Read the Docs build information Build id: 1274143 Project: institute-for-disease-modeling-emod-api Version: latest Commit: a341ddff74f836a4adf40dd495dd9b91ef89fc81 Date: 2023-01-28T00:07:03.440924Z State: finished Success: True [rtd-command-info] start-time: 2023-01-28T00:09:26.321972Z, end-time: 2023-01-28T00:09:28.834691Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emod-api.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2023-01-28T00:09:29.015749Z, end-time: 2023-01-28T00:09:29.245606Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to '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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at a341ddf Bump version: 1.27.9 → 1.27.10 [rtd-command-info] start-time: 2023-01-28T00:09:29.459584Z, end-time: 2023-01-28T00:09:29.521691Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-01-28T00:09:30.641237Z, end-time: 2023-01-28T00:09:36.482938Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/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: 2023-01-28T00:09:36.690686Z, end-time: 2023-01-28T00:09:38.618914Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/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 (22.3.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 32.9 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 66.1.1 Uninstalling setuptools-66.1.1: Successfully uninstalled setuptools-66.1.1 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2023-01-28T00:09:38.795750Z, end-time: 2023-01-28T00:09:46.689234Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I pillow==5.4.1 mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0 setuptools<58.3.0 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 37.9 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 242.2 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.13-py3-none-any.whl (13 kB) Collecting commonmark==0.9.1 Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 178.6 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 191.5 MB/s eta 0:00:00 Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 175.8 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.3 Downloading readthedocs_sphinx_ext-2.2.0-py2.py3-none-any.whl (11 kB) Collecting jinja2<3.1.0 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 217.2 MB/s eta 0:00:00 Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 250.1 MB/s eta 0:00:00 Collecting docutils>=0.11 Downloading docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 239.9 MB/s eta 0:00:00 Collecting requests>=2.0.0 Downloading requests-2.28.2-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 185.5 MB/s eta 0:00:00 Collecting imagesize Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.11.0-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 173.6 MB/s eta 0:00:00 Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 245.6 MB/s eta 0:00:00 Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 205.4 MB/s eta 0:00:00 Collecting Pygments>=2.0 Downloading Pygments-2.14.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 250.3 MB/s eta 0:00:00 Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-23.0-py3-none-any.whl (42 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 164.6 MB/s eta 0:00:00 Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting pytz>=2015.7 Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 499.4/499.4 kB 242.5 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.14-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.6/140.6 kB 220.1 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 166.3 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.12.7-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 192.4 MB/s eta 0:00:00 Collecting charset-normalizer<4,>=2 Downloading charset_normalizer-3.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (170 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.5/170.5 kB 229.2 MB/s eta 0:00:00 Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 208.8 MB/s eta 0:00:00 Building wheels for collected packages: mock Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=1a8626ab799dd3120065ad884cc9eb120760139c45fa6ce8d10b4e9fea6aa9e3 Stored in directory: /tmp/pip-ephem-wheel-cache-vcjk1pxg/wheels/d1/33/8e/f9d24f00cc130866aacfe7c3bc15571217e2b22cc4c4e1b443 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, charset-normalizer, urllib3, sphinxcontrib-serializinghtml, six, setuptools, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark 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 MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-5.4.1 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 setuptools-58.2.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.14 [rtd-command-info] start-time: 2023-01-28T00:09:46.906460Z, end-time: 2023-01-28T00:09:53.955836Z, duration: 7, 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: numpy!=1.19.4 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Collecting pyyaml Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 596.3/596.3 kB 19.6 MB/s eta 0:00:00 Requirement already satisfied: pandas in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (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 4)) (1.5.3) Collecting shapely Downloading shapely-2.0.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 114.2 MB/s eta 0:00:00 Collecting pyproj Downloading pyproj-3.2.1-cp37-cp37m-manylinux2010_x86_64.whl (6.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 200.8 MB/s eta 0:00:00 Collecting geographiclib Downloading geographiclib-2.0-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.3/40.3 kB 167.6 MB/s eta 0:00:00 Collecting scikit-learn Downloading scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.8/24.8 MB 192.4 MB/s eta 0:00:00 Collecting lz4 Downloading lz4-4.3.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 254.6 MB/s eta 0:00:00 Collecting prodict Downloading prodict-0.8.18.tar.gz (4.2 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting graphviz Downloading graphviz-0.20.1-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 169.0 MB/s eta 0:00:00 Collecting parse Downloading parse-1.19.0.tar.gz (30 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 13)) (3.3.2) Requirement already satisfied: python-dateutil>=2.7.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 3)) (2.8.1) 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 3)) (2022.7.1) Requirement already satisfied: certifi in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from pyproj->-r requirements.txt (line 6)) (2022.12.7) Collecting joblib>=0.11 Downloading joblib-1.2.0-py3-none-any.whl (297 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 227.2 MB/s eta 0:00:00 Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 13)) (2.4.7) Collecting pillow>=6.2.0 Downloading Pillow-9.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 211.1 MB/s eta 0:00:00 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 13)) (1.2.0) 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 13)) (0.10.0) 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 13)) (1.16.0) Building wheels for collected packages: prodict, parse Building wheel for prodict (setup.py): started Building wheel for prodict (setup.py): finished with status 'done' Created wheel for prodict: filename=prodict-0.8.18-py3-none-any.whl size=4223 sha256=ece6c79e5418127d8744c8b2e7f8eace762e99791ea82098730126db8c8bd0c6 Stored in directory: /tmp/pip-ephem-wheel-cache-xu1prnp9/wheels/29/89/ca/712fdccd9e7d11126de0f9d9926828406746efd93c5064ef63 Building wheel for parse (setup.py): started Building wheel for parse (setup.py): finished with status 'done' Created wheel for parse: filename=parse-1.19.0-py3-none-any.whl size=24591 sha256=4ce3aa2165249e65045238065ef904bb33d3525964dd1e87bace512aaa0ea161 Stored in directory: /tmp/pip-ephem-wheel-cache-xu1prnp9/wheels/ae/e8/03/b4e651a096c85ca63fd4fba7f0d164dcfb3f46b766c1af0462 Successfully built prodict parse Installing collected packages: prodict, parse, threadpoolctl, shapely, pyyaml, pyproj, pillow, lz4, joblib, graphviz, geographiclib, scikit-learn Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed geographiclib-2.0 graphviz-0.20.1 joblib-1.2.0 lz4-4.3.2 parse-1.19.0 pillow-9.4.0 prodict-0.8.18 pyproj-3.2.1 pyyaml-6.0 scikit-learn-1.0.2 shapely-2.0.0 threadpoolctl-3.1.0 [rtd-command-info] start-time: 2023-01-28T00:09:54.168858Z, end-time: 2023-01-28T00:09:58.888584Z, duration: 4, 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 sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 103.1 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=4.4.0 Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 203.4 MB/s eta 0:00:00 Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting sphinxext.remoteliteralinclude Downloading sphinxext_remoteliteralinclude-0.4.0-py3-none-any.whl (6.4 kB) Collecting sphinx-copybutton~=0.4.0 Downloading sphinx_copybutton-0.4.0-py3-none-any.whl (12 kB) Collecting docutils<0.17 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 239.0 MB/s eta 0:00:00 Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 2)) (1.16.0) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) 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~=4.4.0->-r docs/requirements.txt (line 3)) (3.0.3) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 kB 214.6 MB/s eta 0:00:00 Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2.28.2) Collecting importlib-metadata>=4.4 Downloading importlib_metadata-6.0.0-py3-none-any.whl (21 kB) 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~=4.4.0->-r docs/requirements.txt (line 3)) (2.2.0) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 198.5 MB/s eta 0:00:00 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~=4.4.0->-r docs/requirements.txt (line 3)) (23.0) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.1.5) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 kB 200.8 MB/s eta 0:00:00 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~=4.4.0->-r docs/requirements.txt (line 3)) (1.4.1) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 206.4 MB/s eta 0:00:00 Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) 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~=4.4.0->-r docs/requirements.txt (line 3)) (2.14.0) 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~=4.4.0->-r docs/requirements.txt (line 3)) (0.7.13) 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~=4.4.0->-r docs/requirements.txt (line 3)) (2.11.0) Collecting MarkupSafe<=2.0.1 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 125.7/125.7 kB 201.7 MB/s eta 0:00:00 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~=4.4.0->-r docs/requirements.txt (line 3)) (2022.7.1) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-4.4.0-py3-none-any.whl (26 kB) Collecting zipp>=0.5 Downloading zipp-3.12.0-py3-none-any.whl (6.6 kB) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.26.14) 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>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2022.12.7) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.0.1) Requirement already satisfied: idna<4,>=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>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.4) Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pockets, MarkupSafe, docutils, sphinxcontrib-napoleon, plantweb, Jinja2, importlib-metadata, sphinxext.remoteliteralinclude, sphinx, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton Attempting uninstall: MarkupSafe Found existing installation: MarkupSafe 2.1.2 Uninstalling MarkupSafe-2.1.2: Successfully uninstalled MarkupSafe-2.1.2 Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 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 Jinja2-2.11.3 MarkupSafe-2.0.1 docutils-0.16 importlib-metadata-6.0.0 plantweb-1.2.1 pockets-0.9.1 sphinx-4.4.0 sphinx-copybutton-0.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxcontrib-qthelp-1.0.3 sphinxext.remoteliteralinclude-0.4.0 typing-extensions-4.4.0 zipp-3.12.0 [rtd-command-info] start-time: 2023-01-28T00:09:59.075252Z, end-time: 2023-01-28T00:10:00.134400Z, duration: 1, 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/*' adding license file 'LICENSE' 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/some_config_i_found.py -> build/lib/examples copying examples/write_config_from_default_and_params.py -> 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/spatial_report.py -> build/lib/examples copying examples/migration.py -> build/lib/examples copying examples/weather_file.py -> build/lib/examples copying examples/__init__.py -> build/lib/examples copying examples/insetchart.py -> build/lib/examples copying examples/default_from_schema.py -> build/lib/examples creating build/lib/emod_api copying emod_api/__main__.py -> build/lib/emod_api copying emod_api/peek_camp.py -> build/lib/emod_api copying emod_api/campaign.py -> build/lib/emod_api copying emod_api/__init__.py -> build/lib/emod_api copying emod_api/schema_to_class.py -> build/lib/emod_api copying emod_api/multidim_plotter.py -> build/lib/emod_api creating 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 copying emod_api/weather/__init__.py -> build/lib/emod_api/weather creating build/lib/emod_api/schema copying emod_api/schema/__main__.py -> build/lib/emod_api/schema copying emod_api/schema/get_schema.py -> build/lib/emod_api/schema copying emod_api/schema/dtk_post_process_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__init__.py -> build/lib/emod_api/schema creating build/lib/emod_api/channelreports copying emod_api/channelreports/channels.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/plot_icj_means.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/__main__.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/plot_prop_report.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/__init__.py -> build/lib/emod_api/channelreports 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/__main__.py -> build/lib/emod_api/demographics copying emod_api/demographics/Node.py -> build/lib/emod_api/demographics copying emod_api/demographics/PreDefinedDistributions.py -> build/lib/emod_api/demographics copying emod_api/demographics/__init__.py -> build/lib/emod_api/demographics copying emod_api/demographics/Demographics.py -> build/lib/emod_api/demographics copying emod_api/demographics/Updateable.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsInputDataParsers.py -> build/lib/emod_api/demographics copying emod_api/demographics/BaseInputFile.py -> build/lib/emod_api/demographics copying emod_api/demographics/PropertiesAndAttributes.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsTemplates.py -> build/lib/emod_api/demographics copying emod_api/demographics/grid_construction.py -> build/lib/emod_api/demographics creating build/lib/emod_api/spatialreports copying emod_api/spatialreports/__main__.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/spatial.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/__init__.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/plot_spat_means.py -> build/lib/emod_api/spatialreports creating build/lib/emod_api/serialization copying emod_api/serialization/dtkFileTools.py -> build/lib/emod_api/serialization copying emod_api/serialization/__main__.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileUtility.py -> build/lib/emod_api/serialization copying emod_api/serialization/__init__.py -> build/lib/emod_api/serialization copying emod_api/serialization/CensusAndModPop.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileSupport.py -> build/lib/emod_api/serialization copying emod_api/serialization/SerializedPopulation.py -> build/lib/emod_api/serialization 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/__main__.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_w5ml.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/dtk_pre_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/__init__.py -> build/lib/emod_api/config copying emod_api/config/from_poi_and_binary.py -> build/lib/emod_api/config copying emod_api/config/from_schema.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema.py -> build/lib/emod_api/config creating build/lib/emod_api/migration copying emod_api/migration/__main__.py -> build/lib/emod_api/migration copying emod_api/migration/migration.py -> build/lib/emod_api/migration copying emod_api/migration/__init__.py -> build/lib/emod_api/migration creating build/lib/emod_api/interventions copying emod_api/interventions/common.py -> build/lib/emod_api/interventions copying emod_api/interventions/__main__.py -> build/lib/emod_api/interventions copying emod_api/interventions/outbreak.py -> build/lib/emod_api/interventions copying emod_api/interventions/ccdl.py -> build/lib/emod_api/interventions copying emod_api/interventions/ccdl_viz.py -> build/lib/emod_api/interventions copying emod_api/interventions/migration.py -> build/lib/emod_api/interventions copying emod_api/interventions/__init__.py -> build/lib/emod_api/interventions copying emod_api/interventions/import_pressure.py -> build/lib/emod_api/interventions copying emod_api/interventions/node_multiplier.py -> build/lib/emod_api/interventions copying emod_api/interventions/utils.py -> build/lib/emod_api/interventions copying emod_api/interventions/simple_vaccine.py -> build/lib/emod_api/interventions creating build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__main__.py -> build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__init__.py -> build/lib/emod_api/tabularoutput creating build/lib/emod_api/migration/client copying emod_api/migration/client/__init__.py -> build/lib/emod_api/migration/client copying emod_api/migration/client/client.py -> build/lib/emod_api/migration/client creating build/lib/tests creating build/lib/tests/unittests copying tests/unittests/test_config_imports.py -> build/lib/tests/unittests copying tests/unittests/test_properties_and_attributes.py -> build/lib/tests/unittests copying tests/unittests/test_version.py -> build/lib/tests/unittests copying tests/unittests/__init__.py -> build/lib/tests/unittests copying tests/unittests/test_schema_imports.py -> build/lib/tests/unittests copying tests/unittests/test_demographics_imports.py -> build/lib/tests/unittests copying tests/unittests/test_migration_imports.py -> build/lib/tests/unittests creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/examples copying build/lib/examples/some_config_i_found.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/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/spatial_report.py -> build/bdist.linux-x86_64/egg/examples copying build/lib/examples/migration.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/__init__.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/default_from_schema.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/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 copying build/lib/emod_api/weather/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/weather creating 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/schema/get_schema.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/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/schema creating 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/plot_icj_means.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 copying build/lib/emod_api/channelreports/plot_prop_report.py -> 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/__main__.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/peek_camp.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/__main__.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 copying build/lib/emod_api/demographics/PreDefinedDistributions.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/Demographics.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/Updateable.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/BaseInputFile.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/PropertiesAndAttributes.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/grid_construction.py -> build/bdist.linux-x86_64/egg/emod_api/demographics creating 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/spatialreports/spatial.py -> 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/plot_spat_means.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/campaign.py -> build/bdist.linux-x86_64/egg/emod_api creating 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/__main__.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 copying build/lib/emod_api/serialization/__init__.py -> 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/dtkFileSupport.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/__init__.py -> build/bdist.linux-x86_64/egg/emod_api 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/__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 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/dtk_pre_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/from_poi_and_binary.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/default_from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/schema_to_class.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/multidim_plotter.py -> build/bdist.linux-x86_64/egg/emod_api creating 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 copying build/lib/emod_api/migration/migration.py -> 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 creating build/bdist.linux-x86_64/egg/emod_api/migration/client copying build/lib/emod_api/migration/client/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/migration/client copying build/lib/emod_api/migration/client/client.py -> build/bdist.linux-x86_64/egg/emod_api/migration/client creating build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/common.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/outbreak.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/ccdl.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/ccdl_viz.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/migration.py -> 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/import_pressure.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/node_multiplier.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/utils.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/simple_vaccine.py -> build/bdist.linux-x86_64/egg/emod_api/interventions creating 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 copying build/lib/emod_api/tabularoutput/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput creating build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_config_imports.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_properties_and_attributes.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_version.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_schema_imports.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_demographics_imports.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_migration_imports.py -> build/bdist.linux-x86_64/egg/tests/unittests 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/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/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/spatial_report.py to spatial_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/migration.py to migration.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/__init__.py to __init__.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/default_from_schema.py to default_from_schema.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/weather/__init__.py to __init__.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/schema/get_schema.py to get_schema.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/__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/plot_icj_means.py to plot_icj_means.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/channelreports/plot_prop_report.py to plot_prop_report.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/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/peek_camp.py to peek_camp.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/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Node.py to Node.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/PreDefinedDistributions.py to PreDefinedDistributions.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/Demographics.py to Demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Updateable.py to Updateable.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/BaseInputFile.py to BaseInputFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/PropertiesAndAttributes.py to PropertiesAndAttributes.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/grid_construction.py to grid_construction.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/spatialreports/spatial.py to spatial.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/plot_spat_means.py to plot_spat_means.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/serialization/dtkFileTools.py to dtkFileTools.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/dtkFileUtility.py to dtkFileUtility.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/CensusAndModPop.py to CensusAndModPop.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/SerializedPopulation.py to SerializedPopulation.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/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/__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/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/dtk_pre_process_adhocevents.py to dtk_pre_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/from_poi_and_binary.py to from_poi_and_binary.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/default_from_schema.py to default_from_schema.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/multidim_plotter.py to multidim_plotter.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/migration/migration.py to migration.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/client/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/client/client.py to client.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/common.py to common.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/outbreak.py to outbreak.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/ccdl.py to ccdl.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/ccdl_viz.py to ccdl_viz.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/migration.py to migration.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/import_pressure.py to import_pressure.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/node_multiplier.py to node_multiplier.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/utils.py to utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/simple_vaccine.py to simple_vaccine.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/tabularoutput/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_config_imports.py to test_config_imports.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_properties_and_attributes.py to test_properties_and_attributes.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_version.py to test_version.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_schema_imports.py to test_schema_imports.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demographics_imports.py to test_demographics_imports.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_migration_imports.py to test_migration_imports.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__ emod_api.spatialreports.__pycache__.__main__.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-1.27.10-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-1.27.10-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-1.27.10-py3.7.egg Extracting emod_api-1.27.10-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 1.27.10 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-1.27.10-py3.7.egg Processing dependencies for emod-api==1.27.10 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 parse==1.19.0 Best match: parse 1.19.0 Adding parse 1.19.0 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 graphviz==0.20.1 Best match: graphviz 0.20.1 Adding graphviz 0.20.1 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 prodict==0.8.18 Best match: prodict 0.8.18 Adding prodict 0.8.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for lz4==4.3.2 Best match: lz4 4.3.2 Adding lz4 4.3.2 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 scikit-learn==1.0.2 Best match: scikit-learn 1.0.2 Adding scikit-learn 1.