
Best match: geopy 2.1.0
Adding geopy 2.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for numpy==1.20.2
Best match: numpy 1.20.2
Adding numpy 1.20.2 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.6.2
Best match: scipy 1.6.2
Adding scipy 1.6.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for tqdm==4.59.0
Best match: tqdm 4.59.0
Adding tqdm 4.59.0 to easy-install.pth file
Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for six==1.15.0
Best match: six 1.15.0
Adding six 1.15.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for Pillow==8.1.2
Best match: Pillow 8.1.2
Adding Pillow 8.1.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for importlib-metadata==3.10.0
Best match: importlib-metadata 3.10.0
Adding importlib-metadata 3.10.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for xdg==5.0.1
Best match: xdg 5.0.1
Adding xdg 5.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/envs/latest/bin
Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/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-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Searching for typing-extensions==3.7.4.3
Best match: typing-extensions 3.7.4.3
Adding typing-extensions 3.7.4.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/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-malaria/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-malaria/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-malaria/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-malaria/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for emodpy-malaria==0.0.40

[rtd-command-info] start-time: 2021-04-01T17:23:06.669739Z, end-time: 2021-04-01T17:23:06.754207Z, 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-malaria'
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-malaria'

# -- 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-malaria-docs.tex', u'emodpy-malaria',
     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-malaria-docs', u'emodpy-malaria',
     [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-malaria-docs', u'emodpy-malaria',
     author, 'Institute for Disease Modeling', 'How to use emodpy for malaria 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),
                       'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None),
                       'emod-malaria': ('https://docs.idmod.org/projects/emod-malaria/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': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("v0.0.29", "/en/v0.0.29/"),
    ("v0.0.18", "/en/v0.0.18/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/emodpy-malaria/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/emodpy-malaria/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-emodpy-malaria',
    'name': u'emodpy-malaria',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://docs.idmod.org/projects/emodpy-malaria/en/v0.0.29/',
    '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-malaria',
    'github_version': 'main',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'main',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'main',
    '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': '5cdbba39',
}

# 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-malaria/builds/604445/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2021-04-01T17:23:06.894137Z, end-time: 2021-04-01T17:23:14.737613Z, duration: 7, 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)
rm: cannot remove 'emodpy_malaria_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/idmtools/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 23 source files that are out of date
updating environment: [new config] 23 added, 0 changed, 0 removed
reading sources... [  4%] emodpy_malaria
reading sources... [  8%] emodpy_malaria.config
reading sources... [ 13%] emodpy_malaria.demographics
reading sources... [ 17%] emodpy_malaria.demographics.MalariaDemographics
reading sources... [ 21%] emodpy_malaria.interventions
reading sources... [ 26%] emodpy_malaria.interventions.bednet
reading sources... [ 30%] emodpy_malaria.interventions.common
reading sources... [ 34%] emodpy_malaria.interventions.diag_survey
reading sources... [ 39%] emodpy_malaria.interventions.drug
reading sources... [ 43%] emodpy_malaria.interventions.drug_campaign
reading sources... [ 47%] emodpy_malaria.interventions.irs
reading sources... [ 52%] emodpy_malaria.interventions.ivermectin
reading sources... [ 56%] emodpy_malaria.interventions.mosquitorelease
reading sources... [ 60%] emodpy_malaria.interventions.outdoorrestkill
reading sources... [ 65%] emodpy_malaria.interventions.spacespraying
reading sources... [ 69%] emodpy_malaria.interventions.sugartrap
reading sources... [ 73%] emodpy_malaria.interventions.treatment_seeking
reading sources... [ 78%] emodpy_malaria.interventions.udbednet
reading sources... [ 82%] emodpy_malaria.reporters
reading sources... [ 86%] emodpy_malaria.reporters.builtin
/!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.6.3/configuration.html for details on how to configure idmtools.
reading sources... [ 91%] emodpy_malaria_index
reading sources... [ 95%] index
reading sources... [100%] installation

