Read the Docs build information Build id: 442911 Project: institute-for-disease-modeling-emod-api Version: latest Commit: 2a77f9e6b24b3a31cdec1c0f09e4977d1e4874ff Date: 2020-10-06T18:43:37.075491Z State: finished Success: True [rtd-command-info] start-time: 2020-10-06T18:43:38.830628Z, end-time: 2020-10-06T18:43:39.698392Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emod-api.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2020-10-06T18:43:40.320966Z, end-time: 2020-10-06T18:43:40.502934Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 2a77f9e update emodapi tests (#130) [rtd-command-info] start-time: 2020-10-06T18:43:40.742661Z, end-time: 2020-10-06T18:43:40.801758Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-10-06T18:43:42.440773Z, end-time: 2020-10-06T18:43:47.646146Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-10-06T18:43:47.814654Z, end-time: 2020-10-06T18:43:48.536114Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-10-06T18:43:49.028726Z, end-time: 2020-10-06T18:43:57.150277Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting packaging Downloading 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Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, snowballstemmer, pyparsing, six, packaging, chardet, idna, urllib3, certifi, requests, pytz, babel, MarkupSafe, Jinja2, Pygments, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-50.3.0 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10 [rtd-command-info] start-time: 2020-10-06T18:43:57.345189Z, end-time: 2020-10-06T18:44:03.215285Z, duration: 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wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13704 sha256=f7ec889ae9b28d81484af07d17e6e370a01fdda45743366ba14045dd1de740b3 Stored in directory: /tmp/pip-ephem-wheel-cache-5tc3tys9/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9 Building wheel for wrapt (setup.py): started Building wheel for wrapt (setup.py): finished with status 'done' Created wheel for wrapt: filename=wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl size=70983 sha256=27f2eb6ef2b387ccac8596ea686c4986e1fc92da6046a77083cad7784294133b Stored in directory: /tmp/pip-ephem-wheel-cache-5tc3tys9/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6 Successfully built docopt wrapt Installing collected packages: sphinxcontrib-devhelp, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, sphinxcontrib-programoutput, docopt, py-make, wrapt, deprecated, pyjwt, PyGithub, cached-property, pycparser, cffi, pygit2 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed PyGithub-1.53 cached-property-1.5.2 cffi-1.14.3 deprecated-1.2.10 docopt-0.6.2 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.20 pygit2-1.2.1 pyjwt-1.7.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.16 sphinxcontrib-qthelp-1.0.3 wrapt-1.12.1 [rtd-command-info] start-time: 2020-10-06T18:44:03.345965Z, end-time: 2020-10-06T18:44:05.225053Z, 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/*' 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/emod_api copying emod_api/campaign.py -> build/lib/emod_api copying emod_api/schema_to_class.py -> build/lib/emod_api copying emod_api/__init__.py -> build/lib/emod_api copying emod_api/__main__.py -> build/lib/emod_api creating build/lib/emod_api/serialization copying emod_api/serialization/SerializedPopulation.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileTools.py -> build/lib/emod_api/serialization copying emod_api/serialization/__init__.py -> build/lib/emod_api/serialization copying emod_api/serialization/__main__.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileSupport.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileUtility.py -> build/lib/emod_api/serialization creating build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__init__.py -> build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__main__.py -> build/lib/emod_api/tabularoutput creating build/lib/emod_api/schema copying emod_api/schema/get_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__init__.py -> build/lib/emod_api/schema copying emod_api/schema/dtk_post_process_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__main__.py -> build/lib/emod_api/schema creating build/lib/emod_api/channelreports copying emod_api/channelreports/__init__.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/channels.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/__main__.py -> build/lib/emod_api/channelreports creating build/lib/emod_api/config copying emod_api/config/from_overrides.py -> build/lib/emod_api/config copying emod_api/config/schema_to_config.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/from_poi_and_binary.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema_no_validation.py -> build/lib/emod_api/config copying emod_api/config/dtk_post_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/__init__.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema.py -> build/lib/emod_api/config copying emod_api/config/from_schema.py -> build/lib/emod_api/config copying emod_api/config/__main__.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_w5ml.py -> build/lib/emod_api/config creating build/lib/emod_api/weather copying emod_api/weather/__init__.py -> build/lib/emod_api/weather copying emod_api/weather/weather.py -> build/lib/emod_api/weather copying emod_api/weather/__main__.py -> build/lib/emod_api/weather creating build/lib/emod_api/interventions copying emod_api/interventions/__init__.py -> build/lib/emod_api/interventions copying emod_api/interventions/outbreak.py -> build/lib/emod_api/interventions copying emod_api/interventions/import_pressure.py -> build/lib/emod_api/interventions copying emod_api/interventions/__main__.py -> build/lib/emod_api/interventions copying emod_api/interventions/simple_vaccine.py -> build/lib/emod_api/interventions creating build/lib/emod_api/examples copying emod_api/examples/serialized_file_mc_to_sc.py -> build/lib/emod_api/examples copying emod_api/examples/__init__.py -> build/lib/emod_api/examples copying emod_api/examples/weather_file.py -> build/lib/emod_api/examples copying emod_api/examples/insetchart.py -> build/lib/emod_api/examples copying emod_api/examples/spatial_report.py -> build/lib/emod_api/examples creating build/lib/emod_api/migration copying emod_api/migration/MigrationFile.py -> build/lib/emod_api/migration copying emod_api/migration/__init__.py -> build/lib/emod_api/migration copying emod_api/migration/Migration.py -> build/lib/emod_api/migration copying emod_api/migration/__main__.py -> build/lib/emod_api/migration creating build/lib/emod_api/spatialreports copying emod_api/spatialreports/__init__.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/spatial.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/__main__.py -> build/lib/emod_api/spatialreports creating build/lib/emod_api/demographics copying emod_api/demographics/DemographicsGenerator.py -> build/lib/emod_api/demographics copying emod_api/demographics/demographics_utils.py -> build/lib/emod_api/demographics copying emod_api/demographics/__init__.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsTemplates.py -> build/lib/emod_api/demographics copying emod_api/demographics/Demographics.py -> build/lib/emod_api/demographics copying emod_api/demographics/__main__.py -> build/lib/emod_api/demographics copying emod_api/demographics/BaseInputFile.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsInputDataParsers.py -> build/lib/emod_api/demographics copying emod_api/demographics/Node.py -> build/lib/emod_api/demographics creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/SerializedPopulation.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileTools.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileSupport.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileUtility.py -> build/bdist.linux-x86_64/egg/emod_api/serialization creating build/bdist.linux-x86_64/egg/emod_api/tabularoutput copying build/lib/emod_api/tabularoutput/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput copying build/lib/emod_api/tabularoutput/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput creating build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/get_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/dtk_post_process_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/campaign.