Read the Docs build information Build id: 636269 Project: institute-for-disease-modeling-synthpops-test Version: v1.8.3 Commit: a6be6996b607d4b20d8a695b352f7b15fb34dc94 Date: 2021-05-19T01:17:38.439207Z State: finished Success: True [rtd-command-info] start-time: 2021-05-19T01:17:40.016289Z, end-time: 2021-05-19T01:17:47.180135Z, duration: 7, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/synthpops.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-05-19T01:17:47.365547Z, end-time: 2021-05-19T01:17:47.561742Z, duration: 0, exit-code: 0 git checkout --force a6be6996b607d4b20d8a695b352f7b15fb34dc94 Note: checking out 'a6be6996b607d4b20d8a695b352f7b15fb34dc94'. 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 a6be699 Merge pull request #384 from amath-idm/fix-smalln-fixed-ages [rtd-command-info] start-time: 2021-05-19T01:17:47.670693Z, end-time: 2021-05-19T01:17:47.742106Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-05-19T01:17:48.838997Z, end-time: 2021-05-19T01:17:52.924398Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --system-site-packages 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-synthpops-test/envs/v1.8.3/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-05-19T01:17:53.052873Z, end-time: 2021-05-19T01:17:54.368433Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (21.1.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (56.2.0) [rtd-command-info] start-time: 2021-05-19T01:17:54.475966Z, end-time: 2021-05-19T01:18:03.281419Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting setuptools Downloading setuptools-56.2.0-py3-none-any.whl (785 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting requests>=2.0.0 Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux2010_x86_64.whl (31 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.4-py2.py3-none-any.whl (153 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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=23755 sha256=ce80c958dfb200c910eecf5ea7c8dbaf37d977792bc1b8e0d31fd6fec3fce01d Stored in directory: /tmp/pip-ephem-wheel-cache-qxxl1yhf/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=b1a9716285fdba8c77370d84f7fd021969a23308ff96282988afed2f739f2f3a Stored in directory: /tmp/pip-ephem-wheel-cache-qxxl1yhf/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock 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. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 setuptools-56.2.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4 [rtd-command-info] start-time: 2021-05-19T01:18:03.424310Z, end-time: 2021-05-19T01:18:10.152229Z, duration: 6, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pytest Downloading pytest-6.2.4-py3-none-any.whl (280 kB) Requirement already satisfied: sphinx-rtd-theme in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3) Collecting sphinxcontrib-napoleon Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from -r docs/requirements.txt (line 4)) (1.8.5) Collecting plantweb Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting pandoc Downloading pandoc-1.0.2.tar.gz (488 kB) Collecting pypandoc Downloading pypandoc-1.5.tar.gz (26 kB) Collecting numba==0.48 Downloading numba-0.48.0-1-cp37-cp37m-manylinux2014_x86_64.whl (3.5 MB) Collecting llvmlite<0.32.0,>=0.31.0dev0 Downloading llvmlite-0.31.0-cp37-cp37m-manylinux1_x86_64.whl (20.2 MB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from numba==0.48->-r docs/requirements.txt (line 8)) (56.2.0) Requirement already satisfied: numpy>=1.15 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from numba==0.48->-r docs/requirements.txt (line 8)) (1.19.2) Collecting importlib-metadata>=0.12 Downloading importlib_metadata-4.0.1-py3-none-any.whl (16 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from pytest->-r docs/requirements.txt (line 1)) (20.9) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting attrs>=19.2.0 Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting py>=1.8.2 Downloading py-1.10.0-py2.py3-none-any.whl (97 kB) Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting pluggy<1.0.0a1,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-3.10.0.0-py3-none-any.whl (26 kB) Collecting zipp>=0.5 Downloading zipp-3.4.1-py3-none-any.whl (5.2 kB) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from sphinxcontrib-napoleon->-r docs/requirements.txt (line 3)) (1.16.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.9.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (0.17.1) Requirement already satisfied: sphinxcontrib-websupport in 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx->-r docs/requirements.txt (line 4)) (2.0.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (2020.12.5) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (4.0.0) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (1.26.4) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (2.10) Collecting ply Downloading ply-3.11-py2.py3-none-any.whl (49 kB) Requirement already satisfied: pip>=8.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from pypandoc->-r docs/requirements.txt (line 7)) (21.1.1) Requirement already satisfied: wheel>=0.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from pypandoc->-r docs/requirements.txt (line 7)) (0.36.2) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from packaging->pytest->-r docs/requirements.txt (line 1)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx->-r docs/requirements.txt (line 4)) (1.1.4) Building wheels for collected packages: pandoc, pypandoc Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-1.0.2-py3-none-any.whl size=19992 sha256=7912d772f42e85e3dfcb16d267f226a34ac36769c2e1b9677d0e37cf3499a140 Stored in directory: /tmp/pip-ephem-wheel-cache-o1fww87g/wheels/80/43/26/b24b4f9523170eb4f7de84f914c640da353c74b3197edc22e6 Building wheel for pypandoc (setup.py): started Building wheel for pypandoc (setup.py): finished with status 'done' Created wheel for pypandoc: filename=pypandoc-1.5-py3-none-any.whl size=17037 sha256=41707564f2e17b0c559bfcc8901415597c853dc6dca3983cb30bb9f360111876 Stored in directory: /tmp/pip-ephem-wheel-cache-o1fww87g/wheels/06/a7/1d/3259fbf0089b15d491d9166b97de3a23d1f915bf7591abafc7 Successfully built pandoc pypandoc Installing collected packages: zipp, typing-extensions, importlib-metadata, toml, py, pockets, ply, pluggy, llvmlite, iniconfig, attrs, sphinxcontrib-napoleon, pytest, pypandoc, plantweb, pandoc, numba Successfully installed attrs-21.2.0 importlib-metadata-4.0.1 iniconfig-1.1.1 llvmlite-0.31.0 numba-0.48.0 pandoc-1.0.2 plantweb-1.2.1 pluggy-0.13.1 ply-3.11 pockets-0.9.1 py-1.10.0 pypandoc-1.5 pytest-6.2.4 sphinxcontrib-napoleon-0.7 toml-0.10.2 typing-extensions-3.10.0.0 zipp-3.4.1 [rtd-command-info] start-time: 2021-05-19T01:18:10.263060Z, end-time: 2021-05-19T01:18:39.887194Z, duration: 29, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating synthpops.egg-info writing synthpops.egg-info/PKG-INFO writing dependency_links to synthpops.egg-info/dependency_links.txt writing requirements to synthpops.egg-info/requires.txt writing top-level names to synthpops.egg-info/top_level.txt writing manifest file 'synthpops.egg-info/SOURCES.txt' adding license file 'LICENSE' (matched pattern 'LICEN[CS]E*') reading manifest file 'synthpops.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: manifest_maker: MANIFEST.in, line 4: unknown action 'global-prune' warning: manifest_maker: MANIFEST.in, line 5: unknown action 'global-prune' writing manifest file 'synthpops.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/synthpops copying synthpops/data.py -> build/lib/synthpops copying synthpops/sampling.py -> build/lib/synthpops copying synthpops/config.py -> build/lib/synthpops copying synthpops/contact_networks.py -> build/lib/synthpops copying synthpops/schools.py -> build/lib/synthpops copying synthpops/households.py -> build/lib/synthpops copying synthpops/pop.py -> build/lib/synthpops copying synthpops/version.py -> build/lib/synthpops copying synthpops/workplaces.py -> build/lib/synthpops copying synthpops/data_distributions.py -> build/lib/synthpops copying synthpops/plotting.py -> build/lib/synthpops copying synthpops/base.py -> build/lib/synthpops copying synthpops/defaults.py -> build/lib/synthpops copying synthpops/ltcfs.py -> build/lib/synthpops copying synthpops/__init__.py -> build/lib/synthpops creating build/lib/synthpops/data copying synthpops/data/MUestimates_all_locations.obj -> build/lib/synthpops/data copying synthpops/data/MUestimates_home.obj -> build/lib/synthpops/data copying synthpops/data/MUestimates_other_locations.obj -> build/lib/synthpops/data copying synthpops/data/MUestimates_school.obj -> build/lib/synthpops/data copying synthpops/data/MUestimates_work.obj -> build/lib/synthpops/data copying synthpops/data/Senegal-Dakar-Dakar.json -> build/lib/synthpops/data copying synthpops/data/Senegal-Dakar.json -> build/lib/synthpops/data copying synthpops/data/Senegal.json -> build/lib/synthpops/data copying synthpops/data/usa-Oregon-portland_metro.json -> build/lib/synthpops/data copying synthpops/data/usa-Oregon.json -> build/lib/synthpops/data copying synthpops/data/usa-Washington-Franklin_County.json -> build/lib/synthpops/data copying synthpops/data/usa-Washington-Island_County.json -> build/lib/synthpops/data copying synthpops/data/usa-Washington-Spokane_County.json -> build/lib/synthpops/data copying synthpops/data/usa-Washington-seattle_metro.json -> build/lib/synthpops/data copying synthpops/data/usa-Washington.json -> build/lib/synthpops/data copying synthpops/data/usa.json -> build/lib/synthpops/data creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/data.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/sampling.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/config.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/contact_networks.py -> build/bdist.linux-x86_64/egg/synthpops creating build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Washington-seattle_metro.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/MUestimates_home.obj -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Oregon.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/Senegal.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Oregon-portland_metro.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Washington.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/MUestimates_all_locations.obj -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/MUestimates_school.obj -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/Senegal-Dakar.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/MUestimates_work.obj -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/MUestimates_other_locations.obj -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Washington-Franklin_County.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/Senegal-Dakar-Dakar.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Washington-Spokane_County.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/data/usa-Washington-Island_County.json -> build/bdist.linux-x86_64/egg/synthpops/data copying build/lib/synthpops/schools.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/households.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/pop.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/version.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/workplaces.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/data_distributions.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/plotting.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/base.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/defaults.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/ltcfs.py -> build/bdist.linux-x86_64/egg/synthpops copying build/lib/synthpops/__init__.py -> build/bdist.linux-x86_64/egg/synthpops byte-compiling build/bdist.linux-x86_64/egg/synthpops/data.py to data.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/sampling.py to sampling.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/config.py to config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/contact_networks.py to contact_networks.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/schools.py to schools.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/households.py to households.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/pop.py to pop.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/version.py to version.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/workplaces.py to workplaces.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/data_distributions.py to data_distributions.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/plotting.py to plotting.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/base.py to base.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/defaults.py to defaults.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/ltcfs.py to ltcfs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/synthpops/__init__.py to __init__.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying synthpops.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying synthpops.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying synthpops.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying synthpops.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying synthpops.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... synthpops.__pycache__.config.cpython-37: module references __file__ synthpops.