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  4%] emodpy_malaria
writing output... [  8%] emodpy_malaria.config
writing output... [ 13%] emodpy_malaria.demographics
writing output... [ 17%] emodpy_malaria.demographics.MalariaDemographics
writing output... [ 21%] emodpy_malaria.interventions
writing output... [ 26%] emodpy_malaria.interventions.bednet
writing output... [ 30%] emodpy_malaria.interventions.common
writing output... [ 34%] emodpy_malaria.interventions.diag_survey
writing output... [ 39%] emodpy_malaria.interventions.drug
writing output... [ 43%] emodpy_malaria.interventions.drug_campaign
writing output... [ 47%] emodpy_malaria.interventions.irs
writing output... [ 52%] emodpy_malaria.interventions.ivermectin
writing output... [ 56%] emodpy_malaria.interventions.mosquitorelease
writing output... [ 60%] emodpy_malaria.interventions.outdoorrestkill
writing output... [ 65%] emodpy_malaria.interventions.spacespraying
writing output... [ 69%] emodpy_malaria.interventions.sugartrap
writing output... [ 73%] emodpy_malaria.interventions.treatment_seeking
writing output... [ 78%] emodpy_malaria.interventions.udbednet
writing output... [ 82%] emodpy_malaria.reporters
writing output... [ 86%] emodpy_malaria.reporters.builtin
writing output... [ 91%] emodpy_malaria_index
writing output... [ 95%] 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: 2021-04-01T17:23:14.886785Z, end-time: 2021-04-01T17:23:16.493202Z, 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_malaria_index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... installation emodpy_malaria_index emodpy_malaria emodpy_malaria.demographics emodpy_malaria.demographics.MalariaDemographics emodpy_malaria.interventions emodpy_malaria.interventions.bednet emodpy_malaria.interventions.common emodpy_malaria.interventions.diag_survey emodpy_malaria.interventions.drug emodpy_malaria.interventions.drug_campaign emodpy_malaria.interventions.irs emodpy_malaria.interventions.ivermectin emodpy_malaria.interventions.mosquitorelease emodpy_malaria.interventions.outdoorrestkill emodpy_malaria.interventions.spacespraying emodpy_malaria.interventions.sugartrap emodpy_malaria.interventions.treatment_seeking emodpy_malaria.interventions.udbednet emodpy_malaria.reporters emodpy_malaria.reporters.builtin emodpy_malaria.config 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: 2021-04-01T17:23:16.652668Z, end-time: 2021-04-01T17:23:18.219610Z, 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_malaria_index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing emodpy-malaria-docs.tex... index installation emodpy_malaria_index emodpy_malaria emodpy_malaria.demographics emodpy_malaria.demographics.MalariaDemographics emodpy_malaria.interventions emodpy_malaria.interventions.bednet emodpy_malaria.interventions.common emodpy_malaria.interventions.diag_survey emodpy_malaria.interventions.drug emodpy_malaria.interventions.drug_campaign emodpy_malaria.interventions.irs emodpy_malaria.interventions.ivermectin emodpy_malaria.interventions.mosquitorelease emodpy_malaria.interventions.outdoorrestkill emodpy_malaria.interventions.spacespraying emodpy_malaria.interventions.sugartrap emodpy_malaria.interventions.treatment_seeking emodpy_malaria.interventions.udbednet emodpy_malaria.reporters emodpy_malaria.reporters.builtin emodpy_malaria.config 
resolving references...
done
writing... done
copying TeX support files... copying TeX support files...
done
build succeeded.

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

[rtd-command-info] start-time: 2021-04-01T17:23:18.475234Z, end-time: 2021-04-01T17:23:18.555774Z, 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: 2021-04-01T17:23:18.727229Z, end-time: 2021-04-01T17:23:20.744234Z, duration: 2, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emodpy-malaria -interaction=nonstopmode
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, <GEN1> chunk 1.
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Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
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Latexmk: applying rule 'pdflatex'...
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Run number 1 of rule 'pdflatex'
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Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-malaria"  "emodpy-malaria-docs.tex"'
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Chapter 2.
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[17]
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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
ble op-tions are: *

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\T1/ptm/m/n/10 TRUE_INFECTION_STATUS * BLOOD_SMEAR * PCR * PF_HRP2 *

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[]\T1/pcr/b/n/10 node_property_restrictions \T1/ptm/m/n/10 ^^U List of Node-Pro
p-erty key:value

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ven-

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\T1/ptm/m/n/10 tion. For ex-am-ple, \T1/pcr/m/n/10 [{"NodeProperty1":"PropertyV
alue1"},

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[]\T1/pcr/b/n/10 ind_property_restrictions \T1/ptm/m/n/10 ^^U List of In-di-vid
-u-al-Prop-erty key:value

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\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyV
alue1"},

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[]\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U List of In-di-vid-
u-al-Prop-erty

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\T1/ptm/m/n/10 key:value pairs that cause an in-ter-ven-tion to be aborted. For
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\T1/ptm/m/n/10 am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"}
,
[19]
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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][]
 =

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\T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_coverage:

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[][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [
][]float[][]

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\T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] 
=

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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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\T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][]

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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt
m/m/n/10 ,

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\T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger

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\T1/ptm/m/it/10 = None\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 node_property_restrictions:

