Read the Docs build information Build id: 662046 Project: institute-for-disease-modeling-emodpy-malaria Version: latest Commit: 890db797236bc5b66e6da2a541646189ca61e1c6 Date: 2021-06-23T15:11:26.667491Z State: finished Success: True [rtd-command-info] start-time: 2021-06-23T15:19:12.498911Z, end-time: 2021-06-23T15:19:15.183623Z, 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,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-06-23T15:19:15.310936Z, end-time: 2021-06-23T15:19:15.540431Z, 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. 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Example: git checkout -b HEAD is now at 890db79 Bump version: 0.0.67 → 0.0.68 [rtd-command-info] start-time: 2021-06-23T15:19:15.660073Z, end-time: 2021-06-23T15:19:15.732311Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-06-23T15:19:15.840544Z, end-time: 2021-06-23T15:19:15.908368Z, duration: 0, exit-code: 0 git rev-parse HEAD 890db797236bc5b66e6da2a541646189ca61e1c6 [rtd-command-info] start-time: 2021-06-23T15:19:16.852978Z, end-time: 2021-06-23T15:19:21.148465Z, 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: 2021-06-23T15:19:21.285503Z, end-time: 2021-06-23T15:19:22.618767Z, 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 (21.1.2) 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 (57.0.0) [rtd-command-info] start-time: 2021-06-23T15:19:22.744593Z, end-time: 2021-06-23T15:19:31.473101Z, duration: 8, 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 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) 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 (from sphinx<2) (57.0.0) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting requests>=2.0.0 Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux2010_x86_64.whl (31 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.5-py2.py3-none-any.whl (138 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=9fedba6011cef37bd4ab6dbde0c997f536fe3dedfe333a29f2d9ab51aff221a7 Stored in directory: /tmp/pip-ephem-wheel-cache-4kdgwv7l/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=e1c8b48032e01a44f832398d5ccaf5c65f3ec407b6a0d0f47aee9772f74402b9 Stored in directory: /tmp/pip-ephem-wheel-cache-4kdgwv7l/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 Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 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-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.5 [rtd-command-info] start-time: 2021-06-23T15:19:31.586905Z, end-time: 2021-06-23T15:19:52.840124Z, 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~=1.11.1 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/emodpy/1.11.2/emodpy-1.11.2-py3-none-any.whl (115 kB) Collecting emod-malaria==0.0.0 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/emod-malaria/0.0.0/emod_malaria-0.0.0-py3-none-any.whl (3.4 MB) Collecting matplotlib Downloading matplotlib-3.4.2-cp37-cp37m-manylinux1_x86_64.whl (10.3 MB) Collecting idmtools-models~=1.6.0 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/idmtools-models/1.6.3/idmtools_models-1.6.3-py3-none-any.whl (22 kB) Collecting emod-api~=1.11.0 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/emod-api/1.11.7/emod_api-1.11.7-py3-none-any.whl (106 kB) Collecting astunparse Downloading astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting idmtools-platform-comps~=1.6.0 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/idmtools-platform-comps/1.6.3/idmtools_platform_comps-1.6.3-py3-none-any.whl (158 kB) Collecting bs4 Downloading bs4-0.0.1.tar.gz (1.1 kB) Collecting keyring Downloading keyring-23.0.1-py3-none-any.whl (33 kB) Collecting idmtools~=1.6.0 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/idmtools/1.6.3/idmtools-1.6.3-py3-none-any.whl (137 kB) Collecting astor Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB) Collecting click~=7.1 Downloading click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting shapely Downloading Shapely-1.7.1-cp37-cp37m-manylinux1_x86_64.whl (1.0 MB) Collecting pyproj Downloading pyproj-3.1.0-cp37-cp37m-manylinux2010_x86_64.whl (6.6 MB) Collecting pandas Downloading pandas-1.2.5-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (9.9 MB) Collecting numpy!=1.19.4 Downloading numpy-1.21.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) Collecting pyyaml Downloading PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (636 kB) Collecting geographiclib Downloading geographiclib-1.52-py3-none-any.whl (38 kB) Collecting lz4 Downloading lz4-3.1.3-cp37-cp37m-manylinux2010_x86_64.whl (1.8 MB) Collecting scipy Downloading scipy-1.7.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB) Collecting tabulate<0.9,>=0.8.9 Downloading tabulate-0.8.9-py3-none-any.whl (25 kB) Requirement already satisfied: packaging<21.0,>=20.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from idmtools~=1.6.0->emodpy~=1.11.1->-r requirements.txt (line 1)) (20.9) Collecting diskcache~=5.1.0 Downloading diskcache-5.1.0-py3-none-any.whl (44 kB) Collecting tqdm<5,>=4.52.0 Downloading tqdm-4.61.1-py2.py3-none-any.whl (75 kB) Collecting pipreqs<0.5,>=0.4.10 Downloading pipreqs-0.4.10-py2.py3-none-any.whl (25 kB) Collecting backoff<1.11,>=1.10.0 Downloading backoff-1.10.0-py2.py3-none-any.whl (31 kB) Collecting coloredlogs~=15.0 Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) Collecting pluggy~=0.13.1 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting more-itertools~=8.7.0 Downloading more_itertools-8.7.0-py3-none-any.whl (48 kB) Collecting pygit2<1.6.0,>=1.4.0 Downloading pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl (3.1 MB) Collecting pandas Downloading pandas-1.1.5-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) Collecting humanfriendly>=9.1 Downloading humanfriendly-9.2-py2.py3-none-any.whl (86 kB) Collecting jinja2~=2.11.3 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Collecting pyCOMPS~=2.4.1 Downloading https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/pyCOMPS/2.4.1/pyCOMPS-2.4.1-py2.py3-none-any.whl (55 kB) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from jinja2~=2.11.3->idmtools-models~=1.6.0->emodpy~=1.11.1->-r requirements.txt (line 1)) (2.0.1) Requirement already satisfied: pyparsing>=2.0.2 in 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Requirement already satisfied: future>=0.16.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from pyCOMPS~=2.4.1->idmtools-platform-comps~=1.6.0->emodpy~=1.11.1->-r requirements.txt (line 1)) (0.18.2) Requirement already satisfied: requests>=2.11.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from pyCOMPS~=2.4.1->idmtools-platform-comps~=1.6.0->emodpy~=1.11.1->-r requirements.txt (line 1)) (2.25.1) Collecting xdg>=4.0.1 Downloading xdg-5.1.0-py3-none-any.whl (5.0 kB) Collecting cffi>=1.4.0 Downloading cffi-1.14.5-cp37-cp37m-manylinux1_x86_64.whl (402 kB) Collecting cached-property Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Collecting pycparser Downloading pycparser-2.20-py2.py3-none-any.whl (112 kB) Requirement already satisfied: six>=1.5 in 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.4.1->idmtools-platform-comps~=1.6.0->emodpy~=1.11.1->-r requirements.txt (line 1)) (2.10) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.4.1->idmtools-platform-comps~=1.6.0->emodpy~=1.11.1->-r requirements.txt (line 1)) (1.26.5) Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from astunparse->emodpy~=1.11.1->-r requirements.txt (line 1)) (0.36.2) Collecting beautifulsoup4 Downloading beautifulsoup4-4.9.3-py3-none-any.whl (115 kB) Collecting soupsieve>1.2 Downloading soupsieve-2.2.1-py3-none-any.whl (33 kB) Collecting SecretStorage>=3.2 Downloading SecretStorage-3.3.1-py3-none-any.whl (15 kB) Collecting jeepney>=0.4.2 Downloading jeepney-0.6.0-py3-none-any.whl (45 kB) Collecting cryptography>=2.0 Downloading cryptography-3.4.7-cp36-abi3-manylinux2014_x86_64.whl (3.2 MB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.3.1-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB) Collecting pillow>=6.2.0 Downloading Pillow-8.2.0-cp37-cp37m-manylinux1_x86_64.whl (3.0 MB) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Building wheels for collected packages: bs4, docopt Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1271 sha256=6cd9b72089c76ed76ce780d607fa9dd2072b173c6def3d5d412448e1ad9fd7d5 Stored in directory: /tmp/pip-ephem-wheel-cache-frd0498y/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13724 sha256=e2025a4b90e00b7a84738d80974d509b92e5213534f827c710f9755e24deae0d Stored in directory: /tmp/pip-ephem-wheel-cache-frd0498y/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9 Successfully built bs4 docopt 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, pandas, more-itertools, jeepney, diskcache, cryptography, coloredlogs, backoff, shapely, SecretStorage, scipy, pyproj, pyCOMPS, pillow, lz4, kiwisolver, jinja2, idmtools, geographiclib, cycler, beautifulsoup4, matplotlib, keyring, idmtools-platform-comps, idmtools-models, emod-api, click, bs4, astunparse, astor, emodpy, emod-malaria Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: jinja2 Found existing installation: Jinja2 3.0.1 Uninstalling Jinja2-3.0.1: Successfully uninstalled Jinja2-3.0.1 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-15.0.1 cryptography-3.4.7 cycler-0.10.0 diskcache-5.1.0 docopt-0.6.2 emod-api-1.11.7 emod-malaria-0.0.0 emodpy-1.11.2 geographiclib-1.52 humanfriendly-9.2 idmtools-1.6.3 idmtools-models-1.6.3 idmtools-platform-comps-1.6.3 importlib-metadata-4.5.0 jeepney-0.6.0 jinja2-2.11.3 keyring-23.0.1 kiwisolver-1.3.1 lz4-3.1.3 matplotlib-3.4.2 more-itertools-8.7.0 numpy-1.21.0 pandas-1.1.5 pillow-8.2.0 pipreqs-0.4.10 pluggy-0.13.1 pyCOMPS-2.4.1 pycparser-2.20 pygit2-1.5.0 pyproj-3.1.0 python-dateutil-2.8.1 pyyaml-5.4.1 scipy-1.7.0 shapely-1.7.1 soupsieve-2.2.1 tabulate-0.8.9 tqdm-4.61.1 typing-extensions-3.10.0.0 xdg-5.1.0 yarg-0.1.9 zipp-3.4.1 [rtd-command-info] start-time: 2021-06-23T15:19:52.952697Z, end-time: 2021-06-23T15:19:59.401115Z, duration: 6, 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 Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting pygit2~=1.4.0 Downloading pygit2-1.4.0-cp37-cp37m-manylinux2010_x86_64.whl (3.0 MB) Collecting PyGithub~=1.54 Downloading PyGithub-1.55-py3-none-any.whl (291 kB) Collecting sphinx-copybutton~=0.3.1 Downloading sphinx_copybutton-0.3.3-py3-none-any.whl (12 kB) Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting sphinx~=3.3.1 Downloading Sphinx-3.3.1-py3-none-any.whl (2.9 MB) Collecting sphinxext.remoteliteralinclude Downloading sphinxext_remoteliteralinclude-0.2.0-py3-none-any.whl (6.3 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (0.17.1) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (1.16.0) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (2.25.1) Requirement already satisfied: cached-property in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from pygit2~=1.4.0->-r docs/requirements.txt (line 2)) (1.5.2) Requirement already satisfied: cffi>=1.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from pygit2~=1.4.0->-r docs/requirements.txt (line 2)) (1.14.5) Collecting deprecated Downloading Deprecated-1.2.12-py2.py3-none-any.whl (9.5 kB) Collecting pynacl>=1.4.0 Downloading PyNaCl-1.4.0-cp35-abi3-manylinux1_x86_64.whl (961 kB) Collecting pyjwt>=2.0 Downloading PyJWT-2.1.0-py3-none-any.whl (16 kB) Collecting docutils Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (1.2.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (0.7.12) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2.11.3) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2.9.0) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2.9.1) 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 (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (57.0.0) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (1.1.5) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (20.9) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2.1.0) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2021.1) Requirement already satisfied: pycparser in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from cffi>=1.4.0->pygit2~=1.4.0->-r docs/requirements.txt (line 2)) (2.20) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2.0.1) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (2.10) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (4.0.0) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (2021.5.30) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 1)) (1.26.5) Collecting wrapt<2,>=1.10 Downloading wrapt-1.12.1.tar.gz (27 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.3.1->-r docs/requirements.txt (line 8)) (2.4.7) Building wheels for collected packages: wrapt Building wheel for wrapt (setup.py): started Building wheel for wrapt (setup.py): finished with status 'done' Created wheel for wrapt: filename=wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl size=71043 sha256=43b0e40afa9376c9f951aa4fc2900a1cde9d22e0623444f41731d4a419226fff Stored in directory: /tmp/pip-ephem-wheel-cache-a453_sr_/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6 Successfully built wrapt Installing collected packages: wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, docutils, sphinx, pynacl, pyjwt, pockets, deprecated, sphinxext.remoteliteralinclude, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, sphinx-copybutton, PyGithub, pygit2, plantweb Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: 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 Successfully installed PyGithub-1.55 deprecated-1.2.12 docutils-0.16 plantweb-1.2.1 pockets-0.9.1 pygit2-1.4.0 pyjwt-2.1.0 pynacl-1.4.0 sphinx-3.3.1 sphinx-copybutton-0.3.3 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxcontrib-qthelp-1.0.3 sphinxext.remoteliteralinclude-0.2.0 wrapt-1.12.1 [rtd-command-info] start-time: 2021-06-23T15:19:59.520630Z, end-time: 2021-06-23T15:20:00.507896Z, duration: 0, 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' adding license file 'LICENSE' 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/vector_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/inputeir.