__pycache__.defaults.cpython-37: module references __file__ creating dist creating 'dist/synthpops-1.8.3-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 synthpops-1.8.3-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/synthpops-1.8.3-py3.7.egg Extracting synthpops-1.8.3-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding synthpops 1.8.3 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/synthpops-1.8.3-py3.7.egg Processing dependencies for synthpops==1.8.3 Searching for jsbeautifier Reading https://pypi.org/simple/jsbeautifier/ Downloading https://files.pythonhosted.org/packages/ef/f9/cc78c6f98d7e80dea2fd51d8e4a54a436a17eeec33aee9c92ac43eb7e28d/jsbeautifier-1.13.13.tar.gz#sha256=8ef6d9fa015df8efa578ad7f210184c4a78903b939b5ac877da229ffa5573a12 Best match: jsbeautifier 1.13.13 Processing jsbeautifier-1.13.13.tar.gz Writing /tmp/easy_install-v_4_sqo7/jsbeautifier-1.13.13/setup.cfg Running jsbeautifier-1.13.13/setup.py -q bdist_egg --dist-dir /tmp/easy_install-v_4_sqo7/jsbeautifier-1.13.13/egg-dist-tmp-mmg3bxlu package init file 'jsbeautifier/tests/generated/__init__.py' not found (or not a regular file) warning: no files found matching 'js-beautify' zip_safe flag not set; analyzing archive contents... jsbeautifier.unpackers.__pycache__.__init__.cpython-37: module references __path__ jsbeautifier.unpackers.tests.__pycache__.testmyobfuscate.cpython-37: module references __path__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jsbeautifier-1.13.13-py3.7.egg Extracting jsbeautifier-1.13.13-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding jsbeautifier 1.13.13 to easy-install.pth file Installing js-beautify script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jsbeautifier-1.13.13-py3.7.egg Searching for jsonobject Reading https://pypi.org/simple/jsonobject/ Downloading https://files.pythonhosted.org/packages/62/57/85f98bd8e7c5a46d8a3780cc0af92cbdb67066ac68112236b53b29f0eaaf/jsonobject-0.9.10.tar.gz#sha256=deecaafe0a361b87e2f136b9174063e9969ac036ee7066efd7911f1d608e6e0b Best match: jsonobject 0.9.10 Processing jsonobject-0.9.10.tar.gz Writing /tmp/easy_install-ujbd1yx6/jsonobject-0.9.10/setup.cfg Running jsonobject-0.9.10/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ujbd1yx6/jsonobject-0.9.10/egg-dist-tmp-_d4afxve Warning: 'classifiers' should be a list, got type 'tuple' warning: the 'license_file' option is deprecated, use 'license_files' instead zip_safe flag not set; analyzing archive contents... jsonobject.__pycache__.api.cpython-37: module references __file__ jsonobject.__pycache__.base.cpython-37: module references __file__ jsonobject.__pycache__.base_properties.cpython-37: module references __file__ jsonobject.__pycache__.containers.cpython-37: module references __file__ jsonobject.__pycache__.properties.cpython-37: module references __file__ jsonobject.__pycache__.utils.cpython-37: module references __file__ You are running without Cython installed. It is highly recommended to run pip install cython>=0.29.21,<1.0.0 before you continue creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jsonobject-0.9.10-py3.7-linux-x86_64.egg Extracting jsonobject-0.9.10-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding jsonobject 0.9.10 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jsonobject-0.9.10-py3.7-linux-x86_64.egg Searching for pydot Reading https://pypi.org/simple/pydot/ Downloading https://files.pythonhosted.org/packages/ea/76/75b1bb82e9bad3e3d656556eaa353d8cd17c4254393b08ec9786ac8ed273/pydot-1.4.2-py2.py3-none-any.whl#sha256=66c98190c65b8d2e2382a441b4c0edfdb4f4c025ef9cb9874de478fb0793a451 Best match: pydot 1.4.2 Processing pydot-1.4.2-py2.py3-none-any.whl Installing pydot-1.4.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding pydot 1.4.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/pydot-1.4.2-py3.7.egg Searching for graphviz Reading https://pypi.org/simple/graphviz/ Downloading https://files.pythonhosted.org/packages/86/86/89ba50ba65928001d3161f23bfa03945ed18ea13a1d1d44a772ff1fa4e7a/graphviz-0.16-py2.py3-none-any.whl#sha256=3cad5517c961090dfc679df6402a57de62d97703e2880a1a46147bb0dc1639eb Best match: graphviz 0.16 Processing graphviz-0.16-py2.py3-none-any.whl Installing graphviz-0.16-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding graphviz 0.16 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/graphviz-0.16-py3.7.egg Searching for seaborn Reading https://pypi.org/simple/seaborn/ Downloading https://files.pythonhosted.org/packages/68/ad/6c2406ae175f59ec616714e408979b674fe27b9587f79d59a528ddfbcd5b/seaborn-0.11.1-py3-none-any.whl#sha256=4e1cce9489449a1c6ff3c567f2113cdb41122f727e27a984950d004a88ef3c5c Best match: seaborn 0.11.1 Processing seaborn-0.11.1-py3-none-any.whl Installing seaborn-0.11.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding seaborn 0.11.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/seaborn-0.11.1-py3.7.egg Searching for cmasher Reading https://pypi.org/simple/cmasher/ Downloading https://files.pythonhosted.org/packages/f3/c6/27623300167f32303e425e0bff86ff15362fad5b575d3f82f4ee743b5c3a/cmasher-1.6.1-py3-none-any.whl#sha256=eb94a1f405866449fef74cf530bab62332e9b8f2e609240a4a0709e94ad60e43 Best match: cmasher 1.6.1 Processing cmasher-1.6.1-py3-none-any.whl Installing cmasher-1.6.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding cmasher 1.6.1 to easy-install.pth file Installing cmr script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/cmasher-1.6.1-py3.7.egg Searching for cmocean Reading https://pypi.org/simple/cmocean/ Downloading https://files.pythonhosted.org/packages/48/02/d0f19b00b252fd972e3daec05be73aa811091528f21b90442a15d6a96d89/cmocean-2.0-py3-none-any.whl#sha256=1753f004d84d21c89e76106b2f56e2847808951b2373843bece4dcf532e1a91f Best match: cmocean 2.0 Processing cmocean-2.0-py3-none-any.whl Installing cmocean-2.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding cmocean 2.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/cmocean-2.0-py3.7.egg Searching for networkx>=2.3 Reading https://pypi.org/simple/networkx/ Downloading https://files.pythonhosted.org/packages/f3/b7/c7f488101c0bb5e4178f3cde416004280fd40262433496830de8a8c21613/networkx-2.5.1-py3-none-any.whl#sha256=0635858ed7e989f4c574c2328380b452df892ae85084144c73d8cd819f0c4e06 Best match: networkx 2.5.1 Processing networkx-2.5.1-py3-none-any.whl Installing networkx-2.5.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding networkx 2.5.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/networkx-2.5.1-py3.7.egg Searching for pandas>=1.2.3 Reading https://pypi.org/simple/pandas/ Downloading https://files.pythonhosted.org/packages/51/51/48f3fc47c4e2144da2806dfb6629c4dd1fa3d5a143f9652b141e979a8ca9/pandas-1.2.4-cp37-cp37m-manylinux1_x86_64.whl#sha256=b730add5267f873b3383c18cac4df2527ac4f0f0eed1c6cf37fcb437e25cf558 Best match: pandas 1.2.4 Processing pandas-1.2.4-cp37-cp37m-manylinux1_x86_64.whl Installing pandas-1.2.4-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding pandas 1.2.4 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/pandas-1.2.4-py3.7-linux-x86_64.egg Searching for covasim>=2.0.0 Reading https://pypi.org/simple/covasim/ Downloading https://files.pythonhosted.org/packages/f2/bf/cdd0d322aa04e80b2e66a985a657afd4135e9e8d4c58a68b3bc2fd02ce95/covasim-3.0.3-py3-none-any.whl#sha256=85a085e4d74c736069890c4f20d16cc41117df3cfe8cb081e8a03606817720c7 Best match: covasim 3.0.3 Processing covasim-3.0.3-py3-none-any.whl Installing covasim-3.0.3-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding covasim 3.0.3 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/covasim-3.0.3-py3.7.egg Searching for sciris>=1.1.1 Reading https://pypi.org/simple/sciris/ Downloading https://files.pythonhosted.org/packages/a5/8d/bf0545ef25a10d52c78f1aa08548eab729ce967fe2f782d6315f5454d5a1/sciris-1.1.1-py3-none-any.whl#sha256=a344f9d185aef89912e029d5f0236ceeb9cf59642325f9516469de1e2da4ba6b Best match: sciris 1.1.1 Processing sciris-1.1.1-py3-none-any.whl Installing sciris-1.1.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding sciris 1.1.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/sciris-1.1.1-py3.7.egg Searching for editorconfig>=0.12.2 Reading https://pypi.org/simple/editorconfig/ Downloading https://files.pythonhosted.org/packages/4e/04/e8a79c1db0c55ef03d53c05c61d06c4d6d3be37ef84e5400ce36b4a0fbe9/EditorConfig-0.12.3-py3-none-any.whl#sha256=6b0851425aa875b08b16789ee0eeadbd4ab59666e9ebe728e526314c4a2e52c1 Best match: EditorConfig 0.12.3 Processing EditorConfig-0.12.3-py3-none-any.whl Installing EditorConfig-0.12.3-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding EditorConfig 0.12.3 to easy-install.pth file Installing editorconfig script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/EditorConfig-0.12.3-py3.7.egg Searching for e13tools>=0.9.4 Reading https://pypi.org/simple/e13tools/ Downloading https://files.pythonhosted.org/packages/dd/cc/f699b2af6789be195269fa04747b9bddbe5488b30571a0f1e8c2dfcd9267/e13tools-0.9.6-py3-none-any.whl#sha256=2611f98c176f6fdaecba50ffeeb37c639a921331098bb8c0569773b699cea89b Best match: e13tools 0.9.6 Processing e13tools-0.9.6-py3-none-any.whl Installing e13tools-0.9.6-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding e13tools 0.9.6 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/e13tools-0.9.6-py3.7.egg Searching for colorspacious>=1.1.0 Reading https://pypi.org/simple/colorspacious/ Downloading https://files.pythonhosted.org/packages/ab/a1/318b9aeca7b9856410ededa4f52d6f82174d1a41e64bdd70d951e532675a/colorspacious-1.1.2-py2.py3-none-any.whl#sha256=c78befa603cea5dccb332464e7dd29e96469eebf6cd5133029153d1e69e3fd6f Best match: colorspacious 1.1.2 Processing colorspacious-1.1.2-py2.py3-none-any.whl Installing colorspacious-1.1.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding colorspacious 1.1.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/colorspacious-1.1.2-py3.7.egg Searching for decorator<5,>=4.3 Reading https://pypi.org/simple/decorator/ Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760 Best match: decorator 4.4.2 Processing decorator-4.4.2-py2.py3-none-any.whl Installing decorator-4.4.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding decorator 4.4.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/decorator-4.4.2-py3.7.egg Searching for xlrd==1.2.0 Reading https://pypi.org/simple/xlrd/ Downloading https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl#sha256=e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde Best match: xlrd 1.2.0 Processing xlrd-1.2.0-py2.py3-none-any.whl Installing xlrd-1.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding xlrd 1.2.0 to easy-install.pth file Installing runxlrd.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/xlrd-1.2.0-py3.7.egg Searching for statsmodels Reading https://pypi.org/simple/statsmodels/ Downloading https://files.pythonhosted.org/packages/da/69/8eef30a6237c54f3c0b524140e2975f4b1eea3489b45eb3339574fc8acee/statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=43de84bc08c8b9f778502aed7a476d6e68674e6878718e533b07d569cf0927a9 Best match: statsmodels 0.12.2 Processing statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl Installing statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding statsmodels 0.12.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/statsmodels-0.12.2-py3.7-linux-x86_64.egg Searching for xlsxwriter Reading https://pypi.org/simple/xlsxwriter/ Downloading https://files.pythonhosted.org/packages/2c/ce/74fd8d638a5b82ea0c6f08a5978f741c2655a38c3d6e82f73a0f084377e6/XlsxWriter-1.4.3-py2.py3-none-any.whl#sha256=1a7fac99687020e76aa7dd0d7de4b9b576547ed748e5cd91a99d52a6df54ca16 Best match: XlsxWriter 1.4.3 Processing XlsxWriter-1.4.3-py2.py3-none-any.whl Installing XlsxWriter-1.4.3-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding XlsxWriter 1.4.3 to easy-install.pth file Installing vba_extract.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/XlsxWriter-1.4.3-py3.7.egg Searching for psutil Reading https://pypi.org/simple/psutil/ Downloading https://files.pythonhosted.org/packages/84/da/f7efdcf012b51506938553dbe302aecc22f3f43abd5cffa8320e8e0588d5/psutil-5.8.0-cp37-cp37m-manylinux2010_x86_64.whl#sha256=0dd4465a039d343925cdc29023bb6960ccf4e74a65ad53e768403746a9207023 Best match: psutil 5.8.0 Processing psutil-5.8.0-cp37-cp37m-manylinux2010_x86_64.whl Installing psutil-5.8.0-cp37-cp37m-manylinux2010_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding psutil 5.8.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/psutil-5.8.0-py3.7-linux-x86_64.egg Searching for openpyexcel>=2.5 Reading https://pypi.org/simple/openpyexcel/ Downloading https://files.pythonhosted.org/packages/32/e1/722047fae7a46b658d7fa038cf5b952fbbb150c3c8a31012e4fb76eba27d/openpyexcel-2.5.14-py2.py3-none-any.whl#sha256=f18f4efadbc25a26870885f342e14b6cd6862ca1f4b8195b394fc2681ccdbaab Best match: openpyexcel 2.5.14 Processing openpyexcel-2.5.14-py2.py3-none-any.whl Installing openpyexcel-2.5.14-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding openpyexcel 2.5.14 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/openpyexcel-2.5.14-py3.7.egg Searching for multiprocess Reading https://pypi.org/simple/multiprocess/ Downloading https://files.pythonhosted.org/packages/db/20/458ac043a57322365ac2ed86a911bf7598fc2e49bccb3f94ea810fbb6b9b/multiprocess-0.70.11.1-py37-none-any.whl#sha256=164c77448e357ebee0dc6abc7ee8c823e40e295e629a5fc6d31725109a3a7ee9 Best match: multiprocess 0.70.11.1 Processing multiprocess-0.70.11.1-py37-none-any.whl Installing multiprocess-0.70.11.1-py37-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding multiprocess 0.70.11.