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[][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 ,

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[][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro
up:

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\T1/ptm/m/it/10 any = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it
/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-
[20]
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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
ble op-tions are: *

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\T1/ptm/m/n/10 TRUE_INFECTION_STATUS * BLOOD_SMEAR * PCR * PF_HRP2 *

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[]\T1/pcr/b/n/10 node_property_restrictions \T1/ptm/m/n/10 ^^U List of Node-Pro
p-erty key:value

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\T1/ptm/m/n/10 tion. For ex-am-ple, \T1/pcr/m/n/10 [{"NodeProperty1":"PropertyV
alue1"},

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-u-al-Prop-erty key:value

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\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyV
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[]\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U List of In-di-vid-
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,
[21]
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\T1/ptm/m/it/10 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = 1
\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 re-ceiv-ing_drugs_event:

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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt
m/m/n/10 ,

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\T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger

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\T1/ptm/m/it/10 = None\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 node_property_restrictions:

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[][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 ind_property_restrictions:

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fy-

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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
ble op-tions are: *

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\T1/ptm/m/n/10 TRUE_INFECTION_STATUS * BLOOD_SMEAR * PCR * PF_HRP2 *
[22]
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alue1"},

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\T1/ptm/m/it/10 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = 1
\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 re-ceiv-ing_drugs_event:

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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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\T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lis-ten-ing_duration:

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[][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_covera
ge:

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[][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 DIS-TANCE_ONLY\
TS1/ptm/m/it/10 '\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 node_ids: [][]list[][] = None\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 ex-pire_recent_drugs:

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\T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger

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fy-
[23]
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p-erty key:value

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alue1"},

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ic in-ter-ven-tion.

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alue1"},

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[]\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U ist of In-di-vid-u
-al-Prop-erty

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\T1/ptm/m/n/10 am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"}
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\T1/ptm/m/it/10 TANCE_ONLY\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ev
ent_trigger:
[24]
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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 
, \T1/ptm/m/it/10 cov-

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\T1/ptm/m/it/10 ing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_eff=1\T1/ptm/
m/n/10 ,

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\T1/ptm/m/it/10 in-sec-ti-cide=None\T1/ptm/m/n/10 ,

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[]\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 killing_effect\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/p
tm/m/n/10 ,

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\T1/ptm/m/it/10 killing_duration_box=0\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 killing_exponential_decay_rate=0\T1/pcr/m/n/10 ) 
[25]
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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 
,

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\T1/ptm/m/it/10 by_number=True\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 num-ber=10000\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 per-cent-age=0.1\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 in-fec-tious=0.0\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 species=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 arabiensis\TS1/ptm/m/
it/10 '\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 genome=[[\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 X\TS1/ptm/m/it/10 '\
T1/ptm/m/it/10 ,

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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 X\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ]]\T1/ptm/
m/n/10 ,

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[]\T1/pcr/b/n/10 infectious \T1/ptm/m/n/10 ^^U The frac-tion of vec-tors re-lea
sed that are

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\T1/ptm/m/n/10 `Malaria_Model'!='MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETI
CS'

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\T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 file-

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[]\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 killing_effect\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 in-sec-ti-

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\T1/ptm/m/it/10 killing_predecay_duration=0\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 ,
[26]
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\T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_eff=1\T1/ptm/m/
n/10 ,

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\T1/ptm/m/it/10 stant_duration=100\T1/ptm/m/n/10 ,

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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 ,

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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 
, \T1/ptm/m/it/10 cov-er-

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(./institute-for-disease-modeling-emodpy-malaria.toc) [1] [2] [1] [2]
Chapter 1.
[3] [4]
Chapter 2.
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list[][] =

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\T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger

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\T1/ptm/m/it/10 trig-ger_condition_list: [][]list[][] =
[16]
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[]\T1/pcr/b/n/10 for building, modifying, and writing campaign configuration

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alue1"},
[17]
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\T1/ptm/m/it/10 any = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it
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[18]
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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
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[19]
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][]float[][]

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\T1/ptm/m/it/10 any = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it
/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-
[20]
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[21]
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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt
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[22]
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alue1"},

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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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ge:

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[][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 DIS-TANCE_ONLY\
TS1/ptm/m/it/10 '\T1/ptm/m/n/10 ,

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[23]
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[26]
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[27]
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ntBed-net\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 ,

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[28] [29] [30]
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[]\T1/ptm/m/it/10 manifest\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-sec-ti-cide_name\
T1/ptm/m/n/10 , \T1/ptm/m/it/10 species\T1/ptm/m/n/10 , \T1/ptm/m/it/10 combo\T
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[35] (./institute-for-disease-modeling-emodpy-malaria.ind [36]
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[]\T1/pcr/m/n/10 add() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emodpy_malari
a.interventions.treatment_seeking\T1/ptm/m/n/10 ),