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/schema_to_class.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/__init__.py -> build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/channels.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports creating build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_overrides.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/schema_to_config.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_pre_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_poi_and_binary.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/default_from_schema_no_validation.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_post_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/default_from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_pre_process_w5ml.py -> build/bdist.linux-x86_64/egg/emod_api/config creating build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/weather.py -> build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/weather creating build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/import_pressure.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/simple_vaccine.py -> build/bdist.linux-x86_64/egg/emod_api/interventions creating build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/serialized_file_mc_to_sc.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/weather_file.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/insetchart.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/spatial_report.py -> build/bdist.linux-x86_64/egg/emod_api/examples creating build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/MigrationFile.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 copying build/lib/emod_api/migration/Migration.py -> build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/migration creating build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/spatial.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/__main__.py -> build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsGenerator.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/demographics_utils.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/Demographics.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/BaseInputFile.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsInputDataParsers.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/Node.py -> build/bdist.linux-x86_64/egg/emod_api/demographics byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/SerializedPopulation.py to SerializedPopulation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileTools.py to dtkFileTools.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileSupport.py to dtkFileSupport.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileUtility.py to dtkFileUtility.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/get_schema.py to get_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/dtk_post_process_schema.py to dtk_post_process_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/campaign.py to campaign.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema_to_class.py to schema_to_class.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/channels.py to channels.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_overrides.py to from_overrides.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/schema_to_config.py to schema_to_config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_adhocevents.py to dtk_pre_process_adhocevents.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_poi_and_binary.py to from_poi_and_binary.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema_no_validation.py to default_from_schema_no_validation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_post_process_adhocevents.py to dtk_post_process_adhocevents.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema.py to default_from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_schema.py to from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_w5ml.py to dtk_pre_process_w5ml.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/weather.py to weather.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/outbreak.py to outbreak.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/import_pressure.py to import_pressure.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/simple_vaccine.py to simple_vaccine.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/serialized_file_mc_to_sc.py to serialized_file_mc_to_sc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/weather_file.py to weather_file.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/insetchart.py to insetchart.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/spatial_report.py to spatial_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/MigrationFile.py to MigrationFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/Migration.py to Migration.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/spatial.py to spatial.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsGenerator.py to DemographicsGenerator.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/demographics_utils.py to demographics_utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Demographics.py to Demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/BaseInputFile.py to BaseInputFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsInputDataParsers.py to DemographicsInputDataParsers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Node.py to Node.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... emod_api.config.__pycache__.from_poi_and_binary.cpython-37: module references __file__ emod_api.examples.__pycache__.insetchart.cpython-37: module references __file__ emod_api.examples.__pycache__.spatial_report.cpython-37: module references __file__ emod_api.examples.__pycache__.weather_file.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__ creating dist creating 'dist/emod_api-1.1.0-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-1.1.0-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-1.1.0-py3.7.egg Extracting emod_api-1.1.0-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 1.1.0 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-1.1.0-py3.7.egg Processing dependencies for emod-api==1.1.0 Searching for pyyaml Reading https://pypi.org/simple/pyyaml/ Downloading https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz#sha256=b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d Best match: PyYAML 5.3.1 Processing PyYAML-5.3.1.tar.gz Writing /tmp/easy_install-31rku98f/PyYAML-5.3.1/setup.cfg Running PyYAML-5.3.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-31rku98f/PyYAML-5.3.1/egg-dist-tmp-0bdyugf4 In file included from ext/_yaml.c:596:0: ext/_yaml.h:2:10: fatal error: yaml.h: No such file or directory #include ^~~~~~~~ compilation terminated. Error compiling module, falling back to pure Python zip_safe flag not set; analyzing archive contents... Moving PyYAML-5.3.1-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Adding PyYAML 5.3.1 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/PyYAML-5.3.1-py3.7-linux-x86_64.egg Searching for lz4 Reading https://pypi.org/simple/lz4/ Downloading https://files.pythonhosted.org/packages/28/fd/c414b26c9f76f8dc45fbad92dbec7a2c12ca439434e9877f4140d22cf599/lz4-3.1.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=90d275e08e532a91297fe243041bcc16d4166f84134051580ee181990ae0a3ce Best match: lz4 3.1.0 Processing lz4-3.1.0-cp37-cp37m-manylinux1_x86_64.whl Installing lz4-3.1.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/lz4-3.1.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding lz4 3.1.0 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/lz4-3.1.0-py3.7-linux-x86_64.egg Searching for scipy==1.4.1 Best match: scipy 1.4.1 Adding scipy 1.4.1 to easy-install.pth file Using /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages Searching for pandas==0.25.3 Best match: pandas 0.25.3 pandas 0.25.