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/multiprocess-0.70.11.1-py3.7.egg Searching for memory-profiler Reading https://pypi.org/simple/memory-profiler/ Downloading https://files.pythonhosted.org/packages/8f/fd/d92b3295657f8837e0177e7b48b32d6651436f0293af42b76d134c3bb489/memory_profiler-0.58.0.tar.gz#sha256=01385ac0fec944fcf7969814ec4406c6d8a9c66c079d09276723c5a7680f44e5 Best match: memory-profiler 0.58.0 Processing memory_profiler-0.58.0.tar.gz Writing /tmp/easy_install-z41_qwzv/memory_profiler-0.58.0/setup.cfg Running memory_profiler-0.58.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-z41_qwzv/memory_profiler-0.58.0/egg-dist-tmp-ekqr3657 warning: no files found matching 'mprof.bat' zip_safe flag not set; analyzing archive contents... __pycache__.memory_profiler.cpython-37: module MAY be using inspect.getsourcefile __pycache__.memory_profiler.cpython-37: module MAY be using inspect.stack __pycache__.memory_profiler.cpython-37: module MAY be using inspect.trace creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/memory_profiler-0.58.0-py3.7.egg Extracting memory_profiler-0.58.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding memory-profiler 0.58.0 to easy-install.pth file Installing mprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/memory_profiler-0.58.0-py3.7.egg Searching for line-profiler Reading https://pypi.org/simple/line-profiler/ Downloading https://files.pythonhosted.org/packages/db/32/65574b288b3ac459be2a7495739b7a53fa4a70b785d59fe5a73a33f1c384/line_profiler-3.2.6-cp37-cp37m-manylinux1_x86_64.whl#sha256=0365a1800980a53f9633453eae73a8bb7565f25443b0196acdf5144d2523301f Best match: line-profiler 3.2.6 Processing line_profiler-3.2.6-cp37-cp37m-manylinux1_x86_64.whl Installing line_profiler-3.2.6-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding line-profiler 3.2.6 to easy-install.pth file Installing kernprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/line_profiler-3.2.6-py3.7-linux-x86_64.egg Searching for jsonpickle Reading https://pypi.org/simple/jsonpickle/ Downloading https://files.pythonhosted.org/packages/bb/1a/f2db026d4d682303793559f1c2bb425ba3ec0d6fd7ac63397790443f2461/jsonpickle-2.0.0-py2.py3-none-any.whl#sha256=c1010994c1fbda87a48f8a56698605b598cb0fc6bb7e7927559fc1100e69aeac Best match: jsonpickle 2.0.0 Processing jsonpickle-2.0.0-py2.py3-none-any.whl Installing jsonpickle-2.0.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding jsonpickle 2.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jsonpickle-2.0.0-py3.7.egg Searching for jellyfish Reading https://pypi.org/simple/jellyfish/ Downloading https://files.pythonhosted.org/packages/30/a6/4d039bc827a102f62ce7a7910713e38fdfd7c7a40aa39c72fb14938a1473/jellyfish-0.8.2-cp37-cp37m-manylinux2014_x86_64.whl#sha256=4213dda17b75e09b4a5bac48b7dd2602cf54304af49fd6236d3539f49f614e8a Best match: jellyfish 0.8.2 Processing jellyfish-0.8.2-cp37-cp37m-manylinux2014_x86_64.whl Installing jellyfish-0.8.2-cp37-cp37m-manylinux2014_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding jellyfish 0.8.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jellyfish-0.8.2-py3.7-linux-x86_64.egg Searching for gitpython Reading https://pypi.org/simple/gitpython/ Downloading https://files.pythonhosted.org/packages/27/da/6f6224fdfc47dab57881fe20c0d1bc3122be290198ba0bf26a953a045d92/GitPython-3.1.17-py3-none-any.whl#sha256=29fe82050709760081f588dd50ce83504feddbebdc4da6956d02351552b1c135 Best match: GitPython 3.1.17 Processing GitPython-3.1.17-py3-none-any.whl Installing GitPython-3.1.17-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding GitPython 3.1.17 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/GitPython-3.1.17-py3.7.egg Searching for dill Reading https://pypi.org/simple/dill/ Downloading https://files.pythonhosted.org/packages/52/d6/79f40d230895fa1ce3b6af0d22e0ac79c65175dc069c194b79cc8e05a033/dill-0.3.3-py2.py3-none-any.whl#sha256=78370261be6ea49037ace8c17e0b7dd06d0393af6513cc23f9b222d9367ce389 Best match: dill 0.3.3 Processing dill-0.3.3-py2.py3-none-any.whl Installing dill-0.3.3-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding dill 0.3.3 to easy-install.pth file Installing get_objgraph script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installing undill script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/dill-0.3.3-py3.7.egg Searching for patsy>=0.5 Reading https://pypi.org/simple/patsy/ Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl#sha256=5465be1c0e670c3a965355ec09e9a502bf2c4cbe4875e8528b0221190a8a5d40 Best match: patsy 0.5.1 Processing patsy-0.5.1-py2.py3-none-any.whl Installing patsy-0.5.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding patsy 0.5.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/patsy-0.5.1-py3.7.egg Searching for jdcal Reading https://pypi.org/simple/jdcal/ Downloading https://files.pythonhosted.org/packages/f0/da/572cbc0bc582390480bbd7c4e93d14dc46079778ed915b505dc494b37c57/jdcal-1.4.1-py2.py3-none-any.whl#sha256=1abf1305fce18b4e8aa248cf8fe0c56ce2032392bc64bbd61b5dff2a19ec8bba Best match: jdcal 1.4.1 Processing jdcal-1.4.1-py2.py3-none-any.whl Installing jdcal-1.4.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding jdcal 1.4.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jdcal-1.4.1-py3.7.egg Searching for et-xmlfile Reading https://pypi.org/simple/et-xmlfile/ Downloading https://files.pythonhosted.org/packages/96/c2/3dd434b0108730014f1b96fd286040dc3bcb70066346f7e01ec2ac95865f/et_xmlfile-1.1.0-py3-none-any.whl#sha256=a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada Best match: et-xmlfile 1.1.0 Processing et_xmlfile-1.1.0-py3-none-any.whl Installing et_xmlfile-1.1.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding et-xmlfile 1.1.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/et_xmlfile-1.1.0-py3.7.egg Searching for IPython>=0.13 Reading https://pypi.org/simple/IPython/ Downloading https://files.pythonhosted.org/packages/81/d1/8d0ba7589ea4cbf3e80ef8e20616da2cfc3c33187a64b044372aad517512/ipython-7.23.1-py3-none-any.whl#sha256=f78c6a3972dde1cc9e4041cbf4de583546314ba52d3c97208e5b6b2221a9cb7d Best match: ipython 7.23.1 Processing ipython-7.23.1-py3-none-any.whl Installing ipython-7.23.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding ipython 7.23.1 to easy-install.pth file Installing iptest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installing iptest3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/ipython-7.23.1-py3.7.egg Searching for gitdb<5,>=4.0.1 Reading https://pypi.org/simple/gitdb/ Downloading https://files.pythonhosted.org/packages/ea/e8/f414d1a4f0bbc668ed441f74f44c116d9816833a48bf81d22b697090dba8/gitdb-4.0.7-py3-none-any.whl#sha256=6c4cc71933456991da20917998acbe6cf4fb41eeaab7d6d67fbc05ecd4c865b0 Best match: gitdb 4.0.7 Processing gitdb-4.0.7-py3-none-any.whl Installing gitdb-4.0.7-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding gitdb 4.0.7 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/gitdb-4.0.7-py3.7.egg Searching for traitlets>=4.2 Reading https://pypi.org/simple/traitlets/ Downloading https://files.pythonhosted.org/packages/f6/7d/3ecb0ebd0ce8dcdfa7bd47ab85c1d4a521e6770ef283d0824f5804994dfe/traitlets-5.0.5-py3-none-any.whl#sha256=69ff3f9d5351f31a7ad80443c2674b7099df13cc41fc5fa6e2f6d3b0330b0426 Best match: traitlets 5.0.5 Processing traitlets-5.0.5-py3-none-any.whl Installing traitlets-5.0.5-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding traitlets 5.0.5 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/traitlets-5.0.5-py3.7.egg Searching for prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Reading https://pypi.org/simple/prompt-toolkit/ Downloading https://files.pythonhosted.org/packages/eb/e6/4b4ca4fa94462d4560ba2f4e62e62108ab07be2e16a92e594e43b12d3300/prompt_toolkit-3.0.18-py3-none-any.whl#sha256=bf00f22079f5fadc949f42ae8ff7f05702826a97059ffcc6281036ad40ac6f04 Best match: prompt-toolkit 3.0.18 Processing prompt_toolkit-3.0.18-py3-none-any.whl Installing prompt_toolkit-3.0.18-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding prompt-toolkit 3.0.18 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/prompt_toolkit-3.0.18-py3.7.egg Searching for pickleshare Reading https://pypi.org/simple/pickleshare/ Downloading https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl#sha256=9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56 Best match: pickleshare 0.7.5 Processing pickleshare-0.7.5-py2.py3-none-any.whl Installing pickleshare-0.7.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding pickleshare 0.7.5 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/pickleshare-0.7.5-py3.7.egg Searching for pexpect>4.3 Reading https://pypi.org/simple/pexpect/ Downloading https://files.pythonhosted.org/packages/39/7b/88dbb785881c28a102619d46423cb853b46dbccc70d3ac362d99773a78ce/pexpect-4.8.0-py2.py3-none-any.whl#sha256=0b48a55dcb3c05f3329815901ea4fc1537514d6ba867a152b581d69ae3710937 Best match: pexpect 4.8.0 Processing pexpect-4.8.0-py2.py3-none-any.whl Installing pexpect-4.8.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding pexpect 4.8.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/pexpect-4.8.0-py3.7.egg Searching for matplotlib-inline Reading https://pypi.org/simple/matplotlib-inline/ Downloading https://files.pythonhosted.org/packages/7f/de/6c111d687335729cf8c156394c8d119b0dc3c34b6966ff2a2f7fe4aa79cf/matplotlib_inline-0.1.2-py3-none-any.whl#sha256=5cf1176f554abb4fa98cb362aa2b55c500147e4bdbb07e3fda359143e1da0811 Best match: matplotlib-inline 0.1.2 Processing matplotlib_inline-0.1.2-py3-none-any.whl Installing matplotlib_inline-0.1.2-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding matplotlib-inline 0.1.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/matplotlib_inline-0.1.2-py3.7.egg Searching for jedi>=0.16 Reading https://pypi.org/simple/jedi/ Downloading https://files.pythonhosted.org/packages/f9/36/7aa67ae2663025b49e8426ead0bad983fee1b73f472536e9790655da0277/jedi-0.18.0-py2.py3-none-any.whl#sha256=18456d83f65f400ab0c2d3319e48520420ef43b23a086fdc05dff34132f0fb93 Best match: jedi 0.18.0 Processing jedi-0.18.0-py2.py3-none-any.whl Installing jedi-0.18.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding jedi 0.18.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/jedi-0.18.0-py3.7.egg Searching for backcall Reading https://pypi.org/simple/backcall/ Downloading https://files.pythonhosted.org/packages/4c/1c/ff6546b6c12603d8dd1070aa3c3d273ad4c07f5771689a7b69a550e8c951/backcall-0.2.0-py2.py3-none-any.whl#sha256=fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255 Best match: backcall 0.2.0 Processing backcall-0.2.0-py2.py3-none-any.whl Installing backcall-0.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding backcall 0.2.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/backcall-0.2.0-py3.7.egg Searching for smmap<5,>=3.0.1 Reading https://pypi.org/simple/smmap/ Downloading https://files.pythonhosted.org/packages/68/ee/d540eb5e5996eb81c26ceffac6ee49041d473bc5125f2aa995cf51ec1cf1/smmap-4.0.0-py2.py3-none-any.whl#sha256=a9a7479e4c572e2e775c404dcd3080c8dc49f39918c2cf74913d30c4c478e3c2 Best match: smmap 4.0.0 Processing smmap-4.0.0-py2.py3-none-any.whl Installing smmap-4.0.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding smmap 4.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/smmap-4.0.0-py3.7.egg Searching for ipython-genutils Reading https://pypi.org/simple/ipython-genutils/ Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl#sha256=72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8 Best match: ipython-genutils 0.2.0 Processing ipython_genutils-0.2.0-py2.py3-none-any.whl Installing ipython_genutils-0.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding ipython-genutils 0.2.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/ipython_genutils-0.2.0-py3.7.egg Searching for wcwidth Reading https://pypi.org/simple/wcwidth/ Downloading https://files.pythonhosted.org/packages/59/7c/e39aca596badaf1b78e8f547c807b04dae603a433d3e7a7e04d67f2ef3e5/wcwidth-0.2.5-py2.py3-none-any.whl#sha256=beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784 Best match: wcwidth 0.2.5 Processing wcwidth-0.2.5-py2.py3-none-any.whl Installing wcwidth-0.2.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding wcwidth 0.2.5 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/wcwidth-0.2.5-py3.7.egg Searching for ptyprocess>=0.5 Reading https://pypi.org/simple/ptyprocess/ Downloading https://files.pythonhosted.org/packages/22/a6/858897256d0deac81a172289110f31629fc4cee19b6f01283303e18c8db3/ptyprocess-0.7.0-py2.py3-none-any.whl#sha256=4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35 Best match: ptyprocess 0.7.0 Processing ptyprocess-0.7.0-py2.py3-none-any.whl Installing ptyprocess-0.7.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding ptyprocess 0.7.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/ptyprocess-0.7.0-py3.7.egg Searching for parso<0.9.0,>=0.8.0 Reading https://pypi.org/simple/parso/ Downloading https://files.pythonhosted.org/packages/a9/c4/d5476373088c120ffed82f34c74b266ccae31a68d665b837354d4d8dc8be/parso-0.8.2-py2.py3-none-any.whl#sha256=a8c4922db71e4fdb90e0d0bc6e50f9b273d3397925e5e60a717e719201778d22 Best match: parso 0.8.2 Processing parso-0.8.2-py2.py3-none-any.whl Installing parso-0.8.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Adding parso 0.8.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/parso-0.8.2-py3.7.egg Searching for numba==0.48.0 Best match: numba 0.48.0 Adding numba 0.48.