Read the Docs build information Build id: 833783 Project: institute-for-disease-modeling-emodpy-hiv Version: v1.0.2 Commit: 2aaaaa00fa9ebee1a484d15eca21339c3ca0637c Date: 2022-01-25T21:25:16.091816Z State: finished Success: True [rtd-command-info] start-time: 2022-01-25T21:25:17.966521Z, end-time: 2022-01-25T21:25:19.516387Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emodpy-hiv.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-01-25T21:25:19.765528Z, end-time: 2022-01-25T21:25:19.864152Z, duration: 0, exit-code: 0 git checkout --force 2aaaaa00fa9ebee1a484d15eca21339c3ca0637c Note: checking out '2aaaaa00fa9ebee1a484d15eca21339c3ca0637c'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 2aaaaa0 Bump version: 1.0.1 → 1.0.2 [rtd-command-info] start-time: 2022-01-25T21:25:20.068037Z, end-time: 2022-01-25T21:25:20.133448Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-01-25T21:25:21.315855Z, end-time: 2022-01-25T21:25:26.549743Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2022-01-25T21:25:26.780748Z, end-time: 2022-01-25T21:25:29.371240Z, duration: 2, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (21.3.1) Collecting setuptools<58.3.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/41/f4/a7ca4859317232b1efb64a826b8d2d7299bb77fb60bdb08e2bd1d61cf80d/setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 60.5.0 Uninstalling setuptools-60.5.0: Successfully uninstalled setuptools-60.5.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-01-25T21:25:29.750360Z, end-time: 2022-01-25T21:25:43.774636Z, duration: 14, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting mock==1.0.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/15/45/30273ee91feb60dabb8fbb2da7868520525f02cf910279b3047182feed80/mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ae/2a/0a0ab2833e5270664fb5fae590717f867ac6319b124160c09f1d3291de28/Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c4/85/978c06c898331b72080242f18ab7a6021f1055285fb1db9e6554c79264cd/Sphinx-4.4.0-py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e0/d2/3818e4730e314719e27f639c44164419e40eed826d63753dc480262036e8/sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ed/18/2a7348235e84b53b4abc33bbfe7696a99e9f4f2f97818bf940561cb03d9b/readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8d/14/69b4bad34e3f250afe29a854da03acb6747711f3df06c359fa053fae4e76/docutils-0.18.1-py2.py3-none-any.whl (570 kB) Collecting packaging Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/8e/8de486cbd03baba4deef4142bd643a3e7bbe954a784dc1bb17142572d127/packaging-21.3-py3-none-any.whl (40 kB) Collecting snowballstemmer>=1.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ed/dc/c02e01294f7265e63a7315fe086dd1df7dacb9f840a804da846b96d01b96/snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting docutils>=0.11 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4c/5e/6003a0d1f37725ec2ebd4046b657abb9372202655f96e76795dca8c0063c/docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting sphinxcontrib-qthelp Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/14/05f9206cf4e9cfca1afb5fd224c7cd434dcc3a433d6d9e4e0264d29c6cdb/sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting requests>=2.5.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2d/61/08076519c80041bc0ffa1a8af0cbd3bf3e2b62af10435d269a9d0f40564d/requests-2.27.1-py2.py3-none-any.whl (63 kB) Collecting babel>=1.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/aa/96/4ba93c5f40459dc850d25f9ba93f869a623e77aaecc7a9344e19c01942cf/Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/63/40/c854ef09500e25f6432dcbad0f37df87fd7046d376272292d8654cc71c95/sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) Collecting sphinxcontrib-applehelp Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/dc/47/86022665a9433d89a66f5911b558ddff69861766807ba685de2e324bd6ed/sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting sphinxcontrib-devhelp Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c5/09/5de5ed43a521387f18bdf5f5af31d099605c992fd25372b2b9b825ce48ee/sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting sphinxcontrib-serializinghtml>=1.1.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c6/77/5464ec50dd0f1c1037e3c93249b040c8fc8078fdda97530eeb02424b6eea/sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Collecting Pygments>=2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1d/17/ed4d2df187995561b28f1073df24137cb750e12f9879d291cc8ab67c65d2/Pygments-2.11.2-py3-none-any.whl (1.1 MB) Collecting importlib-metadata>=4.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/58/fd/f82049e9b21773188a72bd1bc53530b900392808f8b823e4c778e7c035f0/importlib_metadata-4.10.1-py3-none-any.whl (17 kB) Collecting imagesize Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/60/d6/5e803b17f4d42e085c365b44fda34deb0d8675a1a910635930b831c43f07/imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting sphinxcontrib-jsmath Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c2/42/4c8646762ee83602e3fb3fbe774c2fac12f317deb0b5dbeeedd2d3ba4b77/sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting Jinja2>=2.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/20/9a/e5d9ec41927401e41aea8af6d16e78b5e612bca4699d417f646a9610a076/Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting pytz>=2015.7 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d3/e3/d9f046b5d1c94a3aeab15f1f867aa414f8ee9d196fae6865f1d6a0ee1a0b/pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting typing-extensions>=3.6.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/e4/baf0031e39cf545f0c9edd5b1a2ea12609b7fcba2d58e118b11753d68cf0/typing_extensions-4.0.1-py3-none-any.whl (22 kB) Collecting zipp>=0.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/52/c5/df7953fe6065185af5956265e3b16f13c2826c2b1ba23d43154f3af453bc/zipp-3.7.0-py3-none-any.whl (5.3 kB) Collecting MarkupSafe>=2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/09/f1/5ca5da61ec071ce1e9c423f66a5bde508957601118be9cd37aeccfeab2f6/MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting idna<4,>=2.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/04/a2/d918dcd22354d8958fe113e1a3630137e0fc8b44859ade3063982eacd2a4/idna-3.3-py3-none-any.whl (61 kB) Collecting urllib3<1.27,>=1.21.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4e/b8/f5a25b22e803f0578e668daa33ba3701bb37858ec80e08a150bd7d2cf1b1/urllib3-1.26.8-py2.py3-none-any.whl (138 kB) Collecting certifi>=2017.4.17 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/37/45/946c02767aabb873146011e665728b680884cd8fe70dde973c640e45b775/certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting charset-normalizer~=2.0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/84/3e/1037abe6498e65d645ce7a22d3402605d49a3b2c7f20c3abb027760da4f0/charset_normalizer-2.0.10-py3-none-any.whl (39 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/80/c1/23fd82ad3121656b585351aba6c19761926bb0db2ebed9e4ff09a43a3fcc/pyparsing-3.0.7-py3-none-any.whl (98 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=23773 sha256=0367db9f365c736e896aa9825b58f4bbb08d98fd982cbd206b68899ca0081ec9 Stored in directory: /tmp/pip-ephem-wheel-cache-xancu5mz/wheels/39/db/d5/e22e622f3ac6beb40ab992464b2b5ae38526942ed4ffff7c05 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=bd78db472b9ffaf820595e237705c784b26ebc15cee74f00ab9789836d662672 Stored in directory: /tmp/pip-ephem-wheel-cache-xancu5mz/wheels/59/f9/bf/01e56e422aee5062f2ae1890a7f6593443981ae37e18fecbfb Successfully built mock future Installing collected packages: zipp, urllib3, typing-extensions, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, requests, Pygments, packaging, Jinja2, importlib-metadata, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.10 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.10.1 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.27.1 snowballstemmer-2.2.0 sphinx-4.4.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.0.1 urllib3-1.26.8 zipp-3.7.0 [rtd-command-info] start-time: 2022-01-25T21:25:43.985519Z, end-time: 2022-01-25T21:26:29.725132Z, duration: 45, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple Collecting emodpy~=1.15 Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.17.1/emodpy-1.17.1-py3-none-any.whl (116 kB) Collecting emod-hiv==0.0.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-hiv/0.0.4/emod_hiv-0.0.4-py3-none-any.whl (44.0 MB) Collecting numpy Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/50/46/292cff79f5b30151b027400efdb3f740ea03271b600751b6696cf550c10d/numpy-1.21.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) Collecting click~=7.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting astunparse Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/03/13dde6512ad7b4557eb792fbcf0c653af6076b81e5941d36ec61f7ce6028/astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting matplotlib Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/bb/eb/fb97c7c75755edf10128ae3f06ba15ffb97b852740ef9311f20113f018eb/matplotlib-3.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB) Collecting keyring Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0d/bb/8e715dbb1886e6d7e4c6a7024c11a7e137559cd85366f25c67c2bdb311c3/keyring-23.5.0-py3-none-any.whl (33 kB) Collecting idmtools-models~=1.6.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.6.4/idmtools_models-1.6.4-py3-none-any.whl (24 kB) Collecting bs4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/ed/7e8b97591f6f456174139ec089c769f89a94a1a4025fe967691de971f314/bs4-0.0.1.tar.gz (1.1 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting emod-api<2.0,>=1.20 Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-api/1.20.1/emod_api-1.20.1-py3-none-any.whl (126 kB) Collecting idmtools~=1.6.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.6.4/idmtools-1.6.4-py3-none-any.whl (162 kB) Collecting idmtools-platform-comps~=1.6.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-platform-comps/1.6.4/idmtools_platform_comps-1.6.4-py3-none-any.whl (177 kB) Collecting astor Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl (27 kB) Collecting scipy Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/58/4f/11f34cfc57ead25752a7992b069c36f5d18421958ebd6466ecd849aeaf86/scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB) Collecting prodict Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5a/0b/594c85ac539dda877198e7d5541982127d0929e3b0e8e6018004cfbd9ac9/prodict-0.8.18.tar.gz (4.2 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sklearn Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1e/7a/dbb3be0ce9bd5c8b7e3d87328e79063f8b263b2b1bfa4774cb1147bfcd3f/sklearn-0.0.tar.gz (1.1 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pyproj Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/57/4648d607dd92d09e9a685a8cc20adeafb0c49ed61397bd77c85392a5eb05/pyproj-3.2.1-cp37-cp37m-manylinux2010_x86_64.whl (6.3 MB) Collecting geographiclib Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/df/60/d1d4c4944f9726228faa80fbe2206c8ddfd9757791b2de2facb8818c5d74/geographiclib-1.52-py3-none-any.whl (38 kB) Collecting pandas Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/0c/23764c4635dcb0a784a787498d56847b90ebf974e65f4ab4053a5d97b1a5/pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) Collecting shapely Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ae/20/33ce377bd24d122a4d54e22ae2c445b9b1be8240edb50040b40add950cd9/Shapely-1.8.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) Collecting lz4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f4/a0/9c588238c16c5bd888b9e6709ddda26c88f77c0337d0274a085e9f404356/lz4-3.1.10-cp37-cp37m-manylinux2010_x86_64.whl (1.8 MB) Collecting pyyaml Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/eb/5f/6e6fe6904e1a9c67bc2ca5629a69e7a5a0b17f079da838bab98a1e548b25/PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB) Collecting coloredlogs~=15.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) Collecting packaging<21.0,>=20.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/89/7ea760b4daa42653ece2380531c90f64788d979110a2ab51049d92f408af/packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting backoff<1.11,>=1.10.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/32/c5dd4f4b0746e9ec05ace2a5045c1fc375ae67ee94355344ad6c7005fd87/backoff-1.10.0-py2.py3-none-any.whl (31 kB) Collecting pygit2<1.6.0,>=1.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/98/ed/41a09ca93374015958a18e37280d02c833238272ce3f2e28b10c6253477d/pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl (3.1 MB) Collecting diskcache~=5.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6a/5e/3deb8f9c83bead2af6f2cda97c4400516488464fede2853875a81e502953/diskcache-5.2.1-py3-none-any.whl (44 kB) Collecting pluggy~=0.13.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting tabulate<0.9,>=0.8.9 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ca/80/7c0cad11bd99985cfe7c09427ee0b4f9bd6b048bd13d4ffb32c6db237dfb/tabulate-0.8.9-py3-none-any.whl (25 kB) Collecting more-itertools~=8.8.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5f/3c/e3ee43177a86b448c3fea1d090238c365ea1a80f015836a8a18fbbaccd63/more_itertools-8.8.0-py3-none-any.whl (48 kB) Collecting pipreqs<0.5,>=0.4.10 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1a/cd/74bbb901d65c375e2e8ab5601a4071d4ef38c745f6d4da74add61f964b9a/pipreqs-0.4.11-py2.py3-none-any.whl (32 kB) Collecting pyyaml Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7a/a5/393c087efdc78091afa2af9f1378762f9821c9c1d7a22c5753fb5ac5f97a/PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (636 kB) Collecting tqdm<5,>=4.52.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/63/f3/b7a1b8e40fd1bd049a34566eb353527bb9b8e9b98f8b6cf803bb64d8ce95/tqdm-4.62.3-py2.py3-none-any.whl (76 kB) Collecting pandas Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fd/70/e8eee0cbddf926bf51958c7d6a86bc69167c300fa2ba8e592330a2377d1b/pandas-1.1.5-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) Requirement already satisfied: jinja2~=3.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from idmtools-models~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (3.0.3) Collecting pyCOMPS~=2.5.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/pyCOMPS/2.5.0/pyCOMPS-2.5.0-py2.py3-none-any.whl (56 kB) Collecting pytest-lazy-fixture~=0.6.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2d/a1/2f2c1c2353350d66c4d110d283e422e4943eb5ad10effa9357ba66f7b5b9/pytest_lazy_fixture-0.6.3-py3-none-any.whl (4.9 kB) Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from astunparse->emodpy~=1.15->-r requirements.txt (line 2)) (0.37.1) Collecting six<2.0,>=1.6.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting beautifulsoup4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/69/bf/f0f194d3379d3f3347478bd267f754fc68c11cbf2fe302a6ab69447b1417/beautifulsoup4-4.10.0-py3-none-any.whl (97 kB) Collecting jeepney>=0.4.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/14/b8/bb3e34d71472140f9bfdf5d77cd063e2cc964b72b1bb0b70fe3c1e7db932/jeepney-0.7.1-py3-none-any.whl (54 kB) Requirement already satisfied: importlib-metadata>=3.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from keyring->emodpy~=1.15->-r requirements.txt (line 2)) (4.10.1) Collecting SecretStorage>=3.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/1e/29cd69fdac7391aa51510dfd42aa70b4e6a826c8cd019ee2a8ab9ec0777f/SecretStorage-3.3.1-py3-none-any.whl (15 kB) Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) (3.0.7) Collecting fonttools>=4.22.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1b/1e/23df4eda86938b503698c24f100462f6e80a8b40094635284e57994722ac/fonttools-4.29.0-py3-none-any.whl (895 kB) Collecting python-dateutil>=2.7 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting pillow>=6.2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/65/c5/85054edda7adce1e9444db026fb1972d81718b1605d0eddda94a6be0709f/Pillow-9.0.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB) Collecting cycler>=0.10 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5c/f9/695d6bedebd747e5eb0fe8fad57b72fdf25411273a39791cde838d5a8f51/cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting kiwisolver>=1.0.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/09/6b/6e567cb2e86d4e5939a9233f8734e26021b6a9c1bc4b1edccba236a84cc2/kiwisolver-1.3.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) Collecting humanfriendly>=9.