Read the Docs build information Build id: 509964 Project: institute-for-disease-modeling-emod-api Version: latest Commit: feadb4db2656e256e27f110c7a69b4bbfbbf06f9 Date: 2020-12-17T01:10:40.323362Z State: finished Success: True [rtd-command-info] start-time: 2020-12-17T01:10:42.012641Z, end-time: 2020-12-17T01:10:43.214403Z, duration: 1, 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: 2020-12-17T01:10:43.584093Z, end-time: 2020-12-17T01:10:43.776501Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. 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 feadb4d Bump version: 1.4.1 → 1.4.2 [rtd-command-info] start-time: 2020-12-17T01:10:43.908701Z, end-time: 2020-12-17T01:10:43.964105Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-12-17T01:10:45.480225Z, end-time: 2020-12-17T01:10:50.365418Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-12-17T01:10:50.596358Z, end-time: 2020-12-17T01:10:52.541547Z, 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/latest/lib/python3.7/site-packages (20.3.3) [rtd-command-info] start-time: 2020-12-17T01:10:52.896079Z, end-time: 2020-12-17T01:11:02.596092Z, 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-2.1.1-py2.py3-none-any.whl (13 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-2.7.3-py3-none-any.whl (950 kB) Collecting pytz>=2015.7 Downloading pytz-2020.4-py2.py3-none-any.whl (509 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=490dac7cef6776f93e1409e08ca227335a03634d6a6a1069935ef834a3520a53 Stored in directory: /tmp/pip-ephem-wheel-cache-h518a4bq/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=0aea058079e3d6602cfc916844f19602afab5fd611327e24cd31246f87a25d91 Stored in directory: /tmp/pip-ephem-wheel-cache-h518a4bq/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-2.7.3 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-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.1 setuptools-51.0.0 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: 2020-12-17T01:11:02.962332Z, end-time: 2020-12-17T01:11:09.554801Z, 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-2.0.0-py3-none-any.whl (111 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: 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/latest/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: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (2020.12.5) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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-8.0.1-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/latest/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 4)) (2020.4) 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=4faa3bac17903c86fc0e2eebf3165fc6b951328ff697f252929e41fd720c7250 Stored in directory: /tmp/pip-ephem-wheel-cache-m8ruya2b/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/latest Can't uninstall 'numpy'. No files were found to uninstall. Successfully installed geographiclib-1.50 geopy-2.0.0 lz4-3.1.1 numpy-1.19.3 pillow-8.0.1 pyproj-3.0.0.post1 pyyaml-5.3.1 shapely-1.7.1 [rtd-command-info] start-time: 2020-12-17T01:11:09.664676Z, end-time: 2020-12-17T01:11:17.224862Z, duration: 7, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/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: requests in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (1.15.0) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (0.14) 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-py3-none-any.whl (290 kB) Collecting sphinx~=3.2.1 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.1.4) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.9.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (20.8) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.2.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.7.3) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.11.2) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (51.0.0) Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 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/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2020.4) 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/latest/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 requests Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (2.10) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB) 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/latest/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 pyjwt Downloading PyJWT-1.7.1-py2.py3-none-any.whl (18 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=ec6886306fd010e1a211f7ae3ff500d3bbdccb3a396aabb8bf030c13f7b753b5 Stored in directory: /tmp/pip-ephem-wheel-cache-1rw9edc3/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=71025 sha256=8a55b3155b9a14fc7a227d1788dc42f131a658d756b0c164b7b3b4644f303f86 Stored in directory: /tmp/pip-ephem-wheel-cache-1rw9edc3/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6 Successfully built docopt wrapt Installing collected packages: urllib3, chardet, wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, requests, pycparser, sphinx, pyjwt, pockets, docopt, deprecated, cffi, cached-property, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, PyGithub, pygit2, py-make, plantweb Attempting uninstall: urllib3 Found existing installation: urllib3 1.26.2 Uninstalling urllib3-1.26.2: Successfully uninstalled urllib3-1.26.2 Attempting uninstall: chardet Found existing installation: chardet 4.0.0 Uninstalling chardet-4.0.0: Successfully uninstalled chardet-4.0.0 Attempting uninstall: requests Found existing installation: requests 2.25.1 Uninstalling requests-2.25.1: Successfully uninstalled requests-2.25.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed PyGithub-1.54 cached-property-1.5.2 cffi-1.14.4 chardet-3.0.4 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 requests-2.24.0 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 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 urllib3-1.25.11 wrapt-1.12.1 [rtd-command-info] start-time: 2020-12-17T01:11:17.375673Z, end-time: 2020-12-17T01:11:18.099288Z, 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/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/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/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-1.4.2-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emod_api-1.4.2-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.2-py3.7.egg Extracting emod_api-1.4.2-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Adding emod-api 1.4.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.2-py3.7.egg Processing dependencies for emod-api==1.4.2 Searching for geopy==2.0.0 Best match: geopy 2.0.0 Adding geopy 2.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for Shapely==1.7.1 Best match: Shapely 1.7.1 Adding Shapely 1.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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/latest/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/latest/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/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for geographiclib==1.50 Best match: geographiclib 1.50 Adding geographiclib 1.50 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for Pillow==8.0.1 Best match: Pillow 8.0.1 Adding Pillow 8.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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 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 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/latest/lib/python3.7/site-packages Searching for certifi==2020.12.5 Best match: certifi 2020.12.5 Adding certifi 2020.12.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/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 pytz==2020.4 Best match: pytz 2020.4 Adding pytz 2020.