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for scipy==1.5.3 Best match: scipy 1.5.3 Adding scipy 1.5.3 to easy-install.pth file Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for numpy==1.19.2 Best match: numpy 1.19.2 numpy 1.19.2 is already the active version in easy-install.pth Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for matplotlib==3.3.2 Best match: matplotlib 3.3.2 matplotlib 3.3.2 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/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-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for pyparsing==2.4.7 Best match: pyparsing 2.4.7 Adding pyparsing 2.4.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for setuptools==56.2.0 Best match: setuptools 56.2.0 Adding setuptools 56.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for llvmlite==0.31.0 Best match: llvmlite 0.31.0 Adding llvmlite 0.31.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for pytz==2021.1 Best match: pytz 2021.1 Adding pytz 2021.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for Pillow==8.0.0 Best match: Pillow 8.0.0 Pillow 8.0.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for certifi==2020.12.5 Best match: certifi 2020.12.5 Adding certifi 2020.12.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 kiwisolver 1.2.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 cycler 0.10.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for importlib-metadata==4.0.1 Best match: importlib-metadata 4.0.1 Adding importlib-metadata 4.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for typing-extensions==3.10.0.0 Best match: typing-extensions 3.10.0.0 Adding typing-extensions 3.10.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for Pygments==2.9.0 Best match: Pygments 2.9.0 Adding Pygments 2.9.0 to easy-install.pth file Installing pygmentize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Searching for zipp==3.4.1 Best match: zipp 3.4.1 Adding zipp 3.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages Finished processing dependencies for synthpops==1.8.3 [rtd-command-info] start-time: 2021-05-19T01:18:41.259152Z, end-time: 2021-05-19T01:18:41.353293Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # 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 # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme from datetime import datetime import synthpops as sp on_rtd = os.environ.get('READTHEDOCS') == 'True' if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "synthpops package" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ # If your documentation 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', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'sphinx.ext.viewcode', # Add a link to the Python source code for classes, functions etc. ] autodoc_default_options = { 'member-order': 'bysource', 'members': None } autodoc_mock_imports = [] napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autoclass_content = "both" # Add __init__ doc (ie. params) to class summaries html_show_sourcelink = False # Remove 'view source code' from top of page (for html, not python) autodoc_member_order = 'bysource' # Keep original ordering add_module_names = False # NB, does not work autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes # 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' master_doc = 'index' # General information about the project. project = 'SynthPops' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for SynthPops version {sp.__version__}.\n' author = '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. version = sp.__version__ # The full version, including alpha/beta/rc tags. release = sp.__version__ # The language for content autogenerated by Sphinx. Refer to documentation # 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 # 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'] # suppress warnings for multiple possible Python references in the namespace # suppress_warnings = ['ref.python'] pygments_style = 'sphinx' # 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 documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] html_logo = "images/IDM_white.png" 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 = { 'rtd_url': 'https://docs.idmod.org/projects/synthpops/en/latest', 'theme_vcs_pageview_mode': 'edit', 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. # if not on_rtd: html_extra_path = ['robots.txt'] # 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 = '%Y-%b-%d' # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_show_sphinx = False # 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 = 'docs.idmod.org/projects/synthpops/en/latest' # Output file base name for HTML help builder. htmlhelp_basename = 'SynthPops' # -- 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': '%XeLaTeX packages' '\\usepackage{xltxtra}' '\\usepackage{fontspec} %%Font package' '\\usepackage{xunicode}' '%%Select fonts' '\\setmainfont[Mapping=tex-text]{nimbusserif}' '\\setsansfont[Mapping=tex-text]{nimbussans}' '\\setmonofont{nimbusmono}', # 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, 'synthpops-docs.tex', u'SynthPops', '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 # -- 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, 'synthpops-docs', 'SynthPops', [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, 'synthpops-docs', 'SynthPops', author, 'Institute for Disease Modeling', 'How to use SynthPops for creating synthetic populations.', 'Miscellaneous'), ] # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file should't rely on extra depencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "v1.8.3", 'version_slug': "v1.8.3", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("v1.9.0", "/en/v1.9.0/"), ("v1.8.4", "/en/v1.8.4/"), ("v1.8.3", "/en/v1.8.3/"), ("v1.8.2", "/en/v1.8.2/"), ("v1.8.1", "/en/v1.8.1/"), ("v1.8.0", "/en/v1.8.0/"), ("v1.7.7", "/en/v1.7.7/"), ("v1.7.6", "/en/v1.7.6/"), ("v1.7.5", "/en/v1.7.5/"), ("v1.6.1", "/en/v1.6.1/"), ("v1.6.0", "/en/v1.6.0/"), ("v1.5.3", "/en/v1.5.3/"), ("v1.5.2", "/en/v1.5.2/"), ("v1.5.1", "/en/v1.5.1/"), ("v1.4.3", "/en/v1.4.3/"), ("v0.5.1", "/en/v0.5.1/"), ("v0.5.0", "/en/v0.5.0/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-synthpops-test', 'name': u'synthpops', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/synthpops/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': 'synthpops', 'github_version': 'v1.8.3', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'v1.8.3', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'v1.8.3', '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': 'a6be6996', } # 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-synthpops-test/builds/636269/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-05-19T01:18:41.466280Z, end-time: 2021-05-19T01:18:58.733047Z, duration: 17, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.5 Covasim 3.0.3 (2021-05-17) — © 2021 by IDM loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [html]: targets for 26 source files that are out of date updating environment: 26 added, 0 changed, 0 removed reading sources... [ 3%] algorithm reading sources... [ 7%] glossary reading sources... [ 11%] households reading sources... [ 15%] index reading sources... [ 19%] input_data reading sources... [ 23%] installation reading sources... [ 26%] modules reading sources... [ 30%] overview reading sources... [ 34%] schools reading sources... [ 38%] synthpops.base reading sources... [ 42%] synthpops.config reading sources... [ 46%] synthpops.contact_networks reading sources... [ 50%] synthpops.data reading sources... [ 53%] synthpops.data_distributions reading sources... [ 57%] synthpops.defaults reading sources... [ 61%] synthpops.households reading sources... [ 65%] synthpops.ltcfs reading sources... [ 69%] synthpops.plotting reading sources... [ 73%] synthpops.pop reading sources... [ 76%] synthpops.sampling reading sources... [ 80%] synthpops.schools reading sources... [ 84%] synthpops.version reading sources... [ 88%] synthpops.workplaces reading sources... [ 92%] usage reading sources... [ 96%] whatsnew reading sources... [100%] workplaces looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 3%] algorithm writing output... [ 7%] glossary writing output... [ 11%] households writing output... [ 15%] index writing output... [ 19%] input_data writing output... [ 23%] installation writing output... [ 26%] modules writing output... [ 30%] overview writing output... [ 34%] schools writing output... [ 38%] synthpops.base writing output... [ 42%] synthpops.config writing output... [ 46%] synthpops.contact_networks writing output... [ 50%] synthpops.data writing output... [ 53%] synthpops.data_distributions writing output... [ 57%] synthpops.defaults writing output... [ 61%] synthpops.households writing output... [ 65%] synthpops.ltcfs writing output... [ 69%] synthpops.plotting writing output... [ 73%] synthpops.pop writing output... [ 76%] synthpops.sampling writing output... [ 80%] synthpops.schools writing output... [ 84%] synthpops.version writing output... [ 88%] synthpops.workplaces writing output... [ 92%] usage writing output... [ 96%] whatsnew writing output... [100%] workplaces generating indices... genindex py-modindex highlighting module code... [ 6%] jsonobject.base_properties highlighting module code... [ 13%] jsonobject.properties highlighting module code... [ 20%] synthpops.base highlighting module code... [ 26%] synthpops.config highlighting module code... [ 33%] synthpops.contact_networks highlighting module code... [ 40%] synthpops.data highlighting module code... [ 46%] synthpops.data_distributions highlighting module code... [ 53%] synthpops.defaults highlighting module code... [ 60%] synthpops.households highlighting module code... [ 66%] synthpops.ltcfs highlighting module code... [ 73%] synthpops.plotting highlighting module code... [ 80%] synthpops.pop highlighting module code... [ 86%] synthpops.sampling highlighting module code... [ 93%] synthpops.schools highlighting module code... [100%] synthpops.workplaces writing additional pages... search opensearch 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... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): [rtd-command-info] start-time: 2021-05-19T01:18:58.890180Z, end-time: 2021-05-19T01:19:04.920638Z, duration: 6, exit-code: 0 python -m sphinx -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v1.8.5 Covasim 3.0.3 (2021-05-17) — © 2021 by IDM loading translations [en]... done making output directory... 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%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation overview whatsnew algorithm usage households schools workplaces input_data modules synthpops.base synthpops.config synthpops.contact_networks synthpops.data synthpops.data_distributions synthpops.defaults synthpops.households synthpops.ltcfs synthpops.plotting synthpops.pop synthpops.sampling synthpops.schools synthpops.version synthpops.workplaces glossary writing... done writing additional files... opensearch copying static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-05-19T01:19:05.059654Z, end-time: 2021-05-19T01:19:10.872767Z, duration: 5, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 Covasim 3.0.3 (2021-05-17) — © 2021 by IDM loading translations [en]... done making output directory... 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%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done processing synthpops-docs.tex...index installation overview whatsnew algorithm usage households schools workplaces input_data modules synthpops.base synthpops.config synthpops.contact_networks synthpops.data synthpops.data_distributions synthpops.defaults synthpops.households synthpops.ltcfs synthpops.plotting synthpops.pop synthpops.sampling synthpops.schools synthpops.version synthpops.workplaces glossary resolving references... writing... done 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). /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/v1.8.3/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. if toctrees[0].get('maxdepth') > 0: WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/v1.8.3/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-05-19T01:19:11.152111Z, end-time: 2021-05-19T01:19:11.236231Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2021-05-19T01:19:11.386144Z, end-time: 2021-05-19T01:19:14.320016Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-synthpops-test -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-synthpops-test" "synthpops-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 (./synthpops-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/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] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) LaTeX Warning: Hyper reference `glossary:term-agent-based-model' on page 5 unde fined on input line 166. LaTeX Warning: Hyper reference `glossary:term-time-step' on page 5 undefined on input line 172. LaTeX Warning: Hyper reference `glossary:term-contact-layers' on page 5 undefin ed on input line 177. LaTeX Warning: Hyper reference `glossary:term-workplace-contact-layer' on page 5 undefined on input line 177. LaTeX Warning: Hyper reference `glossary:term-household-contact-layer' on page 5 undefined on input line 178. LaTeX Warning: Hyper reference `synthpops.pop:synthpops.pop.make_population' on page 5 undefined on input line 197. [5] [6] Chapter 3. [7] Underfull \hbox (badness 10000) in paragraph at lines 247--248 []\T1/ptm/m/n/10 Method to gen-er-ate the count of house-hold sizes for a fixed pop-u-la-tion re-named: \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 247--248 \T1/pcr/m/n/10 households.generate_household_sizes_from_fixed_pop_size \T1/ptm/ m/n/10 ^^U> \T1/pcr/m/n/10 sp.households. [8] Underfull \hbox (badness 10000) in paragraph at lines 310--311 []\T1/ptm/m/n/10 Method name changes: \T1/pcr/m/n/10 sp.get_age_by_brackets_dic () \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 310--311 \T1/pcr/m/n/10 get_age_by_brackets()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp.get_inde x_by_brackets_dic() \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp. 