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/get_latest_schema.py -> 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/vector_config.py -> build/bdist.linux-x86_64/egg/emodpy_malaria 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/inputeir.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/get_latest_schema.py -> 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/vector_config.py to vector_config.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/inputeir.py to inputeir.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/get_latest_schema.py to get_latest_schema.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__ emodpy_malaria.__pycache__.vector_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-0.0.68-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-0.0.68-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-0.0.68-py3.7.egg Extracting emodpy_malaria-0.0.68-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 0.0.68 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-0.0.68-py3.7.egg Processing dependencies for emodpy-malaria==0.0.68 Searching for emod-malaria==0.0.0 Best match: emod-malaria 0.0.0 Adding emod-malaria 0.0.0 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 emodpy==1.11.2 Best match: emodpy 1.11.2 Adding emodpy 1.11.2 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 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 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 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 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-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 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 emod-api==1.11.7 Best match: emod-api 1.11.7 Adding emod-api 1.11.7 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 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 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 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 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 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 importlib-metadata==4.5.0 Best match: importlib-metadata 4.5.0 Adding importlib-metadata 4.5.0 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 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 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 tqdm==4.61.1 Best match: tqdm 4.61.1 Adding tqdm 4.61.1 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 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 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-malaria/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-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 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 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 numpy==1.21.0 Best match: numpy 1.21.0 Adding numpy 1.21.0 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 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 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 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 scipy==1.7.0 Best match: scipy 1.7.0 Adding scipy 1.7.0 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 pyproj==3.1.0 Best match: pyproj 3.1.0 Adding pyproj 3.1.0 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 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 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 geographiclib==1.52 Best match: geographiclib 1.52 Adding geographiclib 1.52 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 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 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 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 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 coloredlogs==15.0.1 Best match: coloredlogs 15.0.1 Adding coloredlogs 15.0.1 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-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 pygit2==1.4.0 Best match: pygit2 1.4.0 Adding pygit2 1.4.0 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 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 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 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 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 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 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-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 MarkupSafe==2.0.1 Best match: MarkupSafe 2.0.1 Adding MarkupSafe 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-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 xdg==5.1.0 Best match: xdg 5.1.0 Adding xdg 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 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 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 certifi==2021.5.30 Best match: certifi 2021.5.30 Adding certifi 2021.5.30 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 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==9.2 Best match: humanfriendly 9.2 Adding humanfriendly 9.2 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 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 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 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 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 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==1.26.5 Best match: urllib3 1.26.5 Adding urllib3 1.26.5 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 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==0.0.68 [rtd-command-info] start-time: 2021-06-23T15:20:01.761470Z, end-time: 2021-06-23T15:20:01.850972Z, duration: 0, exit-code: 0 git rev-parse HEAD 890db797236bc5b66e6da2a541646189ca61e1c6 [rtd-command-info] start-time: 2021-06-23T15:20:02.088489Z, end-time: 2021-06-23T15:20:02.156996Z, 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 from urllib.request import urlretrieve 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 ------------------------------------------------ tags.add('emodpymalaria') # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude' ] 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. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css', '_static/copy_button.css' ] } html_js_files = ['show_block_by_os.js'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a 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/"), ("v0.0.61", "/en/v0.0.61/"), ("v0.0.50", "/en/v0.0.50/"), ("0.0.50", "/en/0.0.50/"), ("v0.0.48", "/en/v0.0.48/"), ("v0.0.45", "/en/v0.0.45/"), ("v0.0.44", "/en/v0.0.44/"), ("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/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-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': '890db797', } # 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/662046/' 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: 2021-06-23T15:20:02.273966Z, end-time: 2021-06-23T15:20:07.249830Z, duration: 4, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.3.1 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 27 source files that are out of date updating environment: [new config] 27 added, 0 changed, 0 removed reading sources... [ 3%] emodpy_malaria reading sources... [ 7%] emodpy_malaria.config reading sources... [ 11%] emodpy_malaria.demographics reading sources... [ 14%] emodpy_malaria.demographics.MalariaDemographics reading sources... [ 18%] emodpy_malaria.interventions reading sources... [ 22%] emodpy_malaria.interventions.bednet reading sources... [ 25%] emodpy_malaria.interventions.common reading sources... [ 29%] emodpy_malaria.interventions.diag_survey reading sources... [ 33%] emodpy_malaria.interventions.drug reading sources... [ 37%] emodpy_malaria.interventions.drug_campaign reading sources... [ 40%] emodpy_malaria.interventions.inputeir reading sources... [ 44%] emodpy_malaria.interventions.irs reading sources... [ 48%] emodpy_malaria.interventions.ivermectin reading sources... [ 51%] emodpy_malaria.interventions.mosquitorelease reading sources... [ 55%] emodpy_malaria.interventions.outdoorrestkill reading sources... [ 59%] emodpy_malaria.interventions.spacespraying reading sources... 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[ 11%] emodpy_malaria.demographics writing output... [ 14%] emodpy_malaria.demographics.MalariaDemographics writing output... [ 18%] emodpy_malaria.interventions writing output... [ 22%] emodpy_malaria.interventions.bednet writing output... [ 25%] emodpy_malaria.interventions.common writing output... [ 29%] emodpy_malaria.interventions.diag_survey writing output... [ 33%] emodpy_malaria.interventions.drug writing output... [ 37%] emodpy_malaria.interventions.drug_campaign writing output... [ 40%] emodpy_malaria.interventions.inputeir writing output... [ 44%] emodpy_malaria.interventions.irs writing output... [ 48%] emodpy_malaria.interventions.ivermectin writing output... [ 51%] emodpy_malaria.interventions.mosquitorelease writing output... [ 55%] emodpy_malaria.interventions.outdoorrestkill writing output... [ 59%] emodpy_malaria.interventions.spacespraying writing output... [ 62%] emodpy_malaria.interventions.sugartrap writing output... [ 66%] emodpy_malaria.interventions.treatment_seeking writing output... [ 70%] emodpy_malaria.interventions.udbednet writing output... [ 74%] emodpy_malaria.reporters writing output... [ 77%] emodpy_malaria.reporters.builtin writing output... [ 81%] emodpy_malaria.vector_config writing output... [ 85%] emodpy_malaria_index writing output... [ 88%] faq writing output... [ 92%] index writing output... [ 96%] installation writing output... [100%] installation-basic generating indices... genindex py-modindex done writing additional pages... search opensearch done 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: 2021-06-23T15:20:07.385683Z, end-time: 2021-06-23T15:20:09.131865Z, duration: 1, exit-code: 0 python -m sphinx -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.3.1 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 installation-basic faq 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.inputeir 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 emodpy_malaria.vector_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: 2021-06-23T15:20:09.277590Z, end-time: 2021-06-23T15:20:10.957460Z, duration: 1, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.3.1 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 installation-basic faq 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.inputeir 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 emodpy_malaria.vector_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: 2021-06-23T15:20:11.178905Z, end-time: 2021-06-23T15:20:11.244884Z, 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: 2021-06-23T15:20:11.361969Z, end-time: 2021-06-23T15:20:13.359155Z, duration: 1, 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, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-malaria" "emodpy-malaria-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emodpy-malaria-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[10] Underfull \hbox (badness 10000) in paragraph at lines 535--535 []\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-age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 block- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \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 , \T1/ptm/m/it/10 re-pelling_eff=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 us-age_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 block-ing_decay_ra te=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 block-ing_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 killing_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 re-pelling_decay_rate=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 pelling_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 us-age_decay_rate=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 us- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 age_predecay_duration=365\T1/ptm/m/n/10 , [11] Underfull \hbox (badness 10000) in paragraph at lines 612--612 []\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-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 612--612 \T1/ptm/m/it/10 block-ing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_eff=1\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 655--655 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 686--686 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 686--686 \T1/ptm/m/it/10 ment_Sensitivity\T1/ptm/m/n/10 , \T1/ptm/m/it/10 De-tec- Underfull \hbox (badness 10000) in paragraph at lines 686--686 \T1/ptm/m/it/10 tion_Threshold\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Di-ag-nos- [12] Overfull \hbox (31.21352pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 get: [][]ob-ject[][] Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6364) in paragraph at lines 755--755 \T1/ptm/m/it/10 start_day: [][]int[][] Underfull \hbox (badness 5203) in paragraph at lines 755--755 \T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-ag-nos- Overfull \hbox (63.55446pt too wide) in paragraph at lines 755--755 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 di-ag-nos- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 tic_threshold: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 float[][] = 40\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 mea-sure- Overfull \hbox (1.01384pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ment_sensitivity: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 event_name: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Di-ag- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 nos-tic Sur-vey\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6364) in paragraph at lines 755--755 \T1/ptm/m/it/10 node_ids: [][]list[][] Overfull \hbox (27.58405pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tive_diagnosis_configs: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 neg-a- Overfull \hbox (27.58405pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tive_diagnosis_configs: Overfull \hbox (6.95406pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ceived_test_event: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ceived_Test\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 IP_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 NP_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 dis-qual-i-fy- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ing_properties: Overfull \hbox (9.814pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ger_condition_list: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 lis-ten- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ing_duration: Overfull \hbox (29.97432pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 gered_campaign_delay: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (47.68343pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 check_eligibility_at_trigger: Overfull \hbox (9.71407pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 pire_recent_drugs: LaTeX Warning: Hyper reference `emodpy_malaria.interventions.common:emodpy_mala ria.interventions.common.MalariaDiagnostic' on page 13 undefined on input line 758. [13] [14] Underfull \hbox (badness 10000) in paragraph at lines 788--791 []\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Type of malaria di-ag-nos-t ic used. De-fault is Underfull \hbox (badness 10000) in paragraph at lines 830--833 []\T1/ptm/m/n/10 In ga-me-to-cytes/microliter, use mea-sure- LaTeX Warning: Hyper reference `emodpy_malaria.interventions.common:emodpy_mala ria.interventions.common.MalariaDiagnostic' on page 15 undefined on input line 854. Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/pcr/b/n/10 measurement_sensitivity \T1/ptm/m/n/10 ^^U Set-ting for \T1/pt m/b/n/10 Mea-sure-ment_Sensitivity \T1/ptm/m/n/10 in [15] Underfull \hbox (badness 10000) in paragraph at lines 876--881 []\T1/pcr/b/n/10 IP_restrictions \T1/ptm/m/n/10 ^^U List of In-di-vid-u-al-Prop -erty key:value pairs that Underfull \hbox (badness 10000) in paragraph at lines 876--881 \T1/ptm/m/n/10 in-di-vid-u-als must have to re-ceive the di-ag-nos-tic in-ter-v en-tion. For Underfull \hbox (badness 10000) in paragraph at lines 876--881 \T1/ptm/m/n/10 ex-am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue 1"}, Underfull \hbox (badness 10000) in paragraph at lines 883--888 []\T1/pcr/b/n/10 NP_restrictions \T1/ptm/m/n/10 ^^U List of Node-Prop-erty key: value pairs Underfull \hbox (badness 10000) in paragraph at lines 883--888 \T1/ptm/m/n/10 that nodes must have to re-ceive the di-ag-nos-tic in-ter-ven-ti on. Underfull \hbox (badness 10000) in paragraph at lines 883--888 \T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 [{"NodeProperty1":"PropertyValue1" }, Underfull \hbox (badness 10000) in paragraph at lines 890--894 []\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U List of In-di-vid- u-al-Prop-erty Underfull \hbox (badness 10000) in paragraph at lines 890--894 \T1/ptm/m/n/10 key:value pairs that cause an in-ter-ven-tion to be aborted. For ex- Underfull \hbox (badness 10000) in paragraph at lines 890--894 \T1/ptm/m/n/10 am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"} , Underfull \hbox (badness 10000) in paragraph at lines 913--916 []\T1/pcr/b/n/10 expire_recent_drugs \T1/ptm/m/n/10 ^^U Adds \T1/pcr/m/n/10 [{" DrugStatus:None"}] \T1/ptm/m/n/10 to \T1/ptm/b/n/10 Prop- Underfull \hbox (badness 10000) in paragraph at lines 934--934 \T1/ptm/m/it/10 drug_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Chloroquine\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emodpy_malaria.config:emodpy_malaria.config.set _team_drug_params' on page 16 undefined on input line 952. [16] Underfull \hbox (badness 10000) in paragraph at lines 1002--1002 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1002--1002 \T1/ptm/m/it/10 drug_code: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cam- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 paign_type: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 MDA\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6775) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: Overfull \hbox (19.21352pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 7344) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-ag- Overfull \hbox (51.55446pt too wide) in paragraph at lines 1033--1033 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 di-ag-nos- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 = 40\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ment_sensitivity: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 fmda_radius: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (6.22408pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 node_selection_type: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 DIS- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 TANCE_ONLY\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 trig-ger_coverage: Underfull \hbox (badness 5667) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 balls: [][]int[][] = 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 treat-ment_delay: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig- Overfull \hbox (17.97432pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 gered_campaign_delay: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 tar-get_group: Overfull \hbox (33.88365pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 drug_ineligibility_duration: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (33.19351pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Overfull \hbox (26.53346pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 dis-qual-i-fy- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ing_properties: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ger_condition_list: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ten-ing_duration: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ent_drug_configs: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 get_residents_only: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 1\T1/ptm/m/n/10 , Overfull \hbox (35.68343pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 check_eligibility_at_trigger: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv- Overfull \hbox (144.47322pt too wide) in paragraph at lines 1033--1033 \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 ) [17] [18] [19] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 1184--1187 []\T1/pcr/b/n/10 ind_property_restrictions \T1/ptm/m/n/10 ^^U The set-ting for \T1/ptm/b/n/10 Prop- Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (57.71327pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 rep-e-ti-tions: [][]int[ ][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 6348) in paragraph at lines 1229--1229 [][]\T1/ptm/m/it/10 int[][] = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [][] list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex-pire_recent_drugs: Overfull \hbox (86.50304pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 6032) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 ing_properties: [][]list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 trig-ger_condition_list: [][]list[][] = LaTeX Warning: Hyper reference `emodpy_malaria.interventions.drug_campaign:emod py_malaria.interventions.drug_campaign.add_drug_campaign' on page 20 undefined on input line 1231. [20] Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (63.71327pt too wide) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][] Underfull \hbox (badness 7504) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 treat-ment_delay: [][]int[ ][] Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 40\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mea-sure-ment_sensitivity: Underfull \hbox (badness 6063) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [ ][]list[][] Overfull \hbox (92.50304pt too wide) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro up: Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \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- Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 check_eligibility_at_trigger: LaTeX Warning: Hyper reference `emodpy_malaria.interventions.drug_campaign:emod py_malaria.interventions.drug_campaign.add_drug_campaign' on page 21 undefined on input line 1246. Underfull \hbox (badness 10000) in paragraph at lines 1245--1248 \T1/ptm/m/n/10 Add an MSAT (mass screen-ing and treat-ment) drug in-ter-ven-tio n to your cam-paign. See [21] Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_coverage: Underfull \hbox (badness 7221) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [ ][]float[][] Underfull \hbox (badness 7595) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (63.71327pt too wide) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][] Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Overfull \hbox (92.50304pt too wide) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro up: Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \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- LaTeX Warning: Hyper reference `emodpy_malaria.interventions.drug_campaign:emod py_malaria.interventions.drug_campaign.add_drug_campaign' on page 22 undefined on input line 1261. Underfull \hbox (badness 7869) in paragraph at lines 1260--1263 \T1/ptm/m/n/10 Add an fMDA (fo-cal mass drug ad-min-is-tra-tion) drug in-ter-ve n-tion to your cam-paign. See Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = Underfull \hbox (badness 6141) in paragraph at lines 1274--1274 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (75.71327pt too wide) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Overfull \hbox (9.55446pt too wide) in paragraph at lines 1274--1274 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Overfull \hbox (104.50304pt too wide) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- LaTeX Warning: Hyper reference `emodpy_malaria.interventions.drug_campaign:emod py_malaria.interventions.drug_campaign.add_drug_campaign' on page 22 undefined on input line 1276. [22] Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (69.71327pt too wide) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 7613) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lis-ten-ing_duration: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_covera ge: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_selection_type: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\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 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 node_ids: [][]list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 ex-pire_recent_drugs: Overfull \hbox (98.50304pt too wide) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- LaTeX Warning: Hyper reference `emodpy_malaria.interventions.drug_campaign:emod py_malaria.interventions.drug_campaign.add_drug_campaign' on page 23 undefined on input line 1291. Underfull \hbox (badness 10000) in paragraph at lines 1304--1304 \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: [23] Underfull \hbox (badness 5091) in paragraph at lines 1363--1363 [][]\T1/ptm/m/it/10 int[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [][]l ist[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 []\T1/ptm/m/it/10 campaign\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 \T1/ptm/m/it/10 monthly_eir: Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 [][]\T1/ptm/m/it/10 list[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name: [24] Underfull \hbox (badness 5274) in paragraph at lines 1428--1428 []\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- Underfull \hbox (badness 10000) in paragraph at lines 1428--1428 \T1/ptm/m/it/10 killing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in- Underfull \hbox (badness 10000) in paragraph at lines 1428--1428 \T1/ptm/m/it/10 sec-ti-cide=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 []\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 [][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo- Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 \T1/ptm/m/it/10 killing_exponential_decay_rate: [25] Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 by_number=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 num-ber=10000\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 frac-tion=0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 in-fec-tious=0.0\T1/ptm/m/n/10 , Overfull \hbox (5.1738pt too wide) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1512--1515 []\T1/pcr/b/n/10 infectious \T1/ptm/m/n/10 ^^U The frac-tion of vec-tors re-lea sed that are Underfull \hbox (badness 10000) in paragraph at lines 1512--1515 \T1/ptm/m/n/10 to be in-fec-tious. One can only use this fea-ture when Overfull \hbox (16.27205pt too wide) in paragraph at lines 1512--1515 \T1/ptm/m/n/10 `Malaria_Model'!='MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETI CS' Underfull \hbox (badness 10000) in paragraph at lines 1539--1539 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (15.52452pt too wide) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 file- Overfull \hbox (30.76479pt too wide) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Overfull \hbox (19.6943pt too wide) in paragraph at lines 1548--1548 []\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_effect\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 in-sec-ti- Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 cide_name=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 get_coverage=1.0\T1/ptm/m/n/10 , Overfull \hbox (41.63394pt too wide) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_predecay_duration=0\T1/ptm/m/n/10 , Overfull \hbox (10.33417pt too wide) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 , [26] Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \T1/ptm/m/it/10 in-sec-ti-cide=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \T1/ptm/m/it/10 stant_duration=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1595--1595 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (3.52452pt too wide) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 file- Overfull \hbox (18.76479pt too wide) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\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- Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 \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 , \T1/ptm/m/it/10 in-sec-ti- Underfull \hbox (badness 10000) in paragraph at lines 1612--1612 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , [27] Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 []\T1/pcr/b/n/10 of individuals to target with the intervention. Default is Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 properties\T1/ptm/m/n/10 ) ^^U \T1/pcr/m/n/10 [ { "trigger":"NewClinicalCase","coverage":0. Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/pcr/m/n/10 8,"agemin":15,"agemax":70, "seek":0.4,"rate":0.3}, Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/pcr/m/n/10 {"trigger":"NewSevereCase","coverage":0.8,"seek":0.6, Underfull \hbox (badness 10000) in paragraph at lines 1655--1657 []\T1/pcr/b/n/10 must have to receive the intervention. 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Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emodpy-malaria.pdf (39 pages, 209883 bytes). Transcript written on institute-for-disease-modeling-emodpy-malaria.log. Latexmk: Index file 'institute-for-disease-modeling-emodpy-malaria.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-emodpy-malaria.ind' from line 'No file institute-for-disease-modeling-emodpy-malaria.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-malaria.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-malaria.pdf' Latexmk: List of undefined refs and citations: Reference `emodpy_malaria.config:module-emodpy_malaria.config' on page 35 undefined on input line 2216 Reference `emodpy_malaria.demographics.MalariaDemographics:module-emodpy_malaria.demographics.MalariaDemographics' on page 35 undefined on input line 2218 Reference `emodpy_malaria.demographics:module-emodpy_malaria.demographics' on page 35 undefined on input line 2217 Reference `emodpy_malaria.interventions.bednet:module-emodpy_malaria.interventions.bednet' on page 35 undefined on input line 2220 Reference `emodpy_malaria.interventions.common:module-emodpy_malaria.interventions.common' on page 35 undefined on input line 2221 Reference `emodpy_malaria.interventions.diag_survey:module-emodpy_malaria.interventions.diag_survey' on page 35 undefined on input line 2222 Reference `emodpy_malaria.interventions.drug:module-emodpy_malaria.interventions.drug' on page 35 undefined on input line 2223 Reference `emodpy_malaria.interventions.drug_campaign:module-emodpy_malaria.interventions.drug_campaign' on page 35 undefined on input line 2224 Reference `emodpy_malaria.interventions.inputeir:module-emodpy_malaria.interventions.inputeir' on page 35 undefined on input line 2225 Reference `emodpy_malaria.interventions.irs:module-emodpy_malaria.interventions.irs' on page 35 undefined on input line 2226 Reference `emodpy_malaria.interventions.ivermectin:module-emodpy_malaria.interventions.ivermectin' on page 35 undefined on input line 2227 Reference `emodpy_malaria.interventions.mosquitorelease:module-emodpy_malaria.interventions.mosquitorelease' on page 35 undefined on input line 2228 Reference `emodpy_malaria.interventions.outdoorrestkill:module-emodpy_malaria.interventions.outdoorrestkill' on page 35 undefined on input line 2229 Reference `emodpy_malaria.interventions.spacespraying:module-emodpy_malaria.interventions.spacespraying' on page 35 undefined on input line 2230 Reference `emodpy_malaria.interventions.sugartrap:module-emodpy_malaria.interventions.sugartrap' on page 35 undefined on input line 2231 Reference `emodpy_malaria.interventions.treatment_seeking:module-emodpy_malaria.interventions.treatment_seeking' on page 35 undefined on input line 2232 Reference `emodpy_malaria.interventions.udbednet:module-emodpy_malaria.interventions.udbednet' on page 35 undefined on input line 2233 Reference `emodpy_malaria.interventions:module-emodpy_malaria.interventions' on page 35 undefined on input line 2219 Reference `emodpy_malaria.reporters.builtin:module-emodpy_malaria.reporters.builtin' on page 35 undefined on input line 2235 Reference `emodpy_malaria.reporters:module-emodpy_malaria.reporters' on page 35 undefined on input line 2234 Reference `emodpy_malaria.vector_config:module-emodpy_malaria.vector_config' on page 35 undefined on input line 2236 Reference `emodpy_malaria:module-emodpy_malaria' on page 35 undefined on input line 2215 Latexmk: Summary of warnings: Latex failed to resolve 22 reference(s) Rule 'makeindex institute-for-disease-modeling-emodpy-malaria.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-emodpy-malaria.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-emodpy-malaria.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-emodpy-malaria.ind" "institute-for-disease-modeling-emodpy-malaria.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-emodpy-malaria.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-emodpy-malaria.idx....done (119 entries accepted, 0 rejected). Sorting entries....done (876 comparisons). Generating output file institute-for-disease-modeling-emodpy-malaria.ind....done (264 lines written, 0 warnings). Output written in institute-for-disease-modeling-emodpy-malaria.ind. Transcript written in institute-for-disease-modeling-emodpy-malaria.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-emodpy-malaria.aux' 'institute-for-disease-modeling-emodpy-malaria.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-malaria" "emodpy-malaria-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emodpy-malaria-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emodpy-malaria.out) (./institute-for-disease-modeling-emodpy-malaria.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./institute-for-disease-modeling-emodpy-malaria.toc) [1] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] [4] Chapter 2. [5] Underfull \hbox (badness 10000) in paragraph at lines 315--317 []\T1/ptm/m/n/10 Install at a com-mand [6] [7] [8] Chapter 3. Overfull \hbox (25.07484pt too wide) in paragraph at lines 373--373 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (59.9842pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Overfull \hbox (22.58472pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 world Overfull \hbox (70.45445pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (65.15454pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 base_file=None\T1/ptm/m/n/10 , Overfull \hbox (60.08455pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 init_prev=0.2\T1/pcr/m/n/10 ) [9] Underfull \hbox (badness 10000) in paragraph at lines 429--429 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 429--429 \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , Overfull \hbox (23.99501pt too wide) in paragraph at lines 429--429 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 429--429 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , Overfull \hbox (9.45456pt too wide) in paragraph at lines 429--429 \T1/ptm/m/it/10 forced_id=1\T1/ptm/m/n/10 , Overfull \hbox (18.08455pt too wide) in paragraph at lines 429--429 \T1/ptm/m/it/10 init_prev=0.2\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 465--465 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (106.44351pt too wide) in paragraph at lines 465--465 \T1/ptm/m/it/10 pop_filename_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 spatial_grid ded_pop_dir\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 491--491 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 491--491 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 491--491 \T1/ptm/m/it/10 frac_rural=0.3\T1/ptm/m/n/10 , Overfull \hbox (9.35394pt too wide) in paragraph at lines 491--491 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_params\TS1/ptm/m/ it/10 '\T1/pcr/m/n/10 ) [10] Underfull \hbox (badness 10000) in paragraph at lines 535--535 []\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-age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 block- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \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 , \T1/ptm/m/it/10 re-pelling_eff=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 us-age_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 block-ing_decay_ra te=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 block-ing_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 killing_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 re-pelling_decay_rate=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 pelling_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 us-age_decay_rate=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 us- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 age_predecay_duration=365\T1/ptm/m/n/10 , [11] Underfull \hbox (badness 10000) in paragraph at lines 612--612 []\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-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 612--612 \T1/ptm/m/it/10 block-ing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_eff=1\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 655--655 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 686--686 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 686--686 \T1/ptm/m/it/10 ment_Sensitivity\T1/ptm/m/n/10 , \T1/ptm/m/it/10 De-tec- Underfull \hbox (badness 10000) in paragraph at lines 686--686 \T1/ptm/m/it/10 tion_Threshold\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Di-ag-nos- [12] Overfull \hbox (31.21352pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 get: [][]ob-ject[][] Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6364) in paragraph at lines 755--755 \T1/ptm/m/it/10 start_day: [][]int[][] Underfull \hbox (badness 5203) in paragraph at lines 755--755 \T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-ag-nos- Overfull \hbox (63.55446pt too wide) in paragraph at lines 755--755 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 di-ag-nos- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 tic_threshold: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 float[][] = 40\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 mea-sure- Overfull \hbox (1.01384pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ment_sensitivity: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 event_name: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Di-ag- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 nos-tic Sur-vey\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6364) in paragraph at lines 755--755 \T1/ptm/m/it/10 node_ids: [][]list[][] Overfull \hbox (27.58405pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tive_diagnosis_configs: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 neg-a- Overfull \hbox (27.58405pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tive_diagnosis_configs: Overfull \hbox (6.95406pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ceived_test_event: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ceived_Test\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 IP_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 NP_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 dis-qual-i-fy- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ing_properties: Overfull \hbox (9.814pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ger_condition_list: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 lis-ten- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ing_duration: Overfull \hbox (29.97432pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 gered_campaign_delay: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (47.68343pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 check_eligibility_at_trigger: Overfull \hbox (9.71407pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 pire_recent_drugs: [13] [14] Underfull \hbox (badness 10000) in paragraph at lines 788--791 []\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Type of malaria di-ag-nos-t ic used. De-fault is Underfull \hbox (badness 10000) in paragraph at lines 830--833 []\T1/ptm/m/n/10 In ga-me-to-cytes/microliter, use mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/pcr/b/n/10 measurement_sensitivity \T1/ptm/m/n/10 ^^U Set-ting for \T1/pt m/b/n/10 Mea-sure-ment_Sensitivity \T1/ptm/m/n/10 in [15] Underfull \hbox (badness 10000) in paragraph at lines 876--881 []\T1/pcr/b/n/10 IP_restrictions \T1/ptm/m/n/10 ^^U List of In-di-vid-u-al-Prop -erty key:value pairs that Underfull \hbox (badness 10000) in paragraph at lines 876--881 \T1/ptm/m/n/10 in-di-vid-u-als must have to re-ceive the di-ag-nos-tic in-ter-v en-tion. For Underfull \hbox (badness 10000) in paragraph at lines 876--881 \T1/ptm/m/n/10 ex-am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue 1"}, Underfull \hbox (badness 10000) in paragraph at lines 883--888 []\T1/pcr/b/n/10 NP_restrictions \T1/ptm/m/n/10 ^^U List of Node-Prop-erty key: value pairs Underfull \hbox (badness 10000) in paragraph at lines 883--888 \T1/ptm/m/n/10 that nodes must have to re-ceive the di-ag-nos-tic in-ter-ven-ti on. Underfull \hbox (badness 10000) in paragraph at lines 883--888 \T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 [{"NodeProperty1":"PropertyValue1" }, Underfull \hbox (badness 10000) in paragraph at lines 890--894 []\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U List of In-di-vid- u-al-Prop-erty Underfull \hbox (badness 10000) in paragraph at lines 890--894 \T1/ptm/m/n/10 key:value