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for geographiclib==2.0 Best match: geographiclib 2.0 Adding geographiclib 2.0 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 pyproj==3.2.1 Best match: pyproj 3.2.1 Adding pyproj 3.2.1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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==2.0.0 Best match: shapely 2.0.0 Adding shapely 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 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==6.0 Best match: PyYAML 6.0 Adding PyYAML 6.0 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 numpy==1.19.2 Best match: numpy 1.19.2 numpy 1.19.2 is already the active version in easy-install.pth Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for Pillow==9.4.0 Best match: Pillow 9.4.0 Adding Pillow 9.4.0 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 pyparsing==2.4.7 Best match: pyparsing 2.4.7 pyparsing 2.4.7 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 cycler 0.10.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for certifi==2022.12.7 Best match: certifi 2022.12.7 Adding certifi 2022.12.7 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 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 joblib==1.2.0 Best match: joblib 1.2.0 Adding joblib 1.2.0 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 threadpoolctl==3.1.0 Best match: threadpoolctl 3.1.0 Adding threadpoolctl 3.1.0 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 pytz==2022.7.1 Best match: pytz 2022.7.1 Adding pytz 2022.7.1 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 six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Finished processing dependencies for emod-api==1.27.10 [rtd-command-info] start-time: 2023-01-28T00:10:04.977664Z, end-time: 2023-01-28T00:10:05.057994Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser from datetime import datetime if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "emod-api" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ tags.add('emodapi') # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx_copybutton', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude', 'sphinx.ext.viewcode' ] 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 = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css', '_static/copy_button.css' ] } html_js_files = ['show_block_by_os.js'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = '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 = {'python': ('https://docs.python.org/3', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("v2.0.1", "/en/v2.0.1/"), ("v1.27.4", "/en/v1.27.4/"), ("v1.27.1", "/en/v1.27.1/"), ("v1.26.1", "/en/v1.26.1/"), ("v1.25.1", "/en/v1.25.1/"), ("v1.24.11", "/en/v1.24.11/"), ("v1.24.8", "/en/v1.24.8/"), ("v1.24.1", "/en/v1.24.1/"), ("v1.23.2", "/en/v1.23.2/"), ("v1.23.1", "/en/v1.23.1/"), ("v1.22.11", "/en/v1.22.11/"), ("v1.22.10", "/en/v1.22.10/"), ("v1.22.9", "/en/v1.22.9/"), ("v1.22.1", "/en/v1.22.1/"), ("v1.22.0", "/en/v1.22.0/"), ("v1.21.1", "/en/v1.21.1/"), ("v1.20.2", "/en/v1.20.2/"), ("v1.20.1", "/en/v1.20.1/"), ("v1.19.13", "/en/v1.19.13/"), ("v1.19.2", "/en/v1.19.2/"), ("v1.18.1", "/en/v1.18.1/"), ("v1.17.4", "/en/v1.17.4/"), ("v1.17.3", "/en/v1.17.3/"), ("v1.17.2", "/en/v1.17.2/"), ("v1.16.10", "/en/v1.16.10/"), ("v1.16.5", "/en/v1.16.5/"), ("v1.16.2", "/en/v1.16.2/"), ("v1.15.6", "/en/v1.15.6/"), ("v1.15.4", "/en/v1.15.4/"), ("v1.15.1", "/en/v1.15.1/"), ("v1.14.7", "/en/v1.14.7/"), ("v1.14.1", "/en/v1.14.1/"), ("v1.13.1", "/en/v1.13.1/"), ("v1.12.1", "/en/v1.12.1/"), ("v1.11.7", "/en/v1.11.7/"), ("v1.11.4", "/en/v1.11.4/"), ("v1.11.0", "/en/v1.11.0/"), ("v1.10.8", "/en/v1.10.8/"), ("v1.10.6", "/en/v1.10.6/"), ("v1.10.5", "/en/v1.10.5/"), ("v1.10.3", "/en/v1.10.3/"), ("v1.10.2", "/en/v1.10.2/"), ("v1.9.2", "/en/v1.9.2/"), ("v1.9.1", "/en/v1.9.1/"), ("v1.8.9", "/en/v1.8.9/"), ("v1.8.8", "/en/v1.8.8/"), ("v1.8.6", "/en/v1.8.6/"), ("v1.8.2", "/en/v1.8.2/"), ("v1.7.5", "/en/v1.7.5/"), ("v1.7.4", "/en/v1.7.4/"), ("v1.7.1", "/en/v1.7.1/"), ("v1.6.3", "/en/v1.6.3/"), ("v1.5.1", "/en/v1.5.1/"), ("v1.5.0", "/en/v1.5.0/"), ], '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': 'a341ddff', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-emod-api/builds/1274143/' 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: 2023-01-28T00:10:05.350489Z, end-time: 2023-01-28T00:11:23.813498Z, duration: 78, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . ../_readthedocs/html Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 66 source files that are out of date updating environment: [new config] 66 added, 0 changed, 0 removed reading sources... [ 1%] emod_api reading sources... [ 3%] emod_api.campaign reading sources... [ 4%] emod_api.channelreports reading sources... [ 6%] emod_api.channelreports.channels reading sources... [ 7%] emod_api.channelreports.plot_icj_means Matplotlib is building the font cache; this may take a moment. reading sources... [ 9%] emod_api.channelreports.plot_prop_report reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 13%] emod_api.config.default_from_schema_no_validation reading sources... [ 15%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 16%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 19%] emod_api.config.from_overrides reading sources... [ 21%] emod_api.config.from_poi_and_binary reading sources... [ 22%] emod_api.config.from_schema reading sources... [ 24%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 25%] emod_api.demographics reading sources... [ 27%] emod_api.demographics.BaseInputFile reading sources... [ 28%] emod_api.demographics.Demographics reading sources... [ 30%] emod_api.demographics.DemographicsGenerator reading sources... [ 31%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 33%] emod_api.demographics.DemographicsTemplates reading sources... [ 34%] emod_api.demographics.Node reading sources... [ 36%] emod_api.demographics.PreDefinedDistributions reading sources... [ 37%] emod_api.demographics.PropertiesAndAttributes reading sources... [ 39%] emod_api.demographics.Updateable reading sources... [ 40%] emod_api.demographics.demographics_utils reading sources... [ 42%] emod_api.demographics.grid_construction reading sources... [ 43%] emod_api.interventions reading sources... [ 45%] emod_api.interventions.ccdl reading sources... [ 46%] emod_api.interventions.ccdl_viz reading sources... [ 48%] emod_api.interventions.common reading sources... [ 50%] emod_api.interventions.import_pressure reading sources... [ 51%] emod_api.interventions.migration reading sources... [ 53%] emod_api.interventions.node_multiplier reading sources... [ 54%] emod_api.interventions.outbreak reading sources... [ 56%] emod_api.interventions.simple_vaccine reading sources... [ 57%] emod_api.interventions.utils reading sources... [ 59%] emod_api.migration reading sources... [ 60%] emod_api.migration.client reading sources... [ 62%] emod_api.migration.client.client reading sources... [ 63%] emod_api.migration.migration reading sources... [ 65%] emod_api.multidim_plotter reading sources... [ 66%] emod_api.peek_camp reading sources... [ 68%] emod_api.schema reading sources... [ 69%] emod_api.schema.dtk_post_process_schema reading sources... [ 71%] emod_api.schema.get_schema reading sources... [ 72%] emod_api.schema_to_class reading sources... [ 74%] emod_api.serialization reading sources... [ 75%] emod_api.serialization.CensusAndModPop reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 78%] emod_api.serialization.dtkFileSupport reading sources... [ 80%] emod_api.serialization.dtkFileTools reading sources... [ 81%] emod_api.serialization.dtkFileUtility reading sources... [ 83%] emod_api.spatialreports reading sources... [ 84%] emod_api.spatialreports.plot_spat_means reading sources... [ 86%] emod_api.spatialreports.spatial reading sources... [ 87%] emod_api.tabularoutput reading sources... [ 89%] emod_api.weather reading sources... [ 90%] emod_api.weather.weather reading sources... [ 92%] faq reading sources... [ 93%] glossary reading sources... [ 95%] index reading sources... [ 96%] installation reading sources... [ 98%] modules reading sources... [100%] plotters looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 1%] emod_api writing output... [ 3%] emod_api.campaign writing output... [ 4%] emod_api.channelreports writing output... [ 6%] emod_api.channelreports.channels writing output... [ 7%] emod_api.channelreports.plot_icj_means writing output... [ 9%] emod_api.channelreports.plot_prop_report writing output... [ 10%] emod_api.config writing output... [ 12%] emod_api.config.default_from_schema writing output... [ 13%] emod_api.config.default_from_schema_no_validation writing output... [ 15%] emod_api.config.dtk_post_process_adhocevents writing output... [ 16%] emod_api.config.dtk_pre_process_adhocevents writing output... [ 18%] emod_api.config.dtk_pre_process_w5ml writing output... [ 19%] emod_api.config.from_overrides writing output... [ 21%] emod_api.config.from_poi_and_binary writing output... [ 22%] emod_api.config.from_schema writing output... [ 24%] emod_api.config.schema_to_config writing output... [ 25%] emod_api.demographics writing output... [ 27%] emod_api.demographics.BaseInputFile writing output... [ 28%] emod_api.demographics.Demographics writing output... [ 30%] emod_api.demographics.DemographicsGenerator writing output... [ 31%] emod_api.demographics.DemographicsInputDataParsers writing output... [ 33%] emod_api.demographics.DemographicsTemplates writing output... [ 34%] emod_api.demographics.Node writing output... [ 36%] emod_api.demographics.PreDefinedDistributions writing output... [ 37%] emod_api.demographics.PropertiesAndAttributes writing output... [ 39%] emod_api.demographics.Updateable writing output... [ 40%] emod_api.demographics.demographics_utils writing output... [ 42%] emod_api.demographics.grid_construction writing output... [ 43%] emod_api.interventions writing output... [ 45%] emod_api.interventions.ccdl writing output... [ 46%] emod_api.interventions.ccdl_viz writing output... [ 48%] emod_api.interventions.common writing output... [ 50%] emod_api.interventions.import_pressure writing output... [ 51%] emod_api.interventions.migration writing output... [ 53%] emod_api.interventions.node_multiplier writing output... [ 54%] emod_api.interventions.outbreak writing output... [ 56%] emod_api.interventions.simple_vaccine writing output... [ 57%] emod_api.interventions.utils writing output... [ 59%] emod_api.migration writing output... [ 60%] emod_api.migration.client writing output... [ 62%] emod_api.migration.client.client writing output... [ 63%] emod_api.migration.migration writing output... [ 65%] emod_api.multidim_plotter writing output... [ 66%] emod_api.peek_camp writing output... [ 68%] emod_api.schema writing output... [ 69%] emod_api.schema.dtk_post_process_schema writing output... [ 71%] emod_api.schema.get_schema writing output... [ 72%] emod_api.schema_to_class writing output... [ 74%] emod_api.serialization writing output... [ 75%] emod_api.serialization.CensusAndModPop writing output... [ 77%] emod_api.serialization.SerializedPopulation writing output... [ 78%] emod_api.serialization.dtkFileSupport writing output... [ 80%] emod_api.serialization.dtkFileTools writing output... [ 81%] emod_api.serialization.dtkFileUtility writing output... [ 83%] emod_api.spatialreports writing output... [ 84%] emod_api.spatialreports.plot_spat_means writing output... [ 86%] emod_api.spatialreports.spatial writing output... [ 87%] emod_api.tabularoutput writing output... [ 89%] emod_api.weather writing output... [ 90%] emod_api.weather.weather writing output... [ 92%] faq writing output... [ 93%] glossary writing output... [ 95%] index writing output... [ 96%] installation writing output... [ 98%] modules writing output... [100%] plotters generating indices... genindex py-modindex done highlighting module code... [ 2%] emod_api.campaign highlighting module code... [ 4%] emod_api.channelreports.channels highlighting module code... [ 6%] emod_api.channelreports.plot_icj_means highlighting module code... [ 8%] emod_api.channelreports.plot_prop_report highlighting module code... [ 10%] emod_api.config.default_from_schema highlighting module code... [ 13%] emod_api.config.default_from_schema_no_validation highlighting module code... [ 15%] emod_api.config.dtk_post_process_adhocevents highlighting module code... [ 17%] emod_api.config.dtk_pre_process_adhocevents highlighting module code... [ 19%] emod_api.config.dtk_pre_process_w5ml highlighting module code... [ 21%] emod_api.config.from_overrides highlighting module code... [ 23%] emod_api.config.from_poi_and_binary highlighting module code... [ 26%] emod_api.config.from_schema highlighting module code... [ 28%] emod_api.config.schema_to_config highlighting module code... [ 30%] emod_api.demographics.BaseInputFile highlighting module code... [ 32%] emod_api.demographics.Demographics highlighting module code... [ 34%] emod_api.demographics.DemographicsGenerator highlighting module code... [ 36%] emod_api.demographics.DemographicsInputDataParsers highlighting module code... [ 39%] emod_api.demographics.DemographicsTemplates highlighting module code... [ 41%] emod_api.demographics.Node highlighting module code... [ 43%] emod_api.demographics.PreDefinedDistributions highlighting module code... [ 45%] emod_api.demographics.PropertiesAndAttributes highlighting module code... [ 47%] emod_api.demographics.Updateable highlighting module code... [ 50%] emod_api.demographics.demographics_utils highlighting module code... [ 52%] emod_api.demographics.grid_construction highlighting module code... [ 54%] emod_api.interventions.ccdl_viz highlighting module code... [ 56%] emod_api.interventions.common highlighting module code... [ 58%] emod_api.interventions.import_pressure highlighting module code... [ 60%] emod_api.interventions.migration highlighting module code... [ 63%] emod_api.interventions.node_multiplier highlighting module code... [ 65%] emod_api.interventions.outbreak highlighting module code... [ 67%] emod_api.interventions.simple_vaccine highlighting module code... [ 69%] emod_api.interventions.utils highlighting module code... [ 71%] emod_api.migration.client.client highlighting module code... [ 73%] emod_api.migration.migration highlighting module code... [ 76%] emod_api.multidim_plotter highlighting module code... [ 78%] emod_api.peek_camp highlighting module code... [ 80%] emod_api.schema.dtk_post_process_schema highlighting module code... [ 82%] emod_api.schema.get_schema highlighting module code... [ 84%] emod_api.schema_to_class highlighting module code... [ 86%] emod_api.serialization.CensusAndModPop highlighting module code... [ 89%] emod_api.serialization.SerializedPopulation highlighting module code... [ 91%] emod_api.serialization.dtkFileSupport highlighting module code... [ 93%] emod_api.serialization.dtkFileTools highlighting module code... [ 95%] emod_api.spatialreports.plot_spat_means highlighting module code... [ 97%] emod_api.spatialreports.spatial highlighting module code... [100%] emod_api.weather.weather writing additional pages... search opensearch done copying images... [ 20%] images/fertility_over_time_doc.png copying images... [ 40%] images/sweep_plot.png copying images... [ 60%] images/spat_plot.png copying images... [ 80%] images/prop_plot.png copying images... [100%] images/colormap_plot.png 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 ../_readthedocs/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: 2023-01-28T00:11:24.082134Z, end-time: 2023-01-28T00:11:34.802083Z, duration: 10, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . ../_readthedocs/htmlzip Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 66 added, 0 changed, 0 removed reading sources... [ 1%] emod_api reading sources... [ 3%] emod_api.campaign reading sources... [ 4%] emod_api.channelreports reading sources... [ 6%] emod_api.channelreports.channels reading sources... [ 7%] emod_api.channelreports.plot_icj_means reading sources... [ 9%] emod_api.channelreports.plot_prop_report reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 13%] emod_api.config.default_from_schema_no_validation reading sources... [ 15%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 16%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 19%] emod_api.config.from_overrides reading sources... [ 21%] emod_api.config.from_poi_and_binary reading sources... [ 22%] emod_api.config.from_schema reading sources... [ 24%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 25%] emod_api.demographics reading sources... [ 27%] emod_api.demographics.BaseInputFile reading sources... [ 28%] emod_api.demographics.Demographics reading sources... [ 30%] emod_api.demographics.DemographicsGenerator reading sources... [ 31%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 33%] emod_api.demographics.DemographicsTemplates reading sources... [ 34%] emod_api.demographics.Node reading sources... [ 36%] emod_api.demographics.PreDefinedDistributions reading sources... [ 37%] emod_api.demographics.PropertiesAndAttributes reading sources... [ 39%] emod_api.demographics.Updateable reading sources... [ 40%] emod_api.demographics.demographics_utils reading sources... [ 42%] emod_api.demographics.grid_construction reading sources... [ 43%] emod_api.interventions reading sources... [ 45%] emod_api.interventions.ccdl reading sources... [ 46%] emod_api.interventions.ccdl_viz reading sources... [ 48%] emod_api.interventions.common reading sources... [ 50%] emod_api.interventions.import_pressure reading sources... [ 51%] emod_api.interventions.migration reading sources... [ 53%] emod_api.interventions.node_multiplier reading sources... [ 54%] emod_api.interventions.outbreak reading sources... [ 56%] emod_api.interventions.simple_vaccine reading sources... [ 57%] emod_api.interventions.utils reading sources... [ 59%] emod_api.migration reading sources... [ 60%] emod_api.migration.client reading sources... [ 62%] emod_api.migration.client.client reading sources... [ 63%] emod_api.migration.migration reading sources... [ 65%] emod_api.multidim_plotter reading sources... [ 66%] emod_api.peek_camp reading sources... [ 68%] emod_api.schema reading sources... [ 69%] emod_api.schema.dtk_post_process_schema reading sources... [ 71%] emod_api.schema.get_schema reading sources... [ 72%] emod_api.schema_to_class reading sources... [ 74%] emod_api.serialization reading sources... [ 75%] emod_api.serialization.CensusAndModPop reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 78%] emod_api.serialization.dtkFileSupport reading sources... [ 80%] emod_api.serialization.dtkFileTools reading sources... [ 81%] emod_api.serialization.dtkFileUtility reading sources... [ 83%] emod_api.spatialreports reading sources... [ 84%] emod_api.spatialreports.plot_spat_means reading sources... [ 86%] emod_api.spatialreports.spatial reading sources... [ 87%] emod_api.tabularoutput reading sources... [ 89%] emod_api.weather reading sources... [ 90%] emod_api.weather.weather reading sources... [ 92%] faq reading sources... [ 93%] glossary reading sources... [ 95%] index reading sources... [ 96%] installation reading sources... [ 98%] modules reading sources... [100%] plotters looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation faq modules emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.channelreports.plot_icj_means emod_api.channelreports.plot_prop_report 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.PreDefinedDistributions emod_api.demographics.PropertiesAndAttributes emod_api.demographics.Updateable emod_api.demographics.demographics_utils emod_api.demographics.grid_construction emod_api.interventions emod_api.interventions.ccdl emod_api.interventions.ccdl_viz emod_api.interventions.common emod_api.interventions.import_pressure emod_api.interventions.migration emod_api.interventions.node_multiplier emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.interventions.utils emod_api.migration emod_api.migration.client emod_api.migration.client.client 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.plot_spat_means emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.multidim_plotter emod_api.peek_camp emod_api.schema_to_class glossary plotters done writing... done writing additional files... opensearchdone copying images... [ 20%] images/fertility_over_time_doc.png copying images... [ 40%] images/sweep_plot.png copying images... [ 60%] images/spat_plot.png copying images... [ 80%] images/prop_plot.png copying images... [100%] images/colormap_plot.png copying static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. 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: 2023-01-28T00:11:35.958944Z, end-time: 2023-01-28T00:11:46.211072Z, duration: 10, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . ../_readthedocs/pdf Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 66 added, 0 changed, 0 removed reading sources... [ 1%] emod_api reading sources... [ 3%] emod_api.campaign reading sources... [ 4%] emod_api.channelreports reading sources... [ 6%] emod_api.channelreports.channels reading sources... [ 7%] emod_api.channelreports.plot_icj_means reading sources... [ 9%] emod_api.channelreports.plot_prop_report reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 13%] emod_api.config.default_from_schema_no_validation reading sources... [ 15%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 16%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 19%] emod_api.config.from_overrides reading sources... [ 21%] emod_api.config.from_poi_and_binary reading sources... [ 22%] emod_api.config.from_schema reading sources... [ 24%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 25%] emod_api.demographics reading sources... [ 27%] emod_api.demographics.BaseInputFile reading sources... [ 28%] emod_api.demographics.Demographics reading sources... [ 30%] emod_api.demographics.DemographicsGenerator reading sources... [ 31%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 33%] emod_api.demographics.DemographicsTemplates reading sources... [ 34%] emod_api.demographics.Node reading sources... [ 36%] emod_api.demographics.PreDefinedDistributions reading sources... [ 37%] emod_api.demographics.PropertiesAndAttributes reading sources... [ 39%] emod_api.demographics.Updateable reading sources... [ 40%] emod_api.demographics.demographics_utils reading sources... [ 42%] emod_api.demographics.grid_construction reading sources... [ 43%] emod_api.interventions reading sources... [ 45%] emod_api.interventions.ccdl reading sources... [ 46%] emod_api.interventions.ccdl_viz reading sources... [ 48%] emod_api.interventions.common reading sources... [ 50%] emod_api.interventions.import_pressure reading sources... [ 51%] emod_api.interventions.migration reading sources... [ 53%] emod_api.interventions.node_multiplier reading sources... [ 54%] emod_api.interventions.outbreak reading sources... [ 56%] emod_api.interventions.simple_vaccine reading sources... [ 57%] emod_api.interventions.utils reading sources... [ 59%] emod_api.migration reading sources... [ 60%] emod_api.migration.client reading sources... [ 62%] emod_api.migration.client.client reading sources... [ 63%] emod_api.migration.migration reading sources... [ 65%] emod_api.multidim_plotter reading sources... [ 66%] emod_api.peek_camp reading sources... [ 68%] emod_api.schema reading sources... [ 69%] emod_api.schema.dtk_post_process_schema reading sources... [ 71%] emod_api.schema.get_schema reading sources... [ 72%] emod_api.schema_to_class reading sources... [ 74%] emod_api.serialization reading sources... [ 75%] emod_api.serialization.CensusAndModPop reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 78%] emod_api.serialization.dtkFileSupport reading sources... [ 80%] emod_api.serialization.dtkFileTools reading sources... [ 81%] emod_api.serialization.dtkFileUtility reading sources... [ 83%] emod_api.spatialreports reading sources... [ 84%] emod_api.spatialreports.plot_spat_means reading sources... [ 86%] emod_api.spatialreports.spatial reading sources... [ 87%] emod_api.tabularoutput reading sources... [ 89%] emod_api.weather reading sources... [ 90%] emod_api.weather.weather reading sources... [ 92%] faq reading sources... [ 93%] glossary reading sources... [ 95%] index reading sources... [ 96%] installation reading sources... [ 98%] modules reading sources... [100%] plotters looking for now-outdated files... none found pickling environment... done checking consistency... done processing emod-api-docs.tex... index installation faq modules emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.channelreports.plot_icj_means emod_api.channelreports.plot_prop_report 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.PreDefinedDistributions emod_api.demographics.PropertiesAndAttributes emod_api.demographics.Updateable emod_api.demographics.demographics_utils emod_api.demographics.grid_construction emod_api.interventions emod_api.interventions.ccdl emod_api.interventions.ccdl_viz emod_api.interventions.common emod_api.interventions.import_pressure emod_api.interventions.migration emod_api.interventions.node_multiplier emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.interventions.utils emod_api.migration emod_api.migration.client emod_api.migration.client.client 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.plot_spat_means emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.multidim_plotter emod_api.peek_camp emod_api.schema_to_class glossary plotters resolving references... done writing... done copying images... [ 20%] images/fertility_over_time_doc.png copying images... [ 40%] images/sweep_plot.png copying images... [ 60%] images/spat_plot.png copying images... [ 80%] images/prop_plot.png copying images... [100%] images/colormap_plot.png copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in ../_readthedocs/pdf. 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/_readthedocs/pdf/_static/searchtools.js [rtd-command-info] start-time: 2023-01-28T00:11:47.477860Z, end-time: 2023-01-28T00:11:47.548454Z, 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: 2023-01-28T00:11:47.805384Z, end-time: 2023-01-28T00:11:53.793326Z, duration: 5, 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. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emod-api" "emod-api-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emod-api-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)) (./sphinxlatexnumfig.sty (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)) (./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emod-api.idx (./institute-for-disease-modeling-emod-api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 246--251 []\T1/qtm/m/n/10 Sure. [5] [6] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 264--267 []\T1/qtm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 268--271 []\T1/qtm/m/n/10 python -m [7] LaTeX Warning: Hyper reference `emod_api.channelreports.channels:emod_api.chann elreports.channels.Header' on page 8 undefined on input line 1. [8] Underfull \hbox (badness 10000) in paragraph at lines 651--654 []\T1/qtm/m/n/10 con-fig = json.load(open(^^Pdefault_config.json^^Q), ob-ject_h ook=s2c.ReadOnlyDict) os.remove( ^^Pde- Overfull \hbox (23.04372pt too wide) in paragraph at lines 660--660 []\T1/qtm/m/it/10 path_to_schema\T1/qtm/m/n/10 , Overfull \hbox (37.0137pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 schema_node=True\T1/qtm/m/n/10 , Overfull \hbox (13.74374pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 as_rod=False\T1/qtm/m/n/10 , Overfull \hbox (40.01373pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 put_filename=None\T1/txtt/m/n/10 )| [9] Overfull \hbox (70.57379pt too wide) in paragraph at lines 675--675 \T1/qtm/m/it/10 put_filename=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 default_config.j son\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , Overfull \hbox (13.51376pt too wide) in paragraph at lines 675--675 \T1/qtm/m/it/10 schema_node=True\T1/txtt/m/n/10 )| Overfull \hbox (53.72368pt too wide) in paragraph at lines 705--705 []\T1/qtm/m/it/10 config_path=None\T1/qtm/m/n/10 , Overfull \hbox (30.34369pt too wide) in paragraph at lines 705--705 \T1/qtm/m/it/10 set_fn=None\T1/qtm/m/n/10 , Overfull \hbox (19.35367pt too wide) in paragraph at lines 705--705 \T1/qtm/m/it/10 fig=None\T1/txtt/m/n/10 )| Overfull \hbox (36.61365pt too wide) in paragraph at lines 740--740 []\T1/qtm/m/it/10 config_path\T1/qtm/m/n/10 , Overfull \hbox (13.23366pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 set_fn\T1/qtm/m/n/10 , Overfull \hbox (4.76366pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 con- Overfull \hbox (42.7586pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 fig_out_path\T1/txtt/m/n/10 )| [10] [11] Underfull \hbox (badness 10000) in paragraph at lines 933--936 []\T1/qtm/m/n/10 builder = s2c.SchemaConfigBuilder( LaTeX Warning: Hyper reference `emod_api.config.from_schema:emod_api.config.fro m_schema.SchemaConfigBuilder' on page 12 undefined on input line 958. [12] LaTeX Warning: Hyper reference `emod_api.demographics.BaseInputFile:emod_api.de mographics.BaseInputFile.BaseInputFile' on page 13 undefined on input line 1096 . [13] Overfull \hbox (2.44467pt too wide) in paragraph at lines 1235--1235 []\T1/qtm/m/it/10 crude_birth_rate=] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \hbox (377.44386pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (349.59387pt too wide) in paragraph at lines 1803--1803 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] Overfull \hbox (5.45383pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 res_in_arcsec=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 custom\TS1/qtm/ m/it/10 '\T1/qtm/m/n/10 , Overfull \hbox (35.91386pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 node_id_from_lat_long=False\T1/txtt/m/n/10 )| [19] Overfull \hbox (309.19406pt too wide) in paragraph at lines 1904--1904 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (281.34407pt too wide) in paragraph at lines 1904--1904 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] Overfull \hbox (9.76408pt too wide) in paragraph at lines 1904--1904 \T1/qtm/m/it/10 load_other_columns_as_attributes=False\T1/qtm/m/n/10 , [20] Overfull \hbox (282.94414pt too wide) in paragraph at lines 1983--1983 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (255.09415pt too wide) in paragraph at lines 1983--1983 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] [21] Overfull \hbox (34.91383pt too wide) in paragraph at lines 2071--2071 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| Overfull \hbox (13.9139pt too wide) in paragraph at lines 2083--2083 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| Overfull \hbox (34.55377pt too wide) in paragraph at lines 2089--2089 \T1/qtm/m/it/10 tra_data_columns=[]\T1/qtm/m/n/10 , Overfull \hbox (66.41374pt too wide) in paragraph at lines 2089--2089 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| LaTeX Warning: Hyper reference `emod_api.demographics.DemographicsTemplates:emo d_api.demographics.DemographicsTemplates.CrudeRate' on page 22 undefined on inp ut line 2115. LaTeX Warning: Hyper reference `emod_api.demographics.DemographicsTemplates:emo d_api.demographics.DemographicsTemplates.CrudeRate' on page 22 undefined on inp ut line 2124. [22] Underfull \hbox (badness 10000) in paragraph at lines 2168--2171 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2198--2201 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2221--2224 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- [23] LaTeX Warning: Hyper reference `emod_api.demographics.PropertiesAndAttributes:e mod_api.demographics.PropertiesAndAttributes.IndividualAttributes' on page 24 u ndefined on input line 2392. LaTeX Warning: Hyper reference `emod_api.demographics.PropertiesAndAttributes:e mod_api.demographics.PropertiesAndAttributes.IndividualProperties' on page 24 u ndefined on input line 2392. LaTeX Warning: Hyper reference `emod_api.demographics.PropertiesAndAttributes:e mod_api.demographics.PropertiesAndAttributes.NodeAttributes' on page 24 undefin ed on input line 2392. Overfull \hbox (43.43935pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][\T1/qtm/m/n/10 emod_api.demographics.PropertiesAndAt tributes.IndividualAttributes\T1/qtm/m/it/10 ] Overfull \hbox (44.23935pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][\T1/qtm/m/n/10 emod_api.demographics.PropertiesAndAt tributes.IndividualProperties\T1/qtm/m/it/10 ] Overfull \hbox (23.78935pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][\T1/qtm/m/n/10 emod_api.demographics.PropertiesAndAt tributes.NodeAttributes\T1/qtm/m/it/10 ] LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 24 undefined on input line 2394. [24] LaTeX Warning: Hyper reference `emod_api.demographics.Node:emod_api.demographic s.Node.Node' on page 25 undefined on input line 2474. LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 25 undefined on input line 2558. LaTeX Warning: Hyper reference `emod_api.demographics.PropertiesAndAttributes:e mod_api.demographics.PropertiesAndAttributes.IndividualProperty' on page 25 und efined on input line 2571. Overfull \hbox (221.87881pt too wide) in paragraph at lines 2571--2571 \T1/qtm/m/it/10 tional[][][\T1/qtm/m/n/10 emod_api.demographics.PropertiesAndAt tributes.IndividualProperty\T1/qtm/m/it/10 ] LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 25 undefined on input line 2573. [25] Overfull \hbox (29.17384pt too wide) in paragraph at lines 2604--2604 []\T1/qtm/m/it/10 age_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (14.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (14.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (9.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (36.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (21.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (21.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (30.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (30.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (89.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (74.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (74.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (5.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (5.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (29.62386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution_male=None\T1/qtm/m/n/10 , Overfull \hbox (36.54384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution_female=None\T1/qtm/m/n/10 , Overfull \hbox (7.93384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/txtt/m/n/10 )| LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 26 undefined on input line 2606. LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 26 undefined on input line 2612. LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 26 undefined on input line 2627. [26] LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 27 undefined on input line 2648. LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 27 undefined on input line 2669. Overfull \hbox (10.98395pt too wide) in paragraph at lines 2703--2703 \T1/qtm/m/it/10 tial_vectors_per_species=None\T1/qtm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.demographics.Updateable:emod_api.demog raphics.Updateable.Updateable' on page 27 undefined on input line 2705. [27] [28] Underfull \hbox (badness 5578) in paragraph at lines 2922--2925 []\T1/qtm/m/n/10 Cre-ate a static de-mo-graph-ics based on the de-mo-graph-ics file spec-i-fied in the con-fig file of the LaTeX Warning: Hyper reference `emod_api.demographics.demographics_utils:emod_a pi.demographics.demographics_utils.set_static_demographics' on page 29 undefine d on input line 2954. [29] [30] LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 31 undefined on input line 3143. Overfull \hbox (5.21407pt too wide) in paragraph at lines 3152--3152 \T1/qtm/m/it/10 Node_Selection_Type=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 DISTANCE_ ONLY\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 31 undefined on input line 3186. LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 31 undefined on input line 3221. [31] LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 32 undefined on input line 3264. LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 32 undefined on input line 3319. [32] LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 33 undefined on input line 3398. Underfull \hbox (badness 10000) in paragraph at lines 3417--3419 []\T1/txtt/bx/n/10 IP. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Target_Property_Value. The value part of the new key[]value pair Underfull \hbox (badness 10000) in paragraph at lines 3429--3431 []\T1/txtt/bx/n/10 Target_Property_Value. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Dail y_Probability. The daily probability that Underfull \hbox (badness 10000) in paragraph at lines 3433--3435 []\T1/txtt/bx/n/10 Daily_Probability. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Maximum_ Duration. The maximum amount of time Underfull \hbox (badness 10000) in paragraph at lines 3433--3435 \T1/txtt/m/sl/10 individuals have to move to a new group. This timing works in Underfull \hbox (badness 10000) in paragraph at lines 3437--3439 []\T1/txtt/bx/n/10 group. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Revert. The number o f days before an individual moves back to Underfull \hbox (badness 10000) in paragraph at lines 3441--3443 []\T1/txtt/bx/n/10 policy. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Intervention_Name. Optional Intervention_Name. Useful if Underfull \hbox (badness 10000) in paragraph at lines 3449--3451 []\T1/txtt/bx/n/10 expired. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Event_Trigger_Expi red. Optional broadcast trigger to be LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 33 undefined on input line 3461. [33] LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 34 undefined on input line 3547. [34] [35] LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 36 undefined on input line 3661. LaTeX Warning: Hyper reference `emod_api.schema_to_class:emod_api.schema_to_cla ss.ReadOnlyDict' on page 36 undefined on input line 3729. Underfull \hbox (badness 10000) in paragraph at lines 3756--3758 []\T1/txtt/bx/n/10 "Delay_Period_Exponential" \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 but without the distribution, which is [36] Overfull \hbox (2.75383pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 ip_targeting=None\T1/qtm/m/n/10 , Overfull \hbox (10.51382pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 get_age_max=45625\T1/qtm/m/n/10 , Overfull \hbox (29.36382pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 get_residents_only=False\T1/qtm/m/n/10 , Overfull \hbox (24.73378pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 check_at_trigger=False\T1/txtt/m/n/10 )| Underfull \hbox (badness 10000) in paragraph at lines 3810--3812 []\T1/txtt/bx/n/10 "Delay_Period_Exponential" \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 but without the distribution, which is [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 []\T1/qtm/m/n/10 {^^PDu-ra-tion_Before_Leaving_Distribution^^Q:^^QGAUSSIAN_DIST RIBUTION^^Q, Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 ^^PDu-ra-tion_Before_Leaving_Gaussian_Mean^^Q: 14, ^^PDu- Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 ra-tion_Before_Leaving_Gaussian_Std_Dev^^Q 3} {^^PDu-ra- Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 tion_Before_Leaving_Distribution^^Q:^^QPOISSON_DISTRIBUTION^^Q, ^^PDu-ra- [42] Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 []\T1/qtm/m/n/10 {^^PDu-ra-tion_At_Node_Distribution^^Q:^^QGAUSSIAN_DISTRIBUTIO N^^Q, ^^PDu-ra- Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 \T1/qtm/m/n/10 tion_At_Node_Gaussian_Mean^^Q: 14, ^^PDu-ra-tion_At_Node_Gaussia n_Std_Dev^^Q Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 \T1/qtm/m/n/10 3} {^^PDu-ra-tion_At_Node_Distribution^^Q:^^QPOISSON_DISTRIBUTIO N^^Q, ^^PDu-ra- Overfull \hbox (17.85501pt too wide) in paragraph at lines 4368--4373 \T1/qtm/m/n/10 from emod_api im-port cam-paign as camp dan = {^^PDu-ra-tion_At_ Node_Distribution^^Q:^^QPOISSON_DISTRIBUTION^^Q, Overfull \hbox (55.02502pt too wide) in paragraph at lines 4368--4373 \T1/qtm/m/n/10 ^^PDu-ra-tion_At_Node_Poisson_Mean^^Q 30} dbl = {^^PDu-ra-tion_B efore_Leaving_Distribution^^Q:^^QGAUSSIAN_DISTRIBUTION^^Q, Underfull \hbox (badness 10000) in paragraph at lines 4374--4380 []\T1/qtm/m/n/10 du-ra- ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4403 ...{CONST(ANT)}] \leavevmode\begin{itemize} [43] [44] [45] [46] [47] Underfull \hbox (badness 10000) in paragraph at lines 4904--4908 []\T1/qtm/m/n/10 EMOD/DTK for-mat mi-gra-tion files (and as-so-ci-ated meta-dat a files) can be writ-ten with mi-gra- [48] LaTeX Warning: Hyper reference `emod_api.migration.migration:emod_api.migration .migration.Migration' on page 49 undefined on input line 5204. Overfull \hbox (57.54393pt too wide) in paragraph at lines 5204--5204 \T1/qtm/m/it/10 emod_api.migration.migration.Migration| [49] [50] [51] [52] LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileSupport:emod_api. serialization.dtkFileSupport.SerialObject' on page 53 undefined on input line 5 634. [53] LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileSupport:emod_api. serialization.dtkFileSupport.SerialObject' on page 54 undefined on input line 5 665. LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFile' on page 54 undefined on input line 5785. LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFile' on page 54 undefined on input line 5800. LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFile' on page 54 undefined on input line 5824. [54] LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFileV3' on page 55 undefined on input line 5848. LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFileV4' on page 55 undefined on input line 5857. [55] LaTeX Warning: Hyper reference `emod_api.spatialreports.spatial:emod_api.spatia lreports.spatial.SpatialNode' on page 56 undefined on input line 1. [56] [57] LaTeX Warning: Hyper reference `emod_api.weather.weather:emod_api.weather.weath er.Metadata' on page 58 undefined on input line 1. LaTeX Warning: Hyper reference `emod_api.weather.weather:emod_api.weather.weath er.WeatherNode' on page 58 undefined on input line 1. [58] Underfull \hbox (badness 6842) in paragraph at lines 6380--6383 []\T1/qtm/m/n/10 Set the (path to) the schema file. And re-set all cam-paign va ri-ables. This is es-sen-tially a [59] [60] Chapter 4. [61] [62] Chapter 5. [63] [64] Chapter 6. LaTeX Warning: Hyper reference `emod_api.channelreports.plot_icj_means:module-e mod_api.channelreports.plot_icj_means' on page 65 undefined on input line 6701. Underfull \hbox (badness 10000) in paragraph at lines 6715--6717 []\T1/txtt/m/n/10 python []m emod_api.channelreports.plot_icj_means [[]h] [[]c CHANNEL] [[]e EXPERIMENT_ID] [[]t [65] [66 <./sweep_plot.png>] Chapter 7. LaTeX Warning: Hyper reference `emod_api.spatialreports.plot_spat_means:module- emod_api.spatialreports.plot_spat_means' on page 67 undefined on input line 675 3. Underfull \hbox (badness 10000) in paragraph at lines 6766--6768 []\T1/txtt/m/n/10 python []m emod_api.spatialreports.plot_spat_means [[]h] [[]c CHANNEL] [[]e EXPERIMENT_ID] [67] [68 <./spat_plot.png>] Chapter 8. Underfull \hbox (badness 10000) in paragraph at lines 6803--6805 []\T1/txtt/m/n/10 python []m emod_api.channelreports.pplot_prop_report.py [[]h] [[]c channelName] [[]p PRIMARY] [69] [70 <./prop_plot.png>] Chapter 9. LaTeX Warning: Hyper reference `emod_api.multidim_plotter:module-emod_api.multi dim_plotter' on page 71 undefined on input line 6866. [71] [72 <./colormap_plot.png>] LaTeX Warning: Reference `emod_api:module-emod_api' on page 73 undefined on inp ut line 6945. LaTeX Warning: Reference `emod_api.campaign:module-emod_api.campaign' on page 7 3 undefined on input line 6946. LaTeX Warning: Reference `emod_api.channelreports:module-emod_api.channelreport s' on page 73 undefined on input line 6947. LaTeX Warning: Reference `emod_api.channelreports.channels:module-emod_api.chan nelreports.channels' on page 73 undefined on input line 6948. LaTeX Warning: Reference `emod_api.channelreports.plot_icj_means:module-emod_ap i.channelreports.plot_icj_means' on page 73 undefined on input line 6949. LaTeX Warning: Reference `emod_api.channelreports.plot_prop_report:module-emod_ api.channelreports.plot_prop_report' on page 73 undefined on input line 6950. LaTeX Warning: Reference `emod_api.config:module-emod_api.config' on page 73 un defined on input line 6951. LaTeX Warning: Reference `emod_api.config.default_from_schema:module-emod_api.c onfig.default_from_schema' on page 73 undefined on input line 6952. LaTeX Warning: Reference `emod_api.config.default_from_schema_no_validation:mod ule-emod_api.config.default_from_schema_no_validation' on page 73 undefined on input line 6953. Overfull \hbox (29.87175pt too wide) in paragraph at lines 6953--6954 []\T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/ 10 , LaTeX Warning: Reference `emod_api.config.dtk_post_process_adhocevents:module-e mod_api.config.dtk_post_process_adhocevents' on page 73 undefined on input line 6954. Overfull \hbox (3.62183pt too wide) in paragraph at lines 6954--6955 []\T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.config.dtk_pre_process_adhocevents:module-em od_api.config.dtk_pre_process_adhocevents' on page 73 undefined on input line 6 955. Underfull \hbox (badness 10000) in paragraph at lines 6955--6956 []\T1/txtt/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.config.dtk_pre_process_w5ml:module-emod_api. config.dtk_pre_process_w5ml' on page 73 undefined on input line 6956. LaTeX Warning: Reference `emod_api.config.from_overrides:module-emod_api.config .from_overrides' on page 73 undefined on input line 6957. LaTeX Warning: Reference `emod_api.config.from_poi_and_binary:module-emod_api.c onfig.from_poi_and_binary' on page 73 undefined on input line 6958. LaTeX Warning: Reference `emod_api.config.from_schema:module-emod_api.config.fr om_schema' on page 73 undefined on input line 6959. LaTeX Warning: Reference `emod_api.config.schema_to_config:module-emod_api.conf ig.schema_to_config' on page 73 undefined on input line 6960. LaTeX Warning: Reference `emod_api.demographics:module-emod_api.demographics' o n page 73 undefined on input line 6961. LaTeX Warning: Reference `emod_api.demographics.BaseInputFile:module-emod_api.d emographics.BaseInputFile' on page 73 undefined on input line 6962. LaTeX Warning: Reference `emod_api.demographics.Demographics:module-emod_api.de mographics.Demographics' on page 73 undefined on input line 6963. LaTeX Warning: Reference `emod_api.demographics.demographics_utils:module-emod_ api.demographics.demographics_utils' on page 73 undefined on input line 6964. LaTeX Warning: Reference `emod_api.demographics.DemographicsGenerator:module-em od_api.demographics.DemographicsGenerator' on page 73 undefined on input line 6 965. Underfull \hbox (badness 10000) in paragraph at lines 6965--6966 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.demographics.DemographicsInputDataParsers:mo dule-emod_api.demographics.DemographicsInputDataParsers' on page 73 undefined o n input line 6966. Overfull \hbox (35.12173pt too wide) in paragraph at lines 6966--6967 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n /10 , LaTeX Warning: Reference `emod_api.demographics.DemographicsTemplates:module-em od_api.demographics.DemographicsTemplates' on page 73 undefined on input line 6 967. Underfull \hbox (badness 10000) in paragraph at lines 6967--6968 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.demographics.grid_construction:module-emod_a pi.demographics.grid_construction' on page 73 undefined on input line 6968. LaTeX Warning: Reference `emod_api.demographics.Node:module-emod_api.demographi cs.Node' on page 73 undefined on input line 6969. LaTeX Warning: Reference `emod_api.demographics.PreDefinedDistributions:module- emod_api.demographics.PreDefinedDistributions' on page 73 undefined on input li ne 6970. Overfull \hbox (8.87181pt too wide) in paragraph at lines 6970--6971 []\T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.demographics.PropertiesAndAttributes:module- emod_api.demographics.PropertiesAndAttributes' on page 73 undefined on input li ne 6971. Overfull \hbox (8.87181pt too wide) in paragraph at lines 6971--6972 []\T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.demographics.Updateable:module-emod_api.demo graphics.Updateable' on page 73 undefined on input line 6972. LaTeX Warning: Reference `emod_api.interventions:module-emod_api.interventions' on page 73 undefined on input line 6973. LaTeX Warning: Reference `emod_api.interventions.ccdl:module-emod_api.intervent ions.ccdl' on page 73 undefined on input line 6974. LaTeX Warning: Reference `emod_api.interventions.ccdl_viz:module-emod_api.inter ventions.ccdl_viz' on page 73 undefined on input line 6975. LaTeX Warning: Reference `emod_api.interventions.common:module-emod_api.interve ntions.common' on page 73 undefined on input line 6976. LaTeX Warning: Reference `emod_api.interventions.import_pressure:module-emod_ap i.interventions.import_pressure' on page 73 undefined on input line 6977. LaTeX Warning: Reference `emod_api.interventions.migration:module-emod_api.inte rventions.migration' on page 73 undefined on input line 6978. LaTeX Warning: Reference `emod_api.interventions.node_multiplier:module-emod_ap i.interventions.node_multiplier' on page 73 undefined on input line 6979. LaTeX Warning: Reference `emod_api.interventions.outbreak:module-emod_api.inter ventions.outbreak' on page 73 undefined on input line 6980. LaTeX Warning: Reference `emod_api.interventions.simple_vaccine:module-emod_api .interventions.simple_vaccine' on page 73 undefined on input line 6981. LaTeX Warning: Reference `emod_api.interventions.utils:module-emod_api.interven tions.utils' on page 73 undefined on input line 6982. LaTeX Warning: Reference `emod_api.migration:module-emod_api.migration' on page 73 undefined on input line 6983. LaTeX Warning: Reference `emod_api.migration.client:module-emod_api.migration.c lient' on page 73 undefined on input line 6984. LaTeX Warning: Reference `emod_api.migration.client.client:module-emod_api.migr ation.client.client' on page 73 undefined on input line 6985. LaTeX Warning: Reference `emod_api.migration.migration:module-emod_api.migratio n.migration' on page 73 undefined on input line 6986. LaTeX Warning: Reference `emod_api.multidim_plotter:module-emod_api.multidim_pl otter' on page 73 undefined on input line 6987. LaTeX Warning: Reference `emod_api.peek_camp:module-emod_api.peek_camp' on page 73 undefined on input line 6988. LaTeX Warning: Reference `emod_api.schema:module-emod_api.schema' on page 73 un defined on input line 6989. LaTeX Warning: Reference `emod_api.schema.dtk_post_process_schema:module-emod_a pi.schema.dtk_post_process_schema' on page 73 undefined on input line 6990. LaTeX Warning: Reference `emod_api.schema.get_schema:module-emod_api.schema.get _schema' on page 73 undefined on input line 6991. LaTeX Warning: Reference `emod_api.schema_to_class:module-emod_api.schema_to_cl ass' on page 73 undefined on input line 6992. LaTeX Warning: Reference `emod_api.serialization:module-emod_api.serialization' on page 73 undefined on input line 6993. LaTeX Warning: Reference `emod_api.serialization.CensusAndModPop:module-emod_ap i.serialization.CensusAndModPop' on page 73 undefined on input line 6994. LaTeX Warning: Reference `emod_api.serialization.dtkFileSupport:module-emod_api .serialization.dtkFileSupport' on page 73 undefined on input line 6995. LaTeX Warning: Reference `emod_api.serialization.dtkFileTools:module-emod_api.s erialization.dtkFileTools' on page 73 undefined on input line 6996. LaTeX Warning: Reference `emod_api.serialization.dtkFileUtility:module-emod_api .serialization.dtkFileUtility' on page 73 undefined on input line 6997. LaTeX Warning: Reference `emod_api.serialization.SerializedPopulation:module-em od_api.serialization.SerializedPopulation' on page 73 undefined on input line 6 998. Underfull \hbox (badness 10000) in paragraph at lines 6998--6999 []\T1/txtt/m/n/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 , LaTeX Warning: Reference `emod_api.spatialreports:module-emod_api.spatialreport s' on page 73 undefined on input line 6999. LaTeX Warning: Reference `emod_api.spatialreports.plot_spat_means:module-emod_a pi.spatialreports.plot_spat_means' on page 73 undefined on input line 7000. LaTeX Warning: Reference `emod_api.spatialreports.spatial:module-emod_api.spati alreports.spatial' on page 73 undefined on input line 7001. LaTeX Warning: Reference `emod_api.tabularoutput:module-emod_api.tabularoutput' on page 73 undefined on input line 7002. LaTeX Warning: Reference `emod_api.weather:module-emod_api.weather' on page 73 undefined on input line 7003. LaTeX Warning: Reference `emod_api.weather.weather:module-emod_api.weather.weat her' on page 73 undefined on input line 7004. [73] No file institute-for-disease-modeling-emod-api.ind. (./institute-for-disease-modeling-emod-api.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emod-api.o ut' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on institute-for-disease-modeling-emod-api.pdf (77 pages, 190624 2 bytes). Transcript written on institute-for-disease-modeling-emod-api.log. Latexmk: Index file 'institute-for-disease-modeling-emod-api.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-emod-api.ind' from line 'No file institute-for-disease-modeling-emod-api.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emod-api.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emod-api.pdf' Latexmk: List of undefined refs and citations: Reference `emod_api.campaign:module-emod_api.campaign' on page 73 undefined on input line 6946 Reference `emod_api.channelreports.channels:module-emod_api.channelreports.channels' on page 73 undefined on input line 6948 Reference `emod_api.channelreports.plot_icj_means:module-emod_api.channelreports.plot_icj_means' on page 73 undefined on input line 6949 Reference `emod_api.channelreports.plot_prop_report:module-emod_api.channelreports.plot_prop_report' on page 73 undefined on input line 6950 Reference `emod_api.channelreports:module-emod_api.channelreports' on page 73 undefined on input line 6947 Reference `emod_api.config.default_from_schema:module-emod_api.config.default_from_schema' on page 73 undefined on input line 6952 Reference `emod_api.config.default_from_schema_no_validation:module-emod_api.config.default_from_schema_no_validation' on page 73 undefined on input line 6953 Reference `emod_api.config.dtk_post_process_adhocevents:module-emod_api.config.dtk_post_process_adhocevents' on page 73 undefined on input line 6954 Reference `emod_api.config.dtk_pre_process_adhocevents:module-emod_api.config.dtk_pre_process_adhocevents' on page 73 undefined on input line 6955 Reference `emod_api.config.dtk_pre_process_w5ml:module-emod_api.config.dtk_pre_process_w5ml' on page 73 undefined on input line 6956 Reference `emod_api.config.from_overrides:module-emod_api.config.from_overrides' on page 73 undefined on input line 6957 Reference `emod_api.config.from_poi_and_binary:module-emod_api.config.from_poi_and_binary' on page 73 undefined on input line 6958 Reference `emod_api.config.from_schema:module-emod_api.config.from_schema' on page 73 undefined on input line 6959 Reference `emod_api.config.schema_to_config:module-emod_api.config.schema_to_config' on page 73 undefined on input line 6960 Reference `emod_api.config:module-emod_api.config' on page 73 undefined on input line 6951 Reference `emod_api.demographics.BaseInputFile:module-emod_api.demographics.BaseInputFile' on page 73 undefined on input line 6962 Reference `emod_api.demographics.Demographics:module-emod_api.demographics.Demographics' on page 73 undefined on input line 6963 Reference `emod_api.demographics.DemographicsGenerator:module-emod_api.demographics.DemographicsGenerator' on page 73 undefined on input line 6965 Reference `emod_api.demographics.DemographicsInputDataParsers:module-emod_api.demographics.DemographicsInputDataParsers' on page 73 undefined on input line 6966 Reference `emod_api.demographics.DemographicsTemplates:module-emod_api.demographics.DemographicsTemplates' on page 73 undefined on input line 6967 Reference `emod_api.demographics.Node:module-emod_api.demographics.Node' on page 73 undefined on input line 6969 Reference `emod_api.demographics.PreDefinedDistributions:module-emod_api.demographics.PreDefinedDistributions' on page 73 undefined on input line 6970 Reference `emod_api.demographics.PropertiesAndAttributes:module-emod_api.demographics.PropertiesAndAttributes' on page 73 undefined on input line 6971 Reference `emod_api.demographics.Updateable:module-emod_api.demographics.Updateable' on page 73 undefined on input line 6972 Reference `emod_api.demographics.demographics_utils:module-emod_api.demographics.demographics_utils' on page 73 undefined on input line 6964 Reference `emod_api.demographics.grid_construction:module-emod_api.demographics.grid_construction' on page 73 undefined on input line 6968 Reference `emod_api.demographics:module-emod_api.demographics' on page 73 undefined on input line 6961 Reference `emod_api.interventions.ccdl:module-emod_api.interventions.ccdl' on page 73 undefined on input line 6974 Reference `emod_api.interventions.ccdl_viz:module-emod_api.interventions.ccdl_viz' on page 73 undefined on input line 6975 Reference `emod_api.interventions.common:module-emod_api.interventions.common' on page 73 undefined on input line 6976 Reference `emod_api.interventions.import_pressure:module-emod_api.interventions.import_pressure' on page 73 undefined on input line 6977 Reference `emod_api.interventions.migration:module-emod_api.interventions.migration' on page 73 undefined on input line 6978 Reference `emod_api.interventions.node_multiplier:module-emod_api.interventions.node_multiplier' on page 73 undefined on input line 6979 Reference `emod_api.interventions.outbreak:module-emod_api.interventions.outbreak' on page 73 undefined on input line 6980 Reference `emod_api.interventions.simple_vaccine:module-emod_api.interventions.simple_vaccine' on page 73 undefined on input line 6981 Reference `emod_api.interventions.utils:module-emod_api.interventions.utils' on page 73 undefined on input line 6982 Reference `emod_api.interventions:module-emod_api.interventions' on page 73 undefined on input line 6973 Reference `emod_api.migration.client.client:module-emod_api.migration.client.client' on page 73 undefined on input line 6985 Reference `emod_api.migration.client:module-emod_api.migration.client' on page 73 undefined on input line 6984 Reference `emod_api.migration.migration:module-emod_api.migration.migration' on page 73 undefined on input line 6986 Reference `emod_api.migration:module-emod_api.migration' on page 73 undefined on input line 6983 Reference `emod_api.multidim_plotter:module-emod_api.multidim_plotter' on page 73 undefined on input line 6987 Reference `emod_api.peek_camp:module-emod_api.peek_camp' on page 73 undefined on input line 6988 Reference `emod_api.schema.dtk_post_process_schema:module-emod_api.schema.dtk_post_process_schema' on page 73 undefined on input line 6990 Reference `emod_api.schema.get_schema:module-emod_api.schema.get_schema' on page 73 undefined on input line 6991 Reference `emod_api.schema:module-emod_api.schema' on page 73 undefined on input line 6989 Reference `emod_api.schema_to_class:module-emod_api.schema_to_class' on page 73 undefined on input line 6992 Reference `emod_api.serialization.CensusAndModPop:module-emod_api.serialization.CensusAndModPop' on page 73 undefined on input line 6994 Reference `emod_api.serialization.SerializedPopulation:module-emod_api.serialization.SerializedPopulation' on page 73 undefined on input line 6998 Reference `emod_api.serialization.dtkFileSupport:module-emod_api.serialization.dtkFileSupport' on page 73 undefined on input line 6995 Reference `emod_api.serialization.dtkFileTools:module-emod_api.serialization.dtkFileTools' on page 73 undefined on input line 6996 Reference `emod_api.serialization.dtkFileUtility:module-emod_api.serialization.dtkFileUtility' on page 73 undefined on input line 6997 Reference `emod_api.serialization:module-emod_api.serialization' on page 73 undefined on input line 6993 Reference `emod_api.spatialreports.plot_spat_means:module-emod_api.spatialreports.plot_spat_means' on page 73 undefined on input line 7000 Reference `emod_api.spatialreports.spatial:module-emod_api.spatialreports.spatial' on page 73 undefined on input line 7001 Reference `emod_api.spatialreports:module-emod_api.spatialreports' on page 73 undefined on input line 6999 Reference `emod_api.tabularoutput:module-emod_api.tabularoutput' on page 73 undefined on input line 7002 Reference `emod_api.weather.weather:module-emod_api.weather.weather' on page 73 undefined on input line 7004 Reference `emod_api.weather:module-emod_api.weather' on page 73 undefined on input line 7003 Reference `emod_api:module-emod_api' on page 73 undefined on input line 6945 Latexmk: Summary of warnings: Latex failed to resolve 60 reference(s) Rule 'makeindex institute-for-disease-modeling-emod-api.