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Also ac-ces-s i-ble pop meth-ods as \T1/pcr/m/n/10 pop. Underfull \hbox (badness 10000) in paragraph at lines 457--458 \T1/pcr/m/n/10 get_household_head_ages_by_size()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pop.plot_household_head_ages_by_size()\T1/ptm/m/n/10 . [11] [12] Chapter 4. LaTeX Warning: Hyper reference `glossary:term-contact-layers' on page 13 undefi ned on input line 527. [13] [14] Chapter 5. LaTeX Warning: Hyper reference `glossary:term-household-contact-layer' on page 15 undefined on input line 576. LaTeX Warning: Hyper reference `glossary:term-school-contact-layer' on page 15 undefined on input line 596. LaTeX Warning: Hyper reference `glossary:term-workplace-contact-layer' on page 15 undefined on input line 608. [15] LaTeX Warning: Hyper reference `glossary:term-contact-layers' on page 16 undefi ned on input line 667. LaTeX Warning: Hyper reference `glossary:term-household-contact-layer' on page 16 undefined on input line 672. [16] [17] LaTeX Warning: Hyper reference `glossary:term-school-contact-layer' on page 18 undefined on input line 819. Underfull \hbox (badness 5374) in paragraph at lines 854--858 []\T1/ptm/b/n/10 Enrollment by age \T1/ptm/m/n/10 spec-i-fy-ing the per-cent-ag e of peo-ple of each age at-tend-ing school. See [18] [19] LaTeX Warning: Hyper reference `glossary:term-workplace-contact-layer' on page 20 undefined on input line 970. LaTeX Warning: Hyper reference `glossary:term-school-contact-layer' on page 20 undefined on input line 972. [20] LaTeX Warning: Hyper reference `glossary:term-location' on page 21 undefined on input line 1042. [21] [22] [23] Overfull \vbox (0.68163pt too high) detected at line 1325 [24] [25] [26] [27] [28] Chapter 6. [29] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 []\T1/ptm/m/it/10 age_by_uid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 homes_by_uids\T1/p tm/m/n/10 , \T1/ptm/m/it/10 stu-dents_by_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm /m/it/10 teach- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 ers_by_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 non_teach ing_staff_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 school_mixing_type='random'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av- er-age_class_size=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_grade_mixing=0.1\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 av-er-age_student_teacher_ratio=20\T1/ptm/m/n/10 , \T1/ptm/m/it /10 av-er-age_teacher_teacher_degree=3\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 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LaTeX Warning: Reference `synthpops.plotting:module-synthpops.plotting' on page 91 undefined on input line 8316. LaTeX Warning: Reference `synthpops.pop:module-synthpops.pop' on page 91 undefi ned on input line 8317. LaTeX Warning: Reference `synthpops.sampling:module-synthpops.sampling' on page 91 undefined on input line 8318. LaTeX Warning: Reference `synthpops.schools:module-synthpops.schools' on page 9 1 undefined on input line 8319. LaTeX Warning: Reference `synthpops.version:module-synthpops.version' on page 9 1 undefined on input line 8320. LaTeX Warning: Reference `synthpops.workplaces:module-synthpops.workplaces' on page 91 undefined on input line 8321. [91] No file institute-for-disease-modeling-synthpops-test.ind. (./institute-for-disease-modeling-synthpops-test.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-synthpops- test.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-synthpops-test.pdf (95 pages, 325788 bytes). Transcript written on institute-for-disease-modeling-synthpops-test.log. Latexmk: Index file 'institute-for-disease-modeling-synthpops-test.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-synthpops-test.ind' from line 'No file institute-for-disease-modeling-synthpops-test.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-synthpops-test.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-synthpops-test.pdf' Latexmk: List of undefined refs and citations: Reference `modules:module-synthpops' on page 91 undefined on input line 8307 Reference `synthpops.base:module-synthpops.base' on page 91 undefined on input line 8308 Reference `synthpops.config:module-synthpops.config' on page 91 undefined on input line 8309 Reference `synthpops.contact_networks:module-synthpops.contact_networks' on page 91 undefined on input line 8310 Reference `synthpops.data:module-synthpops.data' on page 91 undefined on input line 8311 Reference `synthpops.data_distributions:module-synthpops.data_distributions' on page 91 undefined on input line 8312 Reference `synthpops.defaults:module-synthpops.defaults' on page 91 undefined on input line 8313 Reference `synthpops.households:module-synthpops.households' on page 91 undefined on input line 8314 Reference `synthpops.ltcfs:module-synthpops.ltcfs' on page 91 undefined on input line 8315 Reference `synthpops.plotting:module-synthpops.plotting' on page 91 undefined on input line 8316 Reference `synthpops.pop:module-synthpops.pop' on page 91 undefined on input line 8317 Reference `synthpops.sampling:module-synthpops.sampling' on page 91 undefined on input line 8318 Reference `synthpops.schools:module-synthpops.schools' on page 91 undefined on input line 8319 Reference `synthpops.version:module-synthpops.version' on page 91 undefined on input line 8320 Reference `synthpops.workplaces:module-synthpops.workplaces' on page 91 undefined on input line 8321 Latexmk: Summary of warnings: Latex failed to resolve 15 reference(s) Rule 'makeindex institute-for-disease-modeling-synthpops-test.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-synthpops-test.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-synthpops-test.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-synthpops-test.ind" "institute-for-disease-modeling-synthpops-test.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-synthpops-test.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-synthpops-test.idx....done (324 entries accepted, 0 rejected). Sorting entries.....done (2790 comparisons). Generating output file institute-for-disease-modeling-synthpops-test.ind....done (494 lines written, 0 warnings). Output written in institute-for-disease-modeling-synthpops-test.ind. Transcript written in institute-for-disease-modeling-synthpops-test.ilg. 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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-synthpops-test.out) (./institute-for-disease-modeling-synthpops-test.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-synthpops-test.toc [1]) [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6] Chapter 3. [7] Underfull \hbox (badness 10000) in paragraph at lines 247--248 []\T1/ptm/m/n/10 Method to gen-er-ate the count of house-hold sizes for a fixed pop-u-la-tion re-named: \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 247--248 \T1/pcr/m/n/10 households.generate_household_sizes_from_fixed_pop_size \T1/ptm/ m/n/10 ^^U> \T1/pcr/m/n/10 sp.households. [8] Underfull \hbox (badness 10000) in paragraph at lines 310--311 []\T1/ptm/m/n/10 Method name changes: \T1/pcr/m/n/10 sp.get_age_by_brackets_dic () \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 310--311 \T1/pcr/m/n/10 get_age_by_brackets()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp.get_inde x_by_brackets_dic() \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 310--311 \T1/pcr/m/n/10 get_index_by_brackets()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp.get_id s_by_age_dic() \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp.get_ids_by_age()\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 310--311 \T1/pcr/m/n/10 sp.make_contacts_from_microstructure_objects() \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp.make_contacts()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp. [9] Underfull \hbox (badness 10000) in paragraph at lines 378--379 []\T1/ptm/m/it/10 Feature\T1/ptm/m/n/10 : new sum-mary in-for-ma-tion added to pop ob-jects: \T1/pcr/m/n/10 pop.summary.average_age\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 378--379 \T1/pcr/m/n/10 pop.summary.layer_degrees\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pop.sum mary.layer_stats\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 pop.summary. Underfull \hbox (badness 10000) in paragraph at lines 420--421 []\T1/ptm/m/it/10 Feature\T1/ptm/m/n/10 : Added checks for prob-a-bil-ity dis-t ri-bu-tions with meth-ods \T1/pcr/m/n/10 sp. Overfull \hbox (114.26503pt too wide) in paragraph at lines 420--421 \T1/pcr/m/n/10 check_all_probability_distribution_sums()\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sp.check_all_probability_distrubution_nonnegative()\T1/ptm/m/n/10 , Overfull \hbox (78.26503pt too wide) in paragraph at lines 420--421 \T1/pcr/m/n/10 sp.check_probability_distribution_sum()\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 sp.check_probability_distribution_nonnegative()\T1/ptm/m/n/10 . [10] Underfull \hbox (badness 10000) in paragraph at lines 457--458 []\T1/ptm/m/it/10 Feature\T1/ptm/m/n/10 : Added new meth-ods, \T1/pcr/m/n/10 sp .get_household_head_ages_by_size()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 457--458 \T1/pcr/m/n/10 plot_household_head_ages_by_size()\T1/ptm/m/n/10 . Also ac-ces-s i-ble pop meth-ods as \T1/pcr/m/n/10 pop. Underfull \hbox (badness 10000) in paragraph at lines 457--458 \T1/pcr/m/n/10 get_household_head_ages_by_size()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pop.plot_household_head_ages_by_size()\T1/ptm/m/n/10 . [11] [12] Chapter 4. [13] [14] Chapter 5. [15] [16] [17] Underfull \hbox (badness 5374) in paragraph at lines 854--858 []\T1/ptm/b/n/10 Enrollment by age \T1/ptm/m/n/10 spec-i-fy-ing the per-cent-ag e of peo-ple of each age at-tend-ing school. See [18] [19] [20] [21] [22] [23] Overfull \vbox (0.68163pt too high) detected at line 1325 [24] [25] [26] [27] [28] Chapter 6. [29] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 []\T1/ptm/m/it/10 age_by_uid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 homes_by_uids\T1/p tm/m/n/10 , \T1/ptm/m/it/10 stu-dents_by_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm /m/it/10 teach- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 ers_by_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 non_teach ing_staff_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 school_mixing_type='random'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av- er-age_class_size=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_grade_mixing=0.1\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 av-er-age_student_teacher_ratio=20\T1/ptm/m/n/10 , \T1/ptm/m/it /10 av-er-age_teacher_teacher_degree=3\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 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\T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 4181--4181 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_pat h=None\T1/ptm/m/n/10 , [52] Underfull \hbox (badness 10000) in paragraph at lines 4247--4247 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4247--4247 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 4247--4247 \T1/ptm/m/it/10 try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4286--4286 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4286--4286 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , 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Overfull \hbox (14.27411pt too wide) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 coun- Overfull \hbox (6.49422pt too wide) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 try_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 file_path=None\T1/ptm/m/n/10 , Overfull \hbox (7.57417pt too wide) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 use_default=False\T1/pcr/m/n/10 ) [54] Underfull \hbox (badness 10000) in paragraph at lines 4402--4402 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_pat h=None\T1/ptm/m/n/10 , [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 4789--4789 []\T1/ptm/m/it/10 larger_hh_size_array\T1/ptm/m/n/10 , \T1/ptm/m/it/10 larger_h ha_chosen\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4789--4789 \T1/ptm/m/it/10 hha_brackets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cm_age_brackets\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4789--4789 \T1/ptm/m/it/10 cm_age_by_brackets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 house-hold_m atrix\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4831--4831 []\T1/ptm/m/it/10 n_remaining\T1/ptm/m/n/10 , \T1/ptm/m/it/10 hh_sizes\T1/ptm/m /n/10 , \T1/ptm/m/it/10 hha_by_size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 hha_bracket s\T1/ptm/m/n/10 , [58] Underfull \hbox (badness 10000) in paragraph at lines 4882--4882 []\T1/ptm/m/it/10 size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 