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages Searching for numpy==1.18.1 Best match: numpy 1.18.1 numpy 1.18.1 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/3.7.3/lib/python3.7/site-packages Searching for pytz==2020.1 Best match: pytz 2020.1 Adding pytz 2020.1 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 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/3.7.3/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Finished processing dependencies for emod-api==1.1.0 [rtd-command-info] start-time: 2020-10-06T18:44:07.309610Z, end-time: 2020-10-06T18:44:07.377563Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.imgmath', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = ['emod_api.dtk_tools'] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'EMOD-API' copyright = u'2020, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'EMOD-API' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emod-api-docs.tex', u'emod-api', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emod-api-docs', u'emod-api', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'emod-api-docs', u'emod-api', author, 'Institute for Disease Modeling', 'How to use emodpy for disease simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/emod-api/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/emod-api/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-api', 'name': u'emod-api', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/emod-api/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emod-api', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '2a77f9e6', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-10-06T18:44:07.482432Z, end-time: 2020-10-06T18:44:36.697948Z, duration: 29, exit-code: 0 python sphinx-build -T -E -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.2.1 rm: cannot remove 'emod_api_index.rst': No such file or directory rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 51 source files that are out of date updating environment: [new config] 51 added, 0 changed, 0 removed reading sources... [ 1%] emod_api reading sources... [ 3%] emod_api.campaign reading sources... [ 5%] emod_api.channelreports reading sources... [ 7%] emod_api.channelreports.channels reading sources... [ 9%] emod_api.config reading sources... [ 11%] 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... [ 17%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 19%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 21%] emod_api.config.from_overrides reading sources... [ 23%] emod_api.config.from_poi_and_binary reading sources... [ 25%] emod_api.config.from_schema reading sources... [ 27%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 29%] emod_api.demographics reading sources... [ 31%] emod_api.demographics.BaseInputFile reading sources... [ 33%] emod_api.demographics.Demographics reading sources... [ 35%] emod_api.demographics.DemographicsGenerator reading sources... [ 37%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 39%] emod_api.demographics.DemographicsTemplates reading sources... [ 41%] emod_api.demographics.Node reading sources... [ 43%] emod_api.demographics.demographics_utils reading sources... [ 45%] emod_api.examples reading sources... [ 47%] emod_api.examples.insetchart reading sources... [ 49%] emod_api.examples.serialized_file_mc_to_sc reading sources... [ 50%] emod_api.examples.spatial_report reading sources... [ 52%] emod_api.examples.weather_file reading sources... [ 54%] emod_api.interventions reading sources... [ 56%] emod_api.interventions.import_pressure reading sources... [ 58%] emod_api.interventions.outbreak reading sources... [ 60%] emod_api.interventions.simple_vaccine reading sources... [ 62%] emod_api.migration reading sources... [ 64%] emod_api.migration.Migration reading sources... [ 66%] emod_api.migration.MigrationFile reading sources... [ 68%] emod_api.schema reading sources... [ 70%] emod_api.schema.dtk_post_process_schema reading sources... [ 72%] emod_api.schema.get_schema reading sources... [ 74%] emod_api.schema_to_class reading sources... [ 76%] emod_api.serialization reading sources... [ 78%] emod_api.serialization.SerializedPopulation reading sources... [ 80%] emod_api.serialization.dtkFileSupport reading sources... [ 82%] emod_api.serialization.dtkFileTools reading sources... [ 84%] emod_api.serialization.dtkFileUtility reading sources... [ 86%] emod_api.spatialreports reading sources... [ 88%] emod_api.spatialreports.spatial reading sources... [ 90%] emod_api.tabularoutput reading sources... [ 92%] emod_api.weather reading sources... [ 94%] emod_api.weather.weather reading sources... [ 96%] emod_api_index reading sources... [ 98%] glossary reading sources... [100%] index 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... [ 5%] emod_api.channelreports writing output... [ 7%] emod_api.channelreports.channels writing output... [ 9%] emod_api.config writing output... [ 11%] 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... [ 17%] emod_api.config.dtk_pre_process_adhocevents writing output... [ 19%] emod_api.config.dtk_pre_process_w5ml writing output... [ 21%] emod_api.config.from_overrides writing output... [ 23%] emod_api.config.from_poi_and_binary writing output... [ 25%] emod_api.config.from_schema writing output... [ 27%] emod_api.config.schema_to_config writing output... [ 29%] emod_api.demographics writing output... [ 31%] emod_api.demographics.BaseInputFile writing output... [ 33%] emod_api.demographics.Demographics writing output... [ 35%] emod_api.demographics.DemographicsGenerator writing output... [ 37%] emod_api.demographics.DemographicsInputDataParsers writing output... [ 39%] emod_api.demographics.DemographicsTemplates writing output... [ 41%] emod_api.demographics.Node writing output... [ 43%] emod_api.demographics.demographics_utils writing output... [ 45%] emod_api.examples writing output... [ 47%] emod_api.examples.insetchart writing output... [ 49%] emod_api.examples.serialized_file_mc_to_sc writing output... [ 50%] emod_api.examples.spatial_report writing output... [ 52%] emod_api.examples.weather_file writing output... [ 54%] emod_api.interventions writing output... [ 56%] emod_api.interventions.import_pressure writing output... [ 58%] emod_api.interventions.outbreak writing output... [ 60%] emod_api.interventions.simple_vaccine writing output... [ 62%] emod_api.migration writing output... [ 64%] emod_api.migration.Migration writing output... [ 66%] emod_api.migration.MigrationFile writing output... [ 68%] emod_api.schema writing output... [ 70%] emod_api.schema.dtk_post_process_schema writing output... [ 72%] emod_api.schema.get_schema writing output... [ 74%] emod_api.schema_to_class writing output... [ 76%] emod_api.serialization writing output... [ 78%] emod_api.serialization.SerializedPopulation writing output... [ 80%] emod_api.serialization.dtkFileSupport writing output... [ 82%] emod_api.serialization.dtkFileTools writing output... [ 84%] emod_api.serialization.dtkFileUtility writing output... [ 86%] emod_api.spatialreports writing output... [ 88%] emod_api.spatialreports.spatial writing output... [ 90%] emod_api.tabularoutput writing output... [ 92%] emod_api.weather writing output... [ 94%] emod_api.weather.weather writing output... [ 96%] emod_api_index writing output... [ 98%] glossary writing output... [100%] index generating indices... genindex py-modindexdone writing additional pages... search opensearchdone copying static files... ... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) [rtd-command-info] start-time: 2020-10-06T18:44:36.990070Z, end-time: 2020-10-06T18:44:42.627178Z, duration: 5, exit-code: 0 python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 51 added, 0 changed, 0 removed reading sources... [ 1%] emod_api reading sources... [ 3%] emod_api.campaign reading sources... [ 5%] emod_api.channelreports reading sources... [ 7%] emod_api.channelreports.channels reading sources... [ 9%] emod_api.config reading sources... 