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ers.builtin.MalariaPatientJSONReport

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[37]
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[5]
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[6]
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[9] [10]
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[]\T1/pcr/b/n/10 measurement_sensitivity \T1/ptm/m/n/10 ^^U Set-ting for \T1/pt
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[11]
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-erty key:value pairs that

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[]\T1/pcr/b/n/10 expire_recent_drugs \T1/ptm/m/n/10 ^^U Adds \T1/pcr/m/n/10 [{"
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\T1/ptm/m/it/10 drug_code:
[12]
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[][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 MDA\TS1/ptm/m/i
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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt
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\T1/ptm/m/it/10 TANCE_ONLY\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 ind_property_restrictions:

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[][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 ,

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[][]\T1/ptm/m/it/10 bool[][] =

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\T1/ptm/m/it/10 ing_drugs_event_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Received
_Campaign_Drugs\TS1/ptm/m/it/10 '\T1/pcr/m/n/10 ) 
[13] [14] [15] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd)
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[]\T1/pcr/b/n/10 node_property_restrictions \T1/ptm/m/n/10 ^^U List of Node-Pro
p-erty key:value

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\T1/ptm/m/n/10 pairs that nodes must have to re-ceive the di-ag-nos-tic in-ter-
ven-

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alue1"},

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[]\T1/pcr/b/n/10 ind_property_restrictions \T1/ptm/m/n/10 ^^U List of In-di-vid
-u-al-Prop-erty key:value

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\T1/ptm/m/n/10 pairs that in-di-vid-u-als must have to re-ceive the di-ag-nos-t
ic in-ter-ven-tion.

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[]\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U List of In-di-vid-
u-al-Prop-erty

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\T1/ptm/m/n/10 am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"}
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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][]
 =

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\T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] 
=

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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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][] =

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list[][] =

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\T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger

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fy-

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\T1/ptm/m/it/10 ing_properties: [][]list[][] = None\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 trig-ger_condition_list: [][]list[][] =
[16]
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[]\T1/pcr/b/n/10 for building, modifying, and writing campaign configuration

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p-erty key:value

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alue1"},
[17]
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][]

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][]list[][]

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\T1/ptm/m/it/10 any = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it
/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-

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[18]
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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
ble op-tions are: *

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\T1/ptm/m/n/10 TRUE_INFECTION_STATUS * BLOOD_SMEAR * PCR * PF_HRP2 *

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alue1"},

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[19]
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][]float[][]

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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt
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\T1/ptm/m/it/10 any = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it
/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-
[20]
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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
ble op-tions are: *

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[21]
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\T1/ptm/m/it/10 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = 1
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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt
m/m/n/10 ,

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fy-

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[]\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Di-ag-nos-tic type. Avail-a
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\T1/ptm/m/n/10 TRUE_INFECTION_STATUS * BLOOD_SMEAR * PCR * PF_HRP2 *
[22]
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alue1"},

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\T1/ptm/m/it/10 re-ceiv-ing_drugs_event:

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\T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent

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[][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_covera
ge:

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[][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 DIS-TANCE_ONLY\
TS1/ptm/m/it/10 '\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 node_ids: [][]list[][] = None\T1/ptm/m/n/10 ,

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\T1/ptm/m/it/10 ex-pire_recent_drugs:

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\T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger

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fy-
[23]
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p-erty key:value

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alue1"},

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alue1"},

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[]\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U ist of In-di-vid-u
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\T1/ptm/m/it/10 TANCE_ONLY\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ev
ent_trigger:
[24]
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[]\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 
, \T1/ptm/m/it/10 cov-

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\T1/ptm/m/it/10 ing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_eff=1\T1/ptm/
m/n/10 ,

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[27]
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[]\T1/pcr/b/n/10 of individuals to target with the intervention. Default is

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\T1/ptm/m/n/10 (\T1/pcr/m/sl/10 properties\T1/ptm/m/n/10 ) ^^U \T1/pcr/m/n/10 [
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ntBed-net\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 ,

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[28] [29] [30]
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T1/ptm/m/n/10 , \T1/ptm/m/it/10 species\T1/ptm/m/n/10 , \T1/ptm/m/it/10 combo\T
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[35] (./institute-for-disease-modeling-emodpy-malaria.ind [36]
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ers.builtin.MalariaPatientJSONReport

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[39]) (./institute-for-disease-modeling-emodpy-malaria.aux) )
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