larger_household_sizes\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4882--4882 \T1/ptm/m/it/10 heads_of_larger_households\T1/ptm/m/n/10 , \T1/ptm/m/it/10 hha_ brackets\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4882--4882 \T1/ptm/m/it/10 cm_age_brackets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cm_age_by_brack ets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 house- [59] [60] Underfull \hbox (badness 5741) in paragraph at lines 5147--5147 []\T1/ptm/m/it/10 datadir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion\T1/ptm/m/n /10 , \T1/ptm/m/it/10 state_location\T1/ptm/m/n/10 , \T1/ptm/m/it/10 coun-try_l ocation\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ltcf_staff_age_min\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5147--5147 \T1/ptm/m/it/10 ltcf_staff_age_max\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fa-cil-i-tie s\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work-ers_by_age_to_assign_count\T1/ptm/m/n/10 , \T1/ptm/m/it/10 po- Underfull \hbox (badness 10000) in paragraph at lines 5147--5147 \T1/ptm/m/it/10 ten-tial_worker_uids_by_age\T1/ptm/m/n/10 , \T1/ptm/m/it/10 po- ten-tial_worker_uids\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fa-cil-i-ties_by_uids\T1/p tm/m/n/10 , [61] Underfull \hbox (badness 10000) in paragraph at lines 5202--5202 \T1/ptm/m/it/10 po-ten-tial_worker_uids_by_age\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work- [62] Underfull \hbox (badness 10000) in paragraph at lines 5297--5297 []\T1/ptm/m/it/10 ltcfid=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res-i-dent_uids=a rray([]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dtype=int64)\T1/ptm/m/n/10 , [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 []\T1/ptm/m/it/10 n=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 max_contacts=None\T1/p tm/m/n/10 , \T1/ptm/m/it/10 ltcf_pars=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 scho ol_pars=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 with_industry_code=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 with_f acilities=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_default=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 use_two_group_reduction=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av -er-age_LTCF_degree=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ltcf_staff_age_min=20\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 ltcf_staff_age_max=60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 with_scho ol_types=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 school_mixing_type='random'\T1/p tm/m/n/10 , \T1/ptm/m/it/10 av- Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 er-age_class_size=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_gra de_mixing=0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av-er-age_student_teacher_ratio=2 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 av-er-age_teacher_teacher_degree=3\T1/ptm/m/n/10 , \T1/ptm/m/it /10 teacher_age_min=25\T1/ptm/m/n/10 , \T1/ptm/m/it/10 teacher_age_max=75\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 with_non_teaching_staff=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 a v-er-age_student_all_staff_ratio=15\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av-er- [73] [74] [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 6838--6838 []\T1/ptm/m/it/10 student_lists\T1/ptm/m/n/10 , \T1/ptm/m/it/10 teacher_lists\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 non_teaching_staff_lists\T1/ptm/m/n/10 , \T1/ptm /m/it/10 age_by_uid\T1/ptm/m/n/10 , [77] [78] [79] [80] [81] [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7718--7718 []\T1/ptm/m/it/10 scid=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sc_type=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 school_mixing_type=None\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 stu-dent_uids=array([]\T1/ptm/m/n/10 , [84] Underfull \hbox (badness 10000) in paragraph at lines 7738--7739 []\T1/pcr/b/n/10 **school_mixing_type \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 str\T1/pt m/m/n/10 ) ^^U the mix-ing type of the school, `ran- Underfull \hbox (badness 10000) in paragraph at lines 7840--7840 []\T1/ptm/m/it/10 clid=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 stu-dent_uids=array ([]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dtype=int64)\T1/ptm/m/n/10 , \T1/ptm/m/it/1 0 teacher_uids=array([]\T1/ptm/m/n/10 , [85] [86] [87] [88] Chapter 7. [89] [90] [91] (./institute-for-disease-modeling-synthpops-test.ind [92] Underfull \hbox (badness 10000) in paragraph at lines 13--14 []\T1/pcr/m/n/10 add_workplace() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 7981) in paragraph at lines 19--20 []\T1/pcr/m/n/10 assign_facility_staff() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 assign_uids_by_homes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 26--27 []\T1/pcr/m/n/10 binned_values_dist() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/pcr/m/n/10 calculate_which_nbrackets_to_use() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Overfull \hbox (58.1225pt too wide) in paragraph at lines 38--40 []\T1/pcr/m/n/10 check_all_probability_distribution_nonnegative() Overfull \hbox (16.1225pt too wide) in paragraph at lines 40--42 []\T1/pcr/m/n/10 check_all_probability_distribution_sums() Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/pcr/m/n/10 check_array_of_array_entry_lens_arr() Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 check_array_of_arrays_entry_lens() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 7291) in paragraph at lines 51--53 []\T1/pcr/m/n/10 check_household_head_age_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (100.1225pt too wide) in paragraph at lines 53--55 []\T1/pcr/m/n/10 check_household_head_age_distributions_by_family_size() Underfull \hbox (badness 7291) in paragraph at lines 55--57 []\T1/pcr/m/n/10 check_household_size_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Underfull \hbox (badness 10000) in paragraph at lines 57--59 []\T1/pcr/m/n/10 check_location_constraints_satisfied() Underfull \hbox (badness 10000) in paragraph at lines 59--60 []\T1/pcr/m/n/10 check_location_name() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Overfull \hbox (4.1225pt too wide) in paragraph at lines 60--62 []\T1/pcr/m/n/10 check_ltcf_num_residents_distribution() Underfull \hbox (badness 7291) in paragraph at lines 62--64 []\T1/pcr/m/n/10 check_ltcf_num_staff_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (64.1225pt too wide) in paragraph at lines 64--66 []\T1/pcr/m/n/10 check_ltcf_resident_to_staff_ratio_distribution() Overfull \hbox (34.1225pt too wide) in paragraph at lines 70--72 []\T1/pcr/m/n/10 check_probability_distribution_nonnegative() Overfull \hbox (142.1225pt too wide) in paragraph at lines 72--74 []\T1/pcr/m/n/10 check_probability_distribution_nonnegative_age_distributions() Overfull \hbox (94.1225pt too wide) in paragraph at lines 76--78 []\T1/pcr/m/n/10 check_probability_distribution_sum_age_distributions() Underfull \hbox (badness 10000) in paragraph at lines 78--80 []\T1/pcr/m/n/10 check_school_size_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (10.1225pt too wide) in paragraph at lines 82--84 []\T1/pcr/m/n/10 check_school_size_distribution_by_type() [93] Overfull \hbox (4.1225pt too wide) in paragraph at lines 88--90 []\T1/pcr/m/n/10 check_valid_probability_distributions() Overfull \hbox (46.1225pt too wide) in paragraph at lines 90--92 []\T1/pcr/m/n/10 check_workplace_size_counts_by_num_personnel() Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/pcr/m/n/10 compute_layer_degree_description() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 10000) in paragraph at lines 104--105 []\T1/pcr/m/n/10 count_binned_values() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 111--113 []\T1/pcr/m/n/10 count_enrollment_by_school_type() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Underfull \hbox (badness 10000) in paragraph at lines 113--114 []\T1/pcr/m/n/10 count_enrollment_by_school_type() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 Pop Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/pcr/m/n/10 count_layer_degree() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (22.1225pt too wide) in paragraph at lines 122--124 []\T1/pcr/m/n/10 create_reduced_contacts_with_group_types() Underfull \hbox (badness 10000) in paragraph at lines 128--129 []\T1/pcr/m/n/10 default_datadir_path() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 129--130 []\T1/pcr/m/n/10 default_plotting_kwargs() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 plot -ting_kwargs Underfull \hbox (badness 10000) in paragraph at lines 143--144 []\T1/pcr/m/n/10 filter_people() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 10000) in paragraph at lines 148--149 []\T1/pcr/m/n/10 generate_age_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (76.1225pt too wide) in paragraph at lines 157--159 []\T1/pcr/m/n/10 generate_household_size_count_from_fixed_pop_size() Overfull \hbox (4.1225pt too wide) in paragraph at lines 161--163 []\T1/pcr/m/n/10 generate_larger_households_fixed_ages() Overfull \hbox (4.1225pt too wide) in paragraph at lines 163--165 []\T1/pcr/m/n/10 generate_larger_households_infer_ages() Underfull \hbox (badness 10000) in paragraph at lines 168--169 []\T1/pcr/m/n/10 get_age_by_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 get_aggregate_ages() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 10000) in paragraph at lines 170--171 []\T1/pcr/m/n/10 get_aggregate_matrix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 171--172 []\T1/pcr/m/n/10 get_all_households() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 7981) in paragraph at lines 172--173 []\T1/pcr/m/n/10 get_asymmetric_matrix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- [94] Underfull \hbox (badness 10000) in paragraph at lines 181--182 []\T1/pcr/m/n/10 get_contact_counts_by_layer() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Pop Underfull \hbox (badness 10000) in paragraph at lines 182--184 []\T1/pcr/m/n/10 get_contact_matrices() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 184--186 []\T1/pcr/m/n/10 get_contact_matrix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (10.1225pt too wide) in paragraph at lines 186--188 []\T1/pcr/m/n/10 get_default_school_size_distr_brackets() Overfull \hbox (4.1225pt too wide) in paragraph at lines 188--190 []\T1/pcr/m/n/10 get_default_school_size_distr_by_type() Overfull \hbox (10.1225pt too wide) in paragraph at lines 192--194 []\T1/pcr/m/n/10 get_default_school_types_by_age_single() Overfull \hbox (4.1225pt too wide) in paragraph at lines 194--196 []\T1/pcr/m/n/10 get_default_school_types_distr_by_age() Underfull \hbox (badness 10000) in paragraph at lines 196--198 []\T1/pcr/m/n/10 get_employment_rates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 202--204 []\T1/pcr/m/n/10 get_expected_density() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Overfull \hbox (28.1225pt too wide) in paragraph at lines 204--206 []\T1/pcr/m/n/10 get_generated_household_size_distribution() Overfull \hbox (16.1225pt too wide) in paragraph at lines 206--208 []\T1/pcr/m/n/10 get_generated_school_size_distributions() Overfull \hbox (28.1225pt too wide) in paragraph at lines 208--210 []\T1/pcr/m/n/10 get_generated_workplace_size_distribution() Underfull \hbox (badness 7981) in paragraph at lines 210--212 []\T1/pcr/m/n/10 get_head_age_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 212--214 []\T1/pcr/m/n/10 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6] Chapter 3. [7] Underfull \hbox (badness 10000) in paragraph at lines 247--248 []\T1/ptm/m/n/10 Method to gen-er-ate the count of house-hold sizes for a fixed pop-u-la-tion re-named: \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 247--248 \T1/pcr/m/n/10 households.generate_household_sizes_from_fixed_pop_size \T1/ptm/ m/n/10 ^^U> \T1/pcr/m/n/10 sp.households. [8] Underfull \hbox (badness 10000) in paragraph at lines 310--311 []\T1/ptm/m/n/10 Method name changes: \T1/pcr/m/n/10 sp.get_age_by_brackets_dic () \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 310--311 \T1/pcr/m/n/10 get_age_by_brackets()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp.get_inde x_by_brackets_dic() \T1/ptm/m/n/10 -> \T1/pcr/m/n/10 sp. 