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl (86 kB) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from importlib-metadata>=3.6->keyring->emodpy~=1.15->-r requirements.txt (line 2)) (3.7.0) Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from importlib-metadata>=3.6->keyring->emodpy~=1.15->-r requirements.txt (line 2)) (4.0.1) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from jinja2~=3.0.1->idmtools-models~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (2.0.1) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from pandas->emod-api<2.0,>=1.20->emodpy~=1.15->-r requirements.txt (line 2)) (2021.3) Collecting yarg Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8b/90/89a2ff242ccab6a24fbab18dbbabc67c51a6f0ed01f9a0f41689dc177419/yarg-0.1.9-py2.py3-none-any.whl (19 kB) Collecting docopt Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: requests>=2.11.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (2.27.1) Requirement already satisfied: future>=0.16.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (0.18.2) Collecting xdg>=4.0.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ea/09/4a0f30aada49e142b94bbb232c023abcbc6ced7e2a9776533fb14977e9db/xdg-5.1.1-py3-none-any.whl (5.0 kB) Collecting cached-property Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/48/19/f2090f7dad41e225c7f2326e4cfe6fff49e57dedb5b53636c9551f86b069/cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Collecting cffi>=1.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/44/6b/5edf93698ef1dc745774e47e26f5995040dd3604562dd63f5959fcd3a49e/cffi-1.15.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (427 kB) Collecting pytest>=3.2.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/40/76/86f886e750b81a4357b6ed606b2bcf0ce6d6c27ad3c09ebf63ed674fc86e/pytest-6.2.5-py3-none-any.whl (280 kB) Collecting cryptography>=2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d8/0c/c0f8790bdeff9813722811500fd735c40a6c50fe0b4f8f6f4444f7a49cc0/cryptography-36.0.1-cp36-abi3-manylinux_2_24_x86_64.whl (3.6 MB) Collecting soupsieve>1.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/72/a6/fd01694427f1c3fcadfdc5f1de901b813b9ac756f0806ef470cfed1de281/soupsieve-2.3.1-py3-none-any.whl (37 kB) Requirement already satisfied: certifi in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from pyproj->emod-api<2.0,>=1.20->emodpy~=1.15->-r requirements.txt (line 2)) (2021.10.8) Collecting scikit-learn Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/bd/05/e561bc99a615b5c099c7a9355409e5e57c525a108f1c2e156abb005b90a6/scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB) Collecting pycparser Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118 kB) Collecting attrs>=19.2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/be/7abce643bfdf8ca01c48afa2ddf8308c2308b0c3b239a44e57d020afa0ef/attrs-21.4.0-py2.py3-none-any.whl (60 kB) Collecting py>=1.8.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f6/f0/10642828a8dfb741e5f3fbaac830550a518a775c7fff6f04a007259b0548/py-1.11.0-py2.py3-none-any.whl (98 kB) Collecting iniconfig Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9b/dd/b3c12c6d707058fa947864b67f0c4e0c39ef8610988d7baea9578f3c48f3/iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting toml Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/44/6f/7120676b6d73228c96e17f1f794d8ab046fc910d781c8d151120c3f1569e/toml-0.10.2-py2.py3-none-any.whl (16 kB) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (1.26.8) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (3.3) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->-r requirements.txt (line 2)) (2.0.10) Collecting threadpoolctl>=2.0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ff/fe/8aaca2a0db7fd80f0b2cf8a16a034d3eea8102d58ff9331d2aaf1f06766a/threadpoolctl-3.0.0-py3-none-any.whl (14 kB) Collecting joblib>=0.11 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/d5/0163eb0cfa0b673aa4fe1cd3ea9d8a81ea0f32e50807b0c295871e4aab2e/joblib-1.1.0-py2.py3-none-any.whl (306 kB) Building wheels for collected packages: bs4, prodict, sklearn, 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=1272 sha256=3091764546fd2aa692acf5783943f69688169425060b443662f6b5fbed8687e2 Stored in directory: /tmp/pip-ephem-wheel-cache-rveompic/wheels/f1/23/17/3fcd260137068c2aa94da5806487146928f092eae4c2405b28 Building wheel for prodict (setup.py): started Building wheel for prodict (setup.py): finished with status 'done' Created wheel for prodict: filename=prodict-0.8.18-py3-none-any.whl size=4223 sha256=dd81ddaa30713e86320f3dc71d735b96613632698da4cab413d5372675fbebca Stored in directory: /tmp/pip-ephem-wheel-cache-rveompic/wheels/a1/47/0e/cbfbed83f6077c4d538850a09e49b8d78284632fc1d48bf122 Building wheel for sklearn (setup.py): started Building wheel for sklearn (setup.py): finished with status 'done' Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1310 sha256=6a93e5bf8c11580573d2f9b74322de3e42023e7e71e8891d494015eb9f0f0158 Stored in directory: /tmp/pip-ephem-wheel-cache-rveompic/wheels/50/94/aa/ed6f0a3d3e190b800a88139f52ca17b8094f144fd402719641 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=13723 sha256=a90796df96d8063aab8ef26c2fa9979a0959d69c20a29b99b93ae02d891fdf2e Stored in directory: /tmp/pip-ephem-wheel-cache-rveompic/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c Successfully built bs4 prodict sklearn docopt Installing collected packages: six, pycparser, numpy, yarg, toml, threadpoolctl, scipy, python-dateutil, py, pluggy, packaging, joblib, iniconfig, humanfriendly, docopt, cffi, cached-property, attrs, xdg, tqdm, tabulate, soupsieve, scikit-learn, pyyaml, pytest, pygit2, pipreqs, pandas, more-itertools, jeepney, diskcache, cryptography, coloredlogs, backoff, sklearn, shapely, SecretStorage, pytest-lazy-fixture, pyproj, pyCOMPS, prodict, pillow, lz4, kiwisolver, idmtools, geographiclib, fonttools, cycler, beautifulsoup4, matplotlib, keyring, idmtools-platform-comps, idmtools-models, emod-api, click, bs4, astunparse, astor, emodpy, emod-hiv Attempting uninstall: packaging Found existing installation: packaging 21.3 Uninstalling packaging-21.3: Successfully uninstalled packaging-21.3 Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed SecretStorage-3.3.1 astor-0.8.1 astunparse-1.6.3 attrs-21.4.0 backoff-1.10.0 beautifulsoup4-4.10.0 bs4-0.0.1 cached-property-1.5.2 cffi-1.15.0 click-7.1.2 coloredlogs-15.0.1 cryptography-36.0.1 cycler-0.11.0 diskcache-5.2.1 docopt-0.6.2 emod-api-1.20.1 emod-hiv-0.0.4 emodpy-1.17.1 fonttools-4.29.0 geographiclib-1.52 humanfriendly-10.0 idmtools-1.6.4 idmtools-models-1.6.4 idmtools-platform-comps-1.6.4 iniconfig-1.1.1 jeepney-0.7.1 joblib-1.1.0 keyring-23.5.0 kiwisolver-1.3.2 lz4-3.1.10 matplotlib-3.5.1 more-itertools-8.8.0 numpy-1.21.5 packaging-20.9 pandas-1.1.5 pillow-9.0.0 pipreqs-0.4.11 pluggy-0.13.1 prodict-0.8.18 py-1.11.0 pyCOMPS-2.5.0 pycparser-2.21 pygit2-1.5.0 pyproj-3.2.1 pytest-6.2.5 pytest-lazy-fixture-0.6.3 python-dateutil-2.8.2 pyyaml-5.4.1 scikit-learn-1.0.2 scipy-1.7.3 shapely-1.8.0 six-1.16.0 sklearn-0.0 soupsieve-2.3.1 tabulate-0.8.9 threadpoolctl-3.0.0 toml-0.10.2 tqdm-4.62.3 xdg-5.1.1 yarg-0.1.9 [rtd-command-info] start-time: 2022-01-25T21:26:29.899525Z, end-time: 2022-01-25T21:26:37.164110Z, duration: 7, 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/api/pypi/pypi-production/simple Collecting sphinx-rtd-theme~=0.5.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ac/24/2475e8f83519b54b2148d4a56eb1111f9cec630d088c3ffc214492c12107/sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/75/f2/6b7627dfe7b4e418e295e254bb15c3a6455f11f8c0ad0d43113f678049c3/sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/63/b8/34ba32a94cb2b223b941e43b3bcab11281763b95daa8587879eec1eb9a62/Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Collecting plantweb~=1.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d6/6f/9ab1a1c3e33aaa0c0931983578c09336b092c75dce777ea666d3032f756e/plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/30/ee/b7be4b3f45f4e36bfa6c444cd234098e0d09880379c67a43e6bb9ab99a86/sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting py-make Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/59/d5deb42e3485b2bcd9e95a0f58a5b8f9185520dfd0c574702b7fa5741747/py_make-0.1.1-py2.py3-none-any.whl (9.4 kB) Collecting PyGithub~=1.51 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c1/1f/9dc4ba315eeea222473cf4c15d3e665f32d52f859d9d6e73219d0a408969/PyGithub-1.55-py3-none-any.whl (291 kB) Collecting pygit2~=1.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/52/dc/6d865066b127979c26d5f1d8542561697e42b6fb636ec780f7840cc0484d/pygit2-1.2.1-cp37-cp37m-manylinux2010_x86_64.whl (3.0 MB) Collecting sphinxext.remoteliteralinclude Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1b/25/0e9e17e0a13406592ebeabfae2622f44bd114706ca3801052c020b152cf5/sphinxext_remoteliteralinclude-0.3.0-py3-none-any.whl (6.3 kB) Collecting sphinx-copybutton~=0.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/8b/7c9cf5956be80bfd826f2534e2b38ff2310f8c4274a77e4b3b2d846af552/sphinx_copybutton-0.4.0-py3-none-any.whl (12 kB) Collecting docutils<0.17 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/44/8a15e45ffa96e6cf82956dd8d7af9e666357e16b0d93b253903475ee947f/docutils-0.16-py2.py3-none-any.whl (548 kB) Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 2)) (1.16.0) Collecting pockets>=0.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e9/2f/a4583c70fbd8cd04910e2884bcc2bdd670e884061f7b4d70bc13e632a993/pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (20.9) Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.11.2) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.3.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (58.2.0) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.1.5) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.2) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (3.0.3) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.27.1) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.2.0) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.3) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.9.1) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.2) Requirement already satisfied: docopt>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from py-make->-r docs/requirements.txt (line 6)) (0.6.2) Collecting pynacl>=1.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ee/87/f1bb6a595f14a327e8285b9eb54d41fef76c585a0edef0a45f6fc95de125/PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) Collecting pyjwt>=2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2a/4d/67cc66a0c49003dc216fc73db2d05a3b80c7193167fd113da1f2c678ac2a/PyJWT-2.3.0-py3-none-any.whl (16 kB) Collecting deprecated Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/51/6a/c3a0408646408f7283b7bc550c30a32cc791181ec4618592eec13e066ce3/Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB) Requirement already satisfied: cached-property in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from pygit2~=1.2.1->-r docs/requirements.txt (line 8)) (1.5.2) Requirement already satisfied: cffi>=1.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from pygit2~=1.2.1->-r docs/requirements.txt (line 8)) (1.15.0) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2021.3) Requirement already satisfied: pycparser in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from cffi>=1.4.0->pygit2~=1.2.1->-r docs/requirements.txt (line 8)) (2.21) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2021.10.8) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.26.8) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.10) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (3.3) Collecting wrapt<2,>=1.10 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8d/dc/14fe7be60cd15f86acdfc8863c0f59a72c2019d373d0b3fe217830044f9f/wrapt-1.13.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (79 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages (from packaging->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (3.0.7) Installing collected packages: wrapt, docutils, sphinx, pynacl, pyjwt, pockets, deprecated, sphinxext.remoteliteralinclude, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, sphinx-copybutton, PyGithub, pygit2, py-make, 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 4.4.0 Uninstalling Sphinx-4.4.0: Successfully uninstalled Sphinx-4.4.0 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 1.0.0 Uninstalling sphinx-rtd-theme-1.0.0: Successfully uninstalled sphinx-rtd-theme-1.0.0 Attempting uninstall: pygit2 Found existing installation: pygit2 1.5.0 Uninstalling pygit2-1.5.0: Successfully uninstalled pygit2-1.5.0 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. idmtools 1.6.4 requires pygit2<1.6.0,>=1.4.0, but you have pygit2 1.2.1 which is incompatible. Successfully installed PyGithub-1.55 deprecated-1.2.13 docutils-0.16 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pygit2-1.2.1 pyjwt-2.3.0 pynacl-1.5.0 sphinx-3.2.1 sphinx-copybutton-0.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.3.0 wrapt-1.13.3 [rtd-command-info] start-time: 2022-01-25T21:26:37.345369Z, end-time: 2022-01-25T21:26:38.986888Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating emodpy_hiv.egg-info writing emodpy_hiv.egg-info/PKG-INFO writing dependency_links to emodpy_hiv.egg-info/dependency_links.txt writing requirements to emodpy_hiv.egg-info/requires.txt writing top-level names to emodpy_hiv.egg-info/top_level.txt writing manifest file 'emodpy_hiv.egg-info/SOURCES.txt' reading manifest file 'emodpy_hiv.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'emodpy_hiv.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/emodpy_hiv copying emodpy_hiv/download.py -> build/lib/emodpy_hiv copying emodpy_hiv/utils.py -> build/lib/emodpy_hiv copying emodpy_hiv/__init__.py -> build/lib/emodpy_hiv creating build/lib/tests copying tests/__init__.py -> build/lib/tests creating build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/malecirc.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/random.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/yearandsexdiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/modcoinf.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/stipostdebut.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/drawblood.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/reftracker.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/cascade_helpers.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/prep.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/utils.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/art.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/artdropout.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/sigmoiddiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/outbreak.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/delay.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/artstagingbycd4diag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/__init__.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/rapiddiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/pmtct.py -> build/lib/emodpy_hiv/interventions creating build/lib/emodpy_hiv/demographics copying emodpy_hiv/demographics/HIVDemographics.py -> build/lib/emodpy_hiv/demographics copying emodpy_hiv/demographics/DemographicsTemplates.py -> build/lib/emodpy_hiv/demographics copying emodpy_hiv/demographics/__init__.py -> build/lib/emodpy_hiv/demographics creating build/lib/tests/unittests copying tests/unittests/test_intervention.py -> build/lib/tests/unittests copying tests/unittests/test_demographics.py -> build/lib/tests/unittests copying tests/unittests/check_coverage.py -> build/lib/tests/unittests copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests copying tests/unittests/test_import.py -> build/lib/tests/unittests copying tests/unittests/__init__.py -> build/lib/tests/unittests creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/emodpy_hiv copying build/lib/emodpy_hiv/download.py -> build/bdist.linux-x86_64/egg/emodpy_hiv copying build/lib/emodpy_hiv/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv creating build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/malecirc.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/random.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/yearandsexdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/modcoinf.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/stipostdebut.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/drawblood.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/reftracker.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/cascade_helpers.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/prep.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/art.