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[100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.BaseInputFile emod_api.demographics.Demographics emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics_utils emod_api.examples emod_api.examples.insetchart emod_api.examples.serialized_file_mc_to_sc emod_api.examples.spatial_report emod_api.examples.weather_file emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.migration emod_api.migration.Migration emod_api.migration.MigrationFile emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary done writing... done writing additional files... opensearchdone copying static files... ... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) [rtd-command-info] start-time: 2020-10-06T18:44:42.778082Z, end-time: 2020-10-06T18:44:48.373693Z, duration: 5, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 51 added, 0 changed, 0 removed reading sources... [ 1%] emod_api reading sources... [ 3%] emod_api.campaign reading sources... [ 5%] emod_api.channelreports reading sources... [ 7%] emod_api.channelreports.channels reading sources... [ 9%] emod_api.config reading sources... [ 11%] 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... [ 17%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 19%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 21%] emod_api.config.from_overrides reading sources... [ 23%] emod_api.config.from_poi_and_binary reading sources... [ 25%] emod_api.config.from_schema reading sources... [ 27%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 29%] emod_api.demographics reading sources... [ 31%] emod_api.demographics.BaseInputFile reading sources... [ 33%] emod_api.demographics.Demographics reading sources... 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[100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done processing emod-api-docs.tex... index emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.BaseInputFile emod_api.demographics.Demographics emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics_utils emod_api.examples emod_api.examples.insetchart emod_api.examples.serialized_file_mc_to_sc emod_api.examples.spatial_report emod_api.examples.weather_file emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.migration emod_api.migration.Migration emod_api.migration.MigrationFile emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) [rtd-command-info] start-time: 2020-10-06T18:44:48.578813Z, end-time: 2020-10-06T18:44:48.631248Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-10-06T18:44:48.764789Z, end-time: 2020-10-06T18:44:50.801608Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emod-api -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. 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. 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(/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/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 221--221 []\T1/ptm/m/it/10 filename: str = None\T1/ptm/m/n/10 , [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Overfull \hbox (82.64464pt too wide) in paragraph at lines 342--342 []\T1/ptm/m/it/10 path_to_schema\T1/pcr/m/n/10 ) Overfull \hbox (47.68495pt too wide) in paragraph at lines 352--352 []\T1/ptm/m/it/10 config\T1/pcr/m/n/10 ) Overfull \hbox (114.96484pt too wide) in paragraph at lines 366--366 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (95.13463pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 set_fn\T1/pcr/m/n/10 ) [4] Overfull \hbox (126.96484pt too wide) in paragraph at lines 392--392 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (103.63463pt too wide) in paragraph at lines 392--392 \T1/ptm/m/it/10 set_fn\T1/ptm/m/n/10 , Overfull \hbox (95.01491pt too wide) in paragraph at lines 392--392 \T1/ptm/m/it/10 con- Overfull \hbox (133.8048pt too wide) in paragraph at lines 392--392 \T1/ptm/m/it/10 fig_out_path\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 450--450 []\T1/ptm/m/it/10 configjson_path\T1/ptm/m/n/10 , [5] Overfull \hbox (63.52425pt too wide) in paragraph at lines 468--468 []\T1/ptm/m/it/10 start_config_dict\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 468--468 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (66.30441pt too wide) in paragraph at lines 477--477 []\T1/ptm/m/it/10 start_config_path\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 477--477 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (18.36475pt too wide) in paragraph at lines 486--486 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , Overfull \hbox (41.87448pt too wide) in paragraph at lines 486--486 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 495--495 []\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 543--545 []\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder( Underfull \hbox (badness 10000) in paragraph at lines 552--552 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 552--552 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 552--552 \T1/ptm/m/it/10 con-fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/p tm/m/it/10 '\T1/ptm/m/n/10 , [6] Overfull \hbox (28.28418pt too wide) in paragraph at lines 563--563 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (11.09424pt too wide) in paragraph at lines 563--563 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 563--563 \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 563--563 \T1/ptm/m/it/10 fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/ptm/m /it/10 '\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.config.from_schema:emod_api.config.fro m_schema.SchemaConfigBuilder' on page 7 undefined on input line 564. Underfull \hbox (badness 10000) in paragraph at lines 609--609 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , \ T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 609--609 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 forced_id=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 im- Underfull \hbox (badness 10000) in paragraph at lines 629--629 []\T1/ptm/m/it/10 tot_pop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 629--629 \T1/ptm/m/it/10 num_nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--635 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--635 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--635 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_synth_pop\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-plic- Underfull \hbox (badness 10000) in paragraph at lines 653--653 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 653--653 \T1/ptm/m/it/10 world grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 653--653 \T1/ptm/m/it/10 base_file=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-plic- LaTeX Warning: Hyper reference `emod_api.demographics.BaseInputFile:emod_api.de mographics.BaseInputFile.BaseInputFile' on page 7 undefined on input line 654. [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 812--812 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) [8] Overfull \hbox (13.07484pt too wide) in paragraph at lines 831--831 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 831--831 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 916--916 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tion_column_name: [9] Overfull \hbox (54.94496pt too wide) in paragraph at lines 931--932 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [10] Underfull \hbox (badness 10000) in paragraph at lines 979--979 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 979--979 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 979--979 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 994--995 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [11] Overfull \hbox (6.3048pt too wide) in paragraph at lines 1050--1050 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 1050--1050 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 1050--1050 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 1056--1056 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 1062--1062 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 1068--1068 