Read the Docs build information Build id: 533041 Project: institute-for-disease-modeling-emod-api Version: v1.5.0 Commit: 75eefc47c0b76af4496436f144955e1df823018c Date: 2021-01-15T21:41:45.820740Z State: finished Success: True [rtd-command-info] start-time: 2021-01-15T21:41:47.318759Z, end-time: 2021-01-15T21:41:48.250646Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emod-api.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-01-15T21:41:48.868972Z, end-time: 2021-01-15T21:41:49.058880Z, duration: 0, exit-code: 0 git checkout --force 75eefc47c0b76af4496436f144955e1df823018c Note: checking out '75eefc47c0b76af4496436f144955e1df823018c'. 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 75eefc4 Fixed generic schema [rtd-command-info] start-time: 2021-01-15T21:41:49.283276Z, end-time: 2021-01-15T21:41:49.336444Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-01-15T21:41:51.208856Z, end-time: 2021-01-15T21:41:56.975954Z, duration: 5, 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-emod-api/envs/v1.5.0/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-01-15T21:41:57.143887Z, end-time: 2021-01-15T21:41:58.990901Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (20.3.3) [rtd-command-info] start-time: 2021-01-15T21:41:59.302751Z, end-time: 2021-01-15T21:42:09.007510Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) 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 recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.2-py2.py3-none-any.whl (11 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting six Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.4-py3-none-any.whl (950 kB) Collecting pytz>=2015.7 Downloading pytz-2020.5-py2.py3-none-any.whl (510 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 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 idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.2-py2.py3-none-any.whl (136 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting packaging Downloading packaging-20.8-py2.py3-none-any.whl (39 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 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=04f4a1c58b3d106019dde40bd735a711d7091c2b082669f0558cb65e95c6c912 Stored in directory: /tmp/pip-ephem-wheel-cache-rwnw6gp_/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=8e92271bd6e5d66438baac9581533342ee4334401f08264aa913682444769005 Stored in directory: /tmp/pip-ephem-wheel-cache-rwnw6gp_/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 Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.4 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.5 readthedocs-sphinx-ext-2.1.2 recommonmark-0.5.0 requests-2.25.1 setuptools-51.1.2 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2 [rtd-command-info] start-time: 2021-01-15T21:42:09.125177Z, end-time: 2021-01-15T21:42:15.794268Z, duration: 6, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Requirement already satisfied: pandas in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (1.1.3) Requirement already satisfied: scipy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 5)) (1.5.3) Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 8)) (3.3.2) Collecting numpy==1.19.3 Downloading numpy-1.19.3-cp37-cp37m-manylinux2010_x86_64.whl (14.9 MB) Collecting geopy Downloading geopy-2.1.0-py3-none-any.whl (112 kB) Collecting geographiclib<2,>=1.49 Downloading geographiclib-1.50-py3-none-any.whl (38 kB) Collecting lz4 Downloading lz4-3.1.1-cp37-cp37m-manylinux2010_x86_64.whl (1.8 MB) Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (2020.12.5) Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (1.2.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (2.4.7) Requirement already satisfied: python-dateutil>=2.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (2.8.1) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from cycler>=0.10->matplotlib->-r requirements.txt (line 8)) (1.15.0) Collecting pillow>=6.2.0 Downloading Pillow-8.1.0-cp37-cp37m-manylinux1_x86_64.whl (2.2 MB) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 4)) (2020.5) Collecting pyproj Downloading pyproj-3.0.0.post1-cp37-cp37m-manylinux2010_x86_64.whl (6.4 MB) Collecting pyyaml Downloading PyYAML-5.3.1.tar.gz (269 kB) Collecting shapely Downloading Shapely-1.7.1-cp37-cp37m-manylinux1_x86_64.whl (1.0 MB) Building wheels for collected packages: pyyaml Building wheel for pyyaml (setup.py): started Building wheel for pyyaml (setup.py): finished with status 'done' Created wheel for pyyaml: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44620 sha256=9eff250ec9a9300c392501a8d5f72dccebd899ed0904197fc538518c33de3e25 Stored in directory: /tmp/pip-ephem-wheel-cache-lsma4bc5/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653 Successfully built pyyaml Installing collected packages: pillow, numpy, geographiclib, shapely, pyyaml, pyproj, lz4, geopy Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: numpy Found existing installation: numpy 1.19.2 Not uninstalling numpy at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0 Can't uninstall 'numpy'. No files were found to uninstall. Successfully installed geographiclib-1.50 geopy-2.1.0 lz4-3.1.1 numpy-1.19.3 pillow-8.1.0 pyproj-3.0.0.post1 pyyaml-5.3.1 shapely-1.7.1 [rtd-command-info] start-time: 2021-01-15T21:42:16.195645Z, end-time: 2021-01-15T21:42:22.459359Z, duration: 6, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (0.14) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (2.25.1) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (1.15.0) Collecting pygit2~=1.2.1 Downloading pygit2-1.2.1-cp37-cp37m-manylinux2010_x86_64.whl (3.0 MB) Collecting PyGithub~=1.51 Downloading PyGithub-1.54.1-py3-none-any.whl (289 kB) Collecting sphinx~=3.2.1 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.11.2) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.1.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (51.1.2) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.2.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.9.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (20.8) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.7.4) Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.1-py2.py3-none-any.whl (2.8 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading sphinxcontrib_programoutput-0.16-py2.py3-none-any.whl (21 kB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2020.5) Collecting cffi>=1.4.0 Downloading cffi-1.14.4-cp37-cp37m-manylinux1_x86_64.whl (402 kB) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.1.1) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Collecting pyjwt<2.0 Downloading PyJWT-1.7.1-py2.py3-none-any.whl (18 kB) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (2020.12.5) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (2.10) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-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-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (1.26.2) Collecting py-make Downloading py_make-0.1.1-py2.py3-none-any.whl (9.4 kB) Collecting docopt>=0.6.0 Downloading docopt-0.6.2.tar.gz (25 kB) Collecting cached-property Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Collecting deprecated Downloading Deprecated-1.2.10-py2.py3-none-any.whl (8.7 kB) Collecting wrapt<2,>=1.10 Downloading wrapt-1.12.1.tar.gz (27 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages (from packaging->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.4.7) Collecting pycparser Downloading pycparser-2.20-py2.py3-none-any.whl (112 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Building wheels for collected packages: docopt, wrapt Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=db3fef606d8eb433fb07462ff4cfce65f4f16c4fc917e1b32e87a9c7884f3302 Stored in directory: /tmp/pip-ephem-wheel-cache-orvenqcn/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9 Building wheel for wrapt (setup.py): started Building wheel for wrapt (setup.py): finished with status 'done' Created wheel for wrapt: filename=wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl size=71026 sha256=43463d5e7a4739ce822ce8dc3656d94448451d2522de03306ce2f06a9681f0cd Stored in directory: /tmp/pip-ephem-wheel-cache-orvenqcn/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6 Successfully built docopt wrapt Installing collected packages: wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pycparser, sphinx, pyjwt, pockets, docopt, deprecated, cffi, cached-property, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, PyGithub, pygit2, py-make, plantweb Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed PyGithub-1.54.1 cached-property-1.5.2 cffi-1.14.4 deprecated-1.2.10 docopt-0.6.2 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.20 pygit2-1.2.1 pyjwt-1.7.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.16 sphinxcontrib-qthelp-1.0.3 wrapt-1.12.1 [rtd-command-info] start-time: 2021-01-15T21:42:22.818174Z, end-time: 2021-01-15T21:42:23.600818Z, duration: 0, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating emod_api.egg-info writing emod_api.egg-info/PKG-INFO writing dependency_links to emod_api.egg-info/dependency_links.txt writing requirements to emod_api.egg-info/requires.txt writing top-level names to emod_api.egg-info/top_level.txt writing manifest file 'emod_api.egg-info/SOURCES.txt' reading manifest file 'emod_api.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'emod_api/tests/data/*' warning: no directories found matching 'emod_api/dtk_tools/serialization/test-data/*' writing manifest file 'emod_api.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/examples copying examples/serialized_file_mc_to_sc.py -> build/lib/examples copying examples/intervention_from_schema.py -> build/lib/examples copying examples/__init__.py -> build/lib/examples copying examples/weather_file.py -> build/lib/examples copying examples/insetchart.py -> build/lib/examples copying examples/write_config_from_default_and_params.py -> build/lib/examples copying examples/default_from_schema.py -> build/lib/examples copying examples/some_config_i_found.py -> build/lib/examples copying examples/spatial_report.py -> build/lib/examples creating build/lib/emod_api copying emod_api/campaign.py -> build/lib/emod_api copying emod_api/schema_to_class.py -> build/lib/emod_api copying emod_api/__init__.py -> build/lib/emod_api copying emod_api/__main__.py -> build/lib/emod_api creating build/lib/emod_api/serialization copying emod_api/serialization/CensusAndModPop.py -> build/lib/emod_api/serialization copying emod_api/serialization/SerializedPopulation.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileTools.py -> build/lib/emod_api/serialization copying emod_api/serialization/__init__.py -> build/lib/emod_api/serialization copying emod_api/serialization/__main__.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileSupport.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileUtility.py -> build/lib/emod_api/serialization creating build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__init__.py -> build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__main__.py -> build/lib/emod_api/tabularoutput creating build/lib/emod_api/schema copying emod_api/schema/get_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__init__.py -> build/lib/emod_api/schema copying emod_api/schema/dtk_post_process_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__main__.py -> build/lib/emod_api/schema creating build/lib/emod_api/channelreports copying emod_api/channelreports/__init__.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/channels.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/__main__.py -> build/lib/emod_api/channelreports creating build/lib/emod_api/config copying emod_api/config/from_overrides.py -> build/lib/emod_api/config copying emod_api/config/schema_to_config.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/from_poi_and_binary.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema_no_validation.py -> build/lib/emod_api/config copying emod_api/config/dtk_post_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/__init__.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema.py -> build/lib/emod_api/config copying emod_api/config/from_schema.py -> build/lib/emod_api/config copying emod_api/config/__main__.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_w5ml.py -> build/lib/emod_api/config creating build/lib/emod_api/weather copying emod_api/weather/__init__.py -> build/lib/emod_api/weather copying emod_api/weather/weather.py -> build/lib/emod_api/weather copying emod_api/weather/__main__.py -> build/lib/emod_api/weather creating build/lib/emod_api/interventions copying emod_api/interventions/__init__.py -> build/lib/emod_api/interventions copying emod_api/interventions/outbreak.py -> build/lib/emod_api/interventions copying emod_api/interventions/utils.py -> build/lib/emod_api/interventions copying emod_api/interventions/import_pressure.py -> build/lib/emod_api/interventions copying emod_api/interventions/__main__.py -> build/lib/emod_api/interventions copying emod_api/interventions/simple_vaccine.py -> build/lib/emod_api/interventions creating build/lib/emod_api/migration copying emod_api/migration/__init__.py -> build/lib/emod_api/migration copying emod_api/migration/Migration.py -> build/lib/emod_api/migration copying emod_api/migration/__main__.py -> build/lib/emod_api/migration creating build/lib/emod_api/spatialreports copying emod_api/spatialreports/__init__.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/spatial.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/__main__.py -> build/lib/emod_api/spatialreports creating build/lib/emod_api/demographics copying emod_api/demographics/DemographicsGenerator.py -> build/lib/emod_api/demographics copying emod_api/demographics/demographics_utils.py -> build/lib/emod_api/demographics copying emod_api/demographics/__init__.py -> build/lib/emod_api/demographics copying emod_api/demographics/grid_construction.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsTemplates.py -> build/lib/emod_api/demographics copying emod_api/demographics/Demographics.py -> build/lib/emod_api/demographics copying emod_api/demographics/__main__.py -> build/lib/emod_api/demographics copying emod_api/demographics/BaseInputFile.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsInputDataParsers.py -> build/lib/emod_api/demographics copying emod_api/demographics/Node.py -> build/lib/emod_api/demographics creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/examples copying build/lib/examples/serialized_file_mc_to_sc.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/intervention_from_schema.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/__init__.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/weather_file.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/insetchart.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/write_config_from_default_and_params.