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-emod-api.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-emod-api.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-emod-api.ind" "institute-for-disease-modeling-emod-api.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-emod-api.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-emod-api.idx....done (545 entries accepted, 0 rejected). Sorting entries.......done (5115 comparisons). Generating output file institute-for-disease-modeling-emod-api.ind....done (1024 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'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emod-api-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)) (./sphinxlatexnumfig.sty (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)) (./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emod-api.idx (./institute-for-disease-modeling-emod-api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emod-api.out) (./institute-for-disease-modeling-emod-api.out) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./institute-for-disease-modeling-emod-api.toc) [1] [2] [1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 246--251 []\T1/qtm/m/n/10 Sure. [5] [6] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 264--267 []\T1/qtm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 268--271 []\T1/qtm/m/n/10 python -m [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 651--654 []\T1/qtm/m/n/10 con-fig = json.load(open(^^Pdefault_config.json^^Q), ob-ject_h ook=s2c.ReadOnlyDict) os.remove( ^^Pde- Overfull \hbox (23.04372pt too wide) in paragraph at lines 660--660 []\T1/qtm/m/it/10 path_to_schema\T1/qtm/m/n/10 , Overfull \hbox (37.0137pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 schema_node=True\T1/qtm/m/n/10 , Overfull \hbox (13.74374pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 as_rod=False\T1/qtm/m/n/10 , Overfull \hbox (40.01373pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 put_filename=None\T1/txtt/m/n/10 )| [9] Overfull \hbox (70.57379pt too wide) in paragraph at lines 675--675 \T1/qtm/m/it/10 put_filename=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 default_config.j son\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , Overfull \hbox (13.51376pt too wide) in paragraph at lines 675--675 \T1/qtm/m/it/10 schema_node=True\T1/txtt/m/n/10 )| Overfull \hbox (53.72368pt too wide) in paragraph at lines 705--705 []\T1/qtm/m/it/10 config_path=None\T1/qtm/m/n/10 , Overfull \hbox (30.34369pt too wide) in paragraph at lines 705--705 \T1/qtm/m/it/10 set_fn=None\T1/qtm/m/n/10 , Overfull \hbox (19.35367pt too wide) in paragraph at lines 705--705 \T1/qtm/m/it/10 fig=None\T1/txtt/m/n/10 )| Overfull \hbox (36.61365pt too wide) in paragraph at lines 740--740 []\T1/qtm/m/it/10 config_path\T1/qtm/m/n/10 , Overfull \hbox (13.23366pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 set_fn\T1/qtm/m/n/10 , Overfull \hbox (4.76366pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 con- Overfull \hbox (42.7586pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 fig_out_path\T1/txtt/m/n/10 )| [10] [11] Underfull \hbox (badness 10000) in paragraph at lines 933--936 []\T1/qtm/m/n/10 builder = s2c.SchemaConfigBuilder( [12] [13] Overfull \hbox (2.44467pt too wide) in paragraph at lines 1235--1235 []\T1/qtm/m/it/10 crude_birth_rate=] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \hbox (377.44386pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (349.59387pt too wide) in paragraph at lines 1803--1803 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] Overfull \hbox (5.45383pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 res_in_arcsec=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 custom\TS1/qtm/ m/it/10 '\T1/qtm/m/n/10 , Overfull \hbox (35.91386pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 node_id_from_lat_long=False\T1/txtt/m/n/10 )| [19] Overfull \hbox (309.19406pt too wide) in paragraph at lines 1904--1904 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (281.34407pt too wide) in paragraph at lines 1904--1904 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] Overfull \hbox (9.76408pt too wide) in paragraph at lines 1904--1904 \T1/qtm/m/it/10 load_other_columns_as_attributes=False\T1/qtm/m/n/10 , [20] Overfull \hbox (282.94414pt too wide) in paragraph at lines 1983--1983 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (255.09415pt too wide) in paragraph at lines 1983--1983 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] [21] Overfull \hbox (34.91383pt too wide) in paragraph at lines 2071--2071 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| Overfull \hbox (13.9139pt too wide) in paragraph at lines 2083--2083 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| Overfull \hbox (34.55377pt too wide) in paragraph at lines 2089--2089 \T1/qtm/m/it/10 tra_data_columns=[]\T1/qtm/m/n/10 , Overfull \hbox (66.41374pt too wide) in paragraph at lines 2089--2089 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| [22] Underfull \hbox (badness 10000) in paragraph at lines 2168--2171 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2198--2201 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2221--2224 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- [23] Overfull \hbox (43.13435pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.IndividualAttributes[][]\T1/qtm/m/it/10 ] Overfull \hbox (43.93436pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.IndividualProperties[][]\T1/qtm/m/it/10 ] Overfull \hbox (23.48436pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.NodeAttributes[][]\T1/qtm/m/it/10 ] [24] Overfull \hbox (221.57382pt too wide) in paragraph at lines 2571--2571 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.IndividualProperty[][]\T1/qtm/m/it/10 ] [25] Overfull \hbox (29.17384pt too wide) in paragraph at lines 2604--2604 []\T1/qtm/m/it/10 age_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (14.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (14.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (9.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (36.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (21.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (21.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (30.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (30.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (89.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (74.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (74.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (5.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (5.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (29.62386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution_male=None\T1/qtm/m/n/10 , Overfull \hbox (36.54384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution_female=None\T1/qtm/m/n/10 , Overfull \hbox (7.93384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/txtt/m/n/10 )| [26] Overfull \hbox (10.98395pt too wide) in paragraph at lines 2703--2703 \T1/qtm/m/it/10 tial_vectors_per_species=None\T1/qtm/m/n/10 , [27] [28] Underfull \hbox (badness 5578) in paragraph at lines 2922--2925 []\T1/qtm/m/n/10 Cre-ate a static de-mo-graph-ics based on the de-mo-graph-ics file spec-i-fied in the con-fig file of the [29] [30] Overfull \hbox (5.21407pt too wide) in paragraph at lines 3152--3152 \T1/qtm/m/it/10 Node_Selection_Type=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 DISTANCE_ ONLY\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 3417--3419 []\T1/txtt/bx/n/10 IP. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Target_Property_Value. The value part of the new key[]value pair Underfull \hbox (badness 10000) in paragraph at lines 3429--3431 []\T1/txtt/bx/n/10 Target_Property_Value. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Dail y_Probability. The daily probability that Underfull \hbox (badness 10000) in paragraph at lines 3433--3435 []\T1/txtt/bx/n/10 Daily_Probability. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Maximum_ Duration. The maximum amount of time Underfull \hbox (badness 10000) in paragraph at lines 3433--3435 \T1/txtt/m/sl/10 individuals have to move to a new group. This timing works in Underfull \hbox (badness 10000) in paragraph at lines 3437--3439 []\T1/txtt/bx/n/10 group. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Revert. The number o f days before an individual moves back to Underfull \hbox (badness 10000) in paragraph at lines 3441--3443 []\T1/txtt/bx/n/10 policy. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Intervention_Name. Optional Intervention_Name. Useful if Underfull \hbox (badness 10000) in paragraph at lines 3449--3451 []\T1/txtt/bx/n/10 expired. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Event_Trigger_Expi red. Optional broadcast trigger to be [33] [34] [35] Underfull \hbox (badness 10000) in paragraph at lines 3756--3758 []\T1/txtt/bx/n/10 "Delay_Period_Exponential" \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 but without the distribution, which is [36] Overfull \hbox (2.75383pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 ip_targeting=None\T1/qtm/m/n/10 , Overfull \hbox (10.51382pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 get_age_max=45625\T1/qtm/m/n/10 , Overfull \hbox (29.36382pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 get_residents_only=False\T1/qtm/m/n/10 , Overfull \hbox (24.73378pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 check_at_trigger=False\T1/txtt/m/n/10 )| Underfull \hbox (badness 10000) in paragraph at lines 3810--3812 []\T1/txtt/bx/n/10 "Delay_Period_Exponential" \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 but without the distribution, which is [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 []\T1/qtm/m/n/10 {^^PDu-ra-tion_Before_Leaving_Distribution^^Q:^^QGAUSSIAN_DIST RIBUTION^^Q, Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 ^^PDu-ra-tion_Before_Leaving_Gaussian_Mean^^Q: 14, ^^PDu- Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 ra-tion_Before_Leaving_Gaussian_Std_Dev^^Q 3} {^^PDu-ra- Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 tion_Before_Leaving_Distribution^^Q:^^QPOISSON_DISTRIBUTION^^Q, ^^PDu-ra- [42] Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 []\T1/qtm/m/n/10 {^^PDu-ra-tion_At_Node_Distribution^^Q:^^QGAUSSIAN_DISTRIBUTIO N^^Q, ^^PDu-ra- Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 \T1/qtm/m/n/10 tion_At_Node_Gaussian_Mean^^Q: 14, ^^PDu-ra-tion_At_Node_Gaussia n_Std_Dev^^Q Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 \T1/qtm/m/n/10 3} {^^PDu-ra-tion_At_Node_Distribution^^Q:^^QPOISSON_DISTRIBUTIO N^^Q, ^^PDu-ra- Overfull \hbox (17.85501pt too wide) in paragraph at lines 4368--4373 \T1/qtm/m/n/10 from emod_api im-port cam-paign as camp dan = {^^PDu-ra-tion_At_ Node_Distribution^^Q:^^QPOISSON_DISTRIBUTION^^Q, Overfull \hbox (55.02502pt too wide) in paragraph at lines 4368--4373 \T1/qtm/m/n/10 ^^PDu-ra-tion_At_Node_Poisson_Mean^^Q 30} dbl = {^^PDu-ra-tion_B efore_Leaving_Distribution^^Q:^^QGAUSSIAN_DISTRIBUTION^^Q, Underfull \hbox (badness 10000) in paragraph at lines 4374--4380 []\T1/qtm/m/n/10 du-ra- ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4403 ...{CONST(ANT)}] \leavevmode\begin{itemize} [43] [44] [45] [46] [47] Underfull \hbox (badness 10000) in paragraph at lines 4904--4908 []\T1/qtm/m/n/10 EMOD/DTK for-mat mi-gra-tion files (and as-so-ci-ated meta-dat a files) can be writ-ten with mi-gra- [48] Overfull \hbox (57.54393pt too wide) in paragraph at lines 5204--5204 [][]\T1/qtm/m/it/10 emod_api.migration.migration.Migration[][]| [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 6842) in paragraph at lines 6380--6383 []\T1/qtm/m/n/10 Set the (path to) the schema file. And re-set all cam-paign va ri-ables. This is es-sen-tially a [59] [60] Chapter 4. [61] [62] Chapter 5. [63] [64] Chapter 6. Underfull \hbox (badness 10000) in paragraph at lines 6715--6717 []\T1/txtt/m/n/10 python []m emod_api.channelreports.plot_icj_means [[]h] [[]c CHANNEL] [[]e EXPERIMENT_ID] [[]t [65] [66 <./sweep_plot.png>] Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 6766--6768 []\T1/txtt/m/n/10 python []m emod_api.spatialreports.plot_spat_means [[]h] [[]c CHANNEL] [[]e EXPERIMENT_ID] [67] [68 <./spat_plot.png>] Chapter 8. Underfull \hbox (badness 10000) in paragraph at lines 6803--6805 []\T1/txtt/m/n/10 python []m emod_api.channelreports.pplot_prop_report.py [[]h] [[]c channelName] [[]p PRIMARY] [69] [70 <./prop_plot.png>] Chapter 9. [71] [72 <./colormap_plot.png>] Overfull \hbox (29.87175pt too wide) in paragraph at lines 6953--6954 []\T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/ 10 , Overfull \hbox (3.62183pt too wide) in paragraph at lines 6954--6955 []\T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6955--6956 []\T1/txtt/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6965--6966 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 , Overfull \hbox (35.12173pt too wide) in paragraph at lines 6966--6967 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 6967--6968 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 , Overfull \hbox (8.87181pt too wide) in paragraph at lines 6970--6971 []\T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 , Overfull \hbox (8.87181pt too wide) in paragraph at lines 6971--6972 []\T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6998--6999 []\T1/txtt/m/n/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 , [73] (./institute-for-disease-modeling-emod-api.ind [74] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/txtt/m/n/10 accumulateTraceData() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (85.18242pt too wide) in paragraph at lines 10--12 []\T1/txtt/m/n/10 add() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.P ropertiesAndAttributes.IndividualProperties Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/txtt/m/n/10 add_migration_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (137.68227pt too wide) in paragraph at lines 15--17 []\T1/txtt/m/n/10 add_parameter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.PropertiesAndAttributes.IndividualProperties Overfull \hbox (49.44226pt too wide) in paragraph at lines 17--19 []\T1/txtt/m/n/10 add_parameter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.Updateable.Updateable Underfull \hbox (badness 10000) in paragraph at lines 19--21 []\T1/txtt/m/n/10 AddAgeDependentTransmission() Overfull \hbox (33.46252pt too wide) in paragraph at lines 19--21 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/txtt/m/n/10 AddIndividualPropertyAndHINT() Overfull \hbox (33.46252pt too wide) in paragraph at lines 21--23 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/txtt/m/n/10 AgeStructureUNWPP() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Overfull \hbox (15.1475pt too wide) in paragraph at lines 23--25 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/txtt/m/n/10 AgesYears \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration. migration.Migration Overfull \hbox (31.54231pt too wide) in paragraph at lines 28--30 []\T1/txtt/m/n/10 append() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializati on.dtkFileTools.DtkFile.Contents Overfull \hbox (26.68231pt too wide) in paragraph at lines 30--32 []\T1/txtt/m/n/10 append() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializati on.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (8.10747pt too wide) in paragraph at lines 32--34 \T1/qtm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 34--36 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (4.56746pt too wide) in paragraph at lines 34--36 \T1/qtm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 36--38 \T1/qtm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 38--40 \T1/qtm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/qtm/m/n/10 ), Overfull \hbox (73.8823pt too wide) in paragraph at lines 40--42 []\T1/txtt/m/n/10 apply_overlay() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/txtt/m/n/10 apply_to_defaults_or_nodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 42--44 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/txtt/m/n/10 arcsec_to_deg() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 44--46 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Overfull \hbox (51.92223pt too wide) in paragraph at lines 46--48 []\T1/txtt/m/n/10 as_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.ChannelReport Overfull \hbox (30.00221pt too wide) in paragraph at lines 48--50 []\T1/txtt/m/n/10 as_dictionary() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chan nelreports.channels.Channel Overfull \hbox (26.10222pt too wide) in paragraph at lines 50--52 []\T1/txtt/m/n/10 as_dictionary() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chan nelreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 56--58 []\T1/txtt/m/n/10 author \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/txtt/m/n/10 BaseInputFile \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 63--65 \T1/qtm/m/it/10 emod_api.demographics.BaseInputFile\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/txtt/m/n/10 basicNode() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/txtt/m/n/10 BroadcastEvent() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/txtt/m/n/10 BroadcastEventToOtherNodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (4.13228pt too wide) in paragraph at lines 72--74 []\T1/txtt/m/n/10 byte_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/txtt/m/n/10 change_individual_property() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [75] Underfull \hbox (badness 10000) in paragraph at lines 81--83 []\T1/txtt/m/n/10 change_individual_property_scheduled() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Underfull \hbox (badness 10000) in paragraph at lines 83--85 []\T1/txtt/m/n/10 change_individual_property_triggered() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Underfull \hbox (badness 10000) in paragraph at lines 85--87 []\T1/txtt/m/n/10 change_ser_pop() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 85--87 \T1/qtm/m/it/10 emod_api.serialization.CensusAndModPop\T1/qtm/m/n/10 ), Overfull \hbox (46.67224pt too wide) in paragraph at lines 88--90 []\T1/txtt/m/n/10 channel_names \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channe lreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 90--92 []\T1/txtt/m/n/10 ChannelReport \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (20.42232pt too wide) in paragraph at lines 92--94 []\T1/txtt/m/n/10 channels \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelrepo rts.channels.ChannelReport Overfull \hbox (9.38226pt too wide) in paragraph at lines 94--96 []\T1/txtt/m/n/10 chunk_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (9.38226pt too wide) in paragraph at lines 96--98 []\T1/txtt/m/n/10 chunk_sizes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/txtt/m/n/10 chunks \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 100--102 []\T1/txtt/m/n/10 collect() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 100--102 \T1/qtm/m/it/10 emod_api.channelreports.plot_icj_means\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/txtt/m/n/10 collect() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 102--104 \T1/qtm/m/it/10 emod_api.spatialreports.plot_spat_means\T1/qtm/m/n/10 ), Overfull \hbox (29.63231pt too wide) in paragraph at lines 104--106 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileSupport.EllZeeFour Overfull \hbox (13.76231pt too wide) in paragraph at lines 106--108 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileSupport.Snappy Overfull \hbox (43.15228pt too wide) in paragraph at lines 108--110 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 110--112 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (4.13228pt too wide) in paragraph at lines 112--114 []\T1/txtt/m/n/10 compressed \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFile Overfull \hbox (9.38226pt too wide) in paragraph at lines 114--116 []\T1/txtt/m/n/10 compression \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/txtt/m/n/10 ConstantDistribution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.58746pt too wide) in paragraph at lines 116--118 \T1/qtm/m/it/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/txtt/m/n/10 construct() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 118--120 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 120--122 []\T1/txtt/m/n/10 ConstructNodesFromDataFrame() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (46.2575pt too wide) in paragraph at lines 120--122 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (92.52237pt too wide) in paragraph at lines 122--124 []\T1/txtt/m/n/10 copy() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics. PreDefinedDistributions.ConstantDistribution Underfull \hbox (badness 10000) in paragraph at lines 124--126 []\T1/txtt/m/n/10 creation_date \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weathe r.weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 126--128 []\T1/txtt/m/n/10 creation_date \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weathe r.weather.Weather Overfull \hbox (58.51736pt too wide) in paragraph at lines 128--130 []\T1/txtt/m/n/10 CrudeRate \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.d emographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/txtt/m/n/10 data \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports. spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 139--140 []\T1/txtt/m/n/10 data \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.weather .WeatherNode prop- Overfull \hbox (1.23224pt too wide) in paragraph at lines 140--142 []\T1/txtt/m/n/10 datavalue_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weat her.weather.Metadata Overfull \hbox (13.67229pt too wide) in paragraph at lines 146--148 []\T1/txtt/m/n/10 DatavalueCount \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migra tion.