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [12] Underfull \hbox (badness 10000) in paragraph at lines 1141--1143 []\T1/ptm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Overfull \hbox (25.80493pt too wide) in paragraph at lines 1179--1179 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1185--1185 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1191--1191 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1197--1197 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (88.30493pt too wide) in paragraph at lines 1229--1229 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- [13] Underfull \hbox (badness 10000) in paragraph at lines 1238--1241 []\T1/ptm/m/n/10 Requires con-fig en-ables in-fec-tiv-ity scal-ing: e.g.: `En-a ble_Infectivity_Scaling': 1, `En- Overfull \hbox (22.9045pt too wide) in paragraph at lines 1322--1322 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1328--1328 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1328--1328 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1334--1334 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1363--1364 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from [14] Underfull \hbox (badness 10000) in paragraph at lines 1383--1383 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu-tion\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1384--1385 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1411--1411 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1411--1411 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [15] Underfull \hbox 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LaTeX Warning: Reference `emod_api.weather:module-emod_api.weather' on page 31 undefined on input line 2839. LaTeX Warning: Reference `emod_api.weather.weather:module-emod_api.weather.weat her' on page 31 undefined on input line 2840. [31] No file institute-for-disease-modeling-emod-api.ind. (./institute-for-disease-modeling-emod-api.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emod-api.o ut' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emod-api.pdf (35 pages, 183028 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 31 undefined on input line 2794 Reference `emod_api.channelreports.channels:module-emod_api.channelreports.channels' on page 31 undefined on input line 2796 Reference `emod_api.channelreports:module-emod_api.channelreports' on page 31 undefined on input line 2795 Reference `emod_api.config.default_from_schema:module-emod_api.config.default_from_schema' on page 31 undefined on input line 2798 Reference `emod_api.config.default_from_schema_no_validation:module-emod_api.config.default_from_schema_no_validation' on page 31 undefined on input line 2799 Reference `emod_api.config.dtk_post_process_adhocevents:module-emod_api.config.dtk_post_process_adhocevents' on page 31 undefined on input line 2800 Reference `emod_api.config.dtk_pre_process_adhocevents:module-emod_api.config.dtk_pre_process_adhocevents' on page 31 undefined on input line 2801 Reference `emod_api.config.dtk_pre_process_w5ml:module-emod_api.config.dtk_pre_process_w5ml' on page 31 undefined on input line 2802 Reference `emod_api.config.from_overrides:module-emod_api.config.from_overrides' on page 31 undefined on input line 2803 Reference `emod_api.config.from_poi_and_binary:module-emod_api.config.from_poi_and_binary' on page 31 undefined on input line 2804 Reference `emod_api.config.from_schema:module-emod_api.config.from_schema' on page 31 undefined on input line 2805 Reference `emod_api.config.schema_to_config:module-emod_api.config.schema_to_config' on page 31 undefined on input line 2806 Reference `emod_api.config:module-emod_api.config' on page 31 undefined on input line 2797 Reference `emod_api.demographics.BaseInputFile:module-emod_api.demographics.BaseInputFile' on page 31 undefined on input line 2808 Reference `emod_api.demographics.Demographics:module-emod_api.demographics.Demographics' on page 31 undefined on input line 2809 Reference `emod_api.demographics.DemographicsGenerator:module-emod_api.demographics.DemographicsGenerator' on page 31 undefined on input line 2811 Reference `emod_api.demographics.DemographicsInputDataParsers:module-emod_api.demographics.DemographicsInputDataParsers' on page 31 undefined on input line 2812 Reference `emod_api.demographics.DemographicsTemplates:module-emod_api.demographics.DemographicsTemplates' on page 31 undefined on input line 2813 Reference `emod_api.demographics.Node:module-emod_api.demographics.Node' on page 31 undefined on input line 2814 Reference `emod_api.demographics.demographics_utils:module-emod_api.demographics.demographics_utils' on page 31 undefined on input line 2810 Reference `emod_api.demographics:module-emod_api.demographics' on page 31 undefined on input line 2807 Reference `emod_api.examples.insetchart:module-emod_api.examples.insetchart' on page 31 undefined on input line 2816 Reference `emod_api.examples.serialized_file_mc_to_sc:module-emod_api.examples.serialized_file_mc_to_sc' on page 31 undefined on input line 2817 Reference `emod_api.examples.spatial_report:module-emod_api.examples.spatial_report' on page 31 undefined on input line 2818 Reference `emod_api.examples.weather_file:module-emod_api.examples.weather_file' on page 31 undefined on input line 2819 Reference `emod_api.examples:module-emod_api.examples' on page 31 undefined on input line 2815 Reference `emod_api.interventions.import_pressure:module-emod_api.interventions.import_pressure' on page 31 undefined on input line 2821 Reference `emod_api.interventions.outbreak:module-emod_api.interventions.outbreak' on page 31 undefined on input line 2822 Reference `emod_api.interventions.simple_vaccine:module-emod_api.interventions.simple_vaccine' on page 31 undefined on input line 2823 Reference `emod_api.interventions:module-emod_api.interventions' on page 31 undefined on input line 2820 Reference `emod_api.migration.Migration:module-emod_api.migration.Migration' on page 31 undefined on input line 2825 Reference `emod_api.migration.MigrationFile:module-emod_api.migration.MigrationFile' on page 31 undefined on input line 2826 Reference `emod_api.migration:module-emod_api.migration' on page 31 undefined on input line 2824 Reference `emod_api.schema.dtk_post_process_schema:module-emod_api.schema.dtk_post_process_schema' on page 31 undefined on input line 2828 Reference `emod_api.schema.get_schema:module-emod_api.schema.get_schema' on page 31 undefined on input line 2829 Reference `emod_api.schema:module-emod_api.schema' on page 31 undefined on input line 2827 Reference `emod_api.schema_to_class:module-emod_api.schema_to_class' on page 31 undefined on input line 2830 Reference `emod_api.serialization.SerializedPopulation:module-emod_api.serialization.SerializedPopulation' on page 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`emod_api.weather:module-emod_api.weather' on page 31 undefined on input line 2839 Reference `emod_api:module-emod_api' on page 31 undefined on input line 2793 Latexmk: Summary of warnings: Latex failed to resolve 48 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 (372 entries accepted, 0 rejected). Sorting entries......done (3170 comparisons). Generating output file institute-for-disease-modeling-emod-api.ind....done (724 lines written, 0 warnings). Output written in institute-for-disease-modeling-emod-api.ind. Transcript written in institute-for-disease-modeling-emod-api.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-emod-api.aux' 'institute-for-disease-modeling-emod-api.