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/default_from_schema.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/some_config_i_found.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/spatial_report.py -> build/bdist.linux-x86_64/egg/examples creating build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/CensusAndModPop.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/SerializedPopulation.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileTools.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileSupport.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileUtility.py -> build/bdist.linux-x86_64/egg/emod_api/serialization creating build/bdist.linux-x86_64/egg/emod_api/tabularoutput copying build/lib/emod_api/tabularoutput/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput copying build/lib/emod_api/tabularoutput/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput creating build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/get_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/dtk_post_process_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/campaign.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/schema_to_class.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/__init__.py -> build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/channels.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports creating build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_overrides.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/schema_to_config.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_pre_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_poi_and_binary.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/default_from_schema_no_validation.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_post_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/default_from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_pre_process_w5ml.py -> build/bdist.linux-x86_64/egg/emod_api/config creating build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/weather.py -> build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/weather creating build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/utils.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/import_pressure.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/simple_vaccine.py -> build/bdist.linux-x86_64/egg/emod_api/interventions creating build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/Migration.py -> build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/migration creating build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/spatial.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/__main__.py -> build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsGenerator.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/demographics_utils.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/grid_construction.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/Demographics.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/BaseInputFile.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsInputDataParsers.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/Node.py -> build/bdist.linux-x86_64/egg/emod_api/demographics byte-compiling build/bdist.linux-x86_64/egg/examples/serialized_file_mc_to_sc.py to serialized_file_mc_to_sc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/intervention_from_schema.py to intervention_from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/weather_file.py to weather_file.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/insetchart.py to insetchart.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/write_config_from_default_and_params.py to write_config_from_default_and_params.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/default_from_schema.py to default_from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/some_config_i_found.py to some_config_i_found.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/spatial_report.py to spatial_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/CensusAndModPop.py to CensusAndModPop.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/SerializedPopulation.py to SerializedPopulation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileTools.py to dtkFileTools.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileSupport.py to dtkFileSupport.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileUtility.py to dtkFileUtility.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/get_schema.py to get_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/dtk_post_process_schema.py to dtk_post_process_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/campaign.py to campaign.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema_to_class.py to schema_to_class.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/channels.py to channels.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_overrides.py to from_overrides.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/schema_to_config.py to schema_to_config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_adhocevents.py to dtk_pre_process_adhocevents.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_poi_and_binary.py to from_poi_and_binary.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema_no_validation.py to default_from_schema_no_validation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_post_process_adhocevents.py to dtk_post_process_adhocevents.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema.py to default_from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_schema.py to from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_w5ml.py to dtk_pre_process_w5ml.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/weather.py to weather.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/outbreak.py to outbreak.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/utils.py to utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/import_pressure.py to import_pressure.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/simple_vaccine.py to simple_vaccine.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/Migration.py to Migration.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/spatial.py to spatial.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsGenerator.py to DemographicsGenerator.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/demographics_utils.py to demographics_utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/grid_construction.py to grid_construction.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Demographics.py to Demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/BaseInputFile.py to BaseInputFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsInputDataParsers.py to DemographicsInputDataParsers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Node.py to Node.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... emod_api.config.__pycache__.from_poi_and_binary.cpython-37: module references __file__ emod_api.serialization.__pycache__.dtkFileTools.cpython-37: module references __file__ emod_api.serialization.__pycache__.dtkFileUtility.cpython-37: module references __file__ examples.__pycache__.insetchart.cpython-37: module references __file__ examples.__pycache__.spatial_report.cpython-37: module references __file__ examples.__pycache__.weather_file.cpython-37: module references __file__ creating dist creating 'dist/emod_api-1.5.1-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 emod_api-1.5.1-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages/emod_api-1.5.1-py3.7.egg Extracting emod_api-1.5.1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Adding emod-api 1.5.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages/emod_api-1.5.1-py3.7.egg Processing dependencies for emod-api==1.5.1 Searching for geopy==2.1.0 Best match: geopy 2.1.0 Adding geopy 2.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for matplotlib==3.3.2 Best match: matplotlib 3.3.2 Adding matplotlib 3.3.2 to easy-install.pth file Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pyproj==3.0.0.post1 Best match: pyproj 3.0.0.post1 Adding pyproj 3.0.0.post1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for Shapely==1.7.1 Best match: Shapely 1.7.1 Adding Shapely 1.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for scipy==1.5.3 Best match: scipy 1.5.3 scipy 1.5.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pandas==1.1.3 Best match: pandas 1.1.3 pandas 1.1.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for PyYAML==5.3.1 Best match: PyYAML 5.3.1 Adding PyYAML 5.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for lz4==3.1.1 Best match: lz4 3.1.1 Adding lz4 3.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for numpy==1.19.3 Best match: numpy 1.19.3 Adding numpy 1.19.3 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for geographiclib==1.50 Best match: geographiclib 1.50 Adding geographiclib 1.50 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/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 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-emod-api/envs/v1.5.0/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 Pillow==8.1.0 Best match: Pillow 8.1.0 Adding Pillow 8.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/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-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for pytz==2020.5 Best match: pytz 2020.5 Adding pytz 2020.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/site-packages Finished processing dependencies for emod-api==1.5.1 [rtd-command-info] start-time: 2021-01-15T21:42:25.543423Z, end-time: 2021-01-15T21:42:25.617795Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = ['emod_api.dtk_tools'] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'EMOD-API' copyright = u'2020, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'EMOD-API' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emod-api-docs.tex', u'emod-api', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emod-api-docs', u'emod-api', [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, 'emod-api-docs', u'emod-api', author, 'Institute for Disease Modeling', 'How to use emodpy for disease simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'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 # import importlib import sys import os.path from six import string_types 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': "v1.5.0", 'version_slug': "v1.5.0", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-api', 'name': u'emod-api', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/emod-api/en/v1.5.0/', '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': 'emod-api', 'github_version': 'v1.5.0', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'v1.5.0', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'v1.5.0', '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': '75eefc47', } # 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") 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: 2021-01-15T21:42:25.857397Z, end-time: 2021-01-15T21:42:47.909575Z, duration: 22, exit-code: 0 python sphinx-build -T -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.2.1 rm: cannot remove 'emod_api_index.rst': No such file or directory rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 48 source files that are out of date updating environment: [new config] 48 added, 0 changed, 0 removed reading sources... [ 2%] emod_api reading sources... [ 4%] emod_api.campaign reading sources... [ 6%] emod_api.channelreports reading sources... [ 8%] emod_api.channelreports.channels reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 14%] emod_api.config.default_from_schema_no_validation reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 22%] emod_api.config.from_overrides reading sources... [ 25%] emod_api.config.from_poi_and_binary reading sources... [ 27%] emod_api.config.from_schema reading sources... [ 29%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 31%] emod_api.demographics reading sources... [ 33%] emod_api.demographics.BaseInputFile reading sources... [ 35%] emod_api.demographics.Demographics reading sources... [ 37%] emod_api.demographics.DemographicsGenerator reading sources... [ 39%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 41%] emod_api.demographics.DemographicsTemplates reading sources... [ 43%] emod_api.demographics.Node reading sources... [ 45%] emod_api.demographics.demographics_utils reading sources... [ 47%] emod_api.demographics.grid_construction reading sources... [ 50%] emod_api.interventions reading sources... [ 52%] emod_api.interventions.import_pressure reading sources... [ 54%] emod_api.interventions.outbreak reading sources... [ 56%] emod_api.interventions.simple_vaccine reading sources... [ 58%] emod_api.interventions.utils reading sources... [ 60%] emod_api.migration reading sources... [ 62%] emod_api.migration.Migration reading sources... [ 64%] emod_api.schema reading sources... [ 66%] emod_api.schema.dtk_post_process_schema reading sources... [ 68%] emod_api.schema.get_schema reading sources... [ 70%] emod_api.schema_to_class reading sources... [ 72%] emod_api.serialization reading sources... [ 75%] emod_api.serialization.CensusAndModPop reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 79%] emod_api.serialization.dtkFileSupport reading sources... [ 81%] emod_api.serialization.dtkFileTools reading sources... [ 83%] emod_api.serialization.dtkFileUtility reading sources... [ 85%] emod_api.spatialreports reading sources... [ 87%] emod_api.spatialreports.spatial reading sources... [ 89%] emod_api.tabularoutput reading sources... [ 91%] emod_api.weather reading sources... [ 93%] emod_api.weather.weather reading sources... [ 95%] emod_api_index reading sources... [ 97%] glossary reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] emod_api writing output... [ 4%] emod_api.campaign writing output... [ 6%] emod_api.channelreports writing output... [ 8%] emod_api.channelreports.channels writing output... [ 10%] emod_api.config writing output... [ 12%] emod_api.config.default_from_schema writing output... [ 14%] emod_api.config.default_from_schema_no_validation writing output... [ 16%] emod_api.config.dtk_post_process_adhocevents writing output... [ 18%] emod_api.config.dtk_pre_process_adhocevents writing output... [ 20%] emod_api.config.dtk_pre_process_w5ml writing output... [ 22%] emod_api.config.from_overrides writing output... [ 25%] emod_api.config.from_poi_and_binary writing output... [ 27%] emod_api.config.from_schema writing output... [ 29%] emod_api.config.schema_to_config writing output... [ 31%] emod_api.demographics writing output... [ 33%] emod_api.demographics.BaseInputFile writing output... [ 35%] emod_api.demographics.Demographics writing output... [ 37%] emod_api.demographics.DemographicsGenerator writing output... [ 39%] emod_api.demographics.DemographicsInputDataParsers writing output... [ 41%] emod_api.demographics.DemographicsTemplates writing output... [ 43%] emod_api.demographics.Node writing output... [ 45%] emod_api.demographics.demographics_utils writing output... [ 47%] emod_api.demographics.grid_construction writing output... [ 50%] emod_api.interventions writing output... [ 52%] emod_api.interventions.import_pressure writing output... [ 54%] emod_api.interventions.outbreak writing output... [ 56%] emod_api.interventions.simple_vaccine writing output... [ 58%] emod_api.interventions.utils writing output... [ 60%] emod_api.migration writing output... [ 62%] emod_api.migration.Migration writing output... [ 64%] emod_api.schema writing output... [ 66%] emod_api.schema.dtk_post_process_schema writing output... [ 68%] emod_api.schema.get_schema writing output... [ 70%] emod_api.schema_to_class writing output... [ 72%] emod_api.serialization writing output... [ 75%] emod_api.serialization.CensusAndModPop writing output... [ 77%] emod_api.serialization.SerializedPopulation writing output... [ 79%] emod_api.serialization.dtkFileSupport writing output... [ 81%] emod_api.serialization.dtkFileTools writing output... [ 83%] emod_api.serialization.dtkFileUtility writing output... [ 85%] emod_api.spatialreports writing output... [ 87%] emod_api.spatialreports.spatial writing output... [ 89%] emod_api.tabularoutput writing output... [ 91%] emod_api.weather writing output... [ 93%] emod_api.weather.weather writing output... [ 95%] emod_api_index writing output... [ 97%] glossary writing output... [100%] index generating indices... genindex py-modindexdone writing additional pages... search opensearchdone copying static files... ... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) [rtd-command-info] start-time: 2021-01-15T21:42:48.154339Z, end-time: 2021-01-15T21:42:53.937731Z, duration: 5, exit-code: 0 python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 48 added, 0 changed, 0 removed reading sources... [ 2%] emod_api reading sources... [ 4%] emod_api.campaign reading sources... [ 6%] emod_api.channelreports reading sources... [ 8%] emod_api.channelreports.channels reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 14%] emod_api.config.default_from_schema_no_validation reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 22%] emod_api.config.from_overrides reading sources... [ 25%] emod_api.config.from_poi_and_binary reading sources... [ 27%] emod_api.config.from_schema reading sources... [ 29%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 31%] emod_api.demographics reading sources... [ 33%] emod_api.demographics.BaseInputFile reading sources... [ 35%] emod_api.demographics.Demographics reading sources... [ 37%] emod_api.demographics.DemographicsGenerator reading sources... [ 39%] emod_api.demographics.DemographicsInputDataParsers reading sources... 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[ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 79%] emod_api.serialization.dtkFileSupport reading sources... [ 81%] emod_api.serialization.dtkFileTools reading sources... [ 83%] emod_api.serialization.dtkFileUtility reading sources... [ 85%] emod_api.spatialreports reading sources... [ 87%] emod_api.spatialreports.spatial reading sources... [ 89%] emod_api.tabularoutput reading sources... [ 91%] emod_api.weather reading sources... [ 93%] emod_api.weather.weather reading sources... [ 95%] emod_api_index reading sources... [ 97%] glossary reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.BaseInputFile emod_api.demographics.Demographics emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics_utils emod_api.demographics.grid_construction emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.interventions.utils emod_api.migration emod_api.migration.Migration emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.CensusAndModPop emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary done writing... done writing additional files... opensearchdone copying static files... ... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) [rtd-command-info] start-time: 2021-01-15T21:42:54.111993Z, end-time: 2021-01-15T21:42:59.899689Z, duration: 5, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 48 added, 0 changed, 0 removed reading sources... [ 2%] emod_api reading sources... [ 4%] emod_api.campaign reading sources... [ 6%] emod_api.channelreports reading sources... [ 8%] emod_api.channelreports.channels reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 14%] emod_api.config.default_from_schema_no_validation reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 22%] emod_api.config.from_overrides reading sources... [ 25%] emod_api.config.from_poi_and_binary reading sources... [ 27%] emod_api.config.from_schema reading sources... [ 29%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 31%] emod_api.demographics reading sources... [ 33%] emod_api.demographics.BaseInputFile reading sources... [ 35%] emod_api.demographics.Demographics reading sources... [ 37%] emod_api.demographics.DemographicsGenerator reading sources... [ 39%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 41%] emod_api.demographics.DemographicsTemplates reading sources... [ 43%] emod_api.demographics.Node reading sources... [ 45%] emod_api.demographics.demographics_utils reading sources... [ 47%] emod_api.demographics.grid_construction reading sources... [ 50%] emod_api.interventions reading sources... [ 52%] emod_api.interventions.import_pressure reading sources... [ 54%] emod_api.interventions.outbreak reading sources... [ 56%] emod_api.interventions.simple_vaccine reading sources... [ 58%] emod_api.interventions.utils reading sources... [ 60%] emod_api.migration reading sources... [ 62%] emod_api.migration.Migration reading sources... [ 64%] emod_api.schema reading sources... [ 66%] emod_api.schema.dtk_post_process_schema reading sources... [ 68%] emod_api.schema.get_schema reading sources... [ 70%] emod_api.schema_to_class reading sources... [ 72%] emod_api.serialization reading sources... [ 75%] emod_api.serialization.CensusAndModPop reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 79%] emod_api.serialization.dtkFileSupport reading sources... [ 81%] emod_api.serialization.dtkFileTools reading sources... [ 83%] emod_api.serialization.dtkFileUtility reading sources... [ 85%] emod_api.spatialreports reading sources... [ 87%] emod_api.spatialreports.spatial reading sources... [ 89%] emod_api.tabularoutput reading sources... [ 91%] emod_api.weather reading sources... [ 93%] emod_api.weather.weather reading sources... [ 95%] emod_api_index reading sources... [ 97%] glossary reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done processing emod-api-docs.tex... index emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.BaseInputFile emod_api.demographics.Demographics emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics_utils emod_api.demographics.grid_construction emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.interventions.utils emod_api.migration emod_api.migration.Migration emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.CensusAndModPop emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/v1.5.0/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/checkouts/v1.5.0/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-01-15T21:43:00.209687Z, end-time: 2021-01-15T21:43:00.272485Z, 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: 2021-01-15T21:43:00.550953Z, end-time: 2021-01-15T21:43:02.669392Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emod-api -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. 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[7] Underfull \hbox (badness 10000) in paragraph at lines 648--648 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , \ T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 668--668 []\T1/ptm/m/it/10 tot_pop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 668--668 \T1/ptm/m/it/10 num_nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 674--674 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 674--674 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 692--692 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (28.44351pt too wide) in paragraph at lines 692--692 \T1/ptm/m/it/10 pop_filename_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 spatial_grid ded_pop_dir\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 698--698 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 698--698 \T1/ptm/m/it/10 world grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.demographics.BaseInputFile:emod_api.de mographics.BaseInputFile.BaseInputFile' on page 8 undefined on input line 699. [8] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 863--863 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) Overfull \hbox (13.07484pt too wide) in paragraph at lines 882--882 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 882--882 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) [9] Underfull \hbox (badness 10000) in paragraph at lines 967--967 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tion_column_name: [10] Overfull \hbox (54.94496pt too wide) in paragraph at lines 982--983 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [11] Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 1045--1046 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [12] Overfull \hbox (6.3048pt too wide) in paragraph at lines 1101--1101 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 1107--1107 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 1113--1113 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 1119--1119 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [13] Underfull \hbox (badness 10000) in paragraph at lines 1180--1180 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , \T1/ptm/m/it/10 min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1192--1194 []\T1/ptm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Overfull \hbox (22.30493pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (7.6847pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 set- Overfull \hbox (34.0548pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 ting=1.0\T1/pcr/m/n/10 ) Overfull \hbox (10.30493pt too wide) in paragraph at lines 1242--1242 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 pro- Overfull \hbox (58.54413pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 tected_setting=0.0\T1/ptm/m/n/10 , Overfull \hbox (9.20457pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 thresh- Overfull \hbox (53.51486pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 old_age=1825.0\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1248--1248 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1254--1254 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1260--1260 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (88.30493pt too wide) in paragraph at lines 1292--1292 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) [14] Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- Underfull \hbox (badness 10000) in paragraph at lines 1301--1304 []\T1/ptm/m/n/10 Requires con-fig en-ables in-fec-tiv-ity scal-ing: e.g.: `En-a ble_Infectivity_Scaling': 1, `En- Overfull \hbox (22.9045pt too wide) in paragraph at lines 1385--1385 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1391--1391 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1391--1391 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1397--1397 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , [15] Underfull \hbox (badness 10000) in paragraph at lines 1426--1427 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from Underfull \hbox (badness 10000) in paragraph at lines 1446--1446 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu-tion\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1447--1448 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1474--1474 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1474--1474 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1544--1544 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1544--1544 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1570--1570 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1570--1570 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) LaTeX Warning: Hyper reference `emod_api.demographics.demographics_utils:emod_a pi.demographics.demographics_utils.set_static_demographics' on page 17 undefine d on input line 1571. [17] Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 []\T1/ptm/m/it/10 point\T1/ptm/m/n/10 , Overfull \hbox (37.41425pt too wide) in paragraph at lines 1642--1642 \T1/ptm/m/it/10 grid_id_2_cell_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1672--1672 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cam-paign_hook\T1/pt m/m/n/10 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 sv_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Vaccine\TS1/ptm/m/it/ 10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 wan-ing_duration=100\T1/ptm/m/n/10 , [18] Underfull \hbox (badness 10000) in paragraph at lines 1736--1736 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1753--1753 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ini-tial=1.0\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1753--1753 \T1/ptm/m/it/10 box_duration=365\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de- [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 []\T1/ptm/m/it/10 demographics_file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 num_nodes=100\T1/ ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 mig_factor=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_synth_pop\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mi-gra- Overfull \hbox (2.15437pt too wide) in paragraph at lines 2057--2057 []\T1/ptm/m/it/10 demographics_file_path\T1/ptm/m/n/10 , Overfull \hbox (24.70302pt too wide) in paragraph at lines 2089--2089 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2110--2110 []\T1/ptm/m/it/10 input_serpop_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2110--2110 \T1/ptm/m/it/10 mod_fn=None\T1/ptm/m/n/10 , [21] Underfull \hbox (badness 10000) in paragraph at lines 2131--2131 []\T1/ptm/m/it/10 file: [22] Underfull \hbox (badness 10000) in paragraph at lines 2257--2257 []\T1/ptm/m/it/10 name: str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 2292--2292 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- [23] LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileSupport:emod_api. serialization.dtkFileSupport.SerialObject' on page 24 undefined on input line 2 414. 