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Finished processing dependencies for emod-api==1.4.2 [rtd-command-info] start-time: 2020-12-17T01:11:19.577952Z, end-time: 2020-12-17T01:11:19.654497Z, 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': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/emod-api/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/emod-api/en/latest/htmlzip/"), ], '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/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emod-api', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', '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': 'feadb4db', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") 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: 2020-12-17T01:11:19.842994Z, end-time: 2020-12-17T01:12:18.994513Z, duration: 59, exit-code: 0 python sphinx-build -T -E -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 47 source files that are out of date updating environment: [new config] 47 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... [ 17%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 19%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 21%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 23%] 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... [ 34%] emod_api.demographics.BaseInputFile reading sources... [ 36%] emod_api.demographics.Demographics Matplotlib is building the font cache; this may take a moment. reading sources... [ 38%] emod_api.demographics.DemographicsGenerator reading sources... [ 40%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 42%] emod_api.demographics.DemographicsTemplates reading sources... [ 44%] emod_api.demographics.Node reading sources... [ 46%] emod_api.demographics.demographics_utils reading sources... [ 48%] emod_api.demographics.grid_construction reading sources... [ 51%] emod_api.interventions reading sources... [ 53%] emod_api.interventions.import_pressure reading sources... [ 55%] emod_api.interventions.outbreak reading sources... [ 57%] emod_api.interventions.simple_vaccine reading sources... [ 59%] emod_api.migration reading sources... [ 61%] emod_api.migration.Migration reading sources... [ 63%] emod_api.schema reading sources... [ 65%] 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... [ 74%] emod_api.serialization.CensusAndModPop reading sources... [ 76%] emod_api.serialization.SerializedPopulation reading sources... [ 78%] emod_api.serialization.dtkFileSupport reading sources... [ 80%] emod_api.serialization.dtkFileTools reading sources... [ 82%] 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... [ 17%] emod_api.config.dtk_post_process_adhocevents writing output... [ 19%] emod_api.config.dtk_pre_process_adhocevents writing output... [ 21%] emod_api.config.dtk_pre_process_w5ml writing output... [ 23%] 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... [ 34%] emod_api.demographics.BaseInputFile writing output... [ 36%] emod_api.demographics.Demographics writing output... [ 38%] emod_api.demographics.DemographicsGenerator writing output... [ 40%] emod_api.demographics.DemographicsInputDataParsers writing output... [ 42%] emod_api.demographics.DemographicsTemplates writing output... [ 44%] emod_api.demographics.Node writing output... [ 46%] emod_api.demographics.demographics_utils writing output... [ 48%] emod_api.demographics.grid_construction writing output... [ 51%] emod_api.interventions writing output... [ 53%] emod_api.interventions.import_pressure writing output... [ 55%] emod_api.interventions.outbreak writing output... [ 57%] emod_api.interventions.simple_vaccine writing output... [ 59%] emod_api.migration writing output... [ 61%] emod_api.migration.Migration writing output... [ 63%] emod_api.schema writing output... [ 65%] 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... [ 74%] emod_api.serialization.CensusAndModPop writing output... [ 76%] emod_api.serialization.SerializedPopulation writing output... [ 78%] emod_api.serialization.dtkFileSupport writing output... [ 80%] emod_api.serialization.dtkFileTools writing output... [ 82%] 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/latest/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: 2020-12-17T01:12:19.247373Z, end-time: 2020-12-17T01:12:25.123315Z, 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] 47 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... [ 17%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 19%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 21%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 23%] 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... [ 34%] emod_api.demographics.BaseInputFile reading sources... [ 36%] emod_api.demographics.Demographics reading sources... [ 38%] emod_api.demographics.DemographicsGenerator reading sources... [ 40%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 42%] emod_api.demographics.DemographicsTemplates reading sources... [ 44%] emod_api.demographics.Node reading sources... [ 46%] emod_api.demographics.demographics_utils reading sources... [ 48%] emod_api.demographics.grid_construction reading sources... [ 51%] emod_api.interventions reading sources... [ 53%] emod_api.interventions.import_pressure reading sources... [ 55%] emod_api.interventions.outbreak reading sources... [ 57%] emod_api.interventions.simple_vaccine reading sources... [ 59%] emod_api.migration reading sources... [ 61%] emod_api.migration.Migration reading sources... [ 63%] emod_api.schema reading sources... [ 65%] 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... [ 74%] emod_api.serialization.CensusAndModPop reading sources... [ 76%] emod_api.serialization.SerializedPopulation reading sources... [ 78%] emod_api.serialization.dtkFileSupport reading sources... [ 80%] emod_api.serialization.dtkFileTools reading sources... [ 82%] 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.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/latest/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: 2020-12-17T01:12:25.356649Z, end-time: 2020-12-17T01:12:31.174263Z, 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] 47 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... [ 17%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 19%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 21%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 23%] 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... [ 34%] emod_api.demographics.BaseInputFile reading sources... [ 36%] emod_api.demographics.Demographics reading sources... [ 38%] emod_api.demographics.DemographicsGenerator reading sources... [ 40%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 42%] emod_api.demographics.DemographicsTemplates reading sources... [ 44%] emod_api.demographics.Node reading sources... [ 46%] emod_api.demographics.demographics_utils reading sources... [ 48%] emod_api.demographics.grid_construction reading sources... [ 51%] emod_api.interventions reading sources... [ 53%] emod_api.interventions.import_pressure reading sources... [ 55%] emod_api.interventions.outbreak reading sources... [ 57%] emod_api.interventions.simple_vaccine reading sources... [ 59%] emod_api.migration reading sources... [ 61%] emod_api.migration.Migration reading sources... [ 63%] emod_api.schema reading sources... [ 65%] 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... [ 74%] emod_api.serialization.CensusAndModPop reading sources... [ 76%] emod_api.serialization.SerializedPopulation reading sources... [ 78%] emod_api.serialization.dtkFileSupport reading sources... [ 80%] emod_api.serialization.dtkFileTools reading sources... [ 82%] 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.