pairs that cause an in-ter-ven-tion to be aborted. For ex- Underfull \hbox (badness 10000) in paragraph at lines 890--894 \T1/ptm/m/n/10 am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"} , Underfull \hbox (badness 10000) in paragraph at lines 913--916 []\T1/pcr/b/n/10 expire_recent_drugs \T1/ptm/m/n/10 ^^U Adds \T1/pcr/m/n/10 [{" DrugStatus:None"}] \T1/ptm/m/n/10 to \T1/ptm/b/n/10 Prop- Underfull \hbox (badness 10000) in paragraph at lines 934--934 \T1/ptm/m/it/10 drug_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Chloroquine\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1002--1002 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1002--1002 \T1/ptm/m/it/10 drug_code: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cam- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 paign_type: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 MDA\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6775) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: Overfull \hbox (19.21352pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 7344) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-ag- Overfull \hbox (51.55446pt too wide) in paragraph at lines 1033--1033 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 di-ag-nos- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 = 40\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ment_sensitivity: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 fmda_radius: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (6.22408pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 node_selection_type: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 DIS- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 TANCE_ONLY\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 trig-ger_coverage: Underfull \hbox (badness 5667) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 balls: [][]int[][] = 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 treat-ment_delay: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig- Overfull \hbox (17.97432pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 gered_campaign_delay: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 tar-get_group: Overfull \hbox (33.88365pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 drug_ineligibility_duration: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (33.19351pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Overfull \hbox (26.53346pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 dis-qual-i-fy- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ing_properties: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ger_condition_list: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ten-ing_duration: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ent_drug_configs: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 get_residents_only: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 1\T1/ptm/m/n/10 , Overfull \hbox (35.68343pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 check_eligibility_at_trigger: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv- Overfull \hbox (144.47322pt too wide) in paragraph at lines 1033--1033 \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 ) [17] [18] [19] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 1184--1187 []\T1/pcr/b/n/10 ind_property_restrictions \T1/ptm/m/n/10 ^^U The set-ting for \T1/ptm/b/n/10 Prop- Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (57.71327pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 rep-e-ti-tions: [][]int[ ][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 6348) in paragraph at lines 1229--1229 [][]\T1/ptm/m/it/10 int[][] = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [][] list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex-pire_recent_drugs: Overfull \hbox (86.50304pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 6032) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 ing_properties: [][]list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 trig-ger_condition_list: [][]list[][] = [20] Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (63.71327pt too wide) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][] Underfull \hbox (badness 7504) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 treat-ment_delay: [][]int[ ][] Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 40\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mea-sure-ment_sensitivity: Underfull \hbox (badness 6063) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [ ][]list[][] Overfull \hbox (92.50304pt too wide) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro up: Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \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- Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 check_eligibility_at_trigger: Underfull \hbox (badness 10000) in paragraph at lines 1245--1248 \T1/ptm/m/n/10 Add an MSAT (mass screen-ing and treat-ment) drug in-ter-ven-tio n to your cam-paign. See [21] Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_coverage: Underfull \hbox (badness 7221) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [ ][]float[][] Underfull \hbox (badness 7595) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (63.71327pt too wide) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][] Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Overfull \hbox (92.50304pt too wide) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro up: Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \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- Underfull \hbox (badness 7869) in paragraph at lines 1260--1263 \T1/ptm/m/n/10 Add an fMDA (fo-cal mass drug ad-min-is-tra-tion) drug in-ter-ve n-tion to your cam-paign. See Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = Underfull \hbox (badness 6141) in paragraph at lines 1274--1274 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (75.71327pt too wide) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Overfull \hbox (9.55446pt too wide) in paragraph at lines 1274--1274 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Overfull \hbox (104.50304pt too wide) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- [22] Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (69.71327pt too wide) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 7613) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lis-ten-ing_duration: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_covera ge: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_selection_type: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\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 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 node_ids: [][]list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 ex-pire_recent_drugs: Overfull \hbox (98.50304pt too wide) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- Underfull \hbox (badness 10000) in paragraph at lines 1304--1304 \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: [23] Underfull \hbox (badness 5091) in paragraph at lines 1363--1363 [][]\T1/ptm/m/it/10 int[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [][]l ist[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 []\T1/ptm/m/it/10 campaign\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 \T1/ptm/m/it/10 monthly_eir: Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 [][]\T1/ptm/m/it/10 list[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name: [24] Underfull \hbox (badness 5274) in paragraph at lines 1428--1428 []\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- Underfull \hbox (badness 10000) in paragraph at lines 1428--1428 \T1/ptm/m/it/10 killing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in- Underfull \hbox (badness 10000) in paragraph at lines 1428--1428 \T1/ptm/m/it/10 sec-ti-cide=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 []\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 [][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo- Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 \T1/ptm/m/it/10 killing_exponential_decay_rate: [25] Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 by_number=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 num-ber=10000\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 frac-tion=0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 in-fec-tious=0.0\T1/ptm/m/n/10 , Overfull \hbox (5.1738pt too wide) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1512--1515 []\T1/pcr/b/n/10 infectious \T1/ptm/m/n/10 ^^U The frac-tion of vec-tors re-lea sed that are Underfull \hbox (badness 10000) in paragraph at lines 1512--1515 \T1/ptm/m/n/10 to be in-fec-tious. One can only use this fea-ture when Overfull \hbox (16.27205pt too wide) in paragraph at lines 1512--1515 \T1/ptm/m/n/10 `Malaria_Model'!='MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETI CS' Underfull \hbox (badness 10000) in paragraph at lines 1539--1539 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (15.52452pt too wide) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 file- Overfull \hbox (30.76479pt too wide) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Overfull \hbox (19.6943pt too wide) in paragraph at lines 1548--1548 []\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_effect\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 in-sec-ti- Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 cide_name=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 get_coverage=1.0\T1/ptm/m/n/10 , Overfull \hbox (41.63394pt too wide) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_predecay_duration=0\T1/ptm/m/n/10 , Overfull \hbox (10.33417pt too wide) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 , [26] Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \T1/ptm/m/it/10 in-sec-ti-cide=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \T1/ptm/m/it/10 stant_duration=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1595--1595 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (3.52452pt too wide) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 file- Overfull \hbox (18.76479pt too wide) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\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- Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 \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 , \T1/ptm/m/it/10 in-sec-ti- Underfull \hbox (badness 10000) in paragraph at lines 1612--1612 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , [27] Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 []\T1/pcr/b/n/10 of individuals to target with the intervention. Default is Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 properties\T1/ptm/m/n/10 ) ^^U \T1/pcr/m/n/10 [ { "trigger":"NewClinicalCase","coverage":0. Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/pcr/m/n/10 8,"agemin":15,"agemax":70, "seek":0.4,"rate":0.3}, Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/pcr/m/n/10 {"trigger":"NewSevereCase","coverage":0.8,"seek":0.6, Underfull \hbox (badness 10000) in paragraph at lines 1655--1657 []\T1/pcr/b/n/10 must have to receive the intervention. For example, Underfull \hbox (badness 10000) in paragraph at lines 1655--1657 \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 individuals\T1/ptm/m/n/10 ) ^^U \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"}, Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis- Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 0.0013698630136986301\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_e ff: Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 0.0006849315068493151\T1/ptm/m/n/10 , \T1/ptm/m/it/10 iv_name: Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Us-ageDe-pen-de ntBed-net\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 sonal_dependence: [][]dict[][] = None\T1/ptm/m/n/10 , [28] [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 1883--1883 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1883--1883 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: Underfull \hbox (badness 10000) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 dict = \T1/ptm/m/n/10 , Underfull \hbox (badness 6348) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 En-abled: bool = [31] Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 dict = \T1/ptm/m/n/10 , Underfull \hbox (badness 6348) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 En-abled: bool = Underfull \hbox (badness 10000) in paragraph at lines 1958--1958 []\T1/ptm/m/it/10 class_name: Underfull \hbox (badness 10000) in paragraph at lines 1958--1958 \T1/ptm/m/it/10 = \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1958--1958 \T1/ptm/m/it/10 En-abled: Overfull \hbox (0.5943pt too wide) in paragraph at lines 1958--1958 \T1/ptm/m/it/10 Pretty_Format: Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 []\T1/ptm/m/it/10 class_name: Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 pa-ram-e- Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 En-abled: Overfull \hbox (6.5943pt too wide) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 Pretty_Format: Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 []\T1/ptm/m/it/10 class_name: str Underfull \hbox (badness 7291) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram- Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 e-ters: dict = Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 \T1/ptm/m/n/10 , \T1/ptm/m/it/10 En- Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 Pretty_Format: [32] Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 []\T1/ptm/m/it/10 class_name: str = Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: [33] Underfull \hbox (badness 6348) in paragraph at lines 2174--2174 \T1/ptm/m/it/10 block-ing=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing=1.0\T1/pt m/m/n/10 , \T1/ptm/m/it/10 re-pelling=1.0\T1/ptm/m/n/10 , [34] Overfull \hbox (54.6225pt too wide) in paragraph at lines 2218--2219 