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Underfull \hbox (badness 10000) in paragraph at lines 420--421 []\T1/ptm/m/it/10 Feature\T1/ptm/m/n/10 : Added checks for prob-a-bil-ity dis-t ri-bu-tions with meth-ods \T1/pcr/m/n/10 sp. Overfull \hbox (114.26503pt too wide) in paragraph at lines 420--421 \T1/pcr/m/n/10 check_all_probability_distribution_sums()\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sp.check_all_probability_distrubution_nonnegative()\T1/ptm/m/n/10 , Overfull \hbox (78.26503pt too wide) in paragraph at lines 420--421 \T1/pcr/m/n/10 sp.check_probability_distribution_sum()\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 sp.check_probability_distribution_nonnegative()\T1/ptm/m/n/10 . [10] Underfull \hbox (badness 10000) in paragraph at lines 457--458 []\T1/ptm/m/it/10 Feature\T1/ptm/m/n/10 : Added new meth-ods, \T1/pcr/m/n/10 sp .get_household_head_ages_by_size()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sp. Underfull \hbox (badness 10000) in paragraph at lines 457--458 \T1/pcr/m/n/10 plot_household_head_ages_by_size()\T1/ptm/m/n/10 . Also ac-ces-s i-ble pop meth-ods as \T1/pcr/m/n/10 pop. Underfull \hbox (badness 10000) in paragraph at lines 457--458 \T1/pcr/m/n/10 get_household_head_ages_by_size()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pop.plot_household_head_ages_by_size()\T1/ptm/m/n/10 . [11] [12] Chapter 4. [13] [14] Chapter 5. [15] [16] [17] Underfull \hbox (badness 5374) in paragraph at lines 854--858 []\T1/ptm/b/n/10 Enrollment by age \T1/ptm/m/n/10 spec-i-fy-ing the per-cent-ag e of peo-ple of each age at-tend-ing school. See [18] [19] [20] [21] [22] [23] Overfull \vbox (0.68163pt too high) detected at line 1325 [24] [25] [26] [27] [28] Chapter 6. [29] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 []\T1/ptm/m/it/10 age_by_uid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 homes_by_uids\T1/p tm/m/n/10 , \T1/ptm/m/it/10 stu-dents_by_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm /m/it/10 teach- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 ers_by_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 non_teach ing_staff_uid_lists=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 school_mixing_type='random'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av- er-age_class_size=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_grade_mixing=0.1\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 av-er-age_student_teacher_ratio=20\T1/ptm/m/n/10 , \T1/ptm/m/it /10 av-er-age_teacher_teacher_degree=3\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av- Underfull \hbox (badness 10000) in paragraph at lines 1946--1946 \T1/ptm/m/it/10 er-age_student_all_staff_ratio=15\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 av-er-age_additional_staff_degree=20\T1/ptm/m/n/10 , [33] Underfull \hbox (badness 5274) in paragraph at lines 2029--2031 \T1/ptm/m/n/10 Methods to trim large groups of con-tacts down to bet-ter ap-pro x-i-mate a sense of close con- Underfull \hbox (badness 6300) in paragraph at lines 2029--2031 \T1/ptm/m/n/10 tacts (such as class-room sizes or smaller work groups are avail -able via sp.trim_contacts() or [34] Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 []\T1/ptm/m/it/10 popdict\T1/ptm/m/n/10 , \T1/ptm/m/it/10 group_1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 group_2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 set-ting\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 \T1/ptm/m/it/10 av-er-age_degree=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 p_matrix=No ne\T1/ptm/m/n/10 , [35] Underfull \hbox (badness 10000) in paragraph at lines 2189--2189 []\T1/ptm/m/it/10 pop\T1/ptm/m/n/10 , \T1/ptm/m/it/10 layer='H'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ages=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 uids=None\T1/ptm/m/n /10 , [36] [37] [38] [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 2900--2900 []\T1/ptm/m/it/10 location\T1/ptm/m/n/10 , \T1/ptm/m/it/10 prop-erty_name\T1/pt m/m/n/10 , \T1/ptm/m/it/10 tol-er-ance=0.01\T1/ptm/m/n/10 , [41] Underfull \hbox (badness 10000) in paragraph at lines 2932--2932 []\T1/ptm/m/it/10 location\T1/ptm/m/n/10 , \T1/ptm/m/it/10 prop-erty_name\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2958--2958 []\T1/ptm/m/it/10 location\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tol-er-ance=0.01\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 die=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver- [42] [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3454--3454 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- [45] Underfull \hbox (badness 10000) in paragraph at lines 3497--3497 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3497--3497 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nbrack-e ts=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3544--3544 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- [46] Underfull \hbox (badness 10000) in paragraph at lines 3590--3590 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 3635--3635 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- [47] Underfull \hbox (badness 10000) in paragraph at lines 3679--3679 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- Underfull \hbox (badness 7704) in paragraph at lines 3722--3722 []\T1/ptm/m/it/10 datadir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 set-ting_code\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 sheet_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_p ath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-lim-iter=' '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3765--3765 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sheet_name=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_path_dic=None\T1/ptm/m/n/10 , \T1/ptm/m/it /10 de-lim-iter=' '\T1/ptm/m/n/10 , [48] Underfull \hbox (badness 10000) in paragraph at lines 3808--3808 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 3850--3850 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- [49] [50] Underfull \hbox (badness 10000) in paragraph at lines 4017--4017 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 4055--4055 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- [51] Underfull \hbox (badness 10000) in paragraph at lines 4139--4139 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/i t/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 4181--4181 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_pat h=None\T1/ptm/m/n/10 , [52] Underfull \hbox (badness 10000) in paragraph at lines 4247--4247 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion=None\ T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4247--4247 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 4247--4247 \T1/ptm/m/it/10 try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4286--4286 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4286--4286 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4286--4286 \T1/ptm/m/it/10 file_path=None\T1/ptm/m/n/10 , [53] Underfull \hbox (badness 10000) in paragraph at lines 4324--4324 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4324--4324 \T1/ptm/m/it/10 lo-ca-tion=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4324--4324 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4324--4324 \T1/ptm/m/it/10 coun- Underfull \hbox (badness 10000) in paragraph at lines 4324--4324 \T1/ptm/m/it/10 try_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4324--4324 \T1/ptm/m/it/10 file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4363--4363 []\T1/ptm/m/it/10 datadir=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 lo-ca-tion=None\T1/ptm/m/n/10 , Overfull \hbox (14.27411pt too wide) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 state_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 coun- Overfull \hbox (6.49422pt too wide) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 try_location=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 file_path=None\T1/ptm/m/n/10 , Overfull \hbox (7.57417pt too wide) in paragraph at lines 4363--4363 \T1/ptm/m/it/10 use_default=False\T1/pcr/m/n/10 ) [54] Underfull \hbox (badness 10000) in paragraph at lines 4402--4402 \T1/ptm/m/it/10 coun-try_location=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_pat h=None\T1/ptm/m/n/10 , [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 4789--4789 []\T1/ptm/m/it/10 larger_hh_size_array\T1/ptm/m/n/10 , \T1/ptm/m/it/10 larger_h ha_chosen\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4789--4789 \T1/ptm/m/it/10 hha_brackets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cm_age_brackets\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4789--4789 \T1/ptm/m/it/10 cm_age_by_brackets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 house-hold_m atrix\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4831--4831 []\T1/ptm/m/it/10 n_remaining\T1/ptm/m/n/10 , \T1/ptm/m/it/10 hh_sizes\T1/ptm/m /n/10 , \T1/ptm/m/it/10 hha_by_size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 hha_bracket s\T1/ptm/m/n/10 , [58] Underfull \hbox (badness 10000) in paragraph at lines 4882--4882 []\T1/ptm/m/it/10 size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 larger_household_sizes\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4882--4882 \T1/ptm/m/it/10 heads_of_larger_households\T1/ptm/m/n/10 , \T1/ptm/m/it/10 hha_ brackets\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4882--4882 \T1/ptm/m/it/10 cm_age_brackets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cm_age_by_brack ets\T1/ptm/m/n/10 , \T1/ptm/m/it/10 house- [59] [60] Underfull \hbox (badness 5741) in paragraph at lines 5147--5147 []\T1/ptm/m/it/10 datadir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-ca-tion\T1/ptm/m/n /10 , \T1/ptm/m/it/10 state_location\T1/ptm/m/n/10 , \T1/ptm/m/it/10 coun-try_l ocation\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ltcf_staff_age_min\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5147--5147 \T1/ptm/m/it/10 ltcf_staff_age_max\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fa-cil-i-tie s\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work-ers_by_age_to_assign_count\T1/ptm/m/n/10 , \T1/ptm/m/it/10 po- Underfull \hbox (badness 10000) in paragraph at lines 5147--5147 \T1/ptm/m/it/10 ten-tial_worker_uids_by_age\T1/ptm/m/n/10 , \T1/ptm/m/it/10 po- ten-tial_worker_uids\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fa-cil-i-ties_by_uids\T1/p tm/m/n/10 , [61] Underfull \hbox (badness 10000) in paragraph at lines 5202--5202 \T1/ptm/m/it/10 po-ten-tial_worker_uids_by_age\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work- [62] Underfull \hbox (badness 10000) in paragraph at lines 5297--5297 []\T1/ptm/m/it/10 ltcfid=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res-i-dent_uids=a rray([]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dtype=int64)\T1/ptm/m/n/10 , [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 []\T1/ptm/m/it/10 n=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 max_contacts=None\T1/p tm/m/n/10 , \T1/ptm/m/it/10 ltcf_pars=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 scho ol_pars=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 with_industry_code=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 with_f acilities=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_default=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 use_two_group_reduction=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av -er-age_LTCF_degree=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ltcf_staff_age_min=20\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 ltcf_staff_age_max=60\T1/ptm/m/n/10 , \T1/ptm/m/it/10 with_scho ol_types=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 school_mixing_type='random'\T1/p tm/m/n/10 , \T1/ptm/m/it/10 av- Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 er-age_class_size=20\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_gra de_mixing=0.1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av-er-age_student_teacher_ratio=2 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 av-er-age_teacher_teacher_degree=3\T1/ptm/m/n/10 , \T1/ptm/m/it /10 teacher_age_min=25\T1/ptm/m/n/10 , \T1/ptm/m/it/10 teacher_age_max=75\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6364--6364 \T1/ptm/m/it/10 with_non_teaching_staff=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 a v-er-age_student_all_staff_ratio=15\T1/ptm/m/n/10 , \T1/ptm/m/it/10 av-er- [73] [74] [75] [76] Underfull \hbox (badness 10000) in paragraph at lines 6838--6838 []\T1/ptm/m/it/10 student_lists\T1/ptm/m/n/10 , \T1/ptm/m/it/10 teacher_lists\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 non_teaching_staff_lists\T1/ptm/m/n/10 , \T1/ptm /m/it/10 age_by_uid\T1/ptm/m/n/10 , [77] [78] [79] [80] [81] [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7718--7718 []\T1/ptm/m/it/10 scid=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sc_type=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 school_mixing_type=None\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 stu-dent_uids=array([]\T1/ptm/m/n/10 , [84] Underfull \hbox (badness 10000) in paragraph at lines 7738--7739 []\T1/pcr/b/n/10 **school_mixing_type \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 str\T1/pt m/m/n/10 ) ^^U the mix-ing type of the school, `ran- Underfull \hbox (badness 10000) in paragraph at lines 7840--7840 []\T1/ptm/m/it/10 clid=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 stu-dent_uids=array ([]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dtype=int64)\T1/ptm/m/n/10 , \T1/ptm/m/it/1 0 teacher_uids=array([]\T1/ptm/m/n/10 , [85] [86] [87] [88] Chapter 7. [89] [90] [91] (./institute-for-disease-modeling-synthpops-test.ind [92] Underfull \hbox (badness 10000) in paragraph at lines 13--14 []\T1/pcr/m/n/10 add_workplace() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 7981) in paragraph at lines 19--20 []\T1/pcr/m/n/10 assign_facility_staff() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 assign_uids_by_homes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 26--27 []\T1/pcr/m/n/10 binned_values_dist() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/pcr/m/n/10 calculate_which_nbrackets_to_use() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Overfull \hbox (58.1225pt too wide) in paragraph at lines 38--40 []\T1/pcr/m/n/10 check_all_probability_distribution_nonnegative() Overfull \hbox (16.1225pt too wide) in paragraph at lines 40--42 []\T1/pcr/m/n/10 check_all_probability_distribution_sums() Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/pcr/m/n/10 check_array_of_array_entry_lens_arr() Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 