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/latest/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/latest/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2020-12-17T01:12:31.380608Z, end-time: 2020-12-17T01:12:31.441426Z, 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: 2020-12-17T01:12:31.555183Z, end-time: 2020-12-17T01:12:33.673148Z, 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 648--648 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 forced_id=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 im- 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 674--674 \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 im-plic- 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 , Underfull \hbox (badness 10000) in paragraph at lines 698--698 \T1/ptm/m/it/10 base_file=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-plic- 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 (25.80493pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1242--1242 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1248--1248 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1254--1254 []\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 1286--1286 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- [14] Underfull \hbox (badness 10000) in paragraph at lines 1295--1298 []\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 1379--1379 []\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 1385--1385 []\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 1385--1385 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\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 , Underfull \hbox (badness 10000) in paragraph at lines 1420--1421 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from [15] Underfull \hbox (badness 10000) in paragraph at lines 1440--1440 []\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 1441--1442 \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 1468--1468 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1468--1468 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1538--1538 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1538--1538 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1564--1564 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1564--1564 \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 1565. Underfull \hbox (badness 10000) in paragraph at lines 1636--1636 []\T1/ptm/m/it/10 point\T1/ptm/m/n/10 , Overfull \hbox (37.41425pt too wide) in paragraph at lines 1636--1636 \T1/ptm/m/it/10 grid_id_2_cell_id\T1/ptm/m/n/10 , [17] Underfull \hbox (badness 10000) in paragraph at lines 1666--1666 []\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 1709--1709 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1709--1709 \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 , \T1/ptm/m/it/10 wan- Underfull \hbox (badness 10000) in paragraph at lines 1730--1730 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 []\T1/ptm/m/it/10 demographics_file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 \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 2018--2018 \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 2018--2018 \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 2029--2029 []\T1/ptm/m/it/10 demographics_file_path\T1/ptm/m/n/10 , [20] Overfull \hbox (24.70302pt too wide) in paragraph at lines 2061--2061 []\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 2082--2082 []\T1/ptm/m/it/10 input_serpop_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2082--2082 \T1/ptm/m/it/10 mod_fn=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2103--2103 []\T1/ptm/m/it/10 file: [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 2229--2229 []\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 2264--2264 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- [23] Underfull \hbox (badness 7203) in paragraph at lines 2385--2385 \T1/ptm/m/it/10 True, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 date\TS1/ptm/m/it/10 '\ T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Thu Dec 17 Underfull \hbox (badness 5050) in paragraph at lines 2385--2385 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 tool\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : \TS1/ ptm/m/it/10 '\T1/ptm/m/it/10 dtk-File-Tools.py\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver- LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileSupport:emod_api. serialization.dtkFileSupport.SerialObject' on page 24 undefined on input line 2 386. 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[25] Underfull \hbox (badness 10000) in paragraph at lines 2619--2619 \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 2619--2619 \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 3101. LaTeX Warning: Reference `emod_api.campaign:module-emod_api.campaign' on page 3 3 undefined on input line 3102. LaTeX Warning: Reference `emod_api.channelreports:module-emod_api.channelreport s' on page 33 undefined on input line 3103. LaTeX Warning: Reference `emod_api.channelreports.channels:module-emod_api.chan nelreports.channels' on page 33 undefined on input line 3104. LaTeX Warning: Reference `emod_api.config:module-emod_api.config' on page 33 un defined on input line 3105. 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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 3102 Reference `emod_api.channelreports.channels:module-emod_api.channelreports.channels' on page 33 undefined on input line 3104 Reference `emod_api.channelreports:module-emod_api.channelreports' on page 33 undefined on input line 3103 Reference `emod_api.config.default_from_schema:module-emod_api.config.default_from_schema' on page 33 undefined on input line 3106 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 3107 Reference `emod_api.config.dtk_post_process_adhocevents:module-emod_api.config.dtk_post_process_adhocevents' on page 33 undefined on input line 3108 Reference `emod_api.config.dtk_pre_process_adhocevents:module-emod_api.config.dtk_pre_process_adhocevents' on page 33 undefined on input line 3109 Reference `emod_api.config.dtk_pre_process_w5ml:module-emod_api.config.dtk_pre_process_w5ml' on page 33 undefined on input line 3110 Reference `emod_api.config.from_overrides:module-emod_api.config.from_overrides' on page 33 undefined on input line 3111 Reference `emod_api.config.from_poi_and_binary:module-emod_api.config.from_poi_and_binary' on page 33 undefined on input line 3112 Reference `emod_api.config.from_schema:module-emod_api.config.from_schema' on page 33 undefined on input line 3113 Reference `emod_api.config.schema_to_config:module-emod_api.config.schema_to_config' on page 33 undefined on input line 3114 Reference `emod_api.config:module-emod_api.config' on page 33 undefined on input line 3105 Reference `emod_api.demographics.BaseInputFile:module-emod_api.demographics.BaseInputFile' on page 33 undefined on input line 3116 Reference `emod_api.demographics.Demographics:module-emod_api.demographics.Demographics' on page 33 undefined on input line 3117 Reference `emod_api.demographics.DemographicsGenerator:module-emod_api.demographics.DemographicsGenerator' on page 33 undefined on input line 3119 Reference `emod_api.demographics.DemographicsInputDataParsers:module-emod_api.demographics.DemographicsInputDataParsers' on page 33 undefined on input line 3120 Reference `emod_api.demographics.DemographicsTemplates:module-emod_api.demographics.DemographicsTemplates' on page 33 undefined on input line 3121 Reference `emod_api.demographics.Node:module-emod_api.demographics.Node' on page 33 undefined on input line 3123 Reference `emod_api.demographics.demographics_utils:module-emod_api.demographics.demographics_utils' on page 33 undefined on input line 3118 Reference `emod_api.demographics.grid_construction:module-emod_api.demographics.grid_construction' on page 33 undefined on input line 3122 Reference `emod_api.demographics:module-emod_api.demographics' on page 33 undefined on input line 3115 Reference `emod_api.interventions.import_pressure:module-emod_api.interventions.import_pressure' on page 33 undefined on input line 3125 Reference `emod_api.interventions.outbreak:module-emod_api.interventions.outbreak' on page 33 undefined on input line 3126 Reference `emod_api.interventions.simple_vaccine:module-emod_api.interventions.simple_vaccine' on page 33 undefined