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Underfull \hbox (badness 10000) in paragraph at lines 2647--2647 \T1/ptm/m/it/10 List[int] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data: Underfull \hbox (badness 10000) in paragraph at lines 2647--2647 \T1/ptm/m/it/10 numpy.array = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start: [26] [27] [28] [29] [30] Chapter 2. [31] [32] LaTeX Warning: Reference `emod_api:module-emod_api' on page 33 undefined on inp ut line 3135. LaTeX Warning: Reference `emod_api.campaign:module-emod_api.campaign' on page 3 3 undefined on input line 3136. LaTeX Warning: Reference `emod_api.channelreports:module-emod_api.channelreport s' on page 33 undefined on input line 3137. LaTeX Warning: Reference `emod_api.channelreports.channels:module-emod_api.chan nelreports.channels' on page 33 undefined on input line 3138. LaTeX Warning: Reference `emod_api.config:module-emod_api.config' on page 33 un defined on input line 3139. 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Overfull \hbox (30.6225pt too wide) in paragraph at lines 3174--3175 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , LaTeX Warning: Reference `emod_api.spatialreports:module-emod_api.spatialreport s' on page 33 undefined on input line 3175. LaTeX Warning: Reference `emod_api.spatialreports.spatial:module-emod_api.spati alreports.spatial' on page 33 undefined on input line 3176. LaTeX Warning: Reference `emod_api.tabularoutput:module-emod_api.tabularoutput' on page 33 undefined on input line 3177. LaTeX Warning: Reference `emod_api.weather:module-emod_api.weather' on page 33 undefined on input line 3178. LaTeX Warning: Reference `emod_api.weather.weather:module-emod_api.weather.weat her' on page 33 undefined on input line 3179. [33] No file institute-for-disease-modeling-emod-api.ind. (./institute-for-disease-modeling-emod-api.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emod-api.o ut' 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}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on institute-for-disease-modeling-emod-api.pdf (37 pages, 207255 bytes). Transcript written on institute-for-disease-modeling-emod-api.log. Latexmk: Index file 'institute-for-disease-modeling-emod-api.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-emod-api.ind' from line 'No file institute-for-disease-modeling-emod-api.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emod-api.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emod-api.pdf' Latexmk: List of undefined refs and citations: Reference `emod_api.campaign:module-emod_api.campaign' on page 33 undefined on input line 3136 Reference `emod_api.channelreports.channels:module-emod_api.channelreports.channels' on page 33 undefined on input line 3138 Reference `emod_api.channelreports:module-emod_api.channelreports' on page 33 undefined on input line 3137 Reference `emod_api.config.default_from_schema:module-emod_api.config.default_from_schema' on page 33 undefined on input line 3140 Reference `emod_api.config.default_from_schema_no_validation:module-emod_api.config.default_from_schema_no_validation' on page 33 undefined on input line 3141 Reference `emod_api.config.dtk_post_process_adhocevents:module-emod_api.config.dtk_post_process_adhocevents' on page 33 undefined on input line 3142 Reference `emod_api.config.dtk_pre_process_adhocevents:module-emod_api.config.dtk_pre_process_adhocevents' on page 33 undefined on input line 3143 Reference `emod_api.config.dtk_pre_process_w5ml:module-emod_api.config.dtk_pre_process_w5ml' on page 33 undefined on input line 3144 Reference `emod_api.config.from_overrides:module-emod_api.config.from_overrides' on page 33 undefined on input line 3145 Reference `emod_api.config.from_poi_and_binary:module-emod_api.config.from_poi_and_binary' on page 33 undefined on input line 3146 Reference `emod_api.config.from_schema:module-emod_api.config.from_schema' on page 33 undefined on input line 3147 Reference `emod_api.config.schema_to_config:module-emod_api.config.schema_to_config' on page 33 undefined on input line 3148 Reference `emod_api.config:module-emod_api.config' on page 33 undefined on input line 3139 Reference `emod_api.demographics.BaseInputFile:module-emod_api.demographics.BaseInputFile' on page 33 undefined on input line 3150 Reference `emod_api.demographics.Demographics:module-emod_api.demographics.Demographics' on page 33 undefined on input line 3151 Reference `emod_api.demographics.DemographicsGenerator:module-emod_api.demographics.DemographicsGenerator' on page 33 undefined on input line 3153 Reference `emod_api.demographics.DemographicsInputDataParsers:module-emod_api.demographics.DemographicsInputDataParsers' on page 33 undefined on input line 3154 Reference `emod_api.demographics.DemographicsTemplates:module-emod_api.demographics.DemographicsTemplates' on page 33 undefined on input line 3155 Reference `emod_api.demographics.Node:module-emod_api.demographics.Node' on page 33 undefined on input line 3157 Reference `emod_api.demographics.demographics_utils:module-emod_api.demographics.demographics_utils' on page 33 undefined on input line 3152 Reference `emod_api.demographics.grid_construction:module-emod_api.demographics.grid_construction' on page 33 undefined on input line 3156 Reference `emod_api.demographics:module-emod_api.demographics' on page 33 undefined on input line 3149 Reference `emod_api.interventions.import_pressure:module-emod_api.interventions.import_pressure' on page 33 undefined on input line 3159 Reference `emod_api.interventions.outbreak:module-emod_api.interventions.outbreak' on page 33 undefined on input line 3160 Reference `emod_api.interventions.simple_vaccine:module-emod_api.interventions.simple_vaccine' on page 33 undefined on input line 3161 Reference `emod_api.interventions.utils:module-emod_api.interventions.utils' on page 33 undefined on input line 3162 Reference `emod_api.interventions:module-emod_api.interventions' on page 33 undefined on input line 3158 Reference `emod_api.migration.Migration:module-emod_api.migration.Migration' on page 33 undefined on input line 3164 Reference `emod_api.migration:module-emod_api.migration' on page 33 undefined on input line 3163 Reference `emod_api.schema.dtk_post_process_schema:module-emod_api.schema.dtk_post_process_schema' on page 33 undefined on input line 3166 Reference `emod_api.schema.get_schema:module-emod_api.schema.get_schema' on page 33 undefined on input line 3167 Reference `emod_api.schema:module-emod_api.schema' on page 33 undefined on input line 3165 Reference `emod_api.schema_to_class:module-emod_api.schema_to_class' on page 33 undefined on input line 3168 Reference `emod_api.serialization.CensusAndModPop:module-emod_api.serialization.CensusAndModPop' on page 33 undefined on input line 3170 Reference `emod_api.serialization.SerializedPopulation:module-emod_api.serialization.SerializedPopulation' on page 33 undefined on input line 3174 Reference `emod_api.serialization.dtkFileSupport:module-emod_api.serialization.dtkFileSupport' on page 33 undefined on input line 3171 Reference `emod_api.serialization.dtkFileTools:module-emod_api.serialization.dtkFileTools' on page 33 undefined on input line 3172 Reference `emod_api.serialization.dtkFileUtility:module-emod_api.serialization.dtkFileUtility' on page 33 undefined on input line 3173 Reference `emod_api.serialization:module-emod_api.serialization' on page 33 undefined on input line 3169 Reference `emod_api.spatialreports.spatial:module-emod_api.spatialreports.spatial' on page 33 undefined on input line 3176 Reference `emod_api.spatialreports:module-emod_api.spatialreports' on page 33 undefined on input line 3175 Reference `emod_api.tabularoutput:module-emod_api.tabularoutput' on page 33 undefined on input line 3177 Reference `emod_api.weather.weather:module-emod_api.weather.weather' on page 33 undefined on input line 3179 Reference `emod_api.weather:module-emod_api.weather' on page 33 undefined on input line 3178 Reference `emod_api:module-emod_api' on page 33 undefined on input line 3135 Latexmk: Summary of warnings: Latex failed to resolve 45 reference(s) Rule 'makeindex institute-for-disease-modeling-emod-api.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-emod-api.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-emod-api.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-emod-api.ind" "institute-for-disease-modeling-emod-api.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-emod-api.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-emod-api.idx....done (390 entries accepted, 0 rejected). Sorting entries......done (3651 comparisons). Generating output file institute-for-disease-modeling-emod-api.ind....done (761 lines written, 0 warnings). Output written in institute-for-disease-modeling-emod-api.ind. Transcript written in institute-for-disease-modeling-emod-api.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-emod-api.aux' 'institute-for-disease-modeling-emod-api.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emod-api" "emod-api-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tion_column_name: [10] Overfull \hbox (54.94496pt too wide) in paragraph at lines 982--983 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [11] Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 1045--1046 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [12] Overfull \hbox (6.3048pt too wide) in paragraph at lines 1101--1101 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 1107--1107 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 1113--1113 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 1119--1119 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [13] Underfull \hbox (badness 10000) in paragraph at lines 1180--1180 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , \T1/ptm/m/it/10 min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1192--1194 []\T1/ptm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Overfull \hbox (22.30493pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (7.6847pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 set- Overfull \hbox (34.0548pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 ting=1.0\T1/pcr/m/n/10 ) Overfull \hbox (10.30493pt too wide) in paragraph at lines 1242--1242 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 pro- Overfull \hbox (58.54413pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 tected_setting=0.0\T1/ptm/m/n/10 , Overfull \hbox (9.20457pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 thresh- Overfull \hbox (53.51486pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 old_age=1825.0\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1248--1248 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1254--1254 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1260--1260 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (88.30493pt too wide) in paragraph at lines 1292--1292 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) [14] Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- Underfull \hbox (badness 10000) in paragraph at lines 1301--1304 []\T1/ptm/m/n/10 Requires con-fig en-ables in-fec-tiv-ity scal-ing: e.g.: `En-a ble_Infectivity_Scaling': 1, `En- Overfull \hbox (22.9045pt too wide) in paragraph at lines 1385--1385 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1391--1391 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1391--1391 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1397--1397 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , [15] Underfull \hbox (badness 10000) in paragraph at lines 1426--1427 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from Underfull \hbox (badness 10000) in paragraph at lines 1446--1446 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu-tion\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1447--1448 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1474--1474 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1474--1474 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1544--1544 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1544--1544 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1570--1570 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1570--1570 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) [17] Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 []\T1/ptm/m/it/10 point\T1/ptm/m/n/10 , Overfull \hbox (37.41425pt too wide) in paragraph at lines 1642--1642 \T1/ptm/m/it/10 grid_id_2_cell_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1672--1672 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cam-paign_hook\T1/pt m/m/n/10 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 sv_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Vaccine\TS1/ptm/m/it/ 10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 wan-ing_duration=100\T1/ptm/m/n/10 , [18] Underfull \hbox (badness 10000) in paragraph at lines 1736--1736 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1753--1753 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ini-tial=1.0\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1753--1753 \T1/ptm/m/it/10 box_duration=365\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de- [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 []\T1/ptm/m/it/10 demographics_file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 num_nodes=100\T1/ ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 mig_factor=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_synth_pop\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mi-gra- Overfull \hbox (2.15437pt too wide) in paragraph at lines 2057--2057 []\T1/ptm/m/it/10 demographics_file_path\T1/ptm/m/n/10 , Overfull \hbox (24.70302pt too wide) in paragraph at lines 2089--2089 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2110--2110 []\T1/ptm/m/it/10 input_serpop_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2110--2110 \T1/ptm/m/it/10 mod_fn=None\T1/ptm/m/n/10 , [21] Underfull \hbox (badness 10000) in paragraph at lines 2131--2131 []\T1/ptm/m/it/10 file: [22] Underfull \hbox (badness 10000) in paragraph at lines 2257--2257 []\T1/ptm/m/it/10 name: str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 2292--2292 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 2529--2529 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 10000) in paragraph at lines 2543--2543 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 10000) in paragraph at lines 2565--2565 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , [25] Underfull \hbox (badness 10000) in paragraph at lines 2587--2587 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 10000) in paragraph at lines 2647--2647 \T1/ptm/m/it/10 List[int] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data: Underfull \hbox (badness 10000) in paragraph at lines 2647--2647 \T1/ptm/m/it/10 numpy.array = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start: [26] [27] [28] [29] [30] Chapter 2. [31] [32] Overfull \hbox (66.6225pt too wide) in paragraph at lines 3141--3142 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/1 0 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3142--3143 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3143--3144 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 3152--3153 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3153--3154 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3154--3155 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3155--3156 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3156--3157 []\T1/pcr/m/n/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 3159--3160 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3161--3162 []\T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3166--3167 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 3170--3171 []\T1/pcr/m/n/10 emod_api.serialization.CensusAndModPop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3171--3172 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3173--3174 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3174--3175 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , [33] (./institute-for-disease-modeling-emod-api.ind [34] Underfull \hbox (badness 10000) in paragraph at lines 9--11 []\T1/pcr/m/n/10 AddAgeDependentTransmission() Overfull \hbox (34.06111pt too wide) in paragraph at lines 9--11 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 11--13 []\T1/pcr/m/n/10 AddIndividualPropertyAndHINT() Overfull \hbox (34.06111pt too wide) in paragraph at lines 11--13 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/pcr/m/n/10 AddSeasonalForcing() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 13--15 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/pcr/m/n/10 AgeStructureUNWPP() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 15--17 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (8.41116pt too wide) in paragraph at lines 17--19 []\T1/pcr/m/n/10 AgesYears() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration .Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 AIR \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migrati on.Migration at- Overfull \hbox (37.49991pt too wide) in paragraph at lines 20--22 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Contents Overfull \hbox (32.4899pt too wide) in paragraph at lines 22--24 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (7.95116pt too wide) in paragraph at lines 24--26 \T1/ptm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 26--28 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 26--28 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 28--30 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 28--30 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull 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emod_api.chann elreports.channels.Channel Overfull \hbox (37.71117pt too wide) in paragraph at lines 40--42 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 Author() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Mi gration.Migration Underfull \hbox (badness 10000) in paragraph at lines 53--55 []\T1/pcr/m/n/10 BaseInputFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 53--55 \T1/ptm/m/it/10 emod_api.demographics.BaseInputFile\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 55--56 []\T1/pcr/m/n/10 basicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 57--59 []\T1/pcr/m/n/10 byte_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 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(\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile [35] Overfull \hbox (36.91025pt too wide) in paragraph at lines 77--79 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.EllZeeFour Overfull \hbox (21.29066pt too wide) in paragraph at lines 79--81 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Snappy Overfull \hbox (50.91016pt too wide) in paragraph at lines 81--83 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 83--85 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 85--87 []\T1/pcr/m/n/10 compressed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 87--89 []\T1/pcr/m/n/10 compression() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 89--91 []\T1/pcr/m/n/10 ConstantMortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 89--91 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 91--93 []\T1/pcr/m/n/10 construct() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 91--93 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Overfull \hbox (46.65079pt too wide) in paragraph at lines 93--95 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (12.84114pt too wide) in paragraph at lines 95--97 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Metadata Overfull \hbox (7.47115pt too wide) in paragraph at lines 97--99 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports .spatial.SpatialNode Underfull \hbox (badness 10000) in paragraph at lines 110--112 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 110--112 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 112--114 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 112--114 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Overfull \hbox (21.33125pt too wide) in paragraph at lines 114--116 []\T1/pcr/m/n/10 DatavalueCount() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migr ation.Migration.Layer Overfull \hbox (38.41116pt too wide) in paragraph at lines 116--118 []\T1/pcr/m/n/10 DatavalueCount() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migr ation.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/pcr/m/n/10 date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Overfull \hbox (20.41116pt too wide) in paragraph at lines 120--122 []\T1/pcr/m/n/10 DateCreated() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migrati on.Migration.Migration Overfull \hbox (10.77174pt too wide) in paragraph at lines 122--124 []\T1/pcr/m/n/10 default_density \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 124--126 []\T1/pcr/m/n/10 default_population Underfull \hbox (badness 10000) in paragraph at lines 124--126 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node at- Underfull \hbox (badness 7291) in paragraph at lines 126--128 []\T1/pcr/m/n/10 DefaultSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 126--128 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 Demographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 128--130 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 130--132 []\T1/pcr/m/n/10 DemographicsGenerator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 130--132 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 132--134 []\T1/pcr/m/n/10 DemographicsType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 132--134 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 134--136 []\T1/pcr/m/n/10 do_mapping_from_events() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 134--136 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 137--139 []\T1/pcr/m/n/10 dtk_to_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (56.83089pt too wide) in paragraph at lines 139--141 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 141--143 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 DtkFile.Contents \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/pcr/m/n/10 DtkFile.Objects \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 148--150 []\T1/pcr/m/n/10 DtkFileV1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 150--152 []\T1/pcr/m/n/10 DtkFileV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 152--154 []\T1/pcr/m/n/10 DtkFileV2.NodesV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/pcr/m/n/10 DtkFileV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 156--158 []\T1/pcr/m/n/10 DtkFileV3.NodesV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 158--160 []\T1/pcr/m/n/10 DtkFileV4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 160--162 []\T1/pcr/m/n/10 DtkHeader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 162--164 []\T1/pcr/m/n/10 duplicate_nodeID_check() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 162--164 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/pcr/m/n/10 EllZeeFour \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [36] Overfull \hbox (64.1225pt too wide) in paragraph at lines 181--182 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 183--184 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 185--186 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (10.1225pt too wide) in paragraph at lines 203--204 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils Overfull \hbox (28.1225pt too wide) in paragraph at lines 205--206 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 207--208 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 209--210 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (4.1225pt too wide) in paragraph at lines 211--212 []\T1/pcr/m/n/10 emod_api.demographics.grid_construction Overfull \hbox (4.1225pt too wide) in paragraph at lines 231--232 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 247--248 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 259--261 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 259--261 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.demographics.DemographicsTe mplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 261--263 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 271--273 []\T1/pcr/m/n/10 fill_nodes_legacy() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 271--273 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (4.62106pt too wide) in paragraph at lines 273--275 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict [37] Overfull \hbox (36.30013pt too wide) in paragraph at lines 275--277 []\T1/pcr/m/n/10 find() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 277--279 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (81.59949pt too wide) in paragraph at lines 279--281 []\T1/pcr/m/n/10 flush() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 283--285 []\T1/pcr/m/n/10 from_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 283--285 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 285--287 []\T1/pcr/m/n/10 from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 287--289 []\T1/pcr/m/n/10 from_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 287--289 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (8.41116pt too wide) in paragraph at lines 291--293 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration .Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 293--295 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.w eather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 295--297 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 295--297 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 297--299 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 297--299 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 299--301 []\T1/pcr/m/n/10 from_pop_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 299--301 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 301--303 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 301--303 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/pcr/m/n/10 fromBasicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 305--307 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 FullRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 307--309 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (38.41116pt too wide) in paragraph at lines 312--314 []\T1/pcr/m/n/10 GenderDataType() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migr ation.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 314--316 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 314--316 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (80.97084pt too wide) in paragraph at lines 316--318 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.BaseInputFile.BaseInputFile Overfull \hbox (85.96114pt too wide) in paragraph at lines 318--320 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 320--322 []\T1/pcr/m/n/10 generate_headers() Overfull \hbox (29.07082pt too wide) in paragraph at lines 320--322 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.BaseInputFile.BaseInputFi le Underfull \hbox (badness 10000) in paragraph at lines 322--324 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 322--324 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (173.87039pt too wide) in paragraph at lines 324--326 []\T1/pcr/m/n/10 generate_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 327--329 []\T1/pcr/m/n/10 get_bbox() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 327--329 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 329--331 []\T1/pcr/m/n/10 get_class_with_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Overfull \hbox (62.64088pt too wide) in paragraph at lines 331--333 \T1/ptm/m/it/10 mod-ule emod_api.config.default_from_schema_no_validation\T1/pt m/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 336--338 []\T1/pcr/m/n/10 get_grid_cell_id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 336--338 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 338--340 []\T1/pcr/m/n/10 get_next_individual_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 338--340 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/pcr/m/n/10 get_next_infection_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 340--342 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Overfull \hbox (55.96114pt too wide) in paragraph at lines 342--344 []\T1/pcr/m/n/10 get_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 344--346 []\T1/pcr/m/n/10 get_node_ids_from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 344--346 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 346--348 []\T1/pcr/m/n/10 get_node_pops_from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\T1/pcr/m/n/10 get_parameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 348--350 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 351--353 []\T1/pcr/m/n/10 get_waning_from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 353--355 []\T1/pcr/m/n/10 get_xpix_ypix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (26.83089pt too wide) in paragraph at lines 359--361 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport [38] Underfull \hbox (badness 10000) in paragraph at lines 369--371 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports.s patial.SpatialNode Underfull \hbox (badness 7308) in paragraph at lines 371--372 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather. WeatherNode prop- Overfull \hbox (6.84114pt too wide) in paragraph at lines 372--374 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata Overfull \hbox (1.47115pt too wide) in paragraph at lines 374--376 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 376--378 []\T1/pcr/m/n/10 IDREF_GRUMP1DEGREE Underfull \hbox (badness 10000) in paragraph at lines 376--378 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 378--380 []\T1/pcr/m/n/10 IDREF_GRUMP2PT5ARCMIN Underfull \hbox (badness 10000) in paragraph at lines 378--380 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 380--382 []\T1/pcr/m/n/10 IDREF_GRUMP30ARCSEC Underfull \hbox (badness 10000) in paragraph at lines 380--382 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Overfull \hbox (14.41057pt too wide) in paragraph at lines 382--384 []\T1/pcr/m/n/10 IDREF_LEGACY \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migratio n.Migration.Migration Overfull \hbox (20.41116pt too wide) in paragraph at lines 384--386 []\T1/pcr/m/n/10 IdReference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migrati on.