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 153--154 []\T1/txtt/m/n/10 decorate_actual_iv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/txtt/m/n/10 decorate_actual_iv_impl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (14.49223pt too wide) in paragraph at lines 156--158 []\T1/txtt/m/n/10 default_population \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.d emographics.Node.Node Overfull \hbox (15.1475pt too wide) in paragraph at lines 158--160 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 160--162 []\T1/txtt/m/n/10 DelayedIntervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 162--164 []\T1/txtt/m/n/10 Demographics \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 162--164 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 164--166 []\T1/txtt/m/n/10 DemographicsGenerator \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class i n Overfull \hbox (16.85251pt too wide) in paragraph at lines 164--166 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/txtt/m/n/10 DemographicsOverlay \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 166--168 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 168--170 []\T1/txtt/m/n/10 DemographicsType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (16.85251pt too wide) in paragraph at lines 168--170 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/txtt/m/n/10 display() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 170--172 \T1/qtm/m/it/10 emod_api.channelreports.plot_icj_means\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 172--174 []\T1/txtt/m/n/10 do_mapping_from_events() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (4.56746pt too wide) in paragraph at lines 172--174 \T1/qtm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 ), [76] Underfull \hbox (badness 10000) in paragraph at lines 175--177 []\T1/txtt/m/n/10 dtk_to_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (36.17227pt too wide) in paragraph at lines 177--179 []\T1/txtt/m/n/10 dtk_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (5.10228pt too wide) in paragraph at lines 179--181 []\T1/txtt/m/n/10 dtk_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 182--184 []\T1/txtt/m/n/10 DtkFile.Contents \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 184--186 []\T1/txtt/m/n/10 DtkFile.Objects \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (3.18729pt too wide) in paragraph at lines 186--188 []\T1/txtt/m/n/10 DtkFileV1 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (3.18729pt too wide) in paragraph at lines 188--190 []\T1/txtt/m/n/10 DtkFileV2 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/txtt/m/n/10 DtkFileV2.NodesV2 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (3.18729pt too wide) in paragraph at lines 192--194 []\T1/txtt/m/n/10 DtkFileV3 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 194--196 []\T1/txtt/m/n/10 DtkFileV3.NodesV3 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (3.18729pt too wide) in paragraph at lines 196--198 []\T1/txtt/m/n/10 DtkFileV4 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (3.18729pt too wide) in paragraph at lines 198--200 []\T1/txtt/m/n/10 DtkFileV5 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (3.18729pt too wide) in paragraph at lines 200--202 []\T1/txtt/m/n/10 DtkHeader \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (48.0174pt too wide) in paragraph at lines 202--204 []\T1/txtt/m/n/10 DtkRate \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.dem ographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 204--206 []\T1/txtt/m/n/10 duplicate_nodeID_check() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (46.2575pt too wide) in paragraph at lines 204--206 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (19.2323pt too wide) in paragraph at lines 209--211 []\T1/txtt/m/n/10 EllZeeFour \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api. serialization.dtkFileSupport\T1/qtm/m/n/10 ), Overfull \hbox (27.37175pt too wide) in paragraph at lines 227--228 []\T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (1.12183pt too wide) in paragraph at lines 229--230 []\T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (32.62173pt too wide) in paragraph at lines 253--254 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (6.37181pt too wide) in paragraph at lines 261--262 []\T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions Overfull \hbox (6.37181pt too wide) in paragraph at lines 263--264 []\T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes [77] Underfull \hbox (badness 10000) in paragraph at lines 332--334 []\T1/txtt/m/n/10 EveryoneInitiallySusceptible() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 332--334 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/txtt/m/n/10 examine_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/txtt/m/n/10 FAMILY \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.mig ration.Migration Underfull \hbox (badness 10000) in paragraph at lines 342--344 []\T1/txtt/m/n/10 FEMALE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.mig ration.Migration Underfull \hbox (badness 10000) in paragraph at lines 344--346 []\T1/txtt/m/n/10 fill_nodes_legacy() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Overfull \hbox (46.2575pt too wide) in paragraph at lines 344--346 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (31.2124pt too wide) in paragraph at lines 348--350 []\T1/txtt/m/n/10 find() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.se rialization.SerializedPopulation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 350--352 []\T1/txtt/m/n/10 flattenConfig() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (76.32239pt too wide) in paragraph at lines 352--354 []\T1/txtt/m/n/10 flush() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializatio n.SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 356--358 []\T1/txtt/m/n/10 from_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 356--358 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 361--363 []\T1/txtt/m/n/10 from_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 361--363 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 363--365 []\T1/txtt/m/n/10 from_demog_and_param_gravity() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (113.91234pt too wide) in paragraph at lines 367--369 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes Overfull \hbox (180.06232pt too wide) in paragraph at lines 369--371 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes.AgeDistribution Overfull \hbox (197.29231pt too wide) in paragraph at lines 371--373 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes.FertilityDistribution Overfull \hbox (203.09232pt too wide) in paragraph at lines 373--375 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes.MortalityDistribution Overfull \hbox (93.66234pt too wide) in paragraph at lines 375--377 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.NodeAttributes Underfull \hbox (badness 10000) in paragraph at lines 377--379 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather. weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 379--381 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 379--381 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 381--383 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 381--383 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), [78] Underfull \hbox (badness 10000) in paragraph at lines 383--384 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/txtt/m/n/10 from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 384--386 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 386--387 []\T1/txtt/m/n/10 from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 387--389 []\T1/txtt/m/n/10 from_pop_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 387--389 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 389--391 []\T1/txtt/m/n/10 from_template_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 389--391 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 391--393 []\T1/txtt/m/n/10 FullRisk() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 391--393 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (13.67229pt too wide) in paragraph at lines 396--398 []\T1/txtt/m/n/10 GenderDataType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migra tion.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 398--400 []\T1/txtt/m/n/10 generate_demographics() Overfull \hbox (115.38252pt too wide) in paragraph at lines 398--400 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (69.64224pt too wide) in paragraph at lines 400--402 []\T1/txtt/m/n/10 generate_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.BaseInputFile.BaseInputFile Overfull \hbox (73.8823pt too wide) in paragraph at lines 402--404 []\T1/txtt/m/n/10 generate_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.Demographics.Demographics Overfull \hbox (85.3922pt too wide) in paragraph at lines 404--406 []\T1/txtt/m/n/10 generate_headers() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.d emographics.BaseInputFile.BaseInputFile Underfull \hbox (badness 10000) in paragraph at lines 406--408 []\T1/txtt/m/n/10 generate_metadata() Overfull \hbox (115.38252pt too wide) in paragraph at lines 406--408 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (161.05228pt too wide) in paragraph at lines 408--410 []\T1/txtt/m/n/10 generate_nodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.dem ographics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 412--414 []\T1/txtt/m/n/10 get_bbox() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 412--414 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 414--416 []\T1/txtt/m/n/10 get_class_with_defaults() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 416--418 []\T1/txtt/m/n/10 get_colour_from_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule Overfull \hbox (44.89249pt too wide) in paragraph at lines 418--420 \T1/qtm/m/it/10 ule emod_api.config.default_from_schema_no_validation\T1/qtm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 420--422 []\T1/txtt/m/n/10 get_default_config_from_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it /10 in mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 420--422 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 422--424 []\T1/txtt/m/n/10 get_default_for_complex_type() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (93.54231pt too wide) in paragraph at lines 424--426 []\T1/txtt/m/n/10 get_dtk_rate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demog raphics.DemographicsTemplates.CrudeRate Underfull \hbox (badness 10000) in paragraph at lines 427--429 []\T1/txtt/m/n/10 get_fert_dist() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 427--429 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 429--431 []\T1/txtt/m/n/10 get_fert_dist_from_rates() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 429--431 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 431--433 []\T1/txtt/m/n/10 get_grid_cell_id() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 431--433 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 434--436 []\T1/txtt/m/n/10 get_next_individual_suid() Overfull \hbox (77.9025pt too wide) in paragraph at lines 434--436 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 436--438 []\T1/txtt/m/n/10 get_next_infection_suid() Overfull \hbox (77.9025pt too wide) in paragraph at lines 436--438 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 438--440 []\T1/txtt/m/n/10 get_nickname_from_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (47.63237pt too wide) in paragraph at lines 440--442 []\T1/txtt/m/n/10 get_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograph ics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 442--444 []\T1/txtt/m/n/10 get_node_ids_from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 442--444 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Overfull \hbox (34.67223pt too wide) in paragraph at lines 444--446 []\T1/txtt/m/n/10 get_node_offsets() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.m igration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 446--448 []\T1/txtt/m/n/10 get_node_pops_from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 446--448 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 448--450 []\T1/txtt/m/n/10 get_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 448--450 \T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 453--455 []\T1/txtt/m/n/10 get_shape_from_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 456--458 []\T1/txtt/m/n/10 get_waning_from_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 458--460 []\T1/txtt/m/n/10 get_waning_from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 460--462 []\T1/txtt/m/n/10 get_waning_from_points() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 462--464 []\T1/txtt/m/n/10 get_xpix_ypix() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 464--466 []\T1/txtt/m/n/10 getChannels() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 466--468 []\T1/txtt/m/n/10 getTraceName() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [79] Overfull \hbox (9.92235pt too wide) in paragraph at lines 473--475 []\T1/txtt/m/n/10 header \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelreport s.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 475--477 []\T1/txtt/m/n/10 header \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Underfull \hbox (badness 5985) in paragraph at lines 484--486 []\T1/txtt/m/n/10 id \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports.sp atial.SpatialNode prop- Underfull \hbox (badness 10000) in paragraph at lines 487--489 []\T1/txtt/m/n/10 id_reference \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 489--491 []\T1/txtt/m/n/10 id_reference \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Weather Overfull \hbox (34.6714pt too wide) in paragraph at lines 491--493 []\T1/txtt/m/n/10 IDREF_GRUMP1DEGREE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.m igration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 493--495 []\T1/txtt/m/n/10 IDREF_GRUMP2PT5ARCMIN Underfull \hbox (badness 10000) in paragraph at lines 493--495 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 495--497 []\T1/txtt/m/n/10 IDREF_GRUMP30ARCSEC Underfull \hbox (badness 10000) in paragraph at lines 495--497 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Overfull \hbox (3.1715pt too wide) in paragraph at lines 497--499 []\T1/txtt/m/n/10 IDREF_LEGACY \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migrati on.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 501--503 []\T1/txtt/m/n/10 indexFor() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 503--505 []\T1/txtt/m/n/10 IndividualAttributes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 503--505 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Overfull \hbox (14.13748pt too wide) in paragraph at lines 505--507 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 507--509 []\T1/txtt/m/n/10 IndividualAttributes.FertilityDistribution Overfull \hbox (48.58748pt too wide) in paragraph at lines 507--509 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.demographics.PropertiesAndAtt ributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 509--511 []\T1/txtt/m/n/10 IndividualAttributes.MortalityDistribution Overfull \hbox (48.58748pt too wide) in paragraph at lines 509--511 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.demographics.PropertiesAndAtt ributes\T1/qtm/m/n/10 ), Overfull \hbox (16.87178pt too wide) in paragraph at lines 511--513 []\T1/txtt/m/n/10 IndividualAttributes.SusceptibilityDistribution Overfull \hbox (48.58748pt too wide) in paragraph at lines 511--513 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.demographics.PropertiesAndAtt ributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 513--515 []\T1/txtt/m/n/10 IndividualProperties \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 513--515 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 515--517 []\T1/txtt/m/n/10 IndividualProperty \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 515--517 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/txtt/m/n/10 infer_natural_mortality() Overfull \hbox (33.46252pt too wide) in paragraph at lines 517--519 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 519--521 []\T1/txtt/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 519--521 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 521--523 []\T1/txtt/m/n/10 InitAgeUniform() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 521--523 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 523--525 []\T1/txtt/m/n/10 InitPrevUniform() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 523--525 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 525--527 []\T1/txtt/m/n/10 InitRiskExponential() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 525--527 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 527--529 []\T1/txtt/m/n/10 InitRiskLogNormal() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Overfull \hbox (15.1475pt too wide) in paragraph at lines 527--529 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 529--531 []\T1/txtt/m/n/10 InitRiskUniform() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 529--531 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 531--533 []\T1/txtt/m/n/10 InitSusceptConstant() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 531--533 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (29.42224pt too wide) in paragraph at lines 533--535 []\T1/txtt/m/n/10 InterpolationType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.mi gration.migration.Migration Overfull \hbox (2.72234pt too wide) in paragraph at lines 535--537 []\T1/txtt/m/n/10 interval \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialrepo rts.spatial.SpatialReport Overfull \hbox (3.1715pt too wide) in paragraph at lines 537--539 []\T1/txtt/m/n/10 INTERVENTION \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migrati on.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 544--546 []\T1/txtt/m/n/10 lat_lon_from_nodeid() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 547--549 []\T1/txtt/m/n/10 LINEAR_INTERPOLATION Underfull \hbox (badness 10000) in paragraph at lines 547--549 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 549--551 []\T1/txtt/m/n/10 listChannelsAndIPs() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 551--553 []\T1/txtt/m/n/10 load_default_config_as_rod() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 551--553 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 553--555 []\T1/txtt/m/n/10 LOCAL \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migr ation.Migration at- Underfull \hbox (badness 10000) in paragraph at lines 556--558 []\T1/txtt/m/n/10 lon_lat_2_point() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 556--558 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Overfull \hbox (26.81233pt too wide) in paragraph at lines 561--563 []\T1/txtt/m/n/10 main() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.ch annelreports.plot_prop_report\T1/qtm/m/n/10 ), [80] Underfull \hbox (badness 10000) in paragraph at lines 563--565 []\T1/txtt/m/n/10 make_config_from_poi() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 563--565 \T1/qtm/m/it/10 emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 565--567 []\T1/txtt/m/n/10 make_config_from_poi_and_config_dict() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Overfull \hbox (3.8775pt too wide) in paragraph at lines 565--567 \T1/qtm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 567--569 []\T1/txtt/m/n/10 make_config_from_poi_and_config_file() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Overfull \hbox (3.8775pt too wide) in paragraph at lines 567--569 \T1/qtm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 569--571 []\T1/txtt/m/n/10 make_config_from_poi_and_schema() \T1/qtm/m/n/10 (\T1/qtm/m/i t/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 571--572 []\T1/txtt/m/n/10 MALE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migra tion.Migration at- Underfull \hbox (badness 10000) in paragraph at lines 575--576 []\T1/txtt/m/n/10 metadata \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.wea ther.Weather prop- Overfull \hbox (8.4223pt too wide) in paragraph at lines 577--579 []\T1/txtt/m/n/10 MigrationType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migrat ion.migration.Migration Overfull \hbox (2.62189pt too wide) in paragraph at lines 585--586 []| \T1/txtt/m/n/10 emod_api.channelreports.plot_prop_report\T1/qtm/m/n/10 , Overfull \hbox (49.87175pt too wide) in paragraph at lines 588--589 []| \T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/ n/10 , Overfull \hbox (23.62183pt too wide) in paragraph at lines 589--590 []| \T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 590--591 []| \T1/txtt/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 , Overfull \hbox (2.62189pt too wide) in paragraph at lines 599--600 []| \T1/txtt/m/n/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 600--601 []| \T1/txtt/m/n/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 , Overfull \hbox (55.12173pt too wide) in paragraph at lines 601--602 []| \T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m /n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 602--603 []| \T1/txtt/m/n/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 603--604 []| \T1/txtt/m/n/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 , Overfull \hbox (28.87181pt too wide) in paragraph at lines 605--606 []| \T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 , Overfull \hbox (28.87181pt too wide) in paragraph at lines 606--607 []| \T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 612--613 []| \T1/txtt/m/n/10 emod_api.interventions.import_pressure\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 614--615 []| \T1/txtt/m/n/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 625--626 []| \T1/txtt/m/n/10 emod_api.schema.dtk_post_process_schema\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 629--630 []| \T1/txtt/m/n/10 emod_api.serialization.CensusAndModPop\T1/qtm/m/n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 633--634 []| \T1/txtt/m/n/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--636 []| \T1/txtt/m/n/10 emod_api.spatialreports.plot_spat_means\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 640--642 []\T1/txtt/m/n/10 MortalityRateByAge() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Overfull \hbox (15.1475pt too wide) in paragraph at lines 640--642 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 642--644 []\T1/txtt/m/n/10 MortalityStructureNigeriaDHS() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 642--644 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 644--646 []\T1/txtt/m/n/10 MultiInterventionDistributor() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule [81] Underfull \hbox (badness 10000) in paragraph at lines 649--651 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 649--651 \T1/qtm/m/it/10 emod_api.interventions.import_pressure\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 651--653 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 651--653 \T1/qtm/m/it/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 653--655 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 655--657 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 655--657 \T1/qtm/m/it/10 emod_api.interventions.simple_vaccine\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 657--659 []\T1/txtt/m/n/10 new_intervention2() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 657--659 \T1/qtm/m/it/10 emod_api.interventions.simple_vaccine\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 659--661 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 659--661 \T1/qtm/m/it/10 emod_api.interventions.import_pressure\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 661--663 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 661--663 \T1/qtm/m/it/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 663--665 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 665--667 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 665--667 \T1/qtm/m/it/10 emod_api.interventions.simple_vaccine\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 667--669 []\T1/txtt/m/n/10 new_scheduled_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 667--669 \T1/qtm/m/it/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 ), Overfull \hbox (47.63237pt too wide) in paragraph at lines 671--673 []\T1/txtt/m/n/10 node_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograph ics.Demographics.Demographics Overfull \hbox (13.2223pt too wide) in paragraph at lines 673--675 []\T1/txtt/m/n/10 node_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialre ports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 678--680 []\T1/txtt/m/n/10 node_ID_from_lat_long() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule Overfull \hbox (46.2575pt too wide) in paragraph at lines 678--680 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (37.1324pt too wide) in paragraph at lines 680--682 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographic s.Demographics.Demographics Overfull \hbox (2.72234pt too wide) in paragraph at lines 682--684 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialrepo rts.spatial.SpatialReport Underfull \hbox (badness 6808) in paragraph at lines 684--685 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.wea ther.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 685--686 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.wea ther.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 686--688 []\T1/txtt/m/n/10 NodeAttributes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 686--688 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 689--691 []\T1/txtt/m/n/10 NodeCount \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration. migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 691--693 []\T1/txtt/m/n/10 nodeid_from_lat_lon() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (21.38245pt too wide) in paragraph at lines 695--697 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.D emographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 698--700 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Overfull \hbox (65.82242pt too wide) in paragraph at lines 700--702 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization. SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 702--704 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports .spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 706--708 []\T1/txtt/m/n/10 nodes_for_DTK() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 708--710 []\T1/txtt/m/n/10 NoInitialPrevalence() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 708--710 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (62.70738pt too wide) in paragraph at lines 710--712 []\T1/txtt/m/n/10 NoRisk() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api. demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (3.48235pt too wide) in paragraph at lines 712--714 []\T1/txtt/m/n/10 NullPtr \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.ser ialization.dtkFileSupport\T1/qtm/m/n/10 ), Overfull \hbox (41.42226pt too wide) in paragraph at lines 714--716 []\T1/txtt/m/n/10 num_channels \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (10.35226pt too wide) in paragraph at lines 716--718 []\T1/txtt/m/n/10 num_channels \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (51.92223pt too wide) in paragraph at lines 718--720 []\T1/txtt/m/n/10 num_time_steps \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.ChannelReport Overfull \hbox (20.85223pt too wide) in paragraph at lines 720--722 []\T1/txtt/m/n/10 num_time_steps \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 725--727 []\T1/txtt/m/n/10 ONE_FOR_EACH_GENDER Underfull \hbox (badness 10000) in paragraph at lines 725--727 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Overfull \hbox (34.6714pt too wide) in paragraph at lines 732--734 []\T1/txtt/m/n/10 PIECEWISE_CONSTANT \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.m igration.migration.Migration Overfull \hbox (21.05736pt too wide) in paragraph at lines 734--736 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.sp atialreports.plot_spat_means\T1/qtm/m/n/10 ), [82] Underfull \hbox (badness 10000) in paragraph at lines 736--738 []\T1/txtt/m/n/10 plot_from_sql() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 738--740 []\T1/txtt/m/n/10 plotTraces() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 740--742 []\T1/txtt/m/n/10 point_2_grid_cell_id_lookup() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 740--742 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 743--745 []\T1/txtt/m/n/10 processCommandline() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 745--747 []\T1/txtt/m/n/10 PropertyValueChanger() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 753--755 []\T1/txtt/m/n/10 readJsonFile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 756--758 []\T1/txtt/m/n/10 recurser() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 756--758 \T1/qtm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/qtm/m/n/10 ), Overfull \hbox (36.17227pt too wide) in paragraph at lines 760--762 []\T1/txtt/m/n/10 report_type \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (5.10228pt too wide) in paragraph at lines 762--764 []\T1/txtt/m/n/10 report_type \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (51.92223pt too wide) in paragraph at lines 764--766 []\T1/txtt/m/n/10 report_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.ChannelReport Overfull \hbox (20.85223pt too wide) in paragraph at lines 766--768 []\T1/txtt/m/n/10 report_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 768--770 []\T1/txtt/m/n/10 res_in_degrees \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 775--777 []\T1/txtt/m/n/10 SAME_FOR_BOTH_GENDERS Underfull \hbox (badness 10000) in paragraph at lines 775--777 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 778--780 []\T1/txtt/m/n/10 ScheduledCampaignEvent() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 780--782 []\T1/txtt/m/n/10 schema_to_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 780--782 \T1/qtm/m/it/10 emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 782--784 []\T1/txtt/m/n/10 schema_to_config_subnode() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 782--784 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 784--786 []\T1/txtt/m/n/10 SchemaConfigBuilder \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 786--788 []\T1/txtt/m/n/10 SchemaConfigBuilder \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 790--792 []\T1/txtt/m/n/10 seed_by_coverage() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 792--794 []\T1/txtt/m/n/10 SerializedPopulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 792--794 \T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 794--796 []\T1/txtt/m/n/10 SerialObject \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 796--798 []\T1/txtt/m/n/10 set_beautifiers() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 798--800 []\T1/txtt/m/n/10 set_demog_distributions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 798--800 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 800--802 []\T1/txtt/m/n/10 set_growing_demographics() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 800--802 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 802--804 []\T1/txtt/m/n/10 set_immune_mod() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 802--804 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Overfull \hbox (161.05228pt too wide) in paragraph at lines 804--806 []\T1/txtt/m/n/10 set_resolution() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.dem ographics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 