on input line 3127 Reference `emod_api.interventions:module-emod_api.interventions' on page 33 undefined on input line 3124 Reference `emod_api.migration.Migration:module-emod_api.migration.Migration' on page 33 undefined on input line 3129 Reference `emod_api.migration:module-emod_api.migration' on page 33 undefined on input line 3128 Reference `emod_api.schema.dtk_post_process_schema:module-emod_api.schema.dtk_post_process_schema' on page 33 undefined on input line 3131 Reference `emod_api.schema.get_schema:module-emod_api.schema.get_schema' on page 33 undefined on input line 3132 Reference `emod_api.schema:module-emod_api.schema' on page 33 undefined on input line 3130 Reference `emod_api.schema_to_class:module-emod_api.schema_to_class' on page 33 undefined on input line 3133 Reference `emod_api.serialization.CensusAndModPop:module-emod_api.serialization.CensusAndModPop' on page 33 undefined on input line 3135 Reference `emod_api.serialization.SerializedPopulation:module-emod_api.serialization.SerializedPopulation' on page 33 undefined on input line 3139 Reference `emod_api.serialization.dtkFileSupport:module-emod_api.serialization.dtkFileSupport' on page 33 undefined on input line 3136 Reference `emod_api.serialization.dtkFileTools:module-emod_api.serialization.dtkFileTools' on page 33 undefined on input line 3137 Reference `emod_api.serialization.dtkFileUtility:module-emod_api.serialization.dtkFileUtility' on page 33 undefined on input line 3138 Reference `emod_api.serialization:module-emod_api.serialization' on page 33 undefined on input line 3134 Reference `emod_api.spatialreports.spatial:module-emod_api.spatialreports.spatial' on page 33 undefined on input line 3141 Reference `emod_api.spatialreports:module-emod_api.spatialreports' on page 33 undefined on input line 3140 Reference `emod_api.tabularoutput:module-emod_api.tabularoutput' on page 33 undefined on input line 3142 Reference `emod_api.weather.weather:module-emod_api.weather.weather' on page 33 undefined on input line 3144 Reference `emod_api.weather:module-emod_api.weather' on page 33 undefined on input line 3143 Reference `emod_api:module-emod_api' on page 33 undefined on input line 3101 Latexmk: Summary of warnings: Latex failed to resolve 44 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 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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 (385 entries accepted, 0 rejected). Sorting entries......done (3390 comparisons). Generating output file institute-for-disease-modeling-emod-api.ind....done (753 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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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 674--674 \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 im-plic- 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 , Underfull \hbox (badness 10000) in paragraph at lines 698--698 \T1/ptm/m/it/10 base_file=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-plic- [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 (25.80493pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1242--1242 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1248--1248 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1254--1254 []\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 1286--1286 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- [14] Underfull \hbox (badness 10000) in paragraph at lines 1295--1298 []\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 1379--1379 []\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 1385--1385 []\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 1385--1385 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\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 , Underfull \hbox (badness 10000) in paragraph at lines 1420--1421 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from [15] Underfull \hbox (badness 10000) in paragraph at lines 1440--1440 []\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 1441--1442 \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 1468--1468 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1468--1468 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1538--1538 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1538--1538 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1564--1564 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1564--1564 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1636--1636 []\T1/ptm/m/it/10 point\T1/ptm/m/n/10 , Overfull \hbox (37.41425pt too wide) in paragraph at lines 1636--1636 \T1/ptm/m/it/10 grid_id_2_cell_id\T1/ptm/m/n/10 , [17] Underfull \hbox (badness 10000) in paragraph at lines 1666--1666 []\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 1709--1709 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1709--1709 \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 , \T1/ptm/m/it/10 wan- Underfull \hbox (badness 10000) in paragraph at lines 1730--1730 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 []\T1/ptm/m/it/10 demographics_file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 \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 2018--2018 \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 2018--2018 \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 2029--2029 []\T1/ptm/m/it/10 demographics_file_path\T1/ptm/m/n/10 , [20] Overfull \hbox (24.70302pt too wide) in paragraph at lines 2061--2061 []\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 2082--2082 []\T1/ptm/m/it/10 input_serpop_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2082--2082 \T1/ptm/m/it/10 mod_fn=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2103--2103 []\T1/ptm/m/it/10 file: [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 2229--2229 []\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 2264--2264 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- [23] Underfull \hbox (badness 7203) in paragraph at lines 2385--2385 \T1/ptm/m/it/10 True, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 date\TS1/ptm/m/it/10 '\ T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Thu Dec 17 Underfull \hbox (badness 5050) in paragraph at lines 2385--2385 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 tool\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : \TS1/ ptm/m/it/10 '\T1/ptm/m/it/10 dtk-File-Tools.py\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver- [24] Underfull \hbox (badness 10000) in paragraph at lines 2501--2501 []\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 6493) in paragraph at lines 2501--2501 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2501--2501 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2501--2501 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2501--2501 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2515--2515 []\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 6493) in paragraph at lines 2515--2515 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2515--2515 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2515--2515 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2515--2515 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2537--2537 []\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 6493) in paragraph at lines 2537--2537 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2537--2537 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2537--2537 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2537--2537 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2559--2559 []\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 6493) in paragraph at lines 2559--2559 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2559--2559 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2559--2559 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2559--2559 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , [25] Underfull \hbox (badness 10000) in paragraph at