check_array_of_arrays_entry_lens() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 7291) in paragraph at lines 51--53 []\T1/pcr/m/n/10 check_household_head_age_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (100.1225pt too wide) in paragraph at lines 53--55 []\T1/pcr/m/n/10 check_household_head_age_distributions_by_family_size() Underfull \hbox (badness 7291) in paragraph at lines 55--57 []\T1/pcr/m/n/10 check_household_size_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Underfull \hbox (badness 10000) in paragraph at lines 57--59 []\T1/pcr/m/n/10 check_location_constraints_satisfied() Underfull \hbox (badness 10000) in paragraph at lines 59--60 []\T1/pcr/m/n/10 check_location_name() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Overfull \hbox (4.1225pt too wide) in paragraph at lines 60--62 []\T1/pcr/m/n/10 check_ltcf_num_residents_distribution() Underfull \hbox (badness 7291) in paragraph at lines 62--64 []\T1/pcr/m/n/10 check_ltcf_num_staff_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (64.1225pt too wide) in paragraph at lines 64--66 []\T1/pcr/m/n/10 check_ltcf_resident_to_staff_ratio_distribution() Overfull \hbox (34.1225pt too wide) in paragraph at lines 70--72 []\T1/pcr/m/n/10 check_probability_distribution_nonnegative() Overfull \hbox (142.1225pt too wide) in paragraph at lines 72--74 []\T1/pcr/m/n/10 check_probability_distribution_nonnegative_age_distributions() Overfull \hbox (94.1225pt too wide) in paragraph at lines 76--78 []\T1/pcr/m/n/10 check_probability_distribution_sum_age_distributions() Underfull \hbox (badness 10000) in paragraph at lines 78--80 []\T1/pcr/m/n/10 check_school_size_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (10.1225pt too wide) in paragraph at lines 82--84 []\T1/pcr/m/n/10 check_school_size_distribution_by_type() [93] Overfull \hbox (4.1225pt too wide) in paragraph at lines 88--90 []\T1/pcr/m/n/10 check_valid_probability_distributions() Overfull \hbox (46.1225pt too wide) in paragraph at lines 90--92 []\T1/pcr/m/n/10 check_workplace_size_counts_by_num_personnel() Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/pcr/m/n/10 compute_layer_degree_description() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 10000) in paragraph at lines 104--105 []\T1/pcr/m/n/10 count_binned_values() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 111--113 []\T1/pcr/m/n/10 count_enrollment_by_school_type() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Underfull \hbox (badness 10000) in paragraph at lines 113--114 []\T1/pcr/m/n/10 count_enrollment_by_school_type() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 Pop Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/pcr/m/n/10 count_layer_degree() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (22.1225pt too wide) in paragraph at lines 122--124 []\T1/pcr/m/n/10 create_reduced_contacts_with_group_types() Underfull \hbox (badness 10000) in paragraph at lines 128--129 []\T1/pcr/m/n/10 default_datadir_path() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 129--130 []\T1/pcr/m/n/10 default_plotting_kwargs() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 plot -ting_kwargs Underfull \hbox (badness 10000) in paragraph at lines 143--144 []\T1/pcr/m/n/10 filter_people() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 10000) in paragraph at lines 148--149 []\T1/pcr/m/n/10 generate_age_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (76.1225pt too wide) in paragraph at lines 157--159 []\T1/pcr/m/n/10 generate_household_size_count_from_fixed_pop_size() Overfull \hbox (4.1225pt too wide) in paragraph at lines 161--163 []\T1/pcr/m/n/10 generate_larger_households_fixed_ages() Overfull \hbox (4.1225pt too wide) in paragraph at lines 163--165 []\T1/pcr/m/n/10 generate_larger_households_infer_ages() Underfull \hbox (badness 10000) in paragraph at lines 168--169 []\T1/pcr/m/n/10 get_age_by_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 get_aggregate_ages() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 10000) in paragraph at lines 170--171 []\T1/pcr/m/n/10 get_aggregate_matrix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 171--172 []\T1/pcr/m/n/10 get_all_households() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 7981) in paragraph at lines 172--173 []\T1/pcr/m/n/10 get_asymmetric_matrix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- [94] Underfull \hbox (badness 10000) in paragraph at lines 181--182 []\T1/pcr/m/n/10 get_contact_counts_by_layer() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Pop Underfull \hbox (badness 10000) in paragraph at lines 182--184 []\T1/pcr/m/n/10 get_contact_matrices() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 184--186 []\T1/pcr/m/n/10 get_contact_matrix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (10.1225pt too wide) in paragraph at lines 186--188 []\T1/pcr/m/n/10 get_default_school_size_distr_brackets() Overfull \hbox (4.1225pt too wide) in paragraph at lines 188--190 []\T1/pcr/m/n/10 get_default_school_size_distr_by_type() Overfull \hbox (10.1225pt too wide) in paragraph at lines 192--194 []\T1/pcr/m/n/10 get_default_school_types_by_age_single() Overfull \hbox (4.1225pt too wide) in paragraph at lines 194--196 []\T1/pcr/m/n/10 get_default_school_types_distr_by_age() Underfull \hbox (badness 10000) in paragraph at lines 196--198 []\T1/pcr/m/n/10 get_employment_rates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 202--204 []\T1/pcr/m/n/10 get_expected_density() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Overfull \hbox (28.1225pt too wide) in paragraph at lines 204--206 []\T1/pcr/m/n/10 get_generated_household_size_distribution() Overfull \hbox (16.1225pt too wide) in paragraph at lines 206--208 []\T1/pcr/m/n/10 get_generated_school_size_distributions() Overfull \hbox (28.1225pt too wide) in paragraph at lines 208--210 []\T1/pcr/m/n/10 get_generated_workplace_size_distribution() Underfull \hbox (badness 7981) in paragraph at lines 210--212 []\T1/pcr/m/n/10 get_head_age_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 212--214 []\T1/pcr/m/n/10 get_head_age_by_size_distr() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 get_household_head_ages_by_size() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Underfull \hbox (badness 10000) in paragraph at lines 219--220 []\T1/pcr/m/n/10 get_household_head_ages_by_size() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 Pop Underfull \hbox (badness 10000) in paragraph at lines 220--221 []\T1/pcr/m/n/10 get_household_heads() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 224--225 []\T1/pcr/m/n/10 get_household_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 7981) in paragraph at lines 227--228 []\T1/pcr/m/n/10 get_index_by_brackets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Overfull \hbox (148.1225pt too wide) in paragraph at lines 230--232 []\T1/pcr/m/n/10 get_long_term_care_facility_resident_to_staff_ratios_brackets( ) Overfull 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(badness 10000) in paragraph at lines 259--261 []\T1/pcr/m/n/10 get_school_type_age_ranges() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 7981) in paragraph at lines 265--267 []\T1/pcr/m/n/10 get_state_postal_code() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 267--268 []\T1/pcr/m/n/10 get_workplace() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 10000) in paragraph at lines 271--273 []\T1/pcr/m/n/10 get_workplace_size_distr_by_brackets() Underfull \hbox (badness 10000) in paragraph at lines 273--274 []\T1/pcr/m/n/10 get_workplace_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- [95] Underfull \hbox (badness 7888) in paragraph at lines 280--281 []\T1/pcr/m/n/10 household_head_age_brackets \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Lo -ca-tion at- Overfull \hbox (46.1225pt too wide) in paragraph at lines 281--283 []\T1/pcr/m/n/10 household_head_age_distribution_by_family_size Underfull \hbox (badness 7888) in paragraph at lines 283--284 []\T1/pcr/m/n/10 household_size_distribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Lo -ca-tion at- Underfull \hbox (badness 10000) in paragraph at lines 290--291 []\T1/pcr/m/n/10 initialize_empty_households() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Pop Underfull \hbox (badness 10000) in paragraph at lines 296--297 []\T1/pcr/m/n/10 initialize_empty_workplaces() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Pop Underfull \hbox (badness 10000) in paragraph at lines 306--308 []\T1/pcr/m/n/10 load_location() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 7888) in paragraph at lines 318--319 []\T1/pcr/m/n/10 ltcf_num_staff_distribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Lo -ca-tion at- Overfull \hbox (16.1225pt too wide) in paragraph at lines 320--322 []\T1/pcr/m/n/10 ltcf_resident_to_staff_ratio_distribution Underfull \hbox (badness 10000) in paragraph at lines 322--323 []\T1/pcr/m/n/10 ltcf_use_rate_distribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Lo- ca-tion at- Underfull \hbox (badness 10000) in paragraph at lines 326--327 []\T1/pcr/m/n/10 make_contacts() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn -th- Underfull \hbox (badness 10000) in paragraph at lines 351--352 []\T1/pcr/m/n/10 plot_contact_counts() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 357--358 []\T1/pcr/m/n/10 plot_employment_rates_by_age() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Pop Underfull \hbox (badness 10000) in paragraph at lines 360--361 []\T1/pcr/m/n/10 plot_enrollment_rates_by_age() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 Pop Underfull \hbox (badness 10000) in paragraph at lines 361--363 []\T1/pcr/m/n/10 plot_household_head_ages_by_size() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Underfull \hbox (badness 10000) in paragraph at lines 364--365 []\T1/pcr/m/n/10 plot_household_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- [96] Underfull \hbox (badness 10000) in paragraph at lines 370--371 []\T1/pcr/m/n/10 plot_school_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 372--373 []\T1/pcr/m/n/10 plot_workplace_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 378--379 []\T1/pcr/m/n/10 populate_households() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 10000) in paragraph at lines 382--383 []\T1/pcr/m/n/10 populate_parent_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 383--385 []\T1/pcr/m/n/10 populate_parent_data_from_file_path() Underfull \hbox (badness 10000) in paragraph at lines 388--389 []\T1/pcr/m/n/10 populate_workplaces() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le syn-th- Underfull \hbox (badness 5217) in paragraph at lines 391--392 []\T1/pcr/m/n/10 PopulationAgeDistribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 clas s in syn-th- Underfull \hbox (badness 10000) in paragraph at lines 395--397 []\T1/pcr/m/n/10 random_graph_model() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Overfull \hbox (46.1225pt too wide) in paragraph at lines 400--402 []\T1/pcr/m/n/10 remove_ltcf_residents_from_potential_workers() Underfull \hbox (badness 7981) in paragraph at lines 406--408 []\T1/pcr/m/n/10 reset_settings_by_key() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 413--414 []\T1/pcr/m/n/10 sample_from_range() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 414--415 []\T1/pcr/m/n/10 sample_single_arr() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 415--416 []\T1/pcr/m/n/10 sample_single_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e syn-th- Underfull \hbox (badness 10000) in paragraph at lines 416--418 []\T1/pcr/m/n/10 sanitize_location() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule syn-th- Underfull \hbox (badness 10000) in paragraph at lines 425--427 []\T1/pcr/m/n/10 school_size_distribution_by_type \T1/ptm/m/n/10 (\T1/ptm/m/it/ 10 Lo-ca- Underfull \hbox (badness 10000) in paragraph at lines 427--428 []\T1/pcr/m/n/10 school_type \T1/ptm/m/n/10 (\T1/ptm/m/it/10 School-SizeDis-tri -bu-tion-By-Type at- Underfull \hbox (badness 10000) in paragraph at lines 433--434 []\T1/pcr/m/n/10 set_default_pop_pars() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 plot-ti ng_kwargs Underfull \hbox (badness 10000) in paragraph at lines 434--435 []\T1/pcr/m/n/10 set_figure_display_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 plot -ting_kwargs Underfull \hbox (badness 7981) in paragraph at lines 438--439 []\T1/pcr/m/n/10 set_location_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule syn-th- [97] Underfull \hbox (badness 10000) in paragraph at lines 491--493 []\T1/pcr/m/n/10 workplace_size_counts_by_num_personnel [98]) (./institute-for-disease-modeling-synthpops-test.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-synthpops-test.pdf (102 pages, 360666 bytes). Transcript written on institute-for-disease-modeling-synthpops-test.log. Latexmk: Index file 'institute-for-disease-modeling-synthpops-test.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-synthpops-test.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-synthpops-test.pdf' Latexmk: All targets (institute-for-disease-modeling-synthpops-test.pdf) are up-to-date [rtd-command-info] start-time: 2021-05-19T01:19:14.467442Z, end-time: 2021-05-19T01:19:14.541533Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/v1.8.3/docs/_build/latex/institute-for-disease-modeling-synthpops-test.pdf /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/artifacts/v1.8.3/sphinx_pdf/institute-for-disease-modeling-synthpops-test.pdf