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emod-api" "emod-api-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 221--221 []\T1/ptm/m/it/10 filename: str = None\T1/ptm/m/n/10 , [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Overfull \hbox (82.64464pt too wide) in paragraph at lines 342--342 []\T1/ptm/m/it/10 path_to_schema\T1/pcr/m/n/10 ) Overfull \hbox (47.68495pt too wide) in paragraph at lines 352--352 []\T1/ptm/m/it/10 config\T1/pcr/m/n/10 ) Overfull \hbox (114.96484pt too wide) in paragraph at lines 366--366 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (95.13463pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 set_fn\T1/pcr/m/n/10 ) [4] Overfull \hbox (126.96484pt too wide) in paragraph at lines 392--392 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (103.63463pt too wide) in paragraph at lines 392--392 \T1/ptm/m/it/10 set_fn\T1/ptm/m/n/10 , Overfull \hbox (95.01491pt too wide) in paragraph at lines 392--392 \T1/ptm/m/it/10 con- Overfull \hbox (133.8048pt too wide) in paragraph at lines 392--392 \T1/ptm/m/it/10 fig_out_path\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 450--450 []\T1/ptm/m/it/10 configjson_path\T1/ptm/m/n/10 , [5] Overfull \hbox (63.52425pt too wide) in paragraph at lines 468--468 []\T1/ptm/m/it/10 start_config_dict\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 468--468 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (66.30441pt too wide) in paragraph at lines 477--477 []\T1/ptm/m/it/10 start_config_path\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 477--477 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (18.36475pt too wide) in paragraph at lines 486--486 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , Overfull \hbox (41.87448pt too wide) in paragraph at lines 486--486 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 495--495 []\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 543--545 []\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder( Underfull \hbox (badness 10000) in paragraph at lines 552--552 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 552--552 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 552--552 \T1/ptm/m/it/10 con-fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/p tm/m/it/10 '\T1/ptm/m/n/10 , [6] Overfull \hbox (28.28418pt too wide) in paragraph at lines 563--563 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (11.09424pt too wide) in paragraph at lines 563--563 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 563--563 \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 563--563 \T1/ptm/m/it/10 fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/ptm/m /it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 609--609 []\T1/ptm/m/it/10 lat=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon=0\T1/ptm/m/n/10 , \ T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 609--609 \T1/ptm/m/it/10 name=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 forced_id=1\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 im- Underfull \hbox (badness 10000) in paragraph at lines 629--629 []\T1/ptm/m/it/10 tot_pop\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 629--629 \T1/ptm/m/it/10 num_nodes\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--635 []\T1/ptm/m/it/10 tot_pop=1000000.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--635 \T1/ptm/m/it/10 num_nodes=100\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 635--635 \T1/ptm/m/it/10 id_ref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 from_synth_pop\TS1/ptm /m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-plic- Underfull \hbox (badness 10000) in paragraph at lines 653--653 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , \T1/ptm/m/it/10 idref=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Gridded Underfull \hbox (badness 10000) in paragraph at lines 653--653 \T1/ptm/m/it/10 world grump2.5arcmin\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 653--653 \T1/ptm/m/it/10 base_file=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-plic- [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 812--812 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) [8] Overfull \hbox (13.07484pt too wide) in paragraph at lines 831--831 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 831--831 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 831--831 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 916--916 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tion_column_name: [9] Overfull \hbox (54.94496pt too wide) in paragraph at lines 931--932 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [10] Underfull \hbox (badness 10000) in paragraph at lines 979--979 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 979--979 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 979--979 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 994--995 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [11] Overfull \hbox (6.3048pt too wide) in paragraph at lines 1050--1050 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 1050--1050 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 1050--1050 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 1056--1056 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 1062--1062 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 1068--1068 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [12] Underfull \hbox (badness 10000) in paragraph at lines 1141--1143 []\T1/ptm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Overfull \hbox (25.80493pt too wide) in paragraph at lines 1179--1179 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1185--1185 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1191--1191 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1197--1197 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (88.30493pt too wide) in paragraph at lines 1229--1229 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- [13] Underfull \hbox (badness 10000) in paragraph at lines 1238--1241 []\T1/ptm/m/n/10 Requires con-fig en-ables in-fec-tiv-ity scal-ing: e.g.: `En-a ble_Infectivity_Scaling': 1, `En- Overfull \hbox (22.9045pt too wide) in paragraph at lines 1322--1322 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1328--1328 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1328--1328 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1334--1334 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1363--1364 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from [14] Underfull \hbox (badness 10000) in paragraph at lines 1383--1383 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu-tion\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1384--1385 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1411--1411 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1411--1411 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [15] Underfull \hbox (badness 10000) in paragraph at lines 1481--1481 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1481--1481 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1507--1507 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Overfull \hbox (19.2944pt too wide) in paragraph at lines 1557--1557 []\T1/ptm/m/it/10 filename_format\T1/ptm/m/n/10 , Overfull \hbox (3.61461pt too wide) in paragraph at lines 1557--1557 \T1/ptm/m/it/10 core_idx=0\T1/pcr/m/n/10 ) [16] [17] Underfull \hbox (badness 10000) in paragraph at lines 1684--1684 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1694--1694 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1712--1712 []\T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 num_nodes=100\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1712--1712 \T1/ptm/m/it/10 mig_factor=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T 1/ptm/m/n/10 , [18] Overfull \hbox (24.70302pt too wide) in paragraph at lines 1796--1796 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1880--1880 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1880--1880 \T1/ptm/m/it/10 num- Overfull \hbox (9.63463pt too wide) in paragraph at lines 1880--1880 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1892--1892 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1892--1892 \T1/ptm/m/it/10 num- Underfull \hbox 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dle\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1904--1904 []\T1/ptm/m/it/10 prop_values\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1904--1904 \T1/ptm/m/it/10 node\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1919--1919 []\T1/ptm/m/it/10 attribute\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 fil- Underfull \hbox (badness 10000) in