lines 2619--2619 \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 2619--2619 \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 3107--3108 []\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 3108--3109 []\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 3109--3110 []\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 3118--3119 []\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 3119--3120 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3120--3121 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3121--3122 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3122--3123 []\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 3125--3126 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3127--3128 []\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 3131--3132 []\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 3135--3136 []\T1/pcr/m/n/10 emod_api.serialization.CensusAndModPop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3136--3137 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3138--3139 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3139--3140 []\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 136--138 []\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 138--140 []\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 140--142 []\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 143--145 []\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 145--147 []\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 147--149 []\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 149--151 []\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 151--153 []\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 153--155 []\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 155--157 []\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 157--159 []\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 159--161 []\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 161--163 []\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 161--163 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\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 180--181 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 182--183 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 184--185 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (10.1225pt too wide) in paragraph at lines 202--203 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils Overfull \hbox (28.1225pt too wide) in paragraph at lines 204--205 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 206--207 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 208--209 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (4.1225pt too wide) in paragraph at lines 210--211 []\T1/pcr/m/n/10 emod_api.demographics.grid_construction Overfull \hbox (4.1225pt too wide) in paragraph at lines 228--229 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 244--245 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 256--258 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 256--258 \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 258--260 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 268--270 []\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 268--270 \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 270--272 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict Overfull \hbox (36.30013pt too wide) in paragraph at lines 272--274 []\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 274--276 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [37] Overfull \hbox (81.59949pt too wide) in paragraph at lines 276--278 []\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 280--282 []\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 280--282 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 282--284 []\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 284--286 []\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 284--286 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (8.41116pt too wide) in paragraph at lines 288--290 []\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 290--292 []\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 292--294 []\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 292--294 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 294--296 []\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 294--296 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 296--298 []\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 296--298 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 298--300 []\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 298--300 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 300--302 []\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 302--304 []\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 302--304 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 304--306 []\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 304--306 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (38.41116pt too wide) in paragraph at lines 309--311 []\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 311--313 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 311--313 \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 313--315 []\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 315--317 []\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 317--319 []\T1/pcr/m/n/10 generate_headers() Overfull \hbox (29.07082pt too wide) in paragraph at lines 317--319 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.BaseInputFile.BaseInputFi le Underfull \hbox (badness 10000) in paragraph at lines 319--321 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 319--321 \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 321--323 []\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 324--326 []\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 324--326 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 326--328 []\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 328--330 \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 333--335 []\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 333--335 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 335--337 []\T1/pcr/m/n/10 get_next_individual_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 335--337 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 337--339 []\T1/pcr/m/n/10 get_next_infection_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 337--339 \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 339--341 []\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 341--343 []\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 341--343 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 343--345 []\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 345--347 []\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 345--347 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\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 354--356 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 364--366 []\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 366--367 []\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 367--369 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata [38] Overfull \hbox (1.47115pt too wide) in paragraph at lines 369--371 []\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 371--373 []\T1/pcr/m/n/10 IDREF_GRUMP1DEGREE Underfull \hbox (badness 10000) in paragraph at lines 371--373 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 373--375 []\T1/pcr/m/n/10 IDREF_GRUMP2PT5ARCMIN Underfull \hbox (badness 10000) in paragraph at lines 373--375 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 375--377 []\T1/pcr/m/n/10 IDREF_GRUMP30ARCSEC Underfull \hbox (badness 10000) in paragraph at lines 375--377 \T1/ptm/m/n/10 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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 408--410 []\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 410--412 []\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 410--412 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 415--417 []\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 415--417 \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 417--419 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 417--419 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 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paragraph at lines 429--431 []\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 437--438 []| \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 438--439 []| \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 439--440 []| \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 440--441 []| \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 441--442 []| \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 443--444 []| \T1/pcr/m/n/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 , Overfull 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /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 (47 pages, 240783 bytes). Transcript written on institute-for-disease-modeling-emod-api.log. Latexmk: Index file 'institute-for-disease-modeling-emod-api.idx' was written Latexmk: References changed. 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Underfull \hbox (badness 10000) in paragraph at lines 105--107 []\T1/ptm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 108--110 []\T1/ptm/m/n/10 python -m (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] Underfull \hbox (badness 10000) in paragraph at lines 234--234 []\T1/ptm/m/it/10 filename: str = None\T1/ptm/m/n/10 , (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [4] Overfull \hbox (73.14464pt too wide) in paragraph at lines 352--352 []\T1/ptm/m/it/10 schema_path_in\T1/ptm/m/n/10 , Overfull \hbox (27.46486pt too wide) in paragraph at lines 352--352 \T1/ptm/m/it/10 subn- Overfull \hbox (43.09444pt too wide) in paragraph at lines 352--352 \T1/ptm/m/it/10 ode_list\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 355--357 []\T1/ptm/m/n/10 config = json.load(open(^^Pdefault_config.json^^Q), ob-ject_ho ok=s2c.ReadOnlyDict) os.remove( ^^Pde- Overfull \hbox (79.14464pt too wide) in paragraph at lines 363--363 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\T1/ptm/m/it/10 im-plic- [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 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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 (25.80493pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1242--1242 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1242--1242 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1248--1248 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1254--1254 []\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 1286--1286 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1286--1286 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1292--1292 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- [14] Underfull \hbox (badness 10000) in paragraph at lines 1295--1298 []\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 1379--1379 []\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 1385--1385 []\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 1385--1385 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\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 , Underfull \hbox (badness 10000) in paragraph at lines 1420--1421 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from [15] Underfull \hbox (badness 10000) in paragraph at lines 1440--1440 []\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 1441--1442 \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 1468--1468 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1468--1468 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [16] Underfull \hbox (badness 10000) in paragraph at lines 1538--1538 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1538--1538 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1564--1564 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1564--1564 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1636--1636 []\T1/ptm/m/it/10 point\T1/ptm/m/n/10 , Overfull \hbox (37.41425pt too wide) in paragraph at lines 1636--1636 \T1/ptm/m/it/10 grid_id_2_cell_id\T1/ptm/m/n/10 , [17] Underfull \hbox (badness 10000) in paragraph at lines 1666--1666 []\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 1709--1709 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1709--1709 \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 , \T1/ptm/m/it/10 wan- Underfull \hbox (badness 10000) in paragraph at lines 1730--1730 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 []\T1/ptm/m/it/10 demographics_file_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2018--2018 \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 2018--2018 \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 2018--2018 \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 2029--2029 []\T1/ptm/m/it/10 demographics_file_path\T1/ptm/m/n/10 , [20] Overfull \hbox (24.70302pt too wide) in paragraph at lines 2061--2061 []\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 2082--2082 []\T1/ptm/m/it/10 input_serpop_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2082--2082 \T1/ptm/m/it/10 mod_fn=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2103--2103 []\T1/ptm/m/it/10 file: [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 2229--2229 []\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 2264--2264 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- [23] Underfull \hbox (badness 7203) in paragraph at lines 2385--2385 \T1/ptm/m/it/10 True, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 date\TS1/ptm/m/it/10 '\ T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Thu Dec 17 Underfull \hbox (badness 5050) in paragraph at lines 2385--2385 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 tool\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : \TS1/ ptm/m/it/10 '\T1/ptm/m/it/10 dtk-File-Tools.py\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver- [24] Underfull \hbox (badness 10000) in paragraph at lines 2501--2501 []\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 6493) in paragraph at lines 2501--2501 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2501--2501 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2501--2501 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2501--2501 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2515--2515 []\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 6493) in paragraph at lines 2515--2515 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2515--2515 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2515--2515 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2515--2515 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2537--2537 []\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 6493) in paragraph at lines 2537--2537 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2537--2537 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2537--2537 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2537--2537 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2559--2559 []\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 6493) in paragraph at lines 2559--2559 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2559--2559 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2559--2559 \T1/ptm/m/it/10 17 01:12:29 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2559--2559 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , [25] Underfull \hbox (badness 10000) in paragraph at lines 2619--2619 \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 2619--2619 \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 3107--3108 []\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 3108--3109 []\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 3109--3110 []\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 3118--3119 []\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 3119--3120 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3120--3121 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3121--3122 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 3122--3123 []\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 3125--3126 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3127--3128 []\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 3131--3132 []\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 3135--3136 []\T1/pcr/m/n/10 emod_api.serialization.CensusAndModPop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3136--3137 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3138--3139 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3139--3140 []\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 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\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 136--138 []\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 138--140 []\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 140--142 []\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 143--145 []\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 145--147 []\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 147--149 []\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 149--151 []\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 151--153 []\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 153--155 []\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 155--157 []\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 157--159 []\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 159--161 []\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 161--163 []\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 161--163 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\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 180--181 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 182--183 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 184--185 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (10.1225pt too wide) in paragraph at lines 202--203 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils Overfull \hbox (28.1225pt too wide) in paragraph at lines 204--205 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 206--207 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 208--209 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (4.1225pt too wide) in paragraph at lines 210--211 []\T1/pcr/m/n/10 emod_api.demographics.grid_construction Overfull \hbox (4.1225pt too wide) in paragraph at lines 228--229 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 244--245 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 256--258 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 256--258 \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 258--260 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 268--270 []\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 268--270 \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 270--272 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict Overfull \hbox (36.30013pt too wide) in paragraph at lines 272--274 []\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 274--276 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule [37] Overfull \hbox (81.59949pt too wide) in paragraph at lines 276--278 []\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 280--282 []\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 280--282 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 282--284 []\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 284--286 []\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 284--286 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (8.41116pt too wide) in paragraph at lines 288--290 []\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 290--292 []\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 292--294 []\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 292--294 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 294--296 []\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 294--296 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 296--298 []\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 296--298 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 298--300 []\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 298--300 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 300--302 []\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 302--304 []\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 302--304 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 304--306 []\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 304--306 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (38.41116pt too wide) in paragraph at lines 309--311 []\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 311--313 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 311--313 \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 313--315 []\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 315--317 []\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 317--319 []\T1/pcr/m/n/10 generate_headers() Overfull \hbox (29.07082pt too wide) in paragraph at lines 317--319 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.BaseInputFile.BaseInputFi le Underfull \hbox (badness 10000) in paragraph at lines 319--321 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 319--321 \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 321--323 []\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 324--326 []\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 324--326 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 326--328 []\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 328--330 \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 333--335 []\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 333--335 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 335--337 []\T1/pcr/m/n/10 get_next_individual_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 335--337 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 337--339 []\T1/pcr/m/n/10 get_next_infection_suid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 337--339 \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 339--341 []\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 341--343 []\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 341--343 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 343--345 []\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 345--347 []\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 345--347 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\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 354--356 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 364--366 []\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 366--367 []\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 367--369 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata [38] Overfull \hbox (1.47115pt too wide) in paragraph at lines 369--371 []\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 371--373 []\T1/pcr/m/n/10 IDREF_GRUMP1DEGREE Underfull \hbox (badness 10000) in paragraph at lines 371--373 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 373--375 []\T1/pcr/m/n/10 IDREF_GRUMP2PT5ARCMIN Underfull \hbox (badness 10000) in paragraph at lines 373--375 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 375--377 []\T1/pcr/m/n/10 IDREF_GRUMP30ARCSEC Underfull \hbox (badness 10000) in paragraph at lines 375--377 \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 377--379 []\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 379--381 []\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 381--383 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 381--383 