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 386--388 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 386--388 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 388--390 []\T1/pcr/m/n/10 InitAgeUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 388--390 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 390--392 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emod_api.migration.Migration.Migration Overfull \hbox (20.8303pt too wide) in paragraph at lines 398--400 []\T1/pcr/m/n/10 interval() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialrep orts.spatial.SpatialReport Overfull \hbox (14.41057pt too wide) in paragraph at lines 400--402 []\T1/pcr/m/n/10 INTERVENTION \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migratio n.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 406--408 []\T1/pcr/m/n/10 lat_lon_from_nodeid() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 409--411 []\T1/pcr/m/n/10 LINEAR_INTERPOLATION Underfull \hbox (badness 10000) in paragraph at lines 409--411 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 411--413 []\T1/pcr/m/n/10 load_default_config_as_rod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (31.30106pt too wide) in paragraph at lines 411--413 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/pcr/m/n/10 LOCAL \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migra tion.Migration Underfull \hbox (badness 10000) in paragraph at lines 415--417 []\T1/pcr/m/n/10 lon_lat_2_point() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 415--417 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 420--422 []\T1/pcr/m/n/10 make_config_from_poi() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 420--422 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 422--424 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 422--424 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 424--426 []\T1/pcr/m/n/10 make_config_from_poi_and_config_file() Overfull \hbox (16.3614pt too wide) in paragraph at lines 424--426 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 426--428 []\T1/pcr/m/n/10 make_config_from_poi_and_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (3.35153pt too wide) in paragraph at lines 426--428 \T1/ptm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 428--429 []\T1/pcr/m/n/10 MALE \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migrat ion.Migration at- Underfull \hbox (badness 10000) in paragraph at lines 432--433 []\T1/pcr/m/n/10 metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather Overfull \hbox (32.41116pt too wide) in paragraph at lines 434--436 []\T1/pcr/m/n/10 MigrationType() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migra tion.Migration.Migration Overfull \hbox (2.6225pt too wide) in paragraph at lines 442--443 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 443--444 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n /10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 444--445 []| \T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 445--446 []| \T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 446--447 []| \T1/pcr/m/n/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 448--449 []| \T1/pcr/m/n/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 , [39] 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lines 527--529 []\T1/pcr/m/n/10 NodeOffsets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migrati on.Migration.Migration Underfull \hbox (badness 5802) in paragraph at lines 529--531 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Overfull \hbox (81.59949pt too wide) in paragraph at lines 531--533 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Overfull \hbox (2.8303pt too wide) in paragraph at lines 533--535 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreport s.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 536--537 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weath er.Weather prop- [40] Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 nodes_for_DTK() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 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report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 580--582 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 582--584 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 584--586 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Overfull \hbox (4.77174pt too wide) in paragraph at lines 586--588 []\T1/pcr/m/n/10 res_in_degrees \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demogr aphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 591--593 []\T1/pcr/m/n/10 SAME_FOR_BOTH_GENDERS Underfull \hbox (badness 10000) in paragraph at lines 591--593 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 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10000) in paragraph at lines 625--627 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), [41] Overfull \hbox (16.62106pt too wide) in paragraph at lines 627--629 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_t o_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 629--631 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 629--631 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 631--633 []\T1/pcr/m/n/10 set_static_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 631--633 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 633--635 []\T1/pcr/m/n/10 set_suscept_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull 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[]\T1/ptm/m/it/10 path_to_schema\T1/ptm/m/n/10 , Overfull \hbox (96.61464pt too wide) in paragraph at lines 363--363 \T1/ptm/m/it/10 schema_node=True\T1/pcr/m/n/10 ) Overfull \hbox (47.68495pt too wide) in paragraph at lines 373--373 []\T1/ptm/m/it/10 config\T1/pcr/m/n/10 ) Overfull \hbox (114.96484pt too wide) in paragraph at lines 387--387 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (95.13463pt too wide) in paragraph at lines 387--387 \T1/ptm/m/it/10 set_fn\T1/pcr/m/n/10 ) Overfull \hbox (126.96484pt too wide) in paragraph at lines 413--413 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (103.63463pt too wide) in paragraph at lines 413--413 \T1/ptm/m/it/10 set_fn\T1/ptm/m/n/10 , Overfull \hbox (95.01491pt too wide) in paragraph at lines 413--413 \T1/ptm/m/it/10 con- Overfull \hbox (133.8048pt too wide) in paragraph at lines 413--413 \T1/ptm/m/it/10 fig_out_path\T1/pcr/m/n/10 ) [5] Overfull \hbox (7.52466pt too wide) in paragraph at lines 451--451 \T1/ptm/m/it/10 hoc_events\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 481--481 []\T1/ptm/m/it/10 configjson_path\T1/ptm/m/n/10 , Overfull \hbox (63.52425pt too wide) in paragraph at lines 510--510 []\T1/ptm/m/it/10 start_config_dict\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 510--510 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (66.30441pt too wide) in paragraph at lines 519--519 []\T1/ptm/m/it/10 start_config_path\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 519--519 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (18.36475pt too wide) in paragraph at lines 528--528 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , Overfull \hbox (41.87448pt too wide) in paragraph at lines 528--528 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 537--537 []\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 , [6] Underfull \hbox (badness 10000) in paragraph at lines 585--587 []\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder( Underfull \hbox (badness 10000) in paragraph at lines 594--594 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 594--594 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 594--594 \T1/ptm/m/it/10 con-fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/p tm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (28.28418pt too wide) in paragraph at lines 605--605 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (11.09424pt too wide) in paragraph at lines 605--605 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 605--605 \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 605--605 \T1/ptm/m/it/10 fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/ptm/m /it/10 '\T1/ptm/m/n/10 , [7] Underfull \hbox (badness 10000) in paragraph at lines 648--648 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , \ T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 668--668 []\T1/ptm/m/it/10 tot_pop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 668--668 \T1/ptm/m/it/10 num_nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 674--674 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 674--674 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 692--692 []\T1/ptm/m/it/10 pop_filename_in\T1/ptm/m/n/10 , Overfull \hbox (28.44351pt too wide) in paragraph at lines 692--692 \T1/ptm/m/it/10 pop_filename_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 spatial_grid ded_pop_dir\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 698--698 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 698--698 \T1/ptm/m/it/10 world grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , [8] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 863--863 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) Overfull \hbox (13.07484pt too wide) in paragraph at lines 882--882 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 882--882 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 882--882 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) [9] Underfull \hbox (badness 10000) in paragraph at lines 967--967 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 967--967 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 967--967 \T1/ptm/m/it/10 tion_column_name: [10] Overfull \hbox (54.94496pt too wide) in paragraph at lines 982--983 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [11] Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 1030--1030 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 1045--1046 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [12] Overfull \hbox (6.3048pt too wide) in paragraph at lines 1101--1101 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 1107--1107 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 1113--1113 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 1113--1113 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 1119--1119 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 1119--1119 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [13] Underfull \hbox (badness 10000) in paragraph at lines 1180--1180 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , \T1/ptm/m/it/10 min=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1192--1194 []\T1/ptm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Overfull \hbox (22.30493pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (7.6847pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 set- Overfull \hbox (34.0548pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 ting=1.0\T1/pcr/m/n/10 ) Overfull \hbox (10.30493pt too wide) in paragraph at lines 1242--1242 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 pro- Overfull \hbox (58.54413pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 tected_setting=0.0\T1/ptm/m/n/10 , Overfull \hbox (9.20457pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 thresh- Overfull \hbox (53.51486pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 old_age=1825.0\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1248--1248 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1248--1248 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1254--1254 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1260--1260 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (88.30493pt too wide) in paragraph at lines 1292--1292 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) [14] Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1298--1298 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- Underfull \hbox (badness 10000) in paragraph at lines 1301--1304 []\T1/ptm/m/n/10 Requires con-fig en-ables in-fec-tiv-ity scal-ing: e.g.: `En-a ble_Infectivity_Scaling': 1, `En- Overfull \hbox (22.9045pt too wide) in paragraph at lines 1385--1385 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1391--1391 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1391--1391 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1397--1397 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , [15] Underfull \hbox (badness 10000) in paragraph at lines 1426--1427 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from Underfull \hbox (badness 10000) in paragraph at lines 1446--1446 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu-tion\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1447--1448 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1474--1474 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1474--1474 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1544--1544 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1544--1544 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1570--1570 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1570--1570 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) [17] Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 []\T1/ptm/m/it/10 point\T1/ptm/m/n/10 , Overfull \hbox (37.41425pt too wide) in paragraph at lines 1642--1642 \T1/ptm/m/it/10 grid_id_2_cell_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1672--1672 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cam-paign_hook\T1/pt m/m/n/10 , \T1/ptm/m/it/10 cov-er- Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 sv_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Vaccine\TS1/ptm/m/it/ 10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1715--1715 \T1/ptm/m/it/10 wan-ing_duration=100\T1/ptm/m/n/10 , [18] Underfull \hbox (badness 10000) in paragraph at lines 1736--1736 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1753--1753 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ini-tial=1.0\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1753--1753 \T1/ptm/m/it/10 box_duration=365\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de- [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 []\T1/ptm/m/it/10 demographics_file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 num_nodes=100\T1/ ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 mig_factor=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2046--2046 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_synth_pop\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mi-gra- Overfull \hbox (2.15437pt too wide) in paragraph at lines 2057--2057 []\T1/ptm/m/it/10 demographics_file_path\T1/ptm/m/n/10 , Overfull \hbox (24.70302pt too wide) in paragraph at lines 2089--2089 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2110--2110 []\T1/ptm/m/it/10 input_serpop_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2110--2110 \T1/ptm/m/it/10 mod_fn=None\T1/ptm/m/n/10 , [21] Underfull \hbox (badness 10000) in paragraph at lines 2131--2131 []\T1/ptm/m/it/10 file: [22] Underfull \hbox (badness 10000) in paragraph at lines 2257--2257 []\T1/ptm/m/it/10 name: str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 2292--2292 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 2529--2529 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 10000) in paragraph at lines 2543--2543 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 10000) in paragraph at lines 2565--2565 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , [25] Underfull \hbox (badness 10000) in paragraph at lines 2587--2587 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 10000) in paragraph at lines 2647--2647 \T1/ptm/m/it/10 List[int] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data: Underfull \hbox (badness 10000) in paragraph at lines 2647--2647 \T1/ptm/m/it/10 numpy.array = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start: [26] [27] [28] [29] [30] Chapter 2. [31] [32] Overfull \hbox (66.6225pt too wide) in paragraph at lines 3141--3142 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/1 0 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3142--3143 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3143--3144 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 3152--3153 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3153--3154 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3154--3155 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3155--3156 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3156--3157 []\T1/pcr/m/n/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 3159--3160 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3161--3162 []\T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3166--3167 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 3170--3171 []\T1/pcr/m/n/10 emod_api.serialization.CensusAndModPop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3171--3172 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3173--3174 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3174--3175 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , [33] (./institute-for-disease-modeling-emod-api.ind [34] Underfull \hbox (badness 10000) in paragraph at lines 9--11 []\T1/pcr/m/n/10 AddAgeDependentTransmission() Overfull \hbox (34.06111pt too wide) in paragraph at lines 9--11 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 11--13 []\T1/pcr/m/n/10 AddIndividualPropertyAndHINT() Overfull \hbox (34.06111pt too wide) in paragraph at lines 11--13 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/pcr/m/n/10 AddSeasonalForcing() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 13--15 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/pcr/m/n/10 AgeStructureUNWPP() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 15--17 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (8.41116pt too wide) in paragraph at lines 17--19 []\T1/pcr/m/n/10 AgesYears() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration .Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 AIR \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migrati on.Migration at- Overfull \hbox (37.49991pt too wide) in paragraph at lines 20--22 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Contents Overfull \hbox (32.4899pt too wide) in paragraph at lines 22--24 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (7.95116pt too wide) in paragraph at lines 24--26 \T1/ptm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 26--28 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 26--28 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 28--30 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 28--30 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 30--32 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/pcr/m/n/10 apply_to_defaults_or_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 32--34 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 34--36 []\T1/pcr/m/n/10 arcsec_to_deg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 34--36 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 36--38 []\T1/pcr/m/n/10 as_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (41.61118pt too wide) in paragraph at lines 38--40 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Channel Overfull \hbox (37.71117pt too wide) in paragraph at lines 40--42 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 Author() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Mi gration.Migration Underfull \hbox (badness 10000) in paragraph at lines 53--55 []\T1/pcr/m/n/10 BaseInputFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 53--55 \T1/ptm/m/it/10 emod_api.demographics.BaseInputFile\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 55--56 []\T1/pcr/m/n/10 basicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 57--59 []\T1/pcr/m/n/10 byte_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 62--64 []\T1/pcr/m/n/10 change_ser_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 62--64 \T1/ptm/m/it/10 emod_api.serialization.CensusAndModPop\T1/ptm/m/n/10 ), Overfull \hbox (68.83089pt too wide) in paragraph at lines 65--67 []\T1/pcr/m/n/10 channel_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/pcr/m/n/10 ChannelReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (38.83089pt too wide) in paragraph at lines 69--71 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Overfull \hbox (29.59027pt too wide) in paragraph at lines 71--73 []\T1/pcr/m/n/10 chunk_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 73--75 []\T1/pcr/m/n/10 chunk_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile [35] Overfull \hbox (36.91025pt too wide) in paragraph at lines 77--79 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.EllZeeFour Overfull \hbox (21.29066pt too wide) in paragraph at lines 79--81 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Snappy Overfull \hbox (50.91016pt too wide) in paragraph at lines 81--83 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 83--85 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 85--87 []\T1/pcr/m/n/10 compressed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 87--89 []\T1/pcr/m/n/10 compression() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 89--91 []\T1/pcr/m/n/10 ConstantMortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 89--91 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 91--93 []\T1/pcr/m/n/10 construct() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 91--93 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Overfull \hbox (46.65079pt too wide) in paragraph at lines 93--95 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (12.84114pt too wide) in paragraph at lines 95--97 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Metadata Overfull \hbox (7.47115pt too wide) in paragraph at lines 97--99 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports .spatial.SpatialNode Underfull \hbox (badness 10000) in paragraph at lines 110--112 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 110--112 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 112--114 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 112--114 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Overfull \hbox (21.33125pt too wide) in paragraph at lines 114--116 []\T1/pcr/m/n/10 DatavalueCount() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migr ation.Migration.Layer Overfull \hbox (38.41116pt too wide) in paragraph at lines 116--118 []\T1/pcr/m/n/10 DatavalueCount() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migr ation.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/pcr/m/n/10 date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Overfull \hbox (20.41116pt too wide) in paragraph at lines 120--122 []\T1/pcr/m/n/10 DateCreated() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migrati on.Migration.Migration Overfull \hbox (10.77174pt too wide) in paragraph at lines 122--124 []\T1/pcr/m/n/10 default_density \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 124--126 []\T1/pcr/m/n/10 default_population Underfull \hbox (badness 10000) in paragraph at lines 124--126 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node at- Underfull \hbox (badness 7291) in paragraph at lines 126--128 []\T1/pcr/m/n/10 DefaultSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 126--128 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 Demographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 128--130 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 130--132 []\T1/pcr/m/n/10 DemographicsGenerator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 130--132 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 132--134 []\T1/pcr/m/n/10 DemographicsType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 132--134 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 134--136 []\T1/pcr/m/n/10 do_mapping_from_events() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 134--136 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 137--139 []\T1/pcr/m/n/10 dtk_to_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (56.83089pt too wide) in paragraph at lines 139--141 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 141--143 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 DtkFile.Contents \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/pcr/m/n/10 DtkFile.Objects \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 148--150 []\T1/pcr/m/n/10 DtkFileV1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 150--152 []\T1/pcr/m/n/10 DtkFileV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 152--154 []\T1/pcr/m/n/10 DtkFileV2.NodesV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/pcr/m/n/10 DtkFileV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 156--158 []\T1/pcr/m/n/10 DtkFileV3.NodesV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 158--160 []\T1/pcr/m/n/10 DtkFileV4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 160--162 []\T1/pcr/m/n/10 DtkHeader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 162--164 []\T1/pcr/m/n/10 duplicate_nodeID_check() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 162--164 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/pcr/m/n/10 EllZeeFour \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [36] Overfull \hbox (64.1225pt too wide) in paragraph at lines 181--182 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 183--184 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 185--186 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (10.1225pt too wide) in paragraph at lines 203--204 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils Overfull \hbox (28.1225pt too wide) in paragraph at lines 205--206 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 207--208 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 209--210 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (4.1225pt too wide) in paragraph at lines 211--212 []\T1/pcr/m/n/10 emod_api.demographics.grid_construction Overfull \hbox (4.1225pt too wide) in paragraph at lines 231--232 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 247--248 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 259--261 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 259--261 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.demographics.DemographicsTe mplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 261--263 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 271--273 []\T1/pcr/m/n/10 fill_nodes_legacy() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 271--273 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (4.62106pt too wide) in paragraph at lines 273--275 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict [37] Overfull \hbox (36.30013pt too wide) in paragraph at lines 275--277 []\T1/pcr/m/n/10 find() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 277--279 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (81.59949pt too wide) in paragraph at lines 279--281 []\T1/pcr/m/n/10 flush() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 283--285 []\T1/pcr/m/n/10 from_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 283--285 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 285--287 []\T1/pcr/m/n/10 from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 287--289 []\T1/pcr/m/n/10 from_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 287--289 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (8.41116pt too wide) in paragraph at lines 291--293 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration .Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 293--295 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.w eather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 295--297 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 295--297 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 297--299 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 297--299 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 299--301 []\T1/pcr/m/n/10 from_pop_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 299--301 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 301--303 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 301--303 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/pcr/m/n/10 fromBasicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 305--307 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 FullRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 307--309 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (38.41116pt too wide) in paragraph at lines 312--314 []\T1/pcr/m/n/10 GenderDataType() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migr ation.