paragraph at lines 1919--1919 \T1/ptm/m/it/10 ter_fct=>\T1/pcr/m/n/10 ) Overfull \hbox (28.96484pt too wide) in paragraph at lines 1953--1953 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , Overfull \hbox (10.35486pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 in- Overfull \hbox (14.23474pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 fec- Overfull \hbox (17.3048pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 tion\T1/ptm/m/n/10 , Overfull \hbox (55.52435pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 fct=>\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 []\T1/ptm/m/it/10 suid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 kwargs={}\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 copy_ind=None\T1/ptm/m/n/10 , [20] Underfull \hbox (badness 10000) in paragraph at lines 1981--1981 []\T1/ptm/m/it/10 name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 1987--1987 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Overfull \hbox (5.06378pt too wide) in paragraph at lines 1987--1987 \T1/ptm/m/it/10 rentlevel=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 dtk.nodes\TS1/ptm/m /it/10 '\T1/pcr/m/n/10 ) Underfull \hbox (badness 6493) in paragraph at lines 2085--2085 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2085--2085 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2085--2085 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : [21] Underfull \hbox (badness 10000) in paragraph at lines 2201--2201 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2201--2201 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2201--2201 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2201--2201 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2201--2201 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2215--2215 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2215--2215 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2215--2215 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2215--2215 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2215--2215 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2237--2237 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2237--2237 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2237--2237 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2237--2237 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2237--2237 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , [22] Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2259--2259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2322--2322 \T1/ptm/m/it/10 List[int] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data: Underfull \hbox (badness 10000) in paragraph at lines 2322--2322 \T1/ptm/m/it/10 numpy.array = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start: [23] [24] [25] [26] Underfull \hbox (badness 10000) in paragraph at lines 2744--2746 []\T1/ptm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 2747--2749 []\T1/ptm/m/n/10 python -m [27] [28] Chapter 2. [29] [30] Overfull \hbox (66.6225pt too wide) in paragraph at lines 2799--2800 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/1 0 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2800--2801 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2801--2802 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2810--2811 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2811--2812 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 2812--2813 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2813--2814 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2817--2818 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2821--2822 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2823--2824 []\T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2828--2829 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2834--2835 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2835--2836 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , [31] (./institute-for-disease-modeling-emod-api.ind [32] Overfull \hbox (30.30013pt too wide) in paragraph at lines 9--11 []\T1/pcr/m/n/10 add() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.seri alization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 11--13 []\T1/pcr/m/n/10 AddAgeDependentTransmission() Overfull \hbox (34.06111pt too wide) in paragraph at lines 11--13 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/pcr/m/n/10 AddIndividualPropertyAndHINT() Overfull \hbox (34.06111pt too wide) in paragraph at lines 13--15 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (123.59949pt too wide) in paragraph at lines 15--17 []\T1/pcr/m/n/10 addInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serial ization.SerializedPopulation.SerializedPopulation Overfull \hbox (8.17026pt too wide) in paragraph at lines 17--19 \T1/ptm/m/it/10 ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 19--21 []\T1/pcr/m/n/10 AddSeasonalForcing() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 19--21 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 AgeStructureUNWPP() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 21--23 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (37.49991pt too wide) in paragraph at lines 23--25 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Contents Overfull \hbox (32.4899pt too wide) in paragraph at lines 25--27 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (7.95116pt too wide) in paragraph at lines 27--29 \T1/ptm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 29--31 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 33--35 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 35--37 []\T1/pcr/m/n/10 apply_to_defaults_or_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 35--37 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 37--39 []\T1/pcr/m/n/10 arcsec_to_deg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 37--39 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 39--41 []\T1/pcr/m/n/10 as_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (41.61118pt too wide) in paragraph at lines 41--43 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Channel Overfull \hbox (37.71117pt too wide) in paragraph at lines 43--45 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 54--56 []\T1/pcr/m/n/10 BaseInputFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 54--56 \T1/ptm/m/it/10 emod_api.demographics.BaseInputFile\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 56--57 []\T1/pcr/m/n/10 basicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 58--60 []\T1/pcr/m/n/10 byte_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/pcr/m/n/10 changeSusceptibility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 63--65 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (68.83089pt too wide) in paragraph at lines 66--68 []\T1/pcr/m/n/10 channel_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 68--70 []\T1/pcr/m/n/10 ChannelReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (38.83089pt too wide) in paragraph at lines 70--72 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Overfull \hbox (29.59027pt too wide) in paragraph at lines 72--74 []\T1/pcr/m/n/10 chunk_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 74--76 []\T1/pcr/m/n/10 chunk_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile [33] Overfull \hbox (36.91025pt too wide) in paragraph at lines 78--80 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.EllZeeFour Overfull \hbox (21.29066pt too wide) in paragraph at lines 80--82 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Snappy Overfull \hbox (50.91016pt too wide) in paragraph at lines 82--84 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 84--86 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 86--88 []\T1/pcr/m/n/10 compressed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 88--90 []\T1/pcr/m/n/10 compression() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 90--92 []\T1/pcr/m/n/10 ConstantMortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 90--92 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (46.65079pt