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 383--385 []\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 383--385 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 385--387 []\T1/pcr/m/n/10 InitPrevUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 385--387 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 387--389 []\T1/pcr/m/n/10 InitRiskUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 387--389 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 389--391 []\T1/pcr/m/n/10 InitSusceptConstant() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 389--391 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 391--393 []\T1/pcr/m/n/10 InterpolationType() Underfull \hbox (badness 10000) in paragraph at lines 391--393 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Overfull \hbox (20.8303pt too wide) in paragraph at lines 393--395 []\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 395--397 []\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 401--403 []\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 404--406 []\T1/pcr/m/n/10 LINEAR_INTERPOLATION Underfull \hbox (badness 10000) in paragraph at lines 404--406 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 406--408 []\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 406--408 \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 408--410 []\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 410--412 []\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 410--412 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 415--417 []\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 415--417 \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 417--419 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 417--419 \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 419--421 []\T1/pcr/m/n/10 make_config_from_poi_and_config_file() Overfull \hbox (16.3614pt too wide) in paragraph at lines 419--421 \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 421--423 []\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 421--423 \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 423--424 []\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 427--428 []\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 429--431 []\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 437--438 []| \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 438--439 []| \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 439--440 []| \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 440--441 []| \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 441--442 []| \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 443--444 []| \T1/pcr/m/n/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 , Overfull 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lines 521--523 []\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 523--525 []\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 525--527 []\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 527--529 []\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 530--531 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weath er.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 531--533 []\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 533--535 []\T1/pcr/m/n/10 NoInitialPrevalence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 533--535 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), [40] Underfull \hbox (badness 10000) in paragraph at lines 535--537 []\T1/pcr/m/n/10 NoMigrationHeterogeneity() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 535--537 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 NoRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 537--539 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 539--541 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport 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Underfull \hbox (badness 10000) in paragraph at lines 557--559 \T1/ptm/m/it/10 emod_api.demographics.grid_construction\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 561--563 []\T1/pcr/m/n/10 provenance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Overfull \hbox (1.84042pt too wide) in paragraph at lines 566--567 []\T1/pcr/m/n/10 read() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.dtkFileTools\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 568--570 []\T1/pcr/m/n/10 recurser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 568--570 \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 570--572 []\T1/pcr/m/n/10 REGIONAL \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Mi gration.Migration Overfull \hbox (56.83089pt too wide) in paragraph at lines 572--574 []\T1/pcr/m/n/10 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 574--576 []\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 576--578 []\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 578--580 []\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 580--582 []\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 585--587 []\T1/pcr/m/n/10 SAME_FOR_BOTH_GENDERS Underfull \hbox (badness 10000) in paragraph at lines 585--587 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 588--590 []\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 588--590 \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 590--592 []\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 590--592 \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 592--594 []\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 594--596 []\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 596--597 []\T1/pcr/m/n/10 SEA \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Migrati on.Migration at- Underfull \hbox (badness 10000) in paragraph at lines 597--599 []\T1/pcr/m/n/10 seed_by_coverage() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 599--601 []\T1/pcr/m/n/10 SerializedPopulation \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 599--601 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 601--603 []\T1/pcr/m/n/10 SerialObject \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 603--605 []\T1/pcr/m/n/10 set_age_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 603--605 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 605--607 []\T1/pcr/m/n/10 set_age_simple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 605--607 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 607--609 []\T1/pcr/m/n/10 set_boxcar_seasonal() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 607--609 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 609--611 []\T1/pcr/m/n/10 set_demog_distributions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 609--611 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 611--613 []\T1/pcr/m/n/10 set_growing_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 611--613 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 613--615 []\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 613--615 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 615--617 []\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 615--617 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (173.87039pt too wide) in paragraph at lines 617--619 []\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 619--621 []\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 619--621 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Overfull \hbox (16.62106pt too wide) in paragraph at lines 621--623 []\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 623--625 []\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 623--625 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), [41] Underfull \hbox (badness 10000) in paragraph at lines 625--627 []\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 625--627 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 627--629 []\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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