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 314--316 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 314--316 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (80.97084pt too wide) in paragraph at lines 316--318 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.BaseInputFile.BaseInputFile Overfull \hbox (85.96114pt too wide) in paragraph at lines 318--320 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 320--322 []\T1/pcr/m/n/10 generate_headers() Overfull \hbox (29.07082pt too wide) in paragraph at lines 320--322 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.BaseInputFile.BaseInputFi le Underfull \hbox (badness 10000) in paragraph at lines 322--324 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 322--324 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (173.87039pt too wide) in paragraph at lines 324--326 []\T1/pcr/m/n/10 generate_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 327--329 []\T1/pcr/m/n/10 get_bbox() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 327--329 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 329--331 []\T1/pcr/m/n/10 get_class_with_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Overfull \hbox (62.64088pt too wide) in paragraph at lines 331--333 \T1/ptm/m/it/10 mod-ule emod_api.config.default_from_schema_no_validation\T1/pt m/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 336--338 []\T1/pcr/m/n/10 get_grid_cell_id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 336--338 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 338--340 []\T1/pcr/m/n/10 get_next_individual_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 338--340 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/pcr/m/n/10 get_next_infection_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 340--342 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Overfull \hbox (55.96114pt too wide) in paragraph at lines 342--344 []\T1/pcr/m/n/10 get_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 344--346 []\T1/pcr/m/n/10 get_node_ids_from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 344--346 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 346--348 []\T1/pcr/m/n/10 get_node_pops_from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\T1/pcr/m/n/10 get_parameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 348--350 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 351--353 []\T1/pcr/m/n/10 get_waning_from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 353--355 []\T1/pcr/m/n/10 get_xpix_ypix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (26.83089pt too wide) in paragraph at lines 359--361 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport [38] Underfull \hbox (badness 10000) in paragraph at lines 369--371 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports.s patial.SpatialNode Underfull \hbox (badness 7308) in paragraph at lines 371--372 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather. WeatherNode prop- Overfull \hbox (6.84114pt too wide) in paragraph at lines 372--374 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata Overfull \hbox (1.47115pt too wide) in paragraph at lines 374--376 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 376--378 []\T1/pcr/m/n/10 IDREF_GRUMP1DEGREE Underfull \hbox (badness 10000) in paragraph at lines 376--378 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 378--380 []\T1/pcr/m/n/10 IDREF_GRUMP2PT5ARCMIN Underfull \hbox (badness 10000) in paragraph at lines 378--380 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 380--382 []\T1/pcr/m/n/10 IDREF_GRUMP30ARCSEC Underfull \hbox (badness 10000) in paragraph at lines 380--382 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Overfull \hbox (14.41057pt too wide) in paragraph at lines 382--384 []\T1/pcr/m/n/10 IDREF_LEGACY \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migratio n.Migration.Migration Overfull \hbox (20.41116pt too wide) in paragraph at lines 384--386 []\T1/pcr/m/n/10 IdReference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migrati on.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 386--388 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 386--388 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 388--390 []\T1/pcr/m/n/10 InitAgeUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 388--390 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 390--392 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emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/pcr/m/n/10 LOCAL \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migra tion.Migration Underfull \hbox (badness 10000) in paragraph at lines 415--417 []\T1/pcr/m/n/10 lon_lat_2_point() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 415--417 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 420--422 []\T1/pcr/m/n/10 make_config_from_poi() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 420--422 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 422--424 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 422--424 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 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lines 527--529 []\T1/pcr/m/n/10 NodeOffsets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migrati on.Migration.Migration Underfull \hbox (badness 5802) in paragraph at lines 529--531 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Overfull \hbox (81.59949pt too wide) in paragraph at lines 531--533 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Overfull \hbox (2.8303pt too wide) in paragraph at lines 533--535 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreport s.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 536--537 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weath er.Weather prop- [40] Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 nodes_for_DTK() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 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emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 594--596 []\T1/pcr/m/n/10 schema_to_config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 594--596 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 596--598 []\T1/pcr/m/n/10 schema_to_config_subnode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (31.30106pt too wide) in paragraph at lines 596--598 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 598--600 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 600--602 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 602--603 []\T1/pcr/m/n/10 SEA \T1/ptm/m/n/10 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\T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 619--621 []\T1/pcr/m/n/10 set_immune_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 619--621 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 621--623 []\T1/pcr/m/n/10 set_init_prev() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 621--623 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (173.87039pt too wide) in paragraph at lines 623--625 []\T1/pcr/m/n/10 set_resolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 625--627 []\T1/pcr/m/n/10 set_risk_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 625--627 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), [41] Overfull \hbox (16.62106pt too wide) in paragraph at lines 627--629 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_t o_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 629--631 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 629--631 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 631--633 []\T1/pcr/m/n/10 set_static_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 631--633 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 633--635 []\T1/pcr/m/n/10 set_suscept_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 633--635 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 635--637 []\T1/pcr/m/n/10 set_suscept_simple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 635--637 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 637--639 []\T1/pcr/m/n/10 SetConstantSusceptibility() Overfull \hbox (34.06111pt too wide) in paragraph at lines 637--639 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 639--641 []\T1/pcr/m/n/10 SetDefaultFromTemplate() Overfull \hbox (34.06111pt too wide) in paragraph at lines 639--641 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 641--643 []\T1/pcr/m/n/10 SetDefaultIndividualAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 641--643 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 643--645 []\T1/pcr/m/n/10 SetDefaultIndividualProperties() Overfull \hbox (34.06111pt too wide) in paragraph at lines 643--645 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 645--647 []\T1/pcr/m/n/10 SetDefaultNodeAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 645--647 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 647--649 []\T1/pcr/m/n/10 SetDefaultProperties() Overfull \hbox (34.06111pt too wide) in paragraph at lines 647--649 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in 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emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 657--659 []\T1/pcr/m/n/10 SetOverdispersion() Overfull \hbox (34.06111pt too wide) in paragraph at lines 657--659 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 659--661 []\T1/pcr/m/n/10 SimpleSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 659--661 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Overfull \hbox (34.70026pt too wide) in paragraph at lines 661--663 []\T1/pcr/m/n/10 simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFileV1 Overfull \hbox (34.70026pt too wide) in paragraph at lines 663--665 []\T1/pcr/m/n/10 simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFileV2 Overfull \hbox (34.70026pt too wide) in paragraph at lines 665--667 []\T1/pcr/m/n/10 simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFileV3 Overfull \hbox (2.94016pt too wide) in paragraph at lines 667--668 []\T1/pcr/m/n/10 Snappy \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in emod_api.seria lization.dtkFileSupport\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 668--669 []\T1/pcr/m/n/10 SpatialNode \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 669--671 []\T1/pcr/m/n/10 SpatialReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (2.8303pt too wide) in paragraph at lines 671--673 []\T1/pcr/m/n/10 start() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreport s.spatial.SpatialReport Overfull \hbox (50.83089pt too wide) in paragraph at lines 673--675 []\T1/pcr/m/n/10 start_time() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (19.71117pt too wide) in paragraph at lines 675--677 []\T1/pcr/m/n/10 start_time() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (91.05998pt too wide) in paragraph at lines 677--679 []\T1/pcr/m/n/10 STATIC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.D emographicsGenerator.DemographicsType Overfull \hbox (44.83089pt too wide) in paragraph at lines 679--681 []\T1/pcr/m/n/10 step_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (13.71117pt too wide) in paragraph at lines 681--683 []\T1/pcr/m/n/10 step_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelre ports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 683--685 []\T1/pcr/m/n/10 StepFunctionSusceptibility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 683--685 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (50.83089pt too wide) in paragraph at lines 690--692 []\T1/pcr/m/n/10 time_stamp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (19.71117pt too wide) in paragraph at lines 692--694 []\T1/pcr/m/n/10 time_stamp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (32.8303pt too wide) in paragraph at lines 694--696 []\T1/pcr/m/n/10 time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 5741) in paragraph at lines 696--698 []\T1/pcr/m/n/10 title() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreport s.channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 698--699 []\T1/pcr/m/n/10 to_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographic s.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 703--704 []\T1/pcr/m/n/10 to_tuple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 704--706 []\T1/pcr/m/n/10 Tool() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migr ation.Migration Underfull \hbox (badness 10000) in paragraph at lines 706--708 []\T1/pcr/m/n/10 tool() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Overfull \hbox (48.91025pt too wide) in paragraph at lines 711--713 []\T1/pcr/m/n/10 uncompress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileSupport.EllZeeFour Overfull \hbox (33.29066pt too wide) in paragraph at lines 713--715 []\T1/pcr/m/n/10 uncompress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileSupport.Snappy [42] Overfull \hbox (62.91016pt too wide) in paragraph at lines 715--717 []\T1/pcr/m/n/10 uncompress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 717--719 []\T1/pcr/m/n/10 uncompress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 719--721 []\T1/pcr/m/n/10 Uncompressed \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 5741) in paragraph at lines 721--723 []\T1/pcr/m/n/10 units() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreport s.channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 723--725 []\T1/pcr/m/n/10 update_resolution() Underfull \hbox (badness 10000) in paragraph at lines 723--725 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 725--727 []\T1/pcr/m/n/10 update_resolution() Underfull \hbox (badness 10000) in paragraph at lines 725--727 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 730--732 []\T1/pcr/m/n/10 validate_res_in_arcsec() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 730--732 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (5.59027pt too wide) in paragraph at lines 732--734 []\T1/pcr/m/n/10 version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializati on.dtkFileTools.DtkFile Overfull \hbox (81.59949pt too wide) in paragraph at lines 739--741 []\T1/pcr/m/n/10 write() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 741--742 []\T1/pcr/m/n/10 write() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 742--744 []\T1/pcr/m/n/10 write_config_from_default_and_params() Overfull \hbox (75.65076pt too wide) in paragraph at lines 742--744 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.default_from_schema_ no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 744--746 []\T1/pcr/m/n/10 write_default_from_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 746--748 []\T1/pcr/m/n/10 write_default_from_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (31.30106pt too wide) in paragraph at lines 746--748 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Overfull \hbox (50.83089pt too wide) in paragraph at lines 748--750 []\T1/pcr/m/n/10 write_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (32.8303pt too wide) in paragraph at lines 750--752 []\T1/pcr/m/n/10 write_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 754--755 []\T1/pcr/m/n/10 write_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 758--760 []\T1/pcr/m/n/10 xpix_ypix_from_lat_lon() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule [43]) 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