806--808 []\T1/txtt/m/n/10 set_risk_mod() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 806--808 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Overfull \hbox (6.99231pt too wide) in paragraph at lines 808--810 []\T1/txtt/m/n/10 set_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.schema_ to_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 811--813 []\T1/txtt/m/n/10 set_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 811--813 \T1/qtm/m/it/10 emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 813--815 []\T1/txtt/m/n/10 set_static_demographics() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 813--815 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 815--817 []\T1/txtt/m/n/10 SetAgeDistribution() Overfull \hbox (33.46252pt too wide) in paragraph at lines 815--817 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (68.63231pt too wide) in paragraph at lines 817--819 []\T1/txtt/m/n/10 SetBirthRate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demog raphics.Demographics.Demographics Overfull \hbox (84.38226pt too wide) in paragraph at lines 819--821 []\T1/txtt/m/n/10 SetConstantRisk() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.de mographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 821--823 []\T1/txtt/m/n/10 SetConstantSusceptibility() Overfull \hbox (33.46252pt too wide) in paragraph at lines 821--823 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 823--825 []\T1/txtt/m/n/10 SetDefaultFromTemplate() Overfull \hbox (33.46252pt too wide) in paragraph at lines 823--825 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics [83] Underfull \hbox (badness 10000) in paragraph at lines 825--827 []\T1/txtt/m/n/10 SetDefaultIndividualAttributes() Overfull \hbox (33.46252pt too wide) in paragraph at lines 825--827 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 827--829 []\T1/txtt/m/n/10 SetDefaultIndividualProperties() Overfull \hbox (33.46252pt too wide) in paragraph at lines 827--829 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 829--831 []\T1/txtt/m/n/10 SetDefaultNodeAttributes() Overfull \hbox (33.46252pt too wide) in paragraph at lines 829--831 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 831--833 []\T1/txtt/m/n/10 SetDefaultProperties() Overfull \hbox (33.46252pt too wide) in paragraph at lines 831--833 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 833--835 []\T1/txtt/m/n/10 SetDefaultPropertiesFertMort() Overfull \hbox (33.46252pt too wide) in paragraph at lines 833--835 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (1.12183pt too wide) in paragraph at lines 835--837 []\T1/txtt/m/n/10 SetEquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (33.46252pt too wide) in paragraph at lines 835--837 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 837--839 []\T1/txtt/m/n/10 SetEquilibriumVitalDynamics() Overfull \hbox (33.46252pt too wide) in paragraph at lines 837--839 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 839--841 []\T1/txtt/m/n/10 SetEquilibriumVitalDynamicsFromWorldBank() Overfull \hbox (33.46252pt too wide) in paragraph at lines 839--841 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 841--843 []\T1/txtt/m/n/10 SetFertilityOverTimeFromParams() Overfull \hbox (33.46252pt too wide) in paragraph at lines 841--843 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 843--845 []\T1/txtt/m/n/10 SetHeteroRiskExponDist() Overfull \hbox (33.46252pt too wide) in paragraph at lines 843--845 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 845--847 []\T1/txtt/m/n/10 SetHeteroRiskLognormalDist() Overfull \hbox (33.46252pt too wide) in paragraph at lines 845--847 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 847--849 []\T1/txtt/m/n/10 SetHeteroRiskUniformDist() Overfull \hbox (33.46252pt too wide) in paragraph at lines 847--849 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 849--851 []\T1/txtt/m/n/10 SetIndividualAttributesWithFertMort() Overfull \hbox (33.46252pt too wide) in paragraph at lines 849--851 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 851--853 []\T1/txtt/m/n/10 SetInitialAgeExponential() Overfull \hbox (33.46252pt too wide) in paragraph at lines 851--853 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/txtt/m/n/10 SetInitialAgeLikeSubSaharanAfrica() Overfull \hbox (33.46252pt too wide) in paragraph at lines 853--855 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 855--857 []\T1/txtt/m/n/10 SetInitPrevFromUniformDraw() Overfull \hbox (33.46252pt too wide) in paragraph at lines 855--857 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 857--859 []\T1/txtt/m/n/10 SetMigrationPattern() Overfull \hbox (33.46252pt too wide) in paragraph at lines 857--859 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 859--861 []\T1/txtt/m/n/10 SetMinimalNodeAttributes() Overfull \hbox (33.46252pt too wide) in paragraph at lines 859--861 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 861--863 []\T1/txtt/m/n/10 SetMortalityDistribution() Overfull \hbox (33.46252pt too wide) in paragraph at lines 861--863 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/txtt/m/n/10 SetMortalityOverTimeFromData() Overfull \hbox (33.46252pt too wide) in paragraph at lines 863--865 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (89.63225pt too wide) in paragraph at lines 865--867 []\T1/txtt/m/n/10 SetMortalityRate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.d emographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 867--869 []\T1/txtt/m/n/10 SetNodeDefaultFromTemplate() Overfull \hbox (33.46252pt too wide) in paragraph at lines 867--869 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 869--871 []\T1/txtt/m/n/10 SetOneWayMigration() Overfull \hbox (33.46252pt too wide) in paragraph at lines 869--871 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 871--873 []\T1/txtt/m/n/10 SetOverdispersion() Overfull \hbox (33.46252pt too wide) in paragraph at lines 871--873 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 873--875 []\T1/txtt/m/n/10 SetRoundTripMigration() Overfull \hbox (33.46252pt too wide) in paragraph at lines 873--875 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 875--877 []\T1/txtt/m/n/10 SetSimpleVitalDynamics() Overfull \hbox (33.46252pt too wide) in paragraph at lines 875--877 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (15.1475pt too wide) in paragraph at lines 877--879 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (14.49228pt too wide) in paragraph at lines 879--881 []\T1/txtt/m/n/10 simulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFileV1 Overfull \hbox (14.49228pt too wide) in paragraph at lines 881--883 []\T1/txtt/m/n/10 simulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFileV2 Overfull \hbox (14.49228pt too wide) in paragraph at lines 883--885 []\T1/txtt/m/n/10 simulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFileV3 Underfull \hbox (badness 10000) in paragraph at lines 887--889 []\T1/txtt/m/n/10 SpatialReport \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 889--891 []\T1/txtt/m/n/10 StandardDiagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 891--893 []\T1/txtt/m/n/10 start \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports .spatial.SpatialReport Overfull \hbox (30.92229pt too wide) in paragraph at lines 893--895 []\T1/txtt/m/n/10 start_time \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (85.98161pt too wide) in paragraph at lines 897--899 []\T1/txtt/m/n/10 STATIC \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics. DemographicsGenerator.DemographicsType Overfull \hbox (25.6723pt too wide) in paragraph at lines 899--901 []\T1/txtt/m/n/10 step_size \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 903--905 []\T1/txtt/m/n/10 StepFunctionSusceptibility() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 903--905 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), [84] Overfull \hbox (30.92229pt too wide) in paragraph at lines 910--912 []\T1/txtt/m/n/10 time_stamp \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (13.2223pt too wide) in paragraph at lines 914--916 []\T1/txtt/m/n/10 time_steps \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialre ports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 916--918 []\T1/txtt/m/n/10 title \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 918--920 []\T1/txtt/m/n/10 titleFor() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (42.38239pt too wide) in paragraph at lines 921--923 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Demographics.Demographics Overfull \hbox (74.09238pt too wide) in paragraph at lines 923--925 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Demographics.DemographicsOverlay Underfull \hbox (badness 10000) in paragraph at lines 925--926 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Node.Node Overfull \hbox (108.27232pt too wide) in paragraph at lines 926--928 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PreDefinedDistributions.ConstantDistribution Overfull \hbox (103.41237pt too wide) in paragraph at lines 928--930 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes Overfull \hbox (169.56235pt too wide) in paragraph at lines 930--932 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.AgeDistribution Overfull \hbox (186.79234pt too wide) in paragraph at lines 932--934 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.FertilityDistribution Overfull \hbox (192.59235pt too wide) in paragraph at lines 934--936 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.MortalityDistribution Overfull \hbox (208.45236pt too wide) in paragraph at lines 936--938 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.SusceptibilityDistribution Overfull \hbox (106.18236pt too wide) in paragraph at lines 938--940 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualProperties Overfull \hbox (99.51236pt too wide) in paragraph at lines 940--942 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualProperty Overfull \hbox (83.16237pt too wide) in paragraph at lines 942--944 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.NodeAttributes Overfull \hbox (17.94235pt too wide) in paragraph at lines 944--946 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Updateable.Updateable Overfull \hbox (74.09238pt too wide) in paragraph at lines 946--948 []\T1/txtt/m/n/10 to_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Demographics.DemographicsOverlay Underfull \hbox (badness 10000) in paragraph at lines 948--950 []\T1/txtt/m/n/10 to_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration. migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 950--952 []\T1/txtt/m/n/10 to_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 952--953 []\T1/txtt/m/n/10 to_tuple() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 953--954 []\T1/txtt/m/n/10 Tool \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migra tion.Migration prop- Underfull \hbox (badness 10000) in paragraph at lines 956--958 []\T1/txtt/m/n/10 triggered_campaign_delay_event() \T1/qtm/m/n/10 (\T1/qtm/m/it /10 in mod-ule Overfull \hbox (11.6218pt too wide) in paragraph at lines 958--960 []\T1/txtt/m/n/10 triggered_campaign_event_with_optional_delay() Underfull \hbox (badness 10000) in paragraph at lines 960--962 []\T1/txtt/m/n/10 TriggeredCampaignEvent() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (40.13228pt too wide) in paragraph at lines 965--967 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.seriali zation.dtkFileSupport.EllZeeFour Overfull \hbox (24.26228pt too wide) in paragraph at lines 967--969 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.seriali zation.dtkFileSupport.Snappy Overfull \hbox (53.65225pt too wide) in paragraph at lines 969--971 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.seriali zation.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 971--973 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 973--975 []\T1/txtt/m/n/10 Uncompressed \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 975--977 []\T1/txtt/m/n/10 units \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelreports .channels.Channel Overfull \hbox (12.69237pt too wide) in paragraph at lines 977--979 []\T1/txtt/m/n/10 update() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographic s.Updateable.Updateable Overfull \hbox (11.73221pt too wide) in paragraph at lines 979--981 []\T1/txtt/m/n/10 update_resolution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.we ather.weather.Metadata Overfull \hbox (6.7322pt too wide) in paragraph at lines 981--983 []\T1/txtt/m/n/10 update_resolution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.we ather.weather.Weather Overfull \hbox (11.43234pt too wide) in paragraph at lines 983--984 []\T1/txtt/m/n/10 Updateable \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api. demographics.Updateable\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 987--989 []\T1/txtt/m/n/10 validate_res_in_arcsec() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 987--989 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 989--991 []\T1/txtt/m/n/10 version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile Overfull \hbox (76.32239pt too wide) in paragraph at lines 997--999 []\T1/txtt/m/n/10 write() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializatio n.SerializedPopulation.SerializedPopulation Overfull \hbox (2.12732pt too wide) in paragraph at lines 999--1000 []\T1/txtt/m/n/10 write() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1000--1002 []\T1/txtt/m/n/10 write_config_from_default_and_params() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Overfull \hbox (62.11249pt too wide) in paragraph at lines 1000--1002 \T1/qtm/m/it/10 mod-ule emod_api.config.default_from_schema_no_validation\T1/qt m/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1002--1004 []\T1/txtt/m/n/10 write_default_from_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 1004--1006 []\T1/txtt/m/n/10 write_default_from_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 1004--1006 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), [85] Overfull \hbox (41.42226pt too wide) in paragraph at lines 1006--1008 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (23.72227pt too wide) in paragraph at lines 1008--1010 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatial reports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 1010--1012 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 1012--1013 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 1016--1018 []\T1/txtt/m/n/10 xpix_ypix_from_lat_lon() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (63.76735pt too wide) in paragraph at lines 1021--1023 []\T1/txtt/m/n/10 YearlyRate \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api. demographics.DemographicsTemplates\T1/qtm/m/n/10 ), [86]) (./institute-for-disease-modeling-emod-api.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emod-api.o ut' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on institute-for-disease-modeling-emod-api.pdf (90 pages, 196682 9 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. 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' 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.out' 'institute-for-disease-modeling-emod-api.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emod-api" "emod-api-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emod-api-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)))) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)) (./sphinxlatexnumfig.sty (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)) (./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emod-api.idx (./institute-for-disease-modeling-emod-api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emod-api.out) (./institute-for-disease-modeling-emod-api.out) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./institute-for-disease-modeling-emod-api.toc) [1] [2] [1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 246--251 []\T1/qtm/m/n/10 Sure. [5] [6] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 264--267 []\T1/qtm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 268--271 []\T1/qtm/m/n/10 python -m [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 651--654 []\T1/qtm/m/n/10 con-fig = json.load(open(^^Pdefault_config.json^^Q), ob-ject_h ook=s2c.ReadOnlyDict) os.remove( ^^Pde- Overfull \hbox (23.04372pt too wide) in paragraph at lines 660--660 []\T1/qtm/m/it/10 path_to_schema\T1/qtm/m/n/10 , Overfull \hbox (37.0137pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 schema_node=True\T1/qtm/m/n/10 , Overfull \hbox (13.74374pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 as_rod=False\T1/qtm/m/n/10 , Overfull \hbox (40.01373pt too wide) in paragraph at lines 660--660 \T1/qtm/m/it/10 put_filename=None\T1/txtt/m/n/10 )| [9] Overfull \hbox (70.57379pt too wide) in paragraph at lines 675--675 \T1/qtm/m/it/10 put_filename=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 default_config.j son\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , Overfull \hbox (13.51376pt too wide) in paragraph at lines 675--675 \T1/qtm/m/it/10 schema_node=True\T1/txtt/m/n/10 )| Overfull \hbox (53.72368pt too wide) in paragraph at lines 705--705 []\T1/qtm/m/it/10 config_path=None\T1/qtm/m/n/10 , Overfull \hbox (30.34369pt too wide) in paragraph at lines 705--705 \T1/qtm/m/it/10 set_fn=None\T1/qtm/m/n/10 , Overfull \hbox (19.35367pt too wide) in paragraph at lines 705--705 \T1/qtm/m/it/10 fig=None\T1/txtt/m/n/10 )| Overfull \hbox (36.61365pt too wide) in paragraph at lines 740--740 []\T1/qtm/m/it/10 config_path\T1/qtm/m/n/10 , Overfull \hbox (13.23366pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 set_fn\T1/qtm/m/n/10 , Overfull \hbox (4.76366pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 con- Overfull \hbox (42.7586pt too wide) in paragraph at lines 740--740 \T1/qtm/m/it/10 fig_out_path\T1/txtt/m/n/10 )| [10] [11] Underfull \hbox (badness 10000) in paragraph at lines 933--936 []\T1/qtm/m/n/10 builder = s2c.SchemaConfigBuilder( [12] [13] Overfull \hbox (2.44467pt too wide) in paragraph at lines 1235--1235 []\T1/qtm/m/it/10 crude_birth_rate=] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \hbox (377.44386pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (349.59387pt too wide) in paragraph at lines 1803--1803 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] Overfull \hbox (5.45383pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 res_in_arcsec=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 custom\TS1/qtm/ m/it/10 '\T1/qtm/m/n/10 , Overfull \hbox (35.91386pt too wide) in paragraph at lines 1803--1803 \T1/qtm/m/it/10 node_id_from_lat_long=False\T1/txtt/m/n/10 )| [19] Overfull \hbox (309.19406pt too wide) in paragraph at lines 1904--1904 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (281.34407pt too wide) in paragraph at lines 1904--1904 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] Overfull \hbox (9.76408pt too wide) in paragraph at lines 1904--1904 \T1/qtm/m/it/10 load_other_columns_as_attributes=False\T1/qtm/m/n/10 , [20] Overfull \hbox (282.94414pt too wide) in paragraph at lines 1983--1983 \T1/qtm/m/it/10 tional[][][[][]Union[][][emod_api.dtk_tools.demographics.Demogr aphicsGeneratorConcern.DemographicsGeneratorConcern, Overfull \hbox (255.09415pt too wide) in paragraph at lines 1983--1983 [][]\T1/qtm/m/it/10 List[][][emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern]]] [21] Overfull \hbox (34.91383pt too wide) in paragraph at lines 2071--2071 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| Overfull \hbox (13.9139pt too wide) in paragraph at lines 2083--2083 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| Overfull \hbox (34.55377pt too wide) in paragraph at lines 2089--2089 \T1/qtm/m/it/10 tra_data_columns=[]\T1/qtm/m/n/10 , Overfull \hbox (66.41374pt too wide) in paragraph at lines 2089--2089 \T1/qtm/m/it/10 res=0.008333333333333333\T1/txtt/m/n/10 )| [22] Underfull \hbox (badness 10000) in paragraph at lines 2168--2171 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2198--2201 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2221--2224 []\T1/qtm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- [23] Overfull \hbox (43.13435pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.IndividualAttributes[][]\T1/qtm/m/it/10 ] Overfull \hbox (43.93436pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.IndividualProperties[][]\T1/qtm/m/it/10 ] Overfull \hbox (23.48436pt too wide) in paragraph at lines 2392--2392 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.NodeAttributes[][]\T1/qtm/m/it/10 ] [24] Overfull \hbox (221.57382pt too wide) in paragraph at lines 2571--2571 \T1/qtm/m/it/10 tional[][][[][]\T1/qtm/m/n/10 emod_api.demographics.PropertiesA ndAttributes.IndividualProperty[][]\T1/qtm/m/it/10 ] [25] Overfull \hbox (29.17384pt too wide) in paragraph at lines 2604--2604 []\T1/qtm/m/it/10 age_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (14.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (14.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (9.17384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 age_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (36.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (21.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (21.28386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 lence_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (30.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 nity_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (30.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (15.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 risk_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (89.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution_flag=None\T1/qtm/m/n/10 , Overfull \hbox (74.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution1=None\T1/qtm/m/n/10 , Overfull \hbox (74.17386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 tion_heterogeneity_distribution2=None\T1/qtm/m/n/10 , Overfull \hbox (5.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (5.18385pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/qtm/m/n/10 , Overfull \hbox (29.62386pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution_male=None\T1/qtm/m/n/10 , Overfull \hbox (36.54384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution_female=None\T1/qtm/m/n/10 , Overfull \hbox (7.93384pt too wide) in paragraph at lines 2604--2604 \T1/qtm/m/it/10 ity_distribution=None\T1/txtt/m/n/10 )| [26] Overfull \hbox (10.98395pt too wide) in paragraph at lines 2703--2703 \T1/qtm/m/it/10 tial_vectors_per_species=None\T1/qtm/m/n/10 , [27] [28] Underfull \hbox (badness 5578) in paragraph at lines 2922--2925 []\T1/qtm/m/n/10 Cre-ate a static de-mo-graph-ics based on the de-mo-graph-ics file spec-i-fied in the con-fig file of the [29] [30] Overfull \hbox (5.21407pt too wide) in paragraph at lines 3152--3152 \T1/qtm/m/it/10 Node_Selection_Type=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 DISTANCE_ ONLY\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 3417--3419 []\T1/txtt/bx/n/10 IP. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Target_Property_Value. The value part of the new key[]value pair Underfull \hbox (badness 10000) in paragraph at lines 3429--3431 []\T1/txtt/bx/n/10 Target_Property_Value. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Dail y_Probability. The daily probability that Underfull \hbox (badness 10000) in paragraph at lines 3433--3435 []\T1/txtt/bx/n/10 Daily_Probability. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Maximum_ Duration. The maximum amount of time Underfull \hbox (badness 10000) in paragraph at lines 3433--3435 \T1/txtt/m/sl/10 individuals have to move to a new group. This timing works in Underfull \hbox (badness 10000) in paragraph at lines 3437--3439 []\T1/txtt/bx/n/10 group. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Revert. The number o f days before an individual moves back to Underfull \hbox (badness 10000) in paragraph at lines 3441--3443 []\T1/txtt/bx/n/10 policy. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Intervention_Name. Optional Intervention_Name. Useful if Underfull \hbox (badness 10000) in paragraph at lines 3449--3451 []\T1/txtt/bx/n/10 expired. \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 Event_Trigger_Expi red. Optional broadcast trigger to be [33] [34] [35] Underfull \hbox (badness 10000) in paragraph at lines 3756--3758 []\T1/txtt/bx/n/10 "Delay_Period_Exponential" \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 but without the distribution, which is [36] Overfull \hbox (2.75383pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 ip_targeting=None\T1/qtm/m/n/10 , Overfull \hbox (10.51382pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 get_age_max=45625\T1/qtm/m/n/10 , Overfull \hbox (29.36382pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 get_residents_only=False\T1/qtm/m/n/10 , Overfull \hbox (24.73378pt too wide) in paragraph at lines 3784--3784 \T1/qtm/m/it/10 check_at_trigger=False\T1/txtt/m/n/10 )| Underfull \hbox (badness 10000) in paragraph at lines 3810--3812 []\T1/txtt/bx/n/10 "Delay_Period_Exponential" \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 but without the distribution, which is [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 []\T1/qtm/m/n/10 {^^PDu-ra-tion_Before_Leaving_Distribution^^Q:^^QGAUSSIAN_DIST RIBUTION^^Q, Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 ^^PDu-ra-tion_Before_Leaving_Gaussian_Mean^^Q: 14, ^^PDu- Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 ra-tion_Before_Leaving_Gaussian_Std_Dev^^Q 3} {^^PDu-ra- Underfull \hbox (badness 10000) in paragraph at lines 4296--4301 \T1/qtm/m/n/10 tion_Before_Leaving_Distribution^^Q:^^QPOISSON_DISTRIBUTION^^Q, ^^PDu-ra- [42] Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 []\T1/qtm/m/n/10 {^^PDu-ra-tion_At_Node_Distribution^^Q:^^QGAUSSIAN_DISTRIBUTIO N^^Q, ^^PDu-ra- Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 \T1/qtm/m/n/10 tion_At_Node_Gaussian_Mean^^Q: 14, ^^PDu-ra-tion_At_Node_Gaussia n_Std_Dev^^Q Underfull \hbox (badness 10000) in paragraph at lines 4312--4316 \T1/qtm/m/n/10 3} {^^PDu-ra-tion_At_Node_Distribution^^Q:^^QPOISSON_DISTRIBUTIO N^^Q, ^^PDu-ra- Overfull \hbox (17.85501pt too wide) in paragraph at lines 4368--4373 \T1/qtm/m/n/10 from emod_api im-port cam-paign as camp dan = {^^PDu-ra-tion_At_ Node_Distribution^^Q:^^QPOISSON_DISTRIBUTION^^Q, Overfull \hbox (55.02502pt too wide) in paragraph at lines 4368--4373 \T1/qtm/m/n/10 ^^PDu-ra-tion_At_Node_Poisson_Mean^^Q 30} dbl = {^^PDu-ra-tion_B efore_Leaving_Distribution^^Q:^^QGAUSSIAN_DISTRIBUTION^^Q, Underfull \hbox (badness 10000) in paragraph at lines 4374--4380 []\T1/qtm/m/n/10 du-ra- ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.4403 ...