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2222--2223 []\T1/pcr/m/n/10 emodpy_malaria.interventions.diag_survey\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2224--2225 []\T1/pcr/m/n/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2225--2226 []\T1/pcr/m/n/10 emodpy_malaria.interventions.inputeir\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2227--2228 []\T1/pcr/m/n/10 emodpy_malaria.interventions.ivermectin\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2228--2229 []\T1/pcr/m/n/10 emodpy_malaria.interventions.mosquitorelease\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2229--2230 []\T1/pcr/m/n/10 emodpy_malaria.interventions.outdoorrestkill\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2230--2231 []\T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2231--2232 []\T1/pcr/m/n/10 emodpy_malaria.interventions.sugartrap\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 2232--2233 []\T1/pcr/m/n/10 emodpy_malaria.interventions.treatment_seeking\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2233--2234 []\T1/pcr/m/n/10 emodpy_malaria.interventions.udbednet\T1/ptm/m/n/10 , [35] (./institute-for-disease-modeling-emodpy-malaria.ind [36] Overfull \hbox (50.13988pt too wide) in paragraph at lines 8--10 []\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 ), Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/pcr/m/n/10 add_alleles() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/pcr/m/n/10 add_diagnostic_survey() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 12--14 \T1/ptm/m/it/10 emodpy_malaria.interventions.diag_survey\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/pcr/m/n/10 add_drug_campaign() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 14--16 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 add_fMDA() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 16--18 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 add_MDA() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 18--20 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 add_MSAT() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 20--22 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 add_mutation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 add_resistance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 26--28 []\T1/pcr/m/n/10 add_rfMDA() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 26--28 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 28--30 []\T1/pcr/m/n/10 add_rfMSAT() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 28--30 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 30--31 []\T1/pcr/m/n/10 add_trait() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 AntiMalarialDrug() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 \T1/ptm/m/it/10 emodpy_malaria.interventions.common\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 AntiMalarialDrug() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/pcr/m/n/10 BasicBednet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 Bednet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (52.68974pt too wide) in paragraph at lines 45--47 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.FilteredMalariaReport Overfull \hbox (72.70978pt too wide) in paragraph at lines 47--49 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.MalariaPatientJSONReport Overfull \hbox (59.06006pt too wide) in paragraph at lines 49--51 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.MalariaSummaryReport Overfull \hbox (74.48972pt too wide) in paragraph at lines 51--53 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.MalariaTransmissionReport Overfull \hbox (44.06006pt too wide) in paragraph at lines 53--55 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportEventCounter Overfull \hbox (49.04977pt too wide) in paragraph at lines 55--57 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportVectorGenetics Overfull \hbox (33.50998pt too wide) in paragraph at lines 57--59 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportVectorStats Underfull \hbox (badness 10000) in paragraph at lines 62--64 []\T1/pcr/m/n/10 drug_configs_from_code() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 62--64 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Overfull \hbox (52.1225pt too wide) in paragraph at lines 73--74 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics Overfull \hbox (10.1225pt too wide) in paragraph at lines 81--82 []\T1/pcr/m/n/10 emodpy_malaria.interventions.diag_survey Overfull \hbox (22.1225pt too wide) in paragraph at lines 85--86 []\T1/pcr/m/n/10 emodpy_malaria.interventions.drug_campaign [37] Overfull \hbox (4.1225pt too wide) in paragraph at lines 91--92 []\T1/pcr/m/n/10 emodpy_malaria.interventions.ivermectin Overfull \hbox (34.1225pt too wide) in paragraph at lines 93--94 []\T1/pcr/m/n/10 emodpy_malaria.interventions.mosquitorelease Overfull \hbox (34.1225pt too wide) in paragraph at lines 95--96 []\T1/pcr/m/n/10 emodpy_malaria.interventions.outdoorrestkill Overfull \hbox (22.1225pt too wide) in paragraph at lines 97--98 []\T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying Overfull \hbox (46.1225pt too wide) in paragraph at lines 101--102 []\T1/pcr/m/n/10 emodpy_malaria.interventions.treatment_seeking Underfull \hbox (badness 10000) in paragraph at lines 114--116 []\T1/pcr/m/n/10 FilteredMalariaReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/pcr/m/n/10 fmda_cfg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 116--118 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/pcr/m/n/10 from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (36.54083pt too wide) in paragraph at lines 118--120 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 120--122 []\T1/pcr/m/n/10 from_pop_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (36.54083pt too wide) in paragraph at lines 120--122 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 122--124 []\T1/pcr/m/n/10 from_template_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (36.54083pt too wide) in paragraph at lines 122--124 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 127--128 []\T1/pcr/m/n/10 get_drug_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 get_file_from_http() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 130--132 []\T1/pcr/m/n/10 get_species_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 132--134 []\T1/pcr/m/n/10 get_species_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 137--139 []\T1/pcr/m/n/10 InputEIR() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 137--139 \T1/ptm/m/it/10 emodpy_malaria.interventions.inputeir\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 139--141 []\T1/pcr/m/n/10 IRSHousingModification() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 141--143 []\T1/pcr/m/n/10 ivermectin() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 141--143 \T1/ptm/m/it/10 emodpy_malaria.interventions.ivermectin\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 146--148 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] [4] Chapter 2. [5] Underfull \hbox (badness 10000) in paragraph at lines 315--317 []\T1/ptm/m/n/10 Install at a com-mand [6] [7] [8] Chapter 3. Overfull \hbox (25.07484pt too wide) in paragraph at lines 373--373 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (59.9842pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Overfull \hbox (22.58472pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 world Overfull \hbox (70.45445pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (65.15454pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 base_file=None\T1/ptm/m/n/10 , Overfull \hbox (60.08455pt too wide) in paragraph at lines 373--373 \T1/ptm/m/it/10 init_prev=0.2\T1/pcr/m/n/10 ) [9] Underfull \hbox (badness 10000) in paragraph at lines 429--429 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 429--429 \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , Overfull \hbox (23.99501pt too wide) in paragraph at lines 429--429 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 429--429 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , Overfull \hbox (9.45456pt too wide) in paragraph at lines 429--429 \T1/ptm/m/it/10 forced_id=1\T1/ptm/m/n/10 , Overfull \hbox (18.08455pt too wide) in paragraph at lines 429--429 \T1/ptm/m/it/10 init_prev=0.2\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 465--465 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (106.44351pt too wide) in paragraph at lines 465--465 \T1/ptm/m/it/10 pop_filename_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 spatial_grid ded_pop_dir\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 491--491 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 491--491 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 491--491 \T1/ptm/m/it/10 frac_rural=0.3\T1/ptm/m/n/10 , Overfull \hbox (9.35394pt too wide) in paragraph at lines 491--491 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_params\TS1/ptm/m/ it/10 '\T1/pcr/m/n/10 ) [10] Underfull \hbox (badness 10000) in paragraph at lines 535--535 []\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-age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 block- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \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 , \T1/ptm/m/it/10 re-pelling_eff=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 us-age_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 block-ing_decay_ra te=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 block-ing_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 killing_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 re-pelling_decay_rate=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 pelling_predecay_duration=365\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 us-age_decay_rate=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 us- Underfull \hbox (badness 10000) in paragraph at lines 535--535 \T1/ptm/m/it/10 age_predecay_duration=365\T1/ptm/m/n/10 , [11] Underfull \hbox (badness 10000) in paragraph at lines 612--612 []\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-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 612--612 \T1/ptm/m/it/10 block-ing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_eff=1\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 655--655 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 686--686 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 686--686 \T1/ptm/m/it/10 ment_Sensitivity\T1/ptm/m/n/10 , \T1/ptm/m/it/10 De-tec- Underfull \hbox (badness 10000) in paragraph at lines 686--686 \T1/ptm/m/it/10 tion_Threshold\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Di-ag-nos- [12] Overfull \hbox (31.21352pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 get: [][]ob-ject[][] Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Ev-ery-one\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6364) in paragraph at lines 755--755 \T1/ptm/m/it/10 start_day: [][]int[][] Underfull \hbox (badness 5203) in paragraph at lines 755--755 \T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-ag-nos- Overfull \hbox (63.55446pt too wide) in paragraph at lines 755--755 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 di-ag-nos- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 tic_threshold: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 float[][] = 40\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 mea-sure- Overfull \hbox (1.01384pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ment_sensitivity: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 event_name: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Di-ag- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 nos-tic Sur-vey\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6364) in paragraph at lines 755--755 \T1/ptm/m/it/10 node_ids: [][]list[][] Overfull \hbox (27.58405pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tive_diagnosis_configs: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 neg-a- Overfull \hbox (27.58405pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 tive_diagnosis_configs: Overfull \hbox (6.95406pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ceived_test_event: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ceived_Test\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 IP_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 NP_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 dis-qual-i-fy- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ing_properties: Overfull \hbox (9.814pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 ger_condition_list: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 lis-ten- Underfull \hbox (badness 10000) in paragraph at lines 755--755 \T1/ptm/m/it/10 ing_duration: Overfull \hbox (29.97432pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 gered_campaign_delay: Underfull \hbox (badness 10000) in paragraph at lines 755--755 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (47.68343pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 check_eligibility_at_trigger: Overfull \hbox (9.71407pt too wide) in paragraph at lines 755--755 \T1/ptm/m/it/10 pire_recent_drugs: [13] [14] Underfull \hbox (badness 10000) in paragraph at lines 788--791 []\T1/pcr/b/n/10 diagnostic_type \T1/ptm/m/n/10 ^^U Type of malaria di-ag-nos-t ic used. De-fault is Underfull \hbox (badness 10000) in paragraph at lines 830--833 []\T1/ptm/m/n/10 In ga-me-to-cytes/microliter, use mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/pcr/b/n/10 measurement_sensitivity \T1/ptm/m/n/10 ^^U Set-ting for \T1/pt m/b/n/10 Mea-sure-ment_Sensitivity \T1/ptm/m/n/10 in [15] Underfull \hbox (badness 10000) in paragraph at lines 876--881 []\T1/pcr/b/n/10 IP_restrictions \T1/ptm/m/n/10 ^^U List of In-di-vid-u-al-Prop -erty key:value pairs that Underfull \hbox (badness 10000) in paragraph at lines 876--881 \T1/ptm/m/n/10 in-di-vid-u-als must have to re-ceive the