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/artdropout.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/sigmoiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/delay.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/artstagingbycd4diag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/rapiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/pmtct.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions creating build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/demographics/HIVDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv creating build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_intervention.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_demographics.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/check_coverage.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/schema_path_file.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_import.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/download.py to download.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/utils.py to utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/malecirc.py to malecirc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/random.py to random.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/yearandsexdiag.py to yearandsexdiag.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/modcoinf.py to modcoinf.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/stipostdebut.py to stipostdebut.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/drawblood.py to drawblood.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/reftracker.py to reftracker.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/cascade_helpers.py to cascade_helpers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/prep.py to prep.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/utils.py to utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/art.py to art.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artdropout.py to artdropout.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/sigmoiddiag.py to sigmoiddiag.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/outbreak.py to outbreak.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py to artstagingbycd4agnosticdiag.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/delay.py to delay.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4diag.py to artstagingbycd4diag.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/rapiddiag.py to rapiddiag.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/pmtct.py to pmtct.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/HIVDemographics.py to HIVDemographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_intervention.py to test_intervention.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demographics.py to test_demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/check_coverage.py to check_coverage.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/schema_path_file.py to schema_path_file.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_import.py to test_import.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... tests.unittests.__pycache__.schema_path_file.cpython-37: module references __file__ tests.unittests.__pycache__.test_demographics.cpython-37: module references __file__ tests.unittests.__pycache__.test_intervention.cpython-37: module references __file__ creating dist creating 'dist/emodpy_hiv-1.0.2-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emodpy_hiv-1.0.2-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages/emodpy_hiv-1.0.2-py3.7.egg Extracting emodpy_hiv-1.0.2-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Adding emodpy-hiv 1.0.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages/emodpy_hiv-1.0.2-py3.7.egg Processing dependencies for emodpy-hiv==1.0.2 Searching for pygit2<1.6.0,>=1.4.0 Reading https://pypi.org/simple/pygit2/ Downloading https://files.pythonhosted.org/packages/98/ed/41a09ca93374015958a18e37280d02c833238272ce3f2e28b10c6253477d/pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl#sha256=fda3f8dd30608475f24a531e6f968010662ed7b9d4e303525d945c8933d9528f Best match: pygit2 1.5.0 Processing pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl Installing pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Adding pygit2 1.5.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages/pygit2-1.5.0-py3.7-linux-x86_64.egg Searching for numpy==1.21.5 Best match: numpy 1.21.5 Adding numpy 1.21.5 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for emod-hiv==0.0.4 Best match: emod-hiv 0.0.4 Adding emod-hiv 0.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for emodpy==1.17.1 Best match: emodpy 1.17.1 Adding emodpy 1.17.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for matplotlib==3.5.1 Best match: matplotlib 3.5.1 Adding matplotlib 3.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for keyring==23.5.0 Best match: keyring 23.5.0 Adding keyring 23.5.0 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for idmtools==1.6.4 Best match: idmtools 1.6.4 Adding idmtools 1.6.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for emod-api==1.20.1 Best match: emod-api 1.20.1 Adding emod-api 1.20.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for click==7.1.2 Best match: click 7.1.2 Adding click 7.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for bs4==0.0.1 Best match: bs4 0.0.1 Adding bs4 0.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for astor==0.8.1 Best match: astor 0.8.1 Adding astor 0.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for idmtools-models==1.6.4 Best match: idmtools-models 1.6.4 Adding idmtools-models 1.6.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for idmtools-platform-comps==1.6.4 Best match: idmtools-platform-comps 1.6.4 Adding idmtools-platform-comps 1.6.4 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for astunparse==1.6.3 Best match: astunparse 1.6.3 Adding astunparse 1.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for cycler==0.11.0 Best match: cycler 0.11.0 Adding cycler 0.11.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for python-dateutil==2.8.2 Best match: python-dateutil 2.8.2 Adding python-dateutil 2.8.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for fonttools==4.29.0 Best match: fonttools 4.29.0 Adding fonttools 4.29.0 to easy-install.pth file Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for Pillow==9.0.0 Best match: Pillow 9.0.0 Adding Pillow 9.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for packaging==20.9 Best match: packaging 20.9 Adding packaging 20.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pyparsing==3.0.7 Best match: pyparsing 3.0.7 Adding pyparsing 3.0.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for kiwisolver==1.3.2 Best match: kiwisolver 1.3.2 Adding kiwisolver 1.3.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for jeepney==0.7.1 Best match: jeepney 0.7.1 Adding jeepney 0.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for SecretStorage==3.3.1 Best match: SecretStorage 3.3.1 Adding SecretStorage 3.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for importlib-metadata==4.10.1 Best match: importlib-metadata 4.10.1 Adding importlib-metadata 4.10.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pluggy==0.13.1 Best match: pluggy 0.13.1 Adding pluggy 0.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pandas==1.1.5 Best match: pandas 1.1.5 Adding pandas 1.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pipreqs==0.4.11 Best match: pipreqs 0.4.11 Adding pipreqs 0.4.11 to easy-install.pth file Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for coloredlogs==15.0.1 Best match: coloredlogs 15.0.1 Adding coloredlogs 15.0.1 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for diskcache==5.2.1 Best match: diskcache 5.2.1 Adding diskcache 5.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for PyYAML==5.4.1 Best match: PyYAML 5.4.1 Adding PyYAML 5.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for more-itertools==8.8.0 Best match: more-itertools 8.8.0 Adding more-itertools 8.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for tqdm==4.62.3 Best match: tqdm 4.62.3 Adding tqdm 4.62.3 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for backoff==1.10.0 Best match: backoff 1.10.0 Adding backoff 1.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for tabulate==0.8.9 Best match: tabulate 0.8.9 Adding tabulate 0.8.9 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pyproj==3.2.1 Best match: pyproj 3.2.1 Adding pyproj 3.2.1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for Shapely==1.8.0 Best match: Shapely 1.8.0 Adding Shapely 1.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/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-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for prodict==0.8.18 Best match: prodict 0.8.18 Adding prodict 0.8.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for lz4==3.1.10 Best match: lz4 3.1.10 Adding lz4 3.1.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for scipy==1.7.3 Best match: scipy 1.7.3 Adding scipy 1.7.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for sklearn==0.0 Best match: sklearn 0.0 Adding sklearn 0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for beautifulsoup4==4.10.0 Best match: beautifulsoup4 4.10.0 Adding beautifulsoup4 4.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for Jinja2==3.0.3 Best match: Jinja2 3.0.3 Adding Jinja2 3.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pytest-lazy-fixture==0.6.3 Best match: pytest-lazy-fixture 0.6.3 Adding pytest-lazy-fixture 0.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pyCOMPS==2.5.0 Best match: pyCOMPS 2.5.0 Adding pyCOMPS 2.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for wheel==0.37.1 Best match: wheel 0.37.1 Adding wheel 0.37.1 to easy-install.pth file Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for cryptography==36.0.1 Best match: cryptography 36.0.1 Adding cryptography 36.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for zipp==3.7.0 Best match: zipp 3.7.0 Adding zipp 3.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for typing-extensions==4.0.1 Best match: typing-extensions 4.0.1 Adding typing-extensions 4.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pytz==2021.3 Best match: pytz 2021.3 Adding pytz 2021.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for cffi==1.15.0 Best match: cffi 1.15.0 Adding cffi 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for cached-property==1.5.2 Best match: cached-property 1.5.2 Adding cached-property 1.5.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for yarg==0.1.9 Best match: yarg 0.1.9 Adding yarg 0.1.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for docopt==0.6.2 Best match: docopt 0.6.2 Adding docopt 0.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for humanfriendly==10.0 Best match: humanfriendly 10.0 Adding humanfriendly 10.0 to easy-install.pth file Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for certifi==2021.10.8 Best match: certifi 2021.10.8 Adding certifi 2021.10.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for scikit-learn==1.0.2 Best match: scikit-learn 1.0.2 Adding scikit-learn 1.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for soupsieve==2.3.1 Best match: soupsieve 2.3.1 Adding soupsieve 2.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for MarkupSafe==2.0.1 Best match: MarkupSafe 2.0.1 Adding MarkupSafe 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pytest==6.2.5 Best match: pytest 6.2.5 Adding pytest 6.2.5 to easy-install.pth file Installing py.test script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing pytest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for requests==2.27.1 Best match: requests 2.27.1 Adding requests 2.27.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for future==0.18.2 Best match: future 0.18.2 Adding future 0.18.2 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for xdg==5.1.1 Best match: xdg 5.1.1 Adding xdg 5.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for pycparser==2.21 Best match: pycparser 2.21 Adding pycparser 2.21 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for joblib==1.1.0 Best match: joblib 1.1.0 Adding joblib 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for threadpoolctl==3.0.0 Best match: threadpoolctl 3.0.0 Adding threadpoolctl 3.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for iniconfig==1.1.1 Best match: iniconfig 1.1.1 Adding iniconfig 1.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for toml==0.10.2 Best match: toml 0.10.2 Adding toml 0.10.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for attrs==21.4.0 Best match: attrs 21.4.0 Adding attrs 21.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for py==1.11.0 Best match: py 1.11.0 Adding py 1.11.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for idna==3.3 Best match: idna 3.3 Adding idna 3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for charset-normalizer==2.0.10 Best match: charset-normalizer 2.0.10 Adding charset-normalizer 2.0.10 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Searching for urllib3==1.26.8 Best match: urllib3 1.26.8 Adding urllib3 1.26.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/v1.0.2/lib/python3.7/site-packages Finished processing dependencies for emodpy-hiv==1.0.2 [rtd-command-info] start-time: 2022-01-25T21:26:40.780974Z, end-time: 2022-01-25T21:26:40.853096Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser from datetime import datetime if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # -- General configuration ------------------------------------------------ tags.add('emodpyhiv') # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude', 'sphinx_copybutton' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = [] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'emodpy-hiv' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " 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-hiv' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emodpy-hiv-docs.tex', u'emodpy-hiv', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emodpy-hiv-docs', u'emodpy-hiv', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'emodpy-hiv-docs', u'emodpy-hiv', author, 'Institute for Disease Modeling', 'How to use emodpy for HIV simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'python': ('https://docs.python.org/3', None), 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'emodpy_generic': ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'calibra': ('https://docs.idmod.org/projects/idmtools_calibra/en/latest/', None), 'emod-hiv': ('https://docs.idmod.org/projects/emod-hiv/en/latest/', None), 'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "v1.0.2", 'version_slug': "v1.0.2", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("v1.0.2", "/en/v1.0.2/"), ("v1.0.1", "/en/v1.0.1/"), ("v0.0.41", "/en/v0.0.41/"), ("v0.0.38", "/en/v0.0.38/"), ("v0.0.37", "/en/v0.0.37/"), ("v0.0.35", "/en/v0.0.35/"), ("v0.0.22", "/en/v0.0.22/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emodpy-hiv', 'name': u'emodpy-hiv', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/emodpy-hiv/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emodpy-hiv', 'github_version': 'v1.0.2', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'v1.0.2', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'v1.0.2', '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': '2aaaaa00', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'tag' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-emodpy-hiv/builds/833783/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2022-01-25T21:26:41.030010Z, end-time: 2022-01-25T21:26:45.762924Z, duration: 4, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) rm: cannot remove 'emodpy_hiv_index.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools_calibra/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 30 source files that are out of date updating environment: [new config] 30 added, 0 changed, 0 removed reading sources... [ 3%] emodpy_hiv reading sources... [ 6%] emodpy_hiv.demographics reading sources... [ 10%] emodpy_hiv.demographics.DemographicsTemplates reading sources... [ 13%] emodpy_hiv.demographics.HIVDemographics reading sources... [ 16%] emodpy_hiv.download reading sources... [ 20%] emodpy_hiv.interventions reading sources... [ 23%] emodpy_hiv.interventions.art reading sources... [ 26%] emodpy_hiv.interventions.artdropout reading sources... [ 30%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag reading sources... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag reading sources... [ 36%] emodpy_hiv.interventions.cascade_helpers reading sources... [ 40%] emodpy_hiv.interventions.delay reading sources... [ 43%] emodpy_hiv.interventions.drawblood reading sources... [ 46%] emodpy_hiv.interventions.malecirc reading sources... [ 50%] emodpy_hiv.interventions.modcoinf reading sources... [ 53%] emodpy_hiv.interventions.outbreak reading sources... [ 56%] emodpy_hiv.interventions.pmtct reading sources... [ 60%] emodpy_hiv.interventions.prep reading sources... [ 63%] emodpy_hiv.interventions.random reading sources... [ 66%] emodpy_hiv.interventions.rapiddiag reading sources... [ 70%] emodpy_hiv.interventions.reftracker reading sources... [ 73%] emodpy_hiv.interventions.sigmoiddiag reading sources... [ 76%] emodpy_hiv.interventions.stipostdebut reading sources... [ 80%] emodpy_hiv.interventions.utils reading sources... [ 83%] emodpy_hiv.interventions.yearandsexdiag reading sources... [ 86%] emodpy_hiv.utils reading sources... [ 90%] emodpy_hiv_index reading sources... [ 93%] faq reading sources... [ 96%] index reading sources... [100%] installation looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 3%] emodpy_hiv writing output... [ 6%] emodpy_hiv.demographics writing output... [ 10%] emodpy_hiv.demographics.DemographicsTemplates writing output... [ 13%] emodpy_hiv.demographics.HIVDemographics writing output... [ 16%] emodpy_hiv.download writing output... [ 20%] emodpy_hiv.interventions writing output... [ 23%] emodpy_hiv.interventions.art writing output... [ 26%] emodpy_hiv.interventions.artdropout writing output... [ 30%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag writing output... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag writing output... [ 36%] emodpy_hiv.interventions.cascade_helpers writing output... [ 40%] emodpy_hiv.interventions.delay writing output... [ 43%] emodpy_hiv.interventions.drawblood writing output... [ 46%] emodpy_hiv.interventions.malecirc writing output... [ 50%] emodpy_hiv.interventions.modcoinf writing output... [ 53%] emodpy_hiv.interventions.outbreak writing output... [ 56%] emodpy_hiv.interventions.pmtct writing output... [ 60%] emodpy_hiv.interventions.prep writing output... [ 63%] emodpy_hiv.interventions.random writing output... [ 66%] emodpy_hiv.interventions.rapiddiag writing output... [ 70%] emodpy_hiv.interventions.reftracker writing output... [ 73%] emodpy_hiv.interventions.sigmoiddiag writing output... [ 76%] emodpy_hiv.interventions.stipostdebut writing output... [ 80%] emodpy_hiv.interventions.utils writing output... [ 83%] emodpy_hiv.interventions.yearandsexdiag writing output... [ 86%] emodpy_hiv.utils writing output... [ 90%] emodpy_hiv_index writing output... [ 93%] faq writing output... [ 96%] index writing output... [100%] installation generating indices... genindex py-modindexdone writing additional pages... search opensearchdone copying static files... ... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-01-25T21:26:45.965559Z, end-time: 2022-01-25T21:26:47.709202Z, duration: 1, exit-code: 0 python -m sphinx -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] emodpy_hiv_index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation faq emodpy_hiv_index emodpy_hiv emodpy_hiv.demographics emodpy_hiv.demographics.DemographicsTemplates emodpy_hiv.demographics.HIVDemographics emodpy_hiv.interventions emodpy_hiv.interventions.art emodpy_hiv.interventions.artdropout emodpy_hiv.interventions.artstagingbycd4agnosticdiag emodpy_hiv.interventions.artstagingbycd4diag emodpy_hiv.interventions.cascade_helpers emodpy_hiv.interventions.delay emodpy_hiv.interventions.drawblood emodpy_hiv.interventions.malecirc emodpy_hiv.interventions.modcoinf emodpy_hiv.interventions.outbreak emodpy_hiv.interventions.pmtct emodpy_hiv.interventions.prep emodpy_hiv.interventions.random emodpy_hiv.interventions.rapiddiag emodpy_hiv.interventions.reftracker emodpy_hiv.interventions.sigmoiddiag emodpy_hiv.interventions.stipostdebut emodpy_hiv.interventions.utils emodpy_hiv.interventions.yearandsexdiag emodpy_hiv.download emodpy_hiv.utils done writing... done writing additional files... opensearchdone copying static files... ... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-01-25T21:26:47.990769Z, end-time: 2022-01-25T21:26:49.736404Z, duration: 1, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] emodpy_hiv_index looking for now-outdated files... none found pickling environment... done checking consistency... done processing emodpy-hiv-docs.tex... index installation faq emodpy_hiv_index emodpy_hiv emodpy_hiv.demographics emodpy_hiv.demographics.DemographicsTemplates emodpy_hiv.demographics.HIVDemographics emodpy_hiv.interventions emodpy_hiv.interventions.art emodpy_hiv.interventions.artdropout emodpy_hiv.interventions.artstagingbycd4agnosticdiag emodpy_hiv.interventions.artstagingbycd4diag emodpy_hiv.interventions.cascade_helpers emodpy_hiv.interventions.delay emodpy_hiv.interventions.drawblood emodpy_hiv.interventions.malecirc emodpy_hiv.interventions.modcoinf emodpy_hiv.interventions.outbreak emodpy_hiv.interventions.pmtct emodpy_hiv.interventions.prep emodpy_hiv.interventions.random emodpy_hiv.interventions.rapiddiag emodpy_hiv.interventions.reftracker emodpy_hiv.interventions.sigmoiddiag emodpy_hiv.interventions.stipostdebut emodpy_hiv.interventions.utils emodpy_hiv.interventions.yearandsexdiag emodpy_hiv.download emodpy_hiv.utils 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-hiv/checkouts/v1.0.2/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-01-25T21:26:50.023633Z, end-time: 2022-01-25T21:26:50.097230Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2022-01-25T21:26:50.259299Z, end-time: 2022-01-25T21:26:53.915814Z, duration: 3, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emodpy-hiv -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, 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-hiv" "emodpy-hiv-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emodpy-hiv-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emodpy-hiv.idx (./institute-for-disease-modeling-emodpy-hiv.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/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] [1] [2] LaTeX Warning: Hyper reference `faq::doc' on page 1 undefined on input line 107 . [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. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Overfull \vbox (0.72581pt too high) detected at line 2194 [5] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (24.68169pt too high) detected at line 2194 [6] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [7] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (13.68169pt too high) detected at line 2194 [8] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [9] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (13.68169pt too high) detected at line 2194 [10] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [11] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [12] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [13] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [14] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [15] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [16] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [17] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [18] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [19] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [20] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [21] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [22] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [23] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [24] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [25] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [26] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [27] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [28] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [29] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [30] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [31] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [32] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [33] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [34] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [35] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [36] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [37] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [38] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [39] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [40] [41] [42] Chapter 3. Overfull \hbox (16.30493pt too wide) in paragraph at lines 2238--2238 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (45.2442pt too wide) in paragraph at lines 2238--2238 \T1/ptm/m/it/10 key=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 default\TS1/ptm/m/it/10 ' \T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 world Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , [43] Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 []\T1/ptm/m/it/10 rel_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ip_value\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 max_simul_rels_male=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 max_simul_rels_female=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 prob_xtra_rel_male=None\T1/ptm/m/n/10 , [44] Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module- emodpy_hiv.demographics.HIVDemographics' on page 45 undefined on input line 246 6. Underfull \hbox (badness 10000) in paragraph at lines 2498--2498 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (58.44351pt too wide) in paragraph at lines 2498--2498 \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 , LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module- emodpy_hiv.demographics.HIVDemographics' on page 45 undefined on input line 249 9. [45] Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 \T1/ptm/m/it/10 frac_rural=0.3\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module- emodpy_hiv.demographics.HIVDemographics' on page 46 undefined on input line 252 5. LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module- emodpy_hiv.demographics.HIVDemographics' on page 46 undefined on input line 254 8. Underfull \hbox (badness 10000) in paragraph at lines 2574--2574 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2582--2582 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2599--2599 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2599--2599 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2607--2607 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , [46] Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 Pos-i- Overfull \hbox (7.95444pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 Neg-a- Overfull \hbox (7.95444pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , Overfull \hbox (10.18481pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abp_tvmap\T1/ptm/m/n/10 , Overfull \hbox (7.9647pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (11.85474pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (9.62476pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cua_tvmap\T1/ptm/m/n/10 , Overfull \hbox (7.40465pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cbt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (14.79468pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cbw_tvmap\T1/pcr/m/n/10 ) Overfull \hbox (35.40492pt too wide) in paragraph at lines 2635--2635 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (53.58472pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Overfull \hbox (53.73485pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Overfull \hbox (58.18481pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abp_tvmap\T1/ptm/m/n/10 , Overfull \hbox (55.9647pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (59.85474pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (57.62476pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cua_tvmap\T1/ptm/m/n/10 , Overfull \hbox (55.40465pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cbt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (59.29468pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cbw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (63.27452pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Overfull \hbox (28.35486pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cov- Overfull \hbox (22.70485pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 er- Overfull \hbox (47.23497pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , Overfull \hbox (81.2146pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) Overfull \hbox (47.40492pt too wide) in paragraph at lines 2643--2643 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (63.52452pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Overfull \hbox (38.7948pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 file- Overfull \hbox (78.76479pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i- Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Neg- Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 a-tive_Event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 Thresh-old_TVMap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 IP_TVMap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (5.58472pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Overfull \hbox (5.73485pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Overfull \hbox (19.81442pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 thresh_tvmap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 preg- Overfull \hbox (12.9647pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 nant_tvmap\T1/ptm/m/n/10 , Overfull \hbox (2.9647pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 tb_tvmap\T1/ptm/m/n/10 , Overfull \hbox (15.27452pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , Overfull \hbox (33.2146pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) [47] Underfull \hbox (badness 10000) in paragraph at lines 2679--2679 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (15.52452pt too wide) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 file- Overfull \hbox (30.76479pt too wide) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in_trigger\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 out_iv\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 get_sex=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 All\TS1/ptm/m/it/10 ' \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 tar-get_risk=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 in_trigger\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 get_sex=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 All\TS1/ptm/m/it/10 ' \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 tar-get_risk=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Overfull \hbox (4.15442pt too wide) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 event_name=\TS1/ptm/m/it/10 ''\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2729--2729 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (6.87358pt too wide) in paragraph at lines 2729--2729 \T1/ptm/m/it/10 sympto_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 HIVSymptomatic\ TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2737--2737 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (76.8335pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 put_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 HIVPositiveTest\TS 1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 out- Overfull \hbox (72.64357pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 put_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 StartTreatment\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (14.8946pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 lag_time=30\T1/pcr/m/n/10 ) [48] Underfull \hbox (badness 10000) in paragraph at lines 2753--2753 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sig- Overfull \hbox (16.96379pt too wide) in paragraph at lines 2753--2753 \T1/ptm/m/it/10 nal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 StartTreatment\TS1/ptm/m/ it/10 '\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2791--2791 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bcast_event\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 2791--2791 \T1/ptm/m/it/10 pire_event=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2799--2799 