{CONST(ANT)}] \leavevmode\begin{itemize} [43] [44] [45] [46] [47] Underfull \hbox (badness 10000) in paragraph at lines 4904--4908 []\T1/qtm/m/n/10 EMOD/DTK for-mat mi-gra-tion files (and as-so-ci-ated meta-dat a files) can be writ-ten with mi-gra- [48] Overfull \hbox (57.54393pt too wide) in paragraph at lines 5204--5204 [][]\T1/qtm/m/it/10 emod_api.migration.migration.Migration[][]| [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 6842) in paragraph at lines 6380--6383 []\T1/qtm/m/n/10 Set the (path to) the schema file. And re-set all cam-paign va ri-ables. This is es-sen-tially a [59] [60] Chapter 4. [61] [62] Chapter 5. [63] [64] Chapter 6. Underfull \hbox (badness 10000) in paragraph at lines 6715--6717 []\T1/txtt/m/n/10 python []m emod_api.channelreports.plot_icj_means [[]h] [[]c CHANNEL] [[]e EXPERIMENT_ID] [[]t [65] [66 <./sweep_plot.png>] Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 6766--6768 []\T1/txtt/m/n/10 python []m emod_api.spatialreports.plot_spat_means [[]h] [[]c CHANNEL] [[]e EXPERIMENT_ID] [67] [68 <./spat_plot.png>] Chapter 8. Underfull \hbox (badness 10000) in paragraph at lines 6803--6805 []\T1/txtt/m/n/10 python []m emod_api.channelreports.pplot_prop_report.py [[]h] [[]c channelName] [[]p PRIMARY] [69] [70 <./prop_plot.png>] Chapter 9. [71] [72 <./colormap_plot.png>] Overfull \hbox (29.87175pt too wide) in paragraph at lines 6953--6954 []\T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/ 10 , Overfull \hbox (3.62183pt too wide) in paragraph at lines 6954--6955 []\T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6955--6956 []\T1/txtt/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6965--6966 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 , Overfull \hbox (35.12173pt too wide) in paragraph at lines 6966--6967 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 6967--6968 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 , Overfull \hbox (8.87181pt too wide) in paragraph at lines 6970--6971 []\T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 , Overfull \hbox (8.87181pt too wide) in paragraph at lines 6971--6972 []\T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6998--6999 []\T1/txtt/m/n/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 , [73] (./institute-for-disease-modeling-emod-api.ind [74] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/txtt/m/n/10 accumulateTraceData() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (85.18242pt too wide) in paragraph at lines 10--12 []\T1/txtt/m/n/10 add() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.P ropertiesAndAttributes.IndividualProperties Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/txtt/m/n/10 add_migration_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (137.68227pt too wide) in paragraph at lines 15--17 []\T1/txtt/m/n/10 add_parameter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.PropertiesAndAttributes.IndividualProperties Overfull \hbox (49.44226pt too wide) in paragraph at lines 17--19 []\T1/txtt/m/n/10 add_parameter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.Updateable.Updateable Underfull \hbox (badness 10000) in paragraph at lines 19--21 []\T1/txtt/m/n/10 AddAgeDependentTransmission() Overfull \hbox (33.46252pt too wide) in paragraph at lines 19--21 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/txtt/m/n/10 AddIndividualPropertyAndHINT() Overfull \hbox (33.46252pt too wide) in paragraph at lines 21--23 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/txtt/m/n/10 AgeStructureUNWPP() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Overfull \hbox (15.1475pt too wide) in paragraph at lines 23--25 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/txtt/m/n/10 AgesYears \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration. migration.Migration Overfull \hbox (31.54231pt too wide) in paragraph at lines 28--30 []\T1/txtt/m/n/10 append() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializati on.dtkFileTools.DtkFile.Contents Overfull \hbox (26.68231pt too wide) in paragraph at lines 30--32 []\T1/txtt/m/n/10 append() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializati on.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (8.10747pt too wide) in paragraph at lines 32--34 \T1/qtm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 34--36 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (4.56746pt too wide) in paragraph at lines 34--36 \T1/qtm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 36--38 \T1/qtm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/txtt/m/n/10 application() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 38--40 \T1/qtm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/qtm/m/n/10 ), Overfull \hbox (73.8823pt too wide) in paragraph at lines 40--42 []\T1/txtt/m/n/10 apply_overlay() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/txtt/m/n/10 apply_to_defaults_or_nodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 42--44 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/txtt/m/n/10 arcsec_to_deg() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 44--46 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Overfull \hbox (51.92223pt too wide) in paragraph at lines 46--48 []\T1/txtt/m/n/10 as_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.ChannelReport Overfull \hbox (30.00221pt too wide) in paragraph at lines 48--50 []\T1/txtt/m/n/10 as_dictionary() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chan nelreports.channels.Channel Overfull \hbox (26.10222pt too wide) in paragraph at lines 50--52 []\T1/txtt/m/n/10 as_dictionary() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chan nelreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 56--58 []\T1/txtt/m/n/10 author \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/txtt/m/n/10 BaseInputFile \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 63--65 \T1/qtm/m/it/10 emod_api.demographics.BaseInputFile\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/txtt/m/n/10 basicNode() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/txtt/m/n/10 BroadcastEvent() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/txtt/m/n/10 BroadcastEventToOtherNodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (4.13228pt too wide) in paragraph at lines 72--74 []\T1/txtt/m/n/10 byte_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/txtt/m/n/10 change_individual_property() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [75] Underfull \hbox (badness 10000) in paragraph at lines 81--83 []\T1/txtt/m/n/10 change_individual_property_scheduled() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Underfull \hbox (badness 10000) in paragraph at lines 83--85 []\T1/txtt/m/n/10 change_individual_property_triggered() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Underfull \hbox (badness 10000) in paragraph at lines 85--87 []\T1/txtt/m/n/10 change_ser_pop() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 85--87 \T1/qtm/m/it/10 emod_api.serialization.CensusAndModPop\T1/qtm/m/n/10 ), Overfull \hbox (46.67224pt too wide) in paragraph at lines 88--90 []\T1/txtt/m/n/10 channel_names \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channe lreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 90--92 []\T1/txtt/m/n/10 ChannelReport \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (20.42232pt too wide) in paragraph at lines 92--94 []\T1/txtt/m/n/10 channels \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelrepo rts.channels.ChannelReport Overfull \hbox (9.38226pt too wide) in paragraph at lines 94--96 []\T1/txtt/m/n/10 chunk_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (9.38226pt too wide) in paragraph at lines 96--98 []\T1/txtt/m/n/10 chunk_sizes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/txtt/m/n/10 chunks \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 100--102 []\T1/txtt/m/n/10 collect() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 100--102 \T1/qtm/m/it/10 emod_api.channelreports.plot_icj_means\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 102--104 []\T1/txtt/m/n/10 collect() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 102--104 \T1/qtm/m/it/10 emod_api.spatialreports.plot_spat_means\T1/qtm/m/n/10 ), Overfull \hbox (29.63231pt too wide) in paragraph at lines 104--106 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileSupport.EllZeeFour Overfull \hbox (13.76231pt too wide) in paragraph at lines 106--108 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileSupport.Snappy Overfull \hbox (43.15228pt too wide) in paragraph at lines 108--110 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 110--112 []\T1/txtt/m/n/10 compress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (4.13228pt too wide) in paragraph at lines 112--114 []\T1/txtt/m/n/10 compressed \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFile Overfull \hbox (9.38226pt too wide) in paragraph at lines 114--116 []\T1/txtt/m/n/10 compression \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/txtt/m/n/10 ConstantDistribution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.58746pt too wide) in paragraph at lines 116--118 \T1/qtm/m/it/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/txtt/m/n/10 construct() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 118--120 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 120--122 []\T1/txtt/m/n/10 ConstructNodesFromDataFrame() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (46.2575pt too wide) in paragraph at lines 120--122 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (92.52237pt too wide) in paragraph at lines 122--124 []\T1/txtt/m/n/10 copy() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics. PreDefinedDistributions.ConstantDistribution Underfull \hbox (badness 10000) in paragraph at lines 124--126 []\T1/txtt/m/n/10 creation_date \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weathe r.weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 126--128 []\T1/txtt/m/n/10 creation_date \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weathe r.weather.Weather Overfull \hbox (58.51736pt too wide) in paragraph at lines 128--130 []\T1/txtt/m/n/10 CrudeRate \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.d emographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/txtt/m/n/10 data \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports. spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 139--140 []\T1/txtt/m/n/10 data \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.weather .WeatherNode prop- Overfull \hbox (1.23224pt too wide) in paragraph at lines 140--142 []\T1/txtt/m/n/10 datavalue_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weat her.weather.Metadata Overfull \hbox (13.67229pt too wide) in paragraph at lines 146--148 []\T1/txtt/m/n/10 DatavalueCount \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migra tion.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 153--154 []\T1/txtt/m/n/10 decorate_actual_iv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/txtt/m/n/10 decorate_actual_iv_impl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (14.49223pt too wide) in paragraph at lines 156--158 []\T1/txtt/m/n/10 default_population \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.d emographics.Node.Node Overfull \hbox (15.1475pt too wide) in paragraph at lines 158--160 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 160--162 []\T1/txtt/m/n/10 DelayedIntervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 162--164 []\T1/txtt/m/n/10 Demographics \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 162--164 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 164--166 []\T1/txtt/m/n/10 DemographicsGenerator \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class i n Overfull \hbox (16.85251pt too wide) in paragraph at lines 164--166 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/txtt/m/n/10 DemographicsOverlay \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 166--168 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 168--170 []\T1/txtt/m/n/10 DemographicsType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (16.85251pt too wide) in paragraph at lines 168--170 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/txtt/m/n/10 display() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 170--172 \T1/qtm/m/it/10 emod_api.channelreports.plot_icj_means\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 172--174 []\T1/txtt/m/n/10 do_mapping_from_events() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (4.56746pt too wide) in paragraph at lines 172--174 \T1/qtm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 ), [76] Underfull \hbox (badness 10000) in paragraph at lines 175--177 []\T1/txtt/m/n/10 dtk_to_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (36.17227pt too wide) in paragraph at lines 177--179 []\T1/txtt/m/n/10 dtk_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (5.10228pt too wide) in paragraph at lines 179--181 []\T1/txtt/m/n/10 dtk_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 182--184 []\T1/txtt/m/n/10 DtkFile.Contents \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 184--186 []\T1/txtt/m/n/10 DtkFile.Objects \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (3.18729pt too wide) in paragraph at lines 186--188 []\T1/txtt/m/n/10 DtkFileV1 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (3.18729pt too wide) in paragraph at lines 188--190 []\T1/txtt/m/n/10 DtkFileV2 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/txtt/m/n/10 DtkFileV2.NodesV2 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (3.18729pt too wide) in paragraph at lines 192--194 []\T1/txtt/m/n/10 DtkFileV3 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 194--196 []\T1/txtt/m/n/10 DtkFileV3.NodesV3 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (3.18729pt too wide) in paragraph at lines 196--198 []\T1/txtt/m/n/10 DtkFileV4 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (3.18729pt too wide) in paragraph at lines 198--200 []\T1/txtt/m/n/10 DtkFileV5 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (3.18729pt too wide) in paragraph at lines 200--202 []\T1/txtt/m/n/10 DtkHeader \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Overfull \hbox (48.0174pt too wide) in paragraph at lines 202--204 []\T1/txtt/m/n/10 DtkRate \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.dem ographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 204--206 []\T1/txtt/m/n/10 duplicate_nodeID_check() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (46.2575pt too wide) in paragraph at lines 204--206 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (19.2323pt too wide) in paragraph at lines 209--211 []\T1/txtt/m/n/10 EllZeeFour \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api. serialization.dtkFileSupport\T1/qtm/m/n/10 ), Overfull \hbox (27.37175pt too wide) in paragraph at lines 227--228 []\T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (1.12183pt too wide) in paragraph at lines 229--230 []\T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (32.62173pt too wide) in paragraph at lines 253--254 []\T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (6.37181pt too wide) in paragraph at lines 261--262 []\T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions Overfull \hbox (6.37181pt too wide) in paragraph at lines 263--264 []\T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes [77] Underfull \hbox (badness 10000) in paragraph at lines 332--334 []\T1/txtt/m/n/10 EveryoneInitiallySusceptible() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 332--334 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/txtt/m/n/10 examine_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/txtt/m/n/10 FAMILY \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.mig ration.Migration Underfull \hbox (badness 10000) in paragraph at lines 342--344 []\T1/txtt/m/n/10 FEMALE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.mig ration.Migration Underfull \hbox (badness 10000) in paragraph at lines 344--346 []\T1/txtt/m/n/10 fill_nodes_legacy() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Overfull \hbox (46.2575pt too wide) in paragraph at lines 344--346 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (31.2124pt too wide) in paragraph at lines 348--350 []\T1/txtt/m/n/10 find() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.se rialization.SerializedPopulation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 350--352 []\T1/txtt/m/n/10 flattenConfig() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (76.32239pt too wide) in paragraph at lines 352--354 []\T1/txtt/m/n/10 flush() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializatio n.SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 356--358 []\T1/txtt/m/n/10 from_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 356--358 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 361--363 []\T1/txtt/m/n/10 from_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 361--363 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 363--365 []\T1/txtt/m/n/10 from_demog_and_param_gravity() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (113.91234pt too wide) in paragraph at lines 367--369 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes Overfull \hbox (180.06232pt too wide) in paragraph at lines 369--371 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes.AgeDistribution Overfull \hbox (197.29231pt too wide) in paragraph at lines 371--373 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes.FertilityDistribution Overfull \hbox (203.09232pt too wide) in paragraph at lines 373--375 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.IndividualAttributes.MortalityDistribution Overfull \hbox (93.66234pt too wide) in paragraph at lines 375--377 []\T1/txtt/m/n/10 from_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograp hics.PropertiesAndAttributes.NodeAttributes Underfull \hbox (badness 10000) in paragraph at lines 377--379 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather. weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 379--381 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 379--381 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 381--383 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 381--383 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), [78] Underfull \hbox (badness 10000) in paragraph at lines 383--384 []\T1/txtt/m/n/10 from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/txtt/m/n/10 from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 384--386 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 386--387 []\T1/txtt/m/n/10 from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 387--389 []\T1/txtt/m/n/10 from_pop_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 387--389 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 389--391 []\T1/txtt/m/n/10 from_template_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 389--391 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 391--393 []\T1/txtt/m/n/10 FullRisk() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 391--393 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (13.67229pt too wide) in paragraph at lines 396--398 []\T1/txtt/m/n/10 GenderDataType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migra tion.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 398--400 []\T1/txtt/m/n/10 generate_demographics() Overfull \hbox (115.38252pt too wide) in paragraph at lines 398--400 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (69.64224pt too wide) in paragraph at lines 400--402 []\T1/txtt/m/n/10 generate_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.BaseInputFile.BaseInputFile Overfull \hbox (73.8823pt too wide) in paragraph at lines 402--404 []\T1/txtt/m/n/10 generate_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demo graphics.Demographics.Demographics Overfull \hbox (85.3922pt too wide) in paragraph at lines 404--406 []\T1/txtt/m/n/10 generate_headers() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.d emographics.BaseInputFile.BaseInputFile Underfull \hbox (badness 10000) in paragraph at lines 406--408 []\T1/txtt/m/n/10 generate_metadata() Overfull \hbox (115.38252pt too wide) in paragraph at lines 406--408 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (161.05228pt too wide) in paragraph at lines 408--410 []\T1/txtt/m/n/10 generate_nodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.dem ographics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 412--414 []\T1/txtt/m/n/10 get_bbox() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 412--414 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 414--416 []\T1/txtt/m/n/10 get_class_with_defaults() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 416--418 []\T1/txtt/m/n/10 get_colour_from_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule Overfull \hbox (44.89249pt too wide) in paragraph at lines 418--420 \T1/qtm/m/it/10 ule emod_api.config.default_from_schema_no_validation\T1/qtm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 420--422 []\T1/txtt/m/n/10 get_default_config_from_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it /10 in mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 420--422 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 422--424 []\T1/txtt/m/n/10 get_default_for_complex_type() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (93.54231pt too wide) in paragraph at lines 424--426 []\T1/txtt/m/n/10 get_dtk_rate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demog raphics.DemographicsTemplates.CrudeRate Underfull \hbox (badness 10000) in paragraph at lines 427--429 []\T1/txtt/m/n/10 get_fert_dist() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 427--429 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 429--431 []\T1/txtt/m/n/10 get_fert_dist_from_rates() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 429--431 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 431--433 []\T1/txtt/m/n/10 get_grid_cell_id() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 431--433 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 434--436 []\T1/txtt/m/n/10 get_next_individual_suid() Overfull \hbox (77.9025pt too wide) in paragraph at lines 434--436 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 436--438 []\T1/txtt/m/n/10 get_next_infection_suid() Overfull \hbox (77.9025pt too wide) in paragraph at lines 436--438 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 438--440 []\T1/txtt/m/n/10 get_nickname_from_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (47.63237pt too wide) in paragraph at lines 440--442 []\T1/txtt/m/n/10 get_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograph ics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 442--444 []\T1/txtt/m/n/10 get_node_ids_from_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 442--444 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Overfull \hbox (34.67223pt too wide) in paragraph at lines 444--446 []\T1/txtt/m/n/10 get_node_offsets() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.m igration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 446--448 []\T1/txtt/m/n/10 get_node_pops_from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 446--448 \T1/qtm/m/it/10 emod_api.demographics.Demographics\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 448--450 []\T1/txtt/m/n/10 get_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 448--450 \T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 453--455 []\T1/txtt/m/n/10 get_shape_from_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 456--458 []\T1/txtt/m/n/10 get_waning_from_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 458--460 []\T1/txtt/m/n/10 get_waning_from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 460--462 []\T1/txtt/m/n/10 get_waning_from_points() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 462--464 []\T1/txtt/m/n/10 get_xpix_ypix() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 464--466 []\T1/txtt/m/n/10 getChannels() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 466--468 []\T1/txtt/m/n/10 getTraceName() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [79] Overfull \hbox (9.92235pt too wide) in paragraph at lines 473--475 []\T1/txtt/m/n/10 header \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelreport s.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 475--477 []\T1/txtt/m/n/10 header \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Underfull \hbox (badness 5985) in paragraph at lines 484--486 []\T1/txtt/m/n/10 id \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports.sp atial.SpatialNode prop- Underfull \hbox (badness 10000) in paragraph at lines 487--489 []\T1/txtt/m/n/10 id_reference \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 489--491 []\T1/txtt/m/n/10 id_reference \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Weather Overfull \hbox (34.6714pt too wide) in paragraph at lines 491--493 []\T1/txtt/m/n/10 IDREF_GRUMP1DEGREE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.m igration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 493--495 []\T1/txtt/m/n/10 IDREF_GRUMP2PT5ARCMIN Underfull \hbox (badness 10000) in paragraph at lines 493--495 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 495--497 []\T1/txtt/m/n/10 IDREF_GRUMP30ARCSEC Underfull \hbox (badness 10000) in paragraph at lines 495--497 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Overfull \hbox (3.1715pt too wide) in paragraph at lines 497--499 []\T1/txtt/m/n/10 IDREF_LEGACY \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migrati on.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 501--503 []\T1/txtt/m/n/10 indexFor() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 503--505 []\T1/txtt/m/n/10 IndividualAttributes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 503--505 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Overfull \hbox (14.13748pt too wide) in paragraph at lines 505--507 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 507--509 []\T1/txtt/m/n/10 IndividualAttributes.FertilityDistribution Overfull \hbox (48.58748pt too wide) in paragraph at lines 507--509 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.demographics.PropertiesAndAtt ributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 509--511 []\T1/txtt/m/n/10 IndividualAttributes.MortalityDistribution Overfull \hbox (48.58748pt too wide) in paragraph at lines 509--511 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.demographics.PropertiesAndAtt ributes\T1/qtm/m/n/10 ), Overfull \hbox (16.87178pt too wide) in paragraph at lines 511--513 []\T1/txtt/m/n/10 IndividualAttributes.SusceptibilityDistribution Overfull \hbox (48.58748pt too wide) in paragraph at lines 511--513 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.demographics.PropertiesAndAtt ributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 513--515 []\T1/txtt/m/n/10 IndividualProperties \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 513--515 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 515--517 []\T1/txtt/m/n/10 IndividualProperty \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 515--517 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/txtt/m/n/10 infer_natural_mortality() Overfull \hbox (33.46252pt too wide) in paragraph at lines 517--519 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 519--521 []\T1/txtt/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 519--521 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 521--523 []\T1/txtt/m/n/10 InitAgeUniform() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 521--523 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 523--525 []\T1/txtt/m/n/10 InitPrevUniform() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 523--525 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 525--527 []\T1/txtt/m/n/10 InitRiskExponential() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 525--527 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 527--529 []\T1/txtt/m/n/10 InitRiskLogNormal() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Overfull \hbox (15.1475pt too wide) in paragraph at lines 527--529 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 529--531 []\T1/txtt/m/n/10 InitRiskUniform() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 529--531 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 531--533 []\T1/txtt/m/n/10 InitSusceptConstant() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 531--533 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (29.42224pt too wide) in paragraph at lines 533--535 []\T1/txtt/m/n/10 InterpolationType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.mi gration.migration.Migration Overfull \hbox (2.72234pt too wide) in paragraph at lines 535--537 []\T1/txtt/m/n/10 interval \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialrepo rts.spatial.SpatialReport Overfull \hbox (3.1715pt too wide) in paragraph at lines 537--539 []\T1/txtt/m/n/10 INTERVENTION \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migrati on.