di-ag-nos-tic in-ter-v en-tion. For Underfull \hbox (badness 10000) in paragraph at lines 876--881 \T1/ptm/m/n/10 ex-am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue 1"}, Underfull \hbox (badness 10000) in paragraph at lines 883--888 []\T1/pcr/b/n/10 NP_restrictions \T1/ptm/m/n/10 ^^U List of Node-Prop-erty key: value pairs Underfull \hbox (badness 10000) in paragraph at lines 883--888 \T1/ptm/m/n/10 that nodes must have to re-ceive the di-ag-nos-tic in-ter-ven-ti on. Underfull \hbox (badness 10000) in paragraph at lines 883--888 \T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 [{"NodeProperty1":"PropertyValue1" }, Underfull \hbox (badness 10000) in paragraph at lines 890--894 []\T1/pcr/b/n/10 disqualifying_properties \T1/ptm/m/n/10 ^^U List of In-di-vid- u-al-Prop-erty Underfull \hbox (badness 10000) in paragraph at lines 890--894 \T1/ptm/m/n/10 key:value pairs that cause an in-ter-ven-tion to be aborted. For ex- Underfull \hbox (badness 10000) in paragraph at lines 890--894 \T1/ptm/m/n/10 am-ple, \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"} , Underfull \hbox (badness 10000) in paragraph at lines 913--916 []\T1/pcr/b/n/10 expire_recent_drugs \T1/ptm/m/n/10 ^^U Adds \T1/pcr/m/n/10 [{" DrugStatus:None"}] \T1/ptm/m/n/10 to \T1/ptm/b/n/10 Prop- Underfull \hbox (badness 10000) in paragraph at lines 934--934 \T1/ptm/m/it/10 drug_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Chloroquine\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1002--1002 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1002--1002 \T1/ptm/m/it/10 drug_code: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cam- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 paign_type: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 MDA\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 6775) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: Overfull \hbox (19.21352pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 7344) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-ag- Overfull \hbox (51.55446pt too wide) in paragraph at lines 1033--1033 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 di-ag-nos- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 = 40\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mea-sure- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ment_sensitivity: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 fmda_radius: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (6.22408pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 node_selection_type: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 DIS- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 TANCE_ONLY\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 trig-ger_coverage: Underfull \hbox (badness 5667) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 balls: [][]int[][] = 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 treat-ment_delay: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig- Overfull \hbox (17.97432pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 gered_campaign_delay: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 tar-get_group: Overfull \hbox (33.88365pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 drug_ineligibility_duration: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , Overfull \hbox (33.19351pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Overfull \hbox (26.53346pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 dis-qual-i-fy- Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ing_properties: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ger_condition_list: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ten-ing_duration: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 ent_drug_configs: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 get_residents_only: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 int[][] = 1\T1/ptm/m/n/10 , Overfull \hbox (35.68343pt too wide) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 check_eligibility_at_trigger: Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 1033--1033 \T1/ptm/m/it/10 False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv- Overfull \hbox (144.47322pt too wide) in paragraph at lines 1033--1033 \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 ) [17] [18] [19] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 1184--1187 []\T1/pcr/b/n/10 ind_property_restrictions \T1/ptm/m/n/10 ^^U The set-ting for \T1/ptm/b/n/10 Prop- Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (57.71327pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 rep-e-ti-tions: [][]int[ ][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tsteps_btwn_repetitions: Underfull \hbox (badness 6348) in paragraph at lines 1229--1229 [][]\T1/ptm/m/it/10 int[][] = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [][] list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex-pire_recent_drugs: Overfull \hbox (86.50304pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 6032) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 ing_properties: [][]list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 trig-ger_condition_list: [][]list[][] = [20] Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [][]float[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (63.71327pt too wide) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][] Underfull \hbox (badness 7504) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 = 60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 treat-ment_delay: [][]int[ ][] Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 40\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mea-sure-ment_sensitivity: Underfull \hbox (badness 6063) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 float[][] = 0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [ ][]list[][] Overfull \hbox (92.50304pt too wide) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro up: Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \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- Underfull \hbox (badness 10000) in paragraph at lines 1244--1244 \T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 check_eligibility_at_trigger: Underfull \hbox (badness 10000) in paragraph at lines 1245--1248 \T1/ptm/m/n/10 Add an MSAT (mass screen-ing and treat-ment) drug in-ter-ven-tio n to your cam-paign. See [21] Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_days: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_coverage: Underfull \hbox (badness 7221) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age: [ ][]float[][] Underfull \hbox (badness 7595) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 drug_configs: [][]list[][] = Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (63.71327pt too wide) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 tsteps_btwn_repetitions: [][]int[][] Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Overfull \hbox (92.50304pt too wide) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_gro up: Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 \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- Underfull \hbox (badness 7869) in paragraph at lines 1260--1263 \T1/ptm/m/n/10 Add an fMDA (fo-cal mass drug ad-min-is-tra-tion) drug in-ter-ve n-tion to your cam-paign. See Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = Underfull \hbox (badness 6141) in paragraph at lines 1274--1274 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (75.71327pt too wide) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Overfull \hbox (9.55446pt too wide) in paragraph at lines 1274--1274 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 BLOOD_SMEAR_PARASITES\TS1/ptm/m/it/10 '\T1/pt m/m/n/10 , Overfull \hbox (104.50304pt too wide) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1274--1274 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- [22] Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 re-ceiv-ing_drugs_event: Overfull \hbox (69.71327pt too wide) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 emod_api.interventions.common.BroadcastEvent Underfull \hbox (badness 7613) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lis-ten-ing_duration: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 int[][] = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trig-ger_covera ge: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = 0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_selection_type: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\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 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 node_ids: [][]list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 ex-pire_recent_drugs: Overfull \hbox (98.50304pt too wide) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 emod_api.interventions.common.PropertyValueChanger Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 node_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 \T1/ptm/m/it/10 ind_property_restrictions: Underfull \hbox (badness 10000) in paragraph at lines 1289--1289 [][]\T1/ptm/m/it/10 list[][] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-qual-i- fy- Underfull \hbox (badness 10000) in paragraph at lines 1304--1304 \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: [23] Underfull \hbox (badness 5091) in paragraph at lines 1363--1363 [][]\T1/ptm/m/it/10 int[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 node_ids: [][]l ist[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 []\T1/ptm/m/it/10 campaign\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 \T1/ptm/m/it/10 monthly_eir: Underfull \hbox (badness 10000) in paragraph at lines 1396--1396 [][]\T1/ptm/m/it/10 list[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name: [24] Underfull \hbox (badness 5274) in paragraph at lines 1428--1428 []\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- Underfull \hbox (badness 10000) in paragraph at lines 1428--1428 \T1/ptm/m/it/10 killing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in- Underfull \hbox (badness 10000) in paragraph at lines 1428--1428 \T1/ptm/m/it/10 sec-ti-cide=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 []\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 [][]\T1/ptm/m/it/10 float[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo- Underfull \hbox (badness 10000) in paragraph at lines 1449--1449 \T1/ptm/m/it/10 killing_exponential_decay_rate: [25] Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 by_number=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 num-ber=10000\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 frac-tion=0.1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \T1/ptm/m/it/10 in-fec-tious=0.0\T1/ptm/m/n/10 , Overfull \hbox (5.1738pt too wide) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1492--1492 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1512--1515 []\T1/pcr/b/n/10 infectious \T1/ptm/m/n/10 ^^U The frac-tion of vec-tors re-lea sed that are Underfull \hbox (badness 10000) in paragraph at lines 1512--1515 \T1/ptm/m/n/10 to be in-fec-tious. One can only use this fea-ture when Overfull \hbox (16.27205pt too wide) in paragraph at lines 1512--1515 \T1/ptm/m/n/10 `Malaria_Model'!='MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETI CS' Underfull \hbox (badness 10000) in paragraph at lines 1539--1539 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (15.52452pt too wide) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 file- Overfull \hbox (30.76479pt too wide) in paragraph at lines 1539--1539 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Overfull \hbox (19.6943pt too wide) in paragraph at lines 1548--1548 []\T1/ptm/m/it/10 schema_path_container\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_effect\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 in-sec-ti- Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 cide_name=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 get_coverage=1.0\T1/ptm/m/n/10 , Overfull \hbox (41.63394pt too wide) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_predecay_duration=0\T1/ptm/m/n/10 , Overfull \hbox (10.33417pt too wide) in paragraph at lines 1548--1548 \T1/ptm/m/it/10 killing_decay_rate=0\T1/ptm/m/n/10 , [26] Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \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 , Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \T1/ptm/m/it/10 in-sec-ti-cide=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 1587--1587 \T1/ptm/m/it/10 stant_duration=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1595--1595 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (3.52452pt too wide) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 file- Overfull \hbox (18.76479pt too wide) in paragraph at lines 1595--1595 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\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- Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 \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 , \T1/ptm/m/it/10 in-sec-ti- Underfull \hbox (badness 10000) in paragraph at lines 1612--1612 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , [27] Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 []\T1/pcr/b/n/10 of individuals to target with the intervention. Default is Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 properties\T1/ptm/m/n/10 ) ^^U \T1/pcr/m/n/10 [ { "trigger":"NewClinicalCase","coverage":0. Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/pcr/m/n/10 8,"agemin":15,"agemax":70, "seek":0.4,"rate":0.3}, Underfull \hbox (badness 10000) in paragraph at lines 1637--1641 \T1/pcr/m/n/10 {"trigger":"NewSevereCase","coverage":0.8,"seek":0.6, Underfull \hbox (badness 10000) in paragraph at lines 1655--1657 []\T1/pcr/b/n/10 must have to receive the intervention. For example, Underfull \hbox (badness 10000) in paragraph at lines 1655--1657 \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 individuals\T1/ptm/m/n/10 ) ^^U \T1/pcr/m/n/10 [{"IndividualProperty1":"PropertyValue1"}, Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day: [][]int[][] = 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis- Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 0.0013698630136986301\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing_e ff: Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 0.0006849315068493151\T1/ptm/m/n/10 , \T1/ptm/m/it/10 iv_name: Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 [][]\T1/ptm/m/it/10 str[][] = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Us-ageDe-pen-de ntBed-net\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 sonal_dependence: [][]dict[][] = None\T1/ptm/m/n/10 , [28] [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 1883--1883 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1883--1883 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: Underfull \hbox (badness 10000) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 dict = \T1/ptm/m/n/10 , Underfull \hbox (badness 6348) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 En-abled: bool = [31] Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 dict = \T1/ptm/m/n/10 , Underfull \hbox (badness 6348) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 En-abled: bool = Underfull \hbox (badness 10000) in paragraph at lines 1958--1958 []\T1/ptm/m/it/10 class_name: Underfull \hbox (badness 10000) in paragraph at lines 1958--1958 \T1/ptm/m/it/10 = \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1958--1958 \T1/ptm/m/it/10 En-abled: Overfull \hbox (0.5943pt too wide) in paragraph at lines 1958--1958 \T1/ptm/m/it/10 Pretty_Format: Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 []\T1/ptm/m/it/10 class_name: Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 pa-ram-e- Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 En-abled: Overfull \hbox (6.5943pt too wide) in paragraph at lines 1978--1978 \T1/ptm/m/it/10 Pretty_Format: Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 []\T1/ptm/m/it/10 class_name: str Underfull \hbox (badness 7291) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram- Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 e-ters: dict = Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 \T1/ptm/m/n/10 , \T1/ptm/m/it/10 En- Underfull \hbox (badness 10000) in paragraph at lines 1998--1998 \T1/ptm/m/it/10 Pretty_Format: [32] Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 []\T1/ptm/m/it/10 class_name: str = Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: [33] Underfull \hbox (badness 6348) in paragraph at lines 2174--2174 \T1/ptm/m/it/10 block-ing=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 killing=1.0\T1/pt m/m/n/10 , \T1/ptm/m/it/10 re-pelling=1.0\T1/ptm/m/n/10 , [34] Overfull \hbox (54.6225pt too wide) in paragraph at lines 2218--2219 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2222--2223 []\T1/pcr/m/n/10 emodpy_malaria.interventions.diag_survey\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2224--2225 []\T1/pcr/m/n/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2225--2226 []\T1/pcr/m/n/10 emodpy_malaria.interventions.inputeir\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2227--2228 []\T1/pcr/m/n/10 emodpy_malaria.interventions.ivermectin\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2228--2229 []\T1/pcr/m/n/10 emodpy_malaria.interventions.mosquitorelease\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2229--2230 []\T1/pcr/m/n/10 emodpy_malaria.interventions.outdoorrestkill\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2230--2231 []\T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2231--2232 []\T1/pcr/m/n/10 emodpy_malaria.interventions.sugartrap\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 2232--2233 []\T1/pcr/m/n/10 emodpy_malaria.interventions.treatment_seeking\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2233--2234 []\T1/pcr/m/n/10 emodpy_malaria.interventions.udbednet\T1/ptm/m/n/10 , [35] (./institute-for-disease-modeling-emodpy-malaria.ind [36] Overfull \hbox (50.13988pt too wide) in paragraph at lines 8--10 []\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 ), Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/pcr/m/n/10 add_alleles() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/pcr/m/n/10 add_diagnostic_survey() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 12--14 \T1/ptm/m/it/10 emodpy_malaria.interventions.diag_survey\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/pcr/m/n/10 add_drug_campaign() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 14--16 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 add_fMDA() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 16--18 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 add_MDA() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 18--20 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 add_MSAT() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 20--22 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 add_mutation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 add_resistance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 26--28 []\T1/pcr/m/n/10 add_rfMDA() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 26--28 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 28--30 []\T1/pcr/m/n/10 add_rfMSAT() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 28--30 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 30--31 []\T1/pcr/m/n/10 add_trait() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 AntiMalarialDrug() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 \T1/ptm/m/it/10 emodpy_malaria.interventions.common\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 AntiMalarialDrug() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/pcr/m/n/10 BasicBednet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 Bednet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (52.68974pt too wide) in paragraph at lines 45--47 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.FilteredMalariaReport Overfull \hbox (72.70978pt too wide) in paragraph at lines 47--49 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.MalariaPatientJSONReport Overfull \hbox (59.06006pt too wide) in paragraph at lines 49--51 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.MalariaSummaryReport Overfull \hbox (74.48972pt too wide) in paragraph at lines 51--53 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.MalariaTransmissionReport Overfull \hbox (44.06006pt too wide) in paragraph at lines 53--55 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportEventCounter Overfull \hbox (49.04977pt too wide) in paragraph at lines 55--57 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportVectorGenetics Overfull \hbox (33.50998pt too wide) in paragraph at lines 57--59 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportVectorStats Underfull \hbox (badness 10000) in paragraph at lines 62--64 []\T1/pcr/m/n/10 drug_configs_from_code() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 62--64 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Overfull \hbox (52.1225pt too wide) in paragraph at lines 73--74 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics Overfull \hbox (10.1225pt too wide) in paragraph at lines 81--82 []\T1/pcr/m/n/10 emodpy_malaria.interventions.diag_survey Overfull \hbox (22.1225pt too wide) in paragraph at lines 85--86 []\T1/pcr/m/n/10 emodpy_malaria.interventions.drug_campaign [37] Overfull \hbox (4.1225pt too wide) in paragraph at lines 91--92 []\T1/pcr/m/n/10 emodpy_malaria.interventions.ivermectin Overfull \hbox (34.1225pt too wide) in paragraph at lines 93--94 []\T1/pcr/m/n/10 emodpy_malaria.interventions.mosquitorelease Overfull \hbox (34.1225pt too wide) in paragraph at lines 95--96 []\T1/pcr/m/n/10 emodpy_malaria.interventions.outdoorrestkill Overfull \hbox (22.1225pt too wide) in paragraph at lines 97--98 []\T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying Overfull \hbox (46.1225pt too wide) in paragraph at lines 101--102 []\T1/pcr/m/n/10 emodpy_malaria.interventions.treatment_seeking Underfull \hbox (badness 10000) in paragraph at lines 114--116 []\T1/pcr/m/n/10 FilteredMalariaReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/pcr/m/n/10 fmda_cfg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.27083pt too wide) in paragraph at lines 116--118 \T1/ptm/m/it/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/pcr/m/n/10 from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (36.54083pt too wide) in paragraph at lines 118--120 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 120--122 []\T1/pcr/m/n/10 from_pop_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (36.54083pt too wide) in paragraph at lines 120--122 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 122--124 []\T1/pcr/m/n/10 from_template_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (36.54083pt too wide) in paragraph at lines 122--124 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 127--128 []\T1/pcr/m/n/10 get_drug_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 get_file_from_http() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 130--132 []\T1/pcr/m/n/10 get_species_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 132--134 []\T1/pcr/m/n/10 get_species_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 137--139 []\T1/pcr/m/n/10 InputEIR() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 137--139 \T1/ptm/m/it/10 emodpy_malaria.interventions.inputeir\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 139--141 []\T1/pcr/m/n/10 IRSHousingModification() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 141--143 []\T1/pcr/m/n/10 ivermectin() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 141--143 \T1/ptm/m/it/10 emodpy_malaria.interventions.ivermectin\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/pcr/m/n/10 MalariaDemographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (36.54083pt too wide) in paragraph at lines 146--148 \T1/ptm/m/it/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 148--150 []\T1/pcr/m/n/10 MalariaDiagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 148--150 \T1/ptm/m/it/10 emodpy_malaria.interventions.common\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 150--152 []\T1/pcr/m/n/10 MalariaPatientJSONReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 152--154 []\T1/pcr/m/n/10 MalariaSummaryReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/pcr/m/n/10 MalariaTransmissionReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 clas s in Overfull \hbox (74.6225pt too wide) in paragraph at lines 160--161 []| \T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/1 0 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 162--163 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.bednet\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 163--164 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.common\T1/ptm/m/n/10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 164--165 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.diag_survey\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 165--166 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.drug\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 166--167 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.drug_campaign\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 167--168 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.inputeir\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 169--170 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.ivermectin\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 170--171 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.mosquitorelease\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 171--172 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.outdoorrestkill\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 172--173 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 173--174 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.sugartrap\T1/ptm/m/n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 174--175 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.treatment_seeking\T1/ptm/m/n/10 , [38] Overfull \hbox (14.6225pt too wide) in paragraph at lines 175--176 []| \T1/pcr/m/n/10 emodpy_malaria.interventions.udbednet\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 179--181 []\T1/pcr/m/n/10 MosquitoRelease() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (6.12027pt too wide) in paragraph at lines 179--181 \T1/ptm/m/it/10 emodpy_malaria.interventions.mosquitorelease\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 184--186 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 184--186 \T1/ptm/m/it/10 emodpy_malaria.interventions.inputeir\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 186--188 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 188--190 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 192--194 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 194--196 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (6.12027pt too wide) in paragraph at lines 194--196 \T1/ptm/m/it/10 emodpy_malaria.interventions.mosquitorelease\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 196--198 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 196--198 \T1/ptm/m/it/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 198--200 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 200--202 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule 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(\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 261--263 \T1/ptm/m/it/10 emodpy_malaria.interventions.udbednet\T1/ptm/m/n/10 ), [39]) (./institute-for-disease-modeling-emodpy-malaria.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emodpy-malaria.pdf (43 pages, 224829 bytes). 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