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Base_Sensitivity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Base_Specificity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Days_To_Diagnosis=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Treat- Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [49] Underfull \hbox (badness 10000) in paragraph at lines 2852--2852 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2852--2852 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2877 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2877 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=365\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 cov-er-age=0.075\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_properties=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_min_age=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_max_age=125\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- [50] Underfull \hbox (badness 5563) in paragraph at lines 2941--2941 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2949--2949 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2966--2966 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2974--2974 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 3008--3008 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 choices\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3025--3025 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 Neg-a- Underfull \hbox (badness 10000) in paragraph at lines 3044--3044 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3044--3044 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [51] Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 []\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 3061--3061 \T1/ptm/m/it/10 node_ids=None\T1/ptm/m/n/10 , Overfull \hbox (89.26375pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Event_Name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Scheduled_Campaign _Event\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Prop- Overfull \hbox (7.93365pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 erty_Restrictions=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar-get_Age_Min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar- Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 get_Age_Max=45625\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar- Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 date_Period=None\T1/ptm/m/n/10 , Overfull \hbox (21.08447pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 IV_Tracking_Name=None\T1/pcr/m/n/10 ) [52] Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ac- Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 \T1/ptm/m/it/10 tual_intervention\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 Neg- Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 \T1/ptm/m/it/10 a-tive_Event\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ramp_min\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 \T1/ptm/m/it/10 ramp_max\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ramp_midyear\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_max=1\T1/ptm/m/n/10 , Overfull \hbox (3.22461pt too wide) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_midyear=2000\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_rate=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3169--3169 \T1/ptm/m/it/10 Base_Specificity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [53] Underfull \hbox (badness 10000) in paragraph at lines 3196--3196 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3196--3196 \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 3226--3226 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 event_trigger\T1/ptm/m/n /10 , \T1/ptm/m/it/10 de- Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 tvmap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Overfull \hbox (3.2146pt too wide) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 tvmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Overfull \hbox (0.76479pt too wide) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) [54] [55] [56] LaTeX Warning: Reference `emodpy_hiv:module-emodpy_hiv' on page 57 undefined on input line 3299. LaTeX Warning: Reference `emodpy_hiv.demographics:module-emodpy_hiv.demographic s' on page 57 undefined on input line 3300. LaTeX Warning: Reference `emodpy_hiv.demographics.DemographicsTemplates:module- emodpy_hiv.demographics.DemographicsTemplates' on page 57 undefined on input li ne 3301. Overfull \hbox (42.6225pt too wide) in paragraph at lines 3301--3302 []\T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.demographics.HIVDemographics:module-emodpy _hiv.demographics.HIVDemographics' on page 57 undefined on input line 3302. Overfull \hbox (6.6225pt too wide) in paragraph at lines 3302--3303 []\T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.download:module-emodpy_hiv.download' on pa ge 57 undefined on input line 3303. LaTeX Warning: Reference `emodpy_hiv.interventions:module-emodpy_hiv.interventi ons' on page 57 undefined on input line 3304. LaTeX Warning: Reference `emodpy_hiv.interventions.art:module-emodpy_hiv.interv entions.art' on page 57 undefined on input line 3305. LaTeX Warning: Reference `emodpy_hiv.interventions.artdropout:module-emodpy_hiv .interventions.artdropout' on page 57 undefined on input line 3306. LaTeX Warning: Reference `emodpy_hiv.interventions.artstagingbycd4agnosticdiag: module-emodpy_hiv.interventions.artstagingbycd4agnosticdiag' on page 57 undefin ed on input line 3307. Overfull \hbox (84.6225pt too wide) in paragraph at lines 3307--3308 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/ n/10 , LaTeX Warning: Reference `emodpy_hiv.interventions.artstagingbycd4diag:module-e modpy_hiv.interventions.artstagingbycd4diag' on page 57 undefined on input line 3308. Overfull \hbox (36.6225pt too wide) in paragraph at lines 3308--3309 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.interventions.cascade_helpers:module-emodp y_hiv.interventions.cascade_helpers' on page 57 undefined on input line 3309. Overfull \hbox (12.6225pt too wide) in paragraph at lines 3309--3310 []\T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.interventions.delay:module-emodpy_hiv.inte rventions.delay' on page 57 undefined on input line 3310. LaTeX Warning: Reference `emodpy_hiv.interventions.drawblood:module-emodpy_hiv. interventions.drawblood' on page 57 undefined on input line 3311. LaTeX Warning: Reference `emodpy_hiv.interventions.malecirc:module-emodpy_hiv.i nterventions.malecirc' on page 57 undefined on input line 3312. LaTeX Warning: Reference `emodpy_hiv.interventions.modcoinf:module-emodpy_hiv.i nterventions.modcoinf' on page 57 undefined on input line 3313. LaTeX Warning: Reference `emodpy_hiv.interventions.outbreak:module-emodpy_hiv.i nterventions.outbreak' on page 57 undefined on input line 3314. LaTeX Warning: Reference `emodpy_hiv.interventions.pmtct:module-emodpy_hiv.inte rventions.pmtct' on page 57 undefined on input line 3315. LaTeX Warning: Reference `emodpy_hiv.interventions.prep:module-emodpy_hiv.inter ventions.prep' on page 57 undefined on input line 3316. LaTeX Warning: Reference `emodpy_hiv.interventions.random:module-emodpy_hiv.int erventions.random' on page 57 undefined on input line 3317. LaTeX Warning: Reference `emodpy_hiv.interventions.rapiddiag:module-emodpy_hiv. interventions.rapiddiag' on page 57 undefined on input line 3318. LaTeX Warning: Reference `emodpy_hiv.interventions.reftracker:module-emodpy_hiv .interventions.reftracker' on page 57 undefined on input line 3319. LaTeX Warning: Reference `emodpy_hiv.interventions.sigmoiddiag:module-emodpy_hi v.interventions.sigmoiddiag' on page 57 undefined on input line 3320. Underfull \hbox (badness 10000) in paragraph at lines 3320--3321 []\T1/pcr/m/n/10 emodpy_hiv.interventions.sigmoiddiag\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.interventions.stipostdebut:module-emodpy_h iv.interventions.stipostdebut' on page 57 undefined on input line 3321. Underfull \hbox (badness 10000) in paragraph at lines 3321--3322 []\T1/pcr/m/n/10 emodpy_hiv.interventions.stipostdebut\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.interventions.utils:module-emodpy_hiv.inte rventions.utils' on page 57 undefined on input line 3322. LaTeX Warning: Reference `emodpy_hiv.interventions.yearandsexdiag:module-emodpy _hiv.interventions.yearandsexdiag' on page 57 undefined on input line 3323. Overfull \hbox (6.6225pt too wide) in paragraph at lines 3323--3324 []\T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_hiv.utils:module-emodpy_hiv.utils' on page 57 undefined on input line 3324. [57] No file institute-for-disease-modeling-emodpy-hiv.ind. (./institute-for-disease-modeling-emodpy-hiv.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emodpy-hiv .out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. 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-hiv.pdf (61 pages, 2025 40 bytes). Transcript written on institute-for-disease-modeling-emodpy-hiv.log. Latexmk: Index file 'institute-for-disease-modeling-emodpy-hiv.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-emodpy-hiv.ind' from line 'No file institute-for-disease-modeling-emodpy-hiv.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf' Latexmk: List of undefined refs and citations: Reference `emodpy_hiv.demographics.DemographicsTemplates:module-emodpy_hiv.demographics.DemographicsTemplates' on page 57 undefined on input line 3301 Reference `emodpy_hiv.demographics.HIVDemographics:module-emodpy_hiv.demographics.HIVDemographics' on page 57 undefined on input line 3302 Reference `emodpy_hiv.demographics:module-emodpy_hiv.demographics' on page 57 undefined on input line 3300 Reference `emodpy_hiv.download:module-emodpy_hiv.download' on page 57 undefined on input line 3303 Reference `emodpy_hiv.interventions.art:module-emodpy_hiv.interventions.art' on page 57 undefined on input line 3305 Reference `emodpy_hiv.interventions.artdropout:module-emodpy_hiv.interventions.artdropout' on page 57 undefined on input line 3306 Reference `emodpy_hiv.interventions.artstagingbycd4agnosticdiag:module-emodpy_hiv.interventions.artstagingbycd4agnosticdiag' on page 57 undefined on input line 3307 Reference `emodpy_hiv.interventions.artstagingbycd4diag:module-emodpy_hiv.interventions.artstagingbycd4diag' on page 57 undefined on input line 3308 Reference `emodpy_hiv.interventions.cascade_helpers:module-emodpy_hiv.interventions.cascade_helpers' on page 57 undefined on input line 3309 Reference `emodpy_hiv.interventions.delay:module-emodpy_hiv.interventions.delay' on page 57 undefined on input line 3310 Reference `emodpy_hiv.interventions.drawblood:module-emodpy_hiv.interventions.drawblood' on page 57 undefined on input line 3311 Reference `emodpy_hiv.interventions.malecirc:module-emodpy_hiv.interventions.malecirc' on page 57 undefined on input line 3312 Reference `emodpy_hiv.interventions.modcoinf:module-emodpy_hiv.interventions.modcoinf' on page 57 undefined on input line 3313 Reference `emodpy_hiv.interventions.outbreak:module-emodpy_hiv.interventions.outbreak' on page 57 undefined on input line 3314 Reference `emodpy_hiv.interventions.pmtct:module-emodpy_hiv.interventions.pmtct' on page 57 undefined on input line 3315 Reference `emodpy_hiv.interventions.prep:module-emodpy_hiv.interventions.prep' on page 57 undefined on input line 3316 Reference `emodpy_hiv.interventions.random:module-emodpy_hiv.interventions.random' on page 57 undefined on input line 3317 Reference `emodpy_hiv.interventions.rapiddiag:module-emodpy_hiv.interventions.rapiddiag' on page 57 undefined on input line 3318 Reference `emodpy_hiv.interventions.reftracker:module-emodpy_hiv.interventions.reftracker' on page 57 undefined on input line 3319 Reference `emodpy_hiv.interventions.sigmoiddiag:module-emodpy_hiv.interventions.sigmoiddiag' on page 57 undefined on input line 3320 Reference `emodpy_hiv.interventions.stipostdebut:module-emodpy_hiv.interventions.stipostdebut' on page 57 undefined on input line 3321 Reference `emodpy_hiv.interventions.utils:module-emodpy_hiv.interventions.utils' on page 57 undefined on input line 3322 Reference `emodpy_hiv.interventions.yearandsexdiag:module-emodpy_hiv.interventions.yearandsexdiag' on page 57 undefined on input line 3323 Reference `emodpy_hiv.interventions:module-emodpy_hiv.interventions' on page 57 undefined on input line 3304 Reference `emodpy_hiv.utils:module-emodpy_hiv.utils' on page 57 undefined on input line 3324 Reference `emodpy_hiv:module-emodpy_hiv' on page 57 undefined on input line 3299 Latexmk: Summary of warnings: Latex failed to resolve 26 reference(s) Rule 'makeindex institute-for-disease-modeling-emodpy-hiv.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-emodpy-hiv.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-emodpy-hiv.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-emodpy-hiv.ind" "institute-for-disease-modeling-emodpy-hiv.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-emodpy-hiv.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-hiv.idx....done (131 entries accepted, 0 rejected). Sorting entries....done (967 comparisons). Generating output file institute-for-disease-modeling-emodpy-hiv.ind....done (272 lines written, 0 warnings). Output written in institute-for-disease-modeling-emodpy-hiv.ind. Transcript written in institute-for-disease-modeling-emodpy-hiv.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-emodpy-hiv.aux' 'institute-for-disease-modeling-emodpy-hiv.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-hiv" "emodpy-hiv-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emodpy-hiv-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emodpy-hiv.idx (./institute-for-disease-modeling-emodpy-hiv.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emodpy-hiv.out) (./institute-for-disease-modeling-emodpy-hiv.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-hiv.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. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Overfull \vbox (0.72581pt too high) detected at line 2194 [5] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (24.68169pt too high) detected at line 2194 [6] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [7] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (13.68169pt too high) detected at line 2194 [8] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [9] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (13.68169pt too high) detected at line 2194 [10] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [11] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [12] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [13] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [14] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [15] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [16] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [17] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [18] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [19] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [20] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [21] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [22] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [23] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [24] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [25] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [26] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [27] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [28] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [29] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [30] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [31] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [32] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [33] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [34] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [35] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [36] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [37] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [38] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [39] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [40] [41] [42] Chapter 3. Overfull \hbox (16.30493pt too wide) in paragraph at lines 2238--2238 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (45.2442pt too wide) in paragraph at lines 2238--2238 \T1/ptm/m/it/10 key=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 default\TS1/ptm/m/it/10 ' \T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 world Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , [43] Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 []\T1/ptm/m/it/10 rel_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ip_value\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 max_simul_rels_male=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 max_simul_rels_female=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 prob_xtra_rel_male=None\T1/ptm/m/n/10 , [44] Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2498--2498 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (58.44351pt too wide) in paragraph at lines 2498--2498 \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 , [45] Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 \T1/ptm/m/it/10 frac_rural=0.3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2574--2574 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2582--2582 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2599--2599 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2599--2599 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2607--2607 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , [46] Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 Pos-i- Overfull \hbox (7.95444pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 Neg-a- Overfull \hbox (7.95444pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , Overfull \hbox (10.18481pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abp_tvmap\T1/ptm/m/n/10 , Overfull \hbox (7.9647pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (11.85474pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (9.62476pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cua_tvmap\T1/ptm/m/n/10 , Overfull \hbox (7.40465pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cbt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (14.79468pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cbw_tvmap\T1/pcr/m/n/10 ) Overfull \hbox (35.40492pt too wide) in paragraph at lines 2635--2635 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (53.58472pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Overfull \hbox (53.73485pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Overfull \hbox (58.18481pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abp_tvmap\T1/ptm/m/n/10 , Overfull \hbox (55.9647pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (59.85474pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (57.62476pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cua_tvmap\T1/ptm/m/n/10 , Overfull \hbox (55.40465pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cbt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (59.29468pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cbw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (63.27452pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Overfull \hbox (28.35486pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cov- Overfull \hbox (22.70485pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 er- Overfull \hbox (47.23497pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , Overfull \hbox (81.2146pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) Overfull \hbox (47.40492pt too wide) in paragraph at lines 2643--2643 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (63.52452pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Overfull \hbox (38.7948pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 file- Overfull \hbox (78.76479pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i- Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Neg- Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 a-tive_Event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 Thresh-old_TVMap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 IP_TVMap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (5.58472pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Overfull \hbox (5.73485pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Overfull \hbox (19.81442pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 thresh_tvmap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 preg- Overfull \hbox (12.9647pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 nant_tvmap\T1/ptm/m/n/10 , Overfull \hbox (2.9647pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 tb_tvmap\T1/ptm/m/n/10 , Overfull \hbox (15.27452pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , Overfull \hbox (33.2146pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) [47] Underfull \hbox (badness 10000) in paragraph at lines 2679--2679 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (15.52452pt too wide) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 file- Overfull \hbox (30.76479pt too wide) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in_trigger\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 out_iv\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 get_sex=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 All\TS1/ptm/m/it/10 ' \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 tar-get_risk=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 in_trigger\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 get_sex=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 All\TS1/ptm/m/it/10 ' \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 tar-get_risk=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Overfull \hbox (4.15442pt too wide) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 event_name=\TS1/ptm/m/it/10 ''\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2729--2729 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (6.87358pt too wide) in paragraph at lines 2729--2729 \T1/ptm/m/it/10 sympto_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 HIVSymptomatic\ TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2737--2737 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (76.8335pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 put_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 HIVPositiveTest\TS 1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 out- Overfull \hbox (72.64357pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 put_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 StartTreatment\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (14.8946pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 lag_time=30\T1/pcr/m/n/10 ) [48] Underfull \hbox (badness 10000) in paragraph at lines 2753--2753 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sig- Overfull \hbox (16.96379pt too wide) in paragraph at lines 2753--2753 \T1/ptm/m/it/10 nal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 StartTreatment\TS1/ptm/m/ it/10 '\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2791--2791 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bcast_event\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 2791--2791 \T1/ptm/m/it/10 pire_event=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2799--2799 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Base_Sensitivity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Base_Specificity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Days_To_Diagnosis=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Treat- Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [49] Underfull \hbox (badness 10000) in paragraph at lines 2852--2852 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2852--2852 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2877 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2877 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=365\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 cov-er-age=0.075\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_properties=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_min_age=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_max_age=125\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- [50] Underfull \hbox (badness 5563) in paragraph at lines 2941--2941 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2949--2949 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2966--2966 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2974--2974 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 3008--3008 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 choices\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3025--3025 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 Neg-a- Underfull \hbox (badness 10000) in paragraph at lines 3044--3044 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3044--3044 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [51] Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 []\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 3061--3061 \T1/ptm/m/it/10 node_ids=None\T1/ptm/m/n/10 , Overfull \hbox (89.26375pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Event_Name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Scheduled_Campaign _Event\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Prop- Overfull \hbox (7.93365pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 erty_Restrictions=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar-get_Age_Min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar- Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 get_Age_Max=45625\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar- Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 date_Period=None\T1/ptm/m/n/10 , Overfull \hbox (21.08447pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 IV_Tracking_Name=None\T1/pcr/m/n/10 ) [52] Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ac- Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 \T1/ptm/m/it/10 tual_intervention\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 Neg- Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 \T1/ptm/m/it/10 a-tive_Event\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ramp_min\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 \T1/ptm/m/it/10 ramp_max\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ramp_midyear\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_max=1\T1/ptm/m/n/10 , Overfull \hbox (3.22461pt too wide) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_midyear=2000\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_rate=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3169--3169 \T1/ptm/m/it/10 Base_Specificity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [53] Underfull \hbox (badness 10000) in paragraph at lines 3196--3196 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3196--3196 \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 3226--3226 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 event_trigger\T1/ptm/m/n /10 , \T1/ptm/m/it/10 de- Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 tvmap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Overfull \hbox (3.2146pt too wide) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 tvmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Overfull \hbox (0.76479pt too wide) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) [54] [55] [56] Overfull \hbox (42.6225pt too wide) in paragraph at lines 3301--3302 []\T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3302--3303 []\T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/ptm/m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3307--3308 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/ n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3308--3309 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 3309--3310 []\T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3320--3321 []\T1/pcr/m/n/10 emodpy_hiv.interventions.sigmoiddiag\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3321--3322 []\T1/pcr/m/n/10 emodpy_hiv.interventions.stipostdebut\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3323--3324 []\T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 , [57] (./institute-for-disease-modeling-emodpy-hiv.ind [58] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/pcr/m/n/10 add_art_from_trigger() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/pcr/m/n/10 add_choice() \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_default_society() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (23.76091pt too wide) in paragraph at lines 12--14 \T1/ptm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (16.1225pt too wide) in paragraph at lines 14--16 []\T1/pcr/m/n/10 add_or_update_initial_risk_distribution() Overfull \hbox (75.52081pt too wide) in paragraph at lines 14--16 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 add_society_from_template() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.76091pt too wide) in paragraph at lines 16--18 \T1/ptm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 add_test() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 add_triggered_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 apply_assortivity() Overfull \hbox (75.52081pt too wide) in paragraph at lines 22--24 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/pcr/m/n/10 broadcast_event_delayed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 broadcast_event_immediate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 34--35 []\T1/pcr/m/n/10 declutter() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 35--37 []\T1/pcr/m/n/10 DistributeIVByRefTrack() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (40.1225pt too wide) in paragraph at lines 45--46 []\T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates Overfull \hbox (4.1225pt too wide) in paragraph at lines 47--48 []\T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics Overfull \hbox (82.1225pt too wide) in paragraph at lines 57--58 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag Overfull \hbox (34.1225pt too wide) in paragraph at lines 59--60 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag Overfull \hbox (10.1225pt too wide) in paragraph at lines 61--62 []\T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers Overfull \hbox (4.1225pt too wide) in paragraph at lines 89--90 []\T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag [59] Overfull \hbox (103.42084pt too wide) in paragraph at lines 96--98 []\T1/pcr/m/n/10 fertility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demogra phics.HIVDemographics.HIVDemographics Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/pcr/m/n/10 from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 100--102 []\T1/pcr/m/n/10 from_pop_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/pcr/m/n/10 from_template_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 107--109 []\T1/pcr/m/n/10 HIVDemographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (62.6225pt too wide) in paragraph at lines 115--116 []| \T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 116--117 []| \T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 120--121 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.artdropout\T1/ptm/m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 121--122 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/ m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 122--123 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 123--124 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 125--126 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.drawblood\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 126--127 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.malecirc\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 127--128 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.modcoinf\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 128--129 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.outbreak\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 132--133 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.rapiddiag\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 133--134 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.reftracker\T1/ptm/m/n/10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 134--135 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.sigmoiddiag\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 135--136 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.stipostdebut\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 137--138 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 , Overfull \hbox (103.42084pt too wide) in paragraph at lines 139--141 []\T1/pcr/m/n/10 mortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demogra phics.HIVDemographics.HIVDemographics Underfull \hbox (badness 10000) in paragraph at lines 144--145 []\T1/pcr/m/n/10 new_delay() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 145--147 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (37.1202pt too wide) in paragraph at lines 145--147 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 147--149 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (3.33057pt too wide) in paragraph at lines 147--149 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 149--151 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 151--153 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 153--155 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 155--157 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 159--161 \T1/ptm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\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 163--165 []\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 165--167 []\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 167--169 []\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 169--171 []\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 171--173 []\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 173--175 []\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 175--177 []\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 177--179 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [60] Underfull \hbox (badness 10000) in paragraph at lines 179--181 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (37.1202pt too wide) in paragraph at lines 179--181 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 181--183 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (3.33057pt too wide) in paragraph at lines 181--183 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\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 185--187 []\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 187--189 []\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 189--191 []\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 191--193 []\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 193--195 []\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 195--197 []\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 197--199 []\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 199--201 []\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 201--203 []\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 203--205 []\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 205--207 []\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 207--209 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 209--211 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 211--213 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (37.1202pt too wide) in paragraph at lines 211--213 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 213--215 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (3.33057pt too wide) in paragraph at lines 213--215 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 215--217 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 221--223 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 223--225 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 225--227 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 227--229 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 229--231 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 231--233 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 235--237 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 235--237 \T1/ptm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 237--238 []\T1/pcr/m/n/10 non_schema_checks() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 241--243 []\T1/pcr/m/n/10 reset() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 246--248 []\T1/pcr/m/n/10 seed_infection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 248--250 []\T1/pcr/m/n/10 seed_infections() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 250--252 []\T1/pcr/m/n/10 set_coital_act_rate() Overfull \hbox (75.52081pt too wide) in paragraph at lines 250--252 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Overfull \hbox (16.1225pt too wide) in paragraph at lines 252--254 []\T1/pcr/m/n/10 set_concurrency_params_by_type_and_risk() Overfull \hbox (75.52081pt too wide) in paragraph at lines 252--254 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 254--256 []\T1/pcr/m/n/10 set_condom_usage_probs() Overfull \hbox (75.52081pt too wide) in paragraph at lines 254--256 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 256--258 []\T1/pcr/m/n/10 set_pair_form_params() Overfull \hbox (75.52081pt too wide) in paragraph at lines 256--258 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 258--260 []\T1/pcr/m/n/10 set_relationship_duration() Overfull \hbox (75.52081pt too wide) in paragraph at lines 258--260 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 260--262 []\T1/pcr/m/n/10 set_tvmap_lists_from_map() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 265--267 []\T1/pcr/m/n/10 trigger_art() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 267--269 []\T1/pcr/m/n/10 trigger_art_from_pos_test() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 269--271 []\T1/pcr/m/n/10 triggered_event_common() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule [61]) (./institute-for-disease-modeling-emodpy-hiv.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emodpy-hiv .out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (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-hiv.pdf (65 pages, 2174 15 bytes). Transcript written on institute-for-disease-modeling-emodpy-hiv.log. Latexmk: Index file 'institute-for-disease-modeling-emodpy-hiv.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-emodpy-hiv.aux' 'institute-for-disease-modeling-emodpy-hiv.out' 'institute-for-disease-modeling-emodpy-hiv.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-hiv" "emodpy-hiv-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emodpy-hiv-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (./sphinxmulticell.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emodpy-hiv.idx (./institute-for-disease-modeling-emodpy-hiv.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emodpy-hiv.out) (./institute-for-disease-modeling-emodpy-hiv.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-hiv.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. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Overfull \vbox (0.72581pt too high) detected at line 2194 [5] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (24.68169pt too high) detected at line 2194 [6] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [7] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (13.68169pt too high) detected at line 2194 [8] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [9] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (13.68169pt too high) detected at line 2194 [10] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [11] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [12] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [13] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [14] ! Dimension too large. \fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa \fb@putboxa #1\fb@afterfra... l.2194 \end{sphinxVerbatim} Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [15] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [16] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [17] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [18] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [19] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [20] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [21] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [22] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [23] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [24] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [25] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [26] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [27] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [28] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [29] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [30] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [31] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [32] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [33] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [34] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [35] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [36] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [37] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [38] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [39] Underfull \vbox (badness 10000) detected at line 2194 Overfull \vbox (2.68169pt too high) detected at line 2194 [40] [41] [42] Chapter 3. Overfull \hbox (16.30493pt too wide) in paragraph at lines 2238--2238 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (45.2442pt too wide) in paragraph at lines 2238--2238 \T1/ptm/m/it/10 key=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 default\TS1/ptm/m/it/10 ' \T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 world Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , [43] Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 []\T1/ptm/m/it/10 rel_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ip_value\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 max_simul_rels_male=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 max_simul_rels_female=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2334--2334 \T1/ptm/m/it/10 prob_xtra_rel_male=None\T1/ptm/m/n/10 , [44] Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2465--2465 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2498--2498 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (58.44351pt too wide) in paragraph at lines 2498--2498 \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 , [45] Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2524--2524 \T1/ptm/m/it/10 frac_rural=0.3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2574--2574 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2582--2582 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2599--2599 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2599--2599 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2607--2607 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , [46] Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 Pos-i- Overfull \hbox (7.95444pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 Neg-a- Overfull \hbox (7.95444pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , Overfull \hbox (10.18481pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abp_tvmap\T1/ptm/m/n/10 , Overfull \hbox (7.9647pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (11.85474pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 abw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (9.62476pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cua_tvmap\T1/ptm/m/n/10 , Overfull \hbox (7.40465pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cbt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (14.79468pt too wide) in paragraph at lines 2616--2616 \T1/ptm/m/it/10 cbw_tvmap\T1/pcr/m/n/10 ) Overfull \hbox (35.40492pt too wide) in paragraph at lines 2635--2635 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (53.58472pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Overfull \hbox (53.73485pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Overfull \hbox (58.18481pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abp_tvmap\T1/ptm/m/n/10 , Overfull \hbox (55.9647pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (59.85474pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 abw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (57.62476pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cua_tvmap\T1/ptm/m/n/10 , Overfull \hbox (55.40465pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cbt_tvmap\T1/ptm/m/n/10 , Overfull \hbox (59.29468pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cbw_tvmap\T1/ptm/m/n/10 , Overfull \hbox (63.27452pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Overfull \hbox (28.35486pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 cov- Overfull \hbox (22.70485pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 er- Overfull \hbox (47.23497pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , Overfull \hbox (81.2146pt too wide) in paragraph at lines 2635--2635 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) Overfull \hbox (47.40492pt too wide) in paragraph at lines 2643--2643 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (63.52452pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Overfull \hbox (38.7948pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 file- Overfull \hbox (78.76479pt too wide) in paragraph at lines 2643--2643 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i- Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 tive_Event\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Neg- Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 a-tive_Event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 Thresh-old_TVMap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2652--2652 \T1/ptm/m/it/10 IP_TVMap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (5.58472pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Overfull \hbox (5.73485pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Overfull \hbox (19.81442pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 thresh_tvmap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 preg- Overfull \hbox (12.9647pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 nant_tvmap\T1/ptm/m/n/10 , Overfull \hbox (2.9647pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 tb_tvmap\T1/ptm/m/n/10 , Overfull \hbox (15.27452pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , Overfull \hbox (33.2146pt too wide) in paragraph at lines 2671--2671 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) [47] Underfull \hbox (badness 10000) in paragraph at lines 2679--2679 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (15.52452pt too wide) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 file- Overfull \hbox (30.76479pt too wide) in paragraph at lines 2679--2679 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in_trigger\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 out_iv\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 get_sex=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 All\TS1/ptm/m/it/10 ' \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2712--2712 \T1/ptm/m/it/10 tar-get_risk=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 in_trigger\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 age=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 get_sex=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 All\TS1/ptm/m/it/10 ' \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 tar-get_risk=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Overfull \hbox (4.15442pt too wide) in paragraph at lines 2720--2720 \T1/ptm/m/it/10 event_name=\TS1/ptm/m/it/10 ''\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2729--2729 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (6.87358pt too wide) in paragraph at lines 2729--2729 \T1/ptm/m/it/10 sympto_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 HIVSymptomatic\ TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2737--2737 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Overfull \hbox (76.8335pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 put_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 HIVPositiveTest\TS 1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 out- Overfull \hbox (72.64357pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 put_signal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 StartTreatment\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (14.8946pt too wide) in paragraph at lines 2745--2745 \T1/ptm/m/it/10 lag_time=30\T1/pcr/m/n/10 ) [48] Underfull \hbox (badness 10000) in paragraph at lines 2753--2753 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sig- Overfull \hbox (16.96379pt too wide) in paragraph at lines 2753--2753 \T1/ptm/m/it/10 nal=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 StartTreatment\TS1/ptm/m/ it/10 '\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2791--2791 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bcast_event\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 2791--2791 \T1/ptm/m/it/10 pire_event=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2799--2799 