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 544--546 []\T1/txtt/m/n/10 lat_lon_from_nodeid() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 547--549 []\T1/txtt/m/n/10 LINEAR_INTERPOLATION Underfull \hbox (badness 10000) in paragraph at lines 547--549 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 549--551 []\T1/txtt/m/n/10 listChannelsAndIPs() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 551--553 []\T1/txtt/m/n/10 load_default_config_as_rod() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 551--553 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 553--555 []\T1/txtt/m/n/10 LOCAL \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migr ation.Migration at- Underfull \hbox (badness 10000) in paragraph at lines 556--558 []\T1/txtt/m/n/10 lon_lat_2_point() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 556--558 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Overfull \hbox (26.81233pt too wide) in paragraph at lines 561--563 []\T1/txtt/m/n/10 main() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.ch annelreports.plot_prop_report\T1/qtm/m/n/10 ), [80] Underfull \hbox (badness 10000) in paragraph at lines 563--565 []\T1/txtt/m/n/10 make_config_from_poi() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 563--565 \T1/qtm/m/it/10 emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 565--567 []\T1/txtt/m/n/10 make_config_from_poi_and_config_dict() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Overfull \hbox (3.8775pt too wide) in paragraph at lines 565--567 \T1/qtm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 567--569 []\T1/txtt/m/n/10 make_config_from_poi_and_config_file() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Overfull \hbox (3.8775pt too wide) in paragraph at lines 567--569 \T1/qtm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 569--571 []\T1/txtt/m/n/10 make_config_from_poi_and_schema() \T1/qtm/m/n/10 (\T1/qtm/m/i t/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 571--572 []\T1/txtt/m/n/10 MALE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migra tion.Migration at- Underfull \hbox (badness 10000) in paragraph at lines 575--576 []\T1/txtt/m/n/10 metadata \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.wea ther.Weather prop- Overfull \hbox (8.4223pt too wide) in paragraph at lines 577--579 []\T1/txtt/m/n/10 MigrationType \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migrat ion.migration.Migration Overfull \hbox (2.62189pt too wide) in paragraph at lines 585--586 []| \T1/txtt/m/n/10 emod_api.channelreports.plot_prop_report\T1/qtm/m/n/10 , Overfull \hbox (49.87175pt too wide) in paragraph at lines 588--589 []| \T1/txtt/m/n/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/ n/10 , Overfull \hbox (23.62183pt too wide) in paragraph at lines 589--590 []| \T1/txtt/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/qtm/m/n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 590--591 []| \T1/txtt/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/qtm/m/n/10 , Overfull \hbox (2.62189pt too wide) in paragraph at lines 599--600 []| \T1/txtt/m/n/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 600--601 []| \T1/txtt/m/n/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 , Overfull \hbox (55.12173pt too wide) in paragraph at lines 601--602 []| \T1/txtt/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m /n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 602--603 []| \T1/txtt/m/n/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 603--604 []| \T1/txtt/m/n/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 , Overfull \hbox (28.87181pt too wide) in paragraph at lines 605--606 []| \T1/txtt/m/n/10 emod_api.demographics.PreDefinedDistributions\T1/qtm/m/n/10 , Overfull \hbox (28.87181pt too wide) in paragraph at lines 606--607 []| \T1/txtt/m/n/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 612--613 []| \T1/txtt/m/n/10 emod_api.interventions.import_pressure\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 614--615 []| \T1/txtt/m/n/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 625--626 []| \T1/txtt/m/n/10 emod_api.schema.dtk_post_process_schema\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 629--630 []| \T1/txtt/m/n/10 emod_api.serialization.CensusAndModPop\T1/qtm/m/n/10 , Overfull \hbox (18.37184pt too wide) in paragraph at lines 633--634 []| \T1/txtt/m/n/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--636 []| \T1/txtt/m/n/10 emod_api.spatialreports.plot_spat_means\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 640--642 []\T1/txtt/m/n/10 MortalityRateByAge() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Overfull \hbox (15.1475pt too wide) in paragraph at lines 640--642 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 642--644 []\T1/txtt/m/n/10 MortalityStructureNigeriaDHS() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 642--644 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 644--646 []\T1/txtt/m/n/10 MultiInterventionDistributor() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 in mod-ule [81] Underfull \hbox (badness 10000) in paragraph at lines 649--651 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 649--651 \T1/qtm/m/it/10 emod_api.interventions.import_pressure\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 651--653 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 651--653 \T1/qtm/m/it/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 653--655 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 655--657 []\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 655--657 \T1/qtm/m/it/10 emod_api.interventions.simple_vaccine\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 657--659 []\T1/txtt/m/n/10 new_intervention2() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 657--659 \T1/qtm/m/it/10 emod_api.interventions.simple_vaccine\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 659--661 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 659--661 \T1/qtm/m/it/10 emod_api.interventions.import_pressure\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 661--663 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 661--663 \T1/qtm/m/it/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 663--665 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 665--667 []\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 665--667 \T1/qtm/m/it/10 emod_api.interventions.simple_vaccine\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 667--669 []\T1/txtt/m/n/10 new_scheduled_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 667--669 \T1/qtm/m/it/10 emod_api.interventions.node_multiplier\T1/qtm/m/n/10 ), Overfull \hbox (47.63237pt too wide) in paragraph at lines 671--673 []\T1/txtt/m/n/10 node_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograph ics.Demographics.Demographics Overfull \hbox (13.2223pt too wide) in paragraph at lines 673--675 []\T1/txtt/m/n/10 node_count \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialre ports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 678--680 []\T1/txtt/m/n/10 node_ID_from_lat_long() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule Overfull \hbox (46.2575pt too wide) in paragraph at lines 678--680 \T1/qtm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/qtm/m/n/1 0 ), Overfull \hbox (37.1324pt too wide) in paragraph at lines 680--682 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographic s.Demographics.Demographics Overfull \hbox (2.72234pt too wide) in paragraph at lines 682--684 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialrepo rts.spatial.SpatialReport Underfull \hbox (badness 6808) in paragraph at lines 684--685 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.wea ther.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 685--686 []\T1/txtt/m/n/10 node_ids \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather.wea ther.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 686--688 []\T1/txtt/m/n/10 NodeAttributes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (14.13748pt too wide) in paragraph at lines 686--688 \T1/qtm/m/it/10 emod_api.demographics.PropertiesAndAttributes\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 689--691 []\T1/txtt/m/n/10 NodeCount \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration. migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 691--693 []\T1/txtt/m/n/10 nodeid_from_lat_lon() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (21.38245pt too wide) in paragraph at lines 695--697 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.D emographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 698--700 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Overfull \hbox (65.82242pt too wide) in paragraph at lines 700--702 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serialization. SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 702--704 []\T1/txtt/m/n/10 nodes \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports .spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 706--708 []\T1/txtt/m/n/10 nodes_for_DTK() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 708--710 []\T1/txtt/m/n/10 NoInitialPrevalence() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 708--710 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (62.70738pt too wide) in paragraph at lines 710--712 []\T1/txtt/m/n/10 NoRisk() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api. demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (3.48235pt too wide) in paragraph at lines 712--714 []\T1/txtt/m/n/10 NullPtr \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api.ser ialization.dtkFileSupport\T1/qtm/m/n/10 ), Overfull \hbox (41.42226pt too wide) in paragraph at lines 714--716 []\T1/txtt/m/n/10 num_channels \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (10.35226pt too wide) in paragraph at lines 716--718 []\T1/txtt/m/n/10 num_channels \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (51.92223pt too wide) in paragraph at lines 718--720 []\T1/txtt/m/n/10 num_time_steps \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.ChannelReport Overfull \hbox (20.85223pt too wide) in paragraph at lines 720--722 []\T1/txtt/m/n/10 num_time_steps \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 725--727 []\T1/txtt/m/n/10 ONE_FOR_EACH_GENDER Underfull \hbox (badness 10000) in paragraph at lines 725--727 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Overfull \hbox (34.6714pt too wide) in paragraph at lines 732--734 []\T1/txtt/m/n/10 PIECEWISE_CONSTANT \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.m igration.migration.Migration Overfull \hbox (21.05736pt too wide) in paragraph at lines 734--736 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.sp atialreports.plot_spat_means\T1/qtm/m/n/10 ), [82] Underfull \hbox (badness 10000) in paragraph at lines 736--738 []\T1/txtt/m/n/10 plot_from_sql() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 738--740 []\T1/txtt/m/n/10 plotTraces() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 740--742 []\T1/txtt/m/n/10 point_2_grid_cell_id_lookup() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 740--742 \T1/qtm/m/it/10 emod_api.demographics.grid_construction\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 743--745 []\T1/txtt/m/n/10 processCommandline() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 745--747 []\T1/txtt/m/n/10 PropertyValueChanger() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 753--755 []\T1/txtt/m/n/10 readJsonFile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 756--758 []\T1/txtt/m/n/10 recurser() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 756--758 \T1/qtm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/qtm/m/n/10 ), Overfull \hbox (36.17227pt too wide) in paragraph at lines 760--762 []\T1/txtt/m/n/10 report_type \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (5.10228pt too wide) in paragraph at lines 762--764 []\T1/txtt/m/n/10 report_type \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (51.92223pt too wide) in paragraph at lines 764--766 []\T1/txtt/m/n/10 report_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.ChannelReport Overfull \hbox (20.85223pt too wide) in paragraph at lines 766--768 []\T1/txtt/m/n/10 report_version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 768--770 []\T1/txtt/m/n/10 res_in_degrees \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 775--777 []\T1/txtt/m/n/10 SAME_FOR_BOTH_GENDERS Underfull \hbox (badness 10000) in paragraph at lines 775--777 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 778--780 []\T1/txtt/m/n/10 ScheduledCampaignEvent() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 780--782 []\T1/txtt/m/n/10 schema_to_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 780--782 \T1/qtm/m/it/10 emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 782--784 []\T1/txtt/m/n/10 schema_to_config_subnode() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 782--784 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 784--786 []\T1/txtt/m/n/10 SchemaConfigBuilder \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 786--788 []\T1/txtt/m/n/10 SchemaConfigBuilder \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 790--792 []\T1/txtt/m/n/10 seed_by_coverage() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 792--794 []\T1/txtt/m/n/10 SerializedPopulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 792--794 \T1/qtm/m/it/10 emod_api.serialization.SerializedPopulation\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 794--796 []\T1/txtt/m/n/10 SerialObject \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 796--798 []\T1/txtt/m/n/10 set_beautifiers() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 798--800 []\T1/txtt/m/n/10 set_demog_distributions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 798--800 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 800--802 []\T1/txtt/m/n/10 set_growing_demographics() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 800--802 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 802--804 []\T1/txtt/m/n/10 set_immune_mod() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 802--804 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Overfull \hbox (161.05228pt too wide) in paragraph at lines 804--806 []\T1/txtt/m/n/10 set_resolution() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.dem ographics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 806--808 []\T1/txtt/m/n/10 set_risk_mod() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 806--808 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Overfull \hbox (6.99231pt too wide) in paragraph at lines 808--810 []\T1/txtt/m/n/10 set_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.schema_ to_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 811--813 []\T1/txtt/m/n/10 set_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 811--813 \T1/qtm/m/it/10 emod_api.config.from_poi_and_binary\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 813--815 []\T1/txtt/m/n/10 set_static_demographics() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 813--815 \T1/qtm/m/it/10 emod_api.demographics.demographics_utils\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 815--817 []\T1/txtt/m/n/10 SetAgeDistribution() Overfull \hbox (33.46252pt too wide) in paragraph at lines 815--817 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (68.63231pt too wide) in paragraph at lines 817--819 []\T1/txtt/m/n/10 SetBirthRate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demog raphics.Demographics.Demographics Overfull \hbox (84.38226pt too wide) in paragraph at lines 819--821 []\T1/txtt/m/n/10 SetConstantRisk() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.de mographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 821--823 []\T1/txtt/m/n/10 SetConstantSusceptibility() Overfull \hbox (33.46252pt too wide) in paragraph at lines 821--823 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 823--825 []\T1/txtt/m/n/10 SetDefaultFromTemplate() Overfull \hbox (33.46252pt too wide) in paragraph at lines 823--825 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics [83] Underfull \hbox (badness 10000) in paragraph at lines 825--827 []\T1/txtt/m/n/10 SetDefaultIndividualAttributes() Overfull \hbox (33.46252pt too wide) in paragraph at lines 825--827 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 827--829 []\T1/txtt/m/n/10 SetDefaultIndividualProperties() Overfull \hbox (33.46252pt too wide) in paragraph at lines 827--829 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 829--831 []\T1/txtt/m/n/10 SetDefaultNodeAttributes() Overfull \hbox (33.46252pt too wide) in paragraph at lines 829--831 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 831--833 []\T1/txtt/m/n/10 SetDefaultProperties() Overfull \hbox (33.46252pt too wide) in paragraph at lines 831--833 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 833--835 []\T1/txtt/m/n/10 SetDefaultPropertiesFertMort() Overfull \hbox (33.46252pt too wide) in paragraph at lines 833--835 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (1.12183pt too wide) in paragraph at lines 835--837 []\T1/txtt/m/n/10 SetEquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (33.46252pt too wide) in paragraph at lines 835--837 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 837--839 []\T1/txtt/m/n/10 SetEquilibriumVitalDynamics() Overfull \hbox (33.46252pt too wide) in paragraph at lines 837--839 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 839--841 []\T1/txtt/m/n/10 SetEquilibriumVitalDynamicsFromWorldBank() Overfull \hbox (33.46252pt too wide) in paragraph at lines 839--841 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 841--843 []\T1/txtt/m/n/10 SetFertilityOverTimeFromParams() Overfull \hbox (33.46252pt too wide) in paragraph at lines 841--843 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 843--845 []\T1/txtt/m/n/10 SetHeteroRiskExponDist() Overfull \hbox (33.46252pt too wide) in paragraph at lines 843--845 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 845--847 []\T1/txtt/m/n/10 SetHeteroRiskLognormalDist() Overfull \hbox (33.46252pt too wide) in paragraph at lines 845--847 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 847--849 []\T1/txtt/m/n/10 SetHeteroRiskUniformDist() Overfull \hbox (33.46252pt too wide) in paragraph at lines 847--849 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 849--851 []\T1/txtt/m/n/10 SetIndividualAttributesWithFertMort() Overfull \hbox (33.46252pt too wide) in paragraph at lines 849--851 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 851--853 []\T1/txtt/m/n/10 SetInitialAgeExponential() Overfull \hbox (33.46252pt too wide) in paragraph at lines 851--853 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/txtt/m/n/10 SetInitialAgeLikeSubSaharanAfrica() Overfull \hbox (33.46252pt too wide) in paragraph at lines 853--855 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 855--857 []\T1/txtt/m/n/10 SetInitPrevFromUniformDraw() Overfull \hbox (33.46252pt too wide) in paragraph at lines 855--857 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 857--859 []\T1/txtt/m/n/10 SetMigrationPattern() Overfull \hbox (33.46252pt too wide) in paragraph at lines 857--859 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 859--861 []\T1/txtt/m/n/10 SetMinimalNodeAttributes() Overfull \hbox (33.46252pt too wide) in paragraph at lines 859--861 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 861--863 []\T1/txtt/m/n/10 SetMortalityDistribution() Overfull \hbox (33.46252pt too wide) in paragraph at lines 861--863 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/txtt/m/n/10 SetMortalityOverTimeFromData() Overfull \hbox (33.46252pt too wide) in paragraph at lines 863--865 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (89.63225pt too wide) in paragraph at lines 865--867 []\T1/txtt/m/n/10 SetMortalityRate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.d emographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 867--869 []\T1/txtt/m/n/10 SetNodeDefaultFromTemplate() Overfull \hbox (33.46252pt too wide) in paragraph at lines 867--869 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 869--871 []\T1/txtt/m/n/10 SetOneWayMigration() Overfull \hbox (33.46252pt too wide) in paragraph at lines 869--871 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 871--873 []\T1/txtt/m/n/10 SetOverdispersion() Overfull \hbox (33.46252pt too wide) in paragraph at lines 871--873 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 873--875 []\T1/txtt/m/n/10 SetRoundTripMigration() Overfull \hbox (33.46252pt too wide) in paragraph at lines 873--875 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 875--877 []\T1/txtt/m/n/10 SetSimpleVitalDynamics() Overfull \hbox (33.46252pt too wide) in paragraph at lines 875--877 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (15.1475pt too wide) in paragraph at lines 877--879 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), Overfull \hbox (14.49228pt too wide) in paragraph at lines 879--881 []\T1/txtt/m/n/10 simulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFileV1 Overfull \hbox (14.49228pt too wide) in paragraph at lines 881--883 []\T1/txtt/m/n/10 simulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFileV2 Overfull \hbox (14.49228pt too wide) in paragraph at lines 883--885 []\T1/txtt/m/n/10 simulation \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializa tion.dtkFileTools.DtkFileV3 Underfull \hbox (badness 10000) in paragraph at lines 887--889 []\T1/txtt/m/n/10 SpatialReport \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 889--891 []\T1/txtt/m/n/10 StandardDiagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 891--893 []\T1/txtt/m/n/10 start \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialreports .spatial.SpatialReport Overfull \hbox (30.92229pt too wide) in paragraph at lines 893--895 []\T1/txtt/m/n/10 start_time \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (85.98161pt too wide) in paragraph at lines 897--899 []\T1/txtt/m/n/10 STATIC \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographics. DemographicsGenerator.DemographicsType Overfull \hbox (25.6723pt too wide) in paragraph at lines 899--901 []\T1/txtt/m/n/10 step_size \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 903--905 []\T1/txtt/m/n/10 StepFunctionSusceptibility() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (15.1475pt too wide) in paragraph at lines 903--905 \T1/qtm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/qtm/m/n/10 ), [84] Overfull \hbox (30.92229pt too wide) in paragraph at lines 910--912 []\T1/txtt/m/n/10 time_stamp \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (13.2223pt too wide) in paragraph at lines 914--916 []\T1/txtt/m/n/10 time_steps \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatialre ports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 916--918 []\T1/txtt/m/n/10 title \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 918--920 []\T1/txtt/m/n/10 titleFor() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Overfull \hbox (42.38239pt too wide) in paragraph at lines 921--923 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Demographics.Demographics Overfull \hbox (74.09238pt too wide) in paragraph at lines 923--925 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Demographics.DemographicsOverlay Underfull \hbox (badness 10000) in paragraph at lines 925--926 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Node.Node Overfull \hbox (108.27232pt too wide) in paragraph at lines 926--928 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PreDefinedDistributions.ConstantDistribution Overfull \hbox (103.41237pt too wide) in paragraph at lines 928--930 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes Overfull \hbox (169.56235pt too wide) in paragraph at lines 930--932 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.AgeDistribution Overfull \hbox (186.79234pt too wide) in paragraph at lines 932--934 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.FertilityDistribution Overfull \hbox (192.59235pt too wide) in paragraph at lines 934--936 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.MortalityDistribution Overfull \hbox (208.45236pt too wide) in paragraph at lines 936--938 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualAttributes.SusceptibilityDistribution Overfull \hbox (106.18236pt too wide) in paragraph at lines 938--940 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualProperties Overfull \hbox (99.51236pt too wide) in paragraph at lines 940--942 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.IndividualProperty Overfull \hbox (83.16237pt too wide) in paragraph at lines 942--944 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.PropertiesAndAttributes.NodeAttributes Overfull \hbox (17.94235pt too wide) in paragraph at lines 944--946 []\T1/txtt/m/n/10 to_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Updateable.Updateable Overfull \hbox (74.09238pt too wide) in paragraph at lines 946--948 []\T1/txtt/m/n/10 to_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographi cs.Demographics.DemographicsOverlay Underfull \hbox (badness 10000) in paragraph at lines 948--950 []\T1/txtt/m/n/10 to_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration. migration.Migration Underfull \hbox (badness 10000) in paragraph at lines 950--952 []\T1/txtt/m/n/10 to_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 952--953 []\T1/txtt/m/n/10 to_tuple() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 953--954 []\T1/txtt/m/n/10 Tool \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.migration.migra tion.Migration prop- Underfull \hbox (badness 10000) in paragraph at lines 956--958 []\T1/txtt/m/n/10 triggered_campaign_delay_event() \T1/qtm/m/n/10 (\T1/qtm/m/it /10 in mod-ule Overfull \hbox (11.6218pt too wide) in paragraph at lines 958--960 []\T1/txtt/m/n/10 triggered_campaign_event_with_optional_delay() Underfull \hbox (badness 10000) in paragraph at lines 960--962 []\T1/txtt/m/n/10 TriggeredCampaignEvent() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (40.13228pt too wide) in paragraph at lines 965--967 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.seriali zation.dtkFileSupport.EllZeeFour Overfull \hbox (24.26228pt too wide) in paragraph at lines 967--969 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.seriali zation.dtkFileSupport.Snappy Overfull \hbox (53.65225pt too wide) in paragraph at lines 969--971 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.seriali zation.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 971--973 []\T1/txtt/m/n/10 uncompress() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 973--975 []\T1/txtt/m/n/10 Uncompressed \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 975--977 []\T1/txtt/m/n/10 units \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channelreports .channels.Channel Overfull \hbox (12.69237pt too wide) in paragraph at lines 977--979 []\T1/txtt/m/n/10 update() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.demographic s.Updateable.Updateable Overfull \hbox (11.73221pt too wide) in paragraph at lines 979--981 []\T1/txtt/m/n/10 update_resolution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.we ather.weather.Metadata Overfull \hbox (6.7322pt too wide) in paragraph at lines 981--983 []\T1/txtt/m/n/10 update_resolution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.we ather.weather.Weather Overfull \hbox (11.43234pt too wide) in paragraph at lines 983--984 []\T1/txtt/m/n/10 Updateable \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api. demographics.Updateable\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 987--989 []\T1/txtt/m/n/10 validate_res_in_arcsec() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (16.85251pt too wide) in paragraph at lines 987--989 \T1/qtm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 989--991 []\T1/txtt/m/n/10 version \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile Overfull \hbox (76.32239pt too wide) in paragraph at lines 997--999 []\T1/txtt/m/n/10 write() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.serializatio n.SerializedPopulation.SerializedPopulation Overfull \hbox (2.12732pt too wide) in paragraph at lines 999--1000 []\T1/txtt/m/n/10 write() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emod_api.s erialization.dtkFileTools\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1000--1002 []\T1/txtt/m/n/10 write_config_from_default_and_params() \T1/qtm/m/n/10 (\T1/qt m/m/it/10 in Overfull \hbox (62.11249pt too wide) in paragraph at lines 1000--1002 \T1/qtm/m/it/10 mod-ule emod_api.config.default_from_schema_no_validation\T1/qt m/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1002--1004 []\T1/txtt/m/n/10 write_default_from_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 1004--1006 []\T1/txtt/m/n/10 write_default_from_schema() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule Overfull \hbox (31.00249pt too wide) in paragraph at lines 1004--1006 \T1/qtm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/qtm/m/n/10 ), [85] Overfull \hbox (41.42226pt too wide) in paragraph at lines 1006--1008 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (23.72227pt too wide) in paragraph at lines 1008--1010 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.spatial reports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 1010--1012 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 1012--1013 []\T1/txtt/m/n/10 write_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emod_api.weather .weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 1016--1018 []\T1/txtt/m/n/10 xpix_ypix_from_lat_lon() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (63.76735pt too wide) in paragraph at lines 1021--1023 []\T1/txtt/m/n/10 YearlyRate \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in emod_api. demographics.DemographicsTemplates\T1/qtm/m/n/10 ), [86]) (./institute-for-disease-modeling-emod-api.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on institute-for-disease-modeling-emod-api.pdf (90 pages, 196690 5 bytes). Transcript written on institute-for-disease-modeling-emod-api.log. Latexmk: Index file 'institute-for-disease-modeling-emod-api.idx' was written 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: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256