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Base_Sensitivity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Base_Specificity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2808--2808 \T1/ptm/m/it/10 Days_To_Diagnosis=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Treat- Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2827--2827 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [49] Underfull \hbox (badness 10000) in paragraph at lines 2852--2852 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2852--2852 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2877 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2877 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=365\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 cov-er-age=0.075\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_properties=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_min_age=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- Underfull \hbox (badness 10000) in paragraph at lines 2922--2922 \T1/ptm/m/it/10 get_max_age=125\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar- [50] Underfull \hbox (badness 5563) in paragraph at lines 2941--2941 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2949--2949 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 2966--2966 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 2974--2974 []\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 file- Underfull \hbox (badness 10000) in paragraph at lines 3008--3008 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 choices\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3025--3025 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 Neg-a- Underfull \hbox (badness 10000) in paragraph at lines 3044--3044 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3044--3044 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [51] Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 []\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 3061--3061 \T1/ptm/m/it/10 node_ids=None\T1/ptm/m/n/10 , Overfull \hbox (89.26375pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Event_Name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Scheduled_Campaign _Event\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Prop- Overfull \hbox (7.93365pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 erty_Restrictions=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar-get_Age_Min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar- Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 get_Age_Max=45625\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 Tar- Underfull \hbox (badness 10000) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 date_Period=None\T1/ptm/m/n/10 , Overfull \hbox (21.08447pt too wide) in paragraph at lines 3061--3061 \T1/ptm/m/it/10 IV_Tracking_Name=None\T1/pcr/m/n/10 ) [52] Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ac- Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 \T1/ptm/m/it/10 tual_intervention\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3124--3124 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Pos-i-tive_Event\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 Neg- Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 \T1/ptm/m/it/10 a-tive_Event\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ramp_min\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3133--3133 \T1/ptm/m/it/10 ramp_max\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ramp_midyear\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_max=1\T1/ptm/m/n/10 , Overfull \hbox (3.22461pt too wide) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_midyear=2000\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 ramp_rate=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3152--3152 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3169--3169 \T1/ptm/m/it/10 Base_Specificity=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , [53] Underfull \hbox (badness 10000) in paragraph at lines 3196--3196 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3196--3196 \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 3226--3226 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 event_trigger\T1/ptm/m/n /10 , \T1/ptm/m/it/10 de- Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 pos_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 neg_event\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 tvmap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 start_day=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Overfull \hbox (3.2146pt too wide) in paragraph at lines 3254--3254 \T1/ptm/m/it/10 node_ids=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 tvmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Overfull \hbox (0.76479pt too wide) in paragraph at lines 3262--3262 \T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) [54] [55] [56] Overfull \hbox (42.6225pt too wide) in paragraph at lines 3301--3302 []\T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3302--3303 []\T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/ptm/m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3307--3308 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/ n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3308--3309 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 3309--3310 []\T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3320--3321 []\T1/pcr/m/n/10 emodpy_hiv.interventions.sigmoiddiag\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3321--3322 []\T1/pcr/m/n/10 emodpy_hiv.interventions.stipostdebut\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3323--3324 []\T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 , [57] (./institute-for-disease-modeling-emodpy-hiv.ind [58] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/pcr/m/n/10 add_art_from_trigger() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/pcr/m/n/10 add_choice() \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_default_society() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (23.76091pt too wide) in paragraph at lines 12--14 \T1/ptm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (16.1225pt too wide) in paragraph at lines 14--16 []\T1/pcr/m/n/10 add_or_update_initial_risk_distribution() Overfull \hbox (75.52081pt too wide) in paragraph at lines 14--16 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 add_society_from_template() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.76091pt too wide) in paragraph at lines 16--18 \T1/ptm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 add_test() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 add_triggered_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 apply_assortivity() Overfull \hbox (75.52081pt too wide) in paragraph at lines 22--24 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/pcr/m/n/10 broadcast_event_delayed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 broadcast_event_immediate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 34--35 []\T1/pcr/m/n/10 declutter() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 35--37 []\T1/pcr/m/n/10 DistributeIVByRefTrack() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (40.1225pt too wide) in paragraph at lines 45--46 []\T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates Overfull \hbox (4.1225pt too wide) in paragraph at lines 47--48 []\T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics Overfull \hbox (82.1225pt too wide) in paragraph at lines 57--58 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag Overfull \hbox (34.1225pt too wide) in paragraph at lines 59--60 []\T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag Overfull \hbox (10.1225pt too wide) in paragraph at lines 61--62 []\T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers Overfull \hbox (4.1225pt too wide) in paragraph at lines 89--90 []\T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag [59] Overfull \hbox (103.42084pt too wide) in paragraph at lines 96--98 []\T1/pcr/m/n/10 fertility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demogra phics.HIVDemographics.HIVDemographics Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/pcr/m/n/10 from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 100--102 []\T1/pcr/m/n/10 from_pop_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/pcr/m/n/10 from_template_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 107--109 []\T1/pcr/m/n/10 HIVDemographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (62.6225pt too wide) in paragraph at lines 115--116 []| \T1/pcr/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 116--117 []| \T1/pcr/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 120--121 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.artdropout\T1/ptm/m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 121--122 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/ m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 122--123 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 123--124 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 125--126 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.drawblood\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 126--127 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.malecirc\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 127--128 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.modcoinf\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 128--129 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.outbreak\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 132--133 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.rapiddiag\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 133--134 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.reftracker\T1/ptm/m/n/10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 134--135 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.sigmoiddiag\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 135--136 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.stipostdebut\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 137--138 []| \T1/pcr/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 , Overfull \hbox (103.42084pt too wide) in paragraph at lines 139--141 []\T1/pcr/m/n/10 mortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demogra phics.HIVDemographics.HIVDemographics Underfull \hbox (badness 10000) in paragraph at lines 144--145 []\T1/pcr/m/n/10 new_delay() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 145--147 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (37.1202pt too wide) in paragraph at lines 145--147 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 147--149 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (3.33057pt too wide) in paragraph at lines 147--149 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 149--151 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 151--153 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 153--155 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 155--157 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/pcr/m/n/10 new_diagnostic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 159--161 \T1/ptm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\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 163--165 []\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 165--167 []\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 167--169 []\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 169--171 []\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 171--173 []\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 173--175 []\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 175--177 []\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 177--179 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [60] Underfull \hbox (badness 10000) in paragraph at lines 179--181 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (37.1202pt too wide) in paragraph at lines 179--181 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 181--183 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (3.33057pt too wide) in paragraph at lines 181--183 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\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 185--187 []\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 187--189 []\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 189--191 []\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 191--193 []\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 193--195 []\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 195--197 []\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 197--199 []\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 199--201 []\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 201--203 []\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 203--205 []\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 205--207 []\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 207--209 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 209--211 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 211--213 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (37.1202pt too wide) in paragraph at lines 211--213 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 213--215 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (3.33057pt too wide) in paragraph at lines 213--215 \T1/ptm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 215--217 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 221--223 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 223--225 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 225--227 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 227--229 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 229--231 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 231--233 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 235--237 []\T1/pcr/m/n/10 new_intervention_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 235--237 \T1/ptm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 237--238 []\T1/pcr/m/n/10 non_schema_checks() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 241--243 []\T1/pcr/m/n/10 reset() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 246--248 []\T1/pcr/m/n/10 seed_infection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 248--250 []\T1/pcr/m/n/10 seed_infections() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 250--252 []\T1/pcr/m/n/10 set_coital_act_rate() Overfull \hbox (75.52081pt too wide) in paragraph at lines 250--252 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Overfull \hbox (16.1225pt too wide) in paragraph at lines 252--254 []\T1/pcr/m/n/10 set_concurrency_params_by_type_and_risk() Overfull \hbox (75.52081pt too wide) in paragraph at lines 252--254 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 254--256 []\T1/pcr/m/n/10 set_condom_usage_probs() Overfull \hbox (75.52081pt too wide) in paragraph at lines 254--256 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 256--258 []\T1/pcr/m/n/10 set_pair_form_params() Overfull \hbox (75.52081pt too wide) in paragraph at lines 256--258 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 258--260 []\T1/pcr/m/n/10 set_relationship_duration() Overfull \hbox (75.52081pt too wide) in paragraph at lines 258--260 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo graphics Underfull \hbox (badness 10000) in paragraph at lines 260--262 []\T1/pcr/m/n/10 set_tvmap_lists_from_map() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 265--267 []\T1/pcr/m/n/10 trigger_art() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 267--269 []\T1/pcr/m/n/10 trigger_art_from_pos_test() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 269--271 []\T1/pcr/m/n/10 triggered_event_common() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule [61]) (./institute-for-disease-modeling-emodpy-hiv.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-hiv.pdf (65 pages, 2176 43 bytes). Transcript written on institute-for-disease-modeling-emodpy-hiv.log. Latexmk: Index file 'institute-for-disease-modeling-emodpy-hiv.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 [rtd-command-info] start-time: 2022-01-25T21:26:54.141884Z, end-time: 2022-01-25T21:26:54.220665Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/checkouts/v1.0.2/docs/_build/latex/institute-for-disease-modeling-emodpy-hiv.pdf /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/artifacts/v1.0.2/sphinx_pdf/institute-for-disease-modeling-emodpy-hiv.pdf