too wide) in paragraph at lines 92--94 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 94--95 []\T1/pcr/m/n/10 Coordinate \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 95--97 []\T1/pcr/m/n/10 createIndividual() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 95--97 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (12.84114pt too wide) in paragraph at lines 97--99 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Metadata Overfull \hbox (7.47115pt too wide) in paragraph at lines 99--101 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 106--108 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports .spatial.SpatialNode Underfull \hbox (badness 10000) in paragraph at lines 112--114 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 112--114 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 114--116 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 114--116 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/pcr/m/n/10 date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 118--119 []\T1/pcr/m/n/10 decode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (10.77174pt too wide) in paragraph at lines 119--121 []\T1/pcr/m/n/10 default_density \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 121--123 []\T1/pcr/m/n/10 default_population Underfull \hbox (badness 10000) in paragraph at lines 121--123 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node at- Underfull \hbox (badness 7291) in paragraph at lines 123--125 []\T1/pcr/m/n/10 DefaultSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 123--125 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 125--127 []\T1/pcr/m/n/10 Demographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 125--127 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 127--129 []\T1/pcr/m/n/10 DemographicsGenerator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 127--129 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 129--131 []\T1/pcr/m/n/10 DemographicsType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 129--131 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/pcr/m/n/10 dtk_to_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (56.83089pt too wide) in paragraph at lines 133--135 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 135--137 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/pcr/m/n/10 DtkFile.Contents \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 DtkFile.Objects \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 142--144 []\T1/pcr/m/n/10 DtkFileV1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 DtkFileV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/pcr/m/n/10 DtkFileV2.NodesV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 148--150 []\T1/pcr/m/n/10 DtkFileV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 150--152 []\T1/pcr/m/n/10 DtkFileV3.NodesV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 152--154 []\T1/pcr/m/n/10 DtkFileV4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/pcr/m/n/10 DtkHeader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 156--157 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\T1/pcr/m/n/10 duplicate_nodeID_check() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 161--163 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/pcr/m/n/10 EllZeeFour \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [34] Overfull \hbox (64.1225pt too wide) in paragraph at lines 180--181 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 182--183 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 184--185 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (10.1225pt too wide) in paragraph at lines 202--203 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils Overfull \hbox (28.1225pt too wide) in paragraph at lines 204--205 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 206--207 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 208--209 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (22.1225pt too wide) in paragraph at lines 216--217 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc Overfull \hbox (4.1225pt too wide) in paragraph at lines 238--239 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 252--253 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 264--266 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 264--266 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.demographics.DemographicsTe mplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 266--268 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 272--274 []\T1/pcr/m/n/10 fill_nodes_legacy() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 272--274 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (4.62106pt too wide) in paragraph at lines 274--276 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict [35] Overfull \hbox (36.30013pt too wide) in paragraph at lines 276--278 []\T1/pcr/m/n/10 find() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 278--280 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (81.59949pt too wide) in paragraph at lines 280--282 []\T1/pcr/m/n/10 flush() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 284--286 []\T1/pcr/m/n/10 from_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 284--286 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 288--290 []\T1/pcr/m/n/10 from_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 288--290 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.w eather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 292--294 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 292--294 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 294--296 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 294--296 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 296--298 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 296--298 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 298--300 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 300--302 []\T1/pcr/m/n/10 fromBasicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 300--302 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 302--304 []\T1/pcr/m/n/10 FullRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 302--304 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 307--309 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (80.97084pt too wide) in paragraph at lines 309--311 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.BaseInputFile.BaseInputFile Overfull \hbox (85.96114pt too wide) in paragraph at lines 311--313 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 313--315 []\T1/pcr/m/n/10 generate_headers() Overfull \hbox (29.07082pt too wide) in paragraph at lines 313--315 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.BaseInputFile.BaseInputFi le Underfull \hbox (badness 10000) in paragraph at lines 315--317 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 315--317 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (173.87039pt too wide) in paragraph at lines 317--319 []\T1/pcr/m/n/10 generate_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 319--321 []\T1/pcr/m/n/10 generatePopulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 319--321 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 321--323 []\T1/pcr/m/n/10 get_class_with_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Overfull \hbox (62.64088pt too wide) in paragraph at lines 323--325 \T1/ptm/m/it/10 mod-ule emod_api.config.default_from_schema_no_validation\T1/pt m/m/n/10 ), Overfull \hbox (55.96114pt too wide) in paragraph at lines 325--327 []\T1/pcr/m/n/10 get_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 327--329 []\T1/pcr/m/n/10 get_node_ids_from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 327--329 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 329--331 []\T1/pcr/m/n/10 get_node_pops_from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (105.59949pt too wide) in paragraph at lines 331--333 []\T1/pcr/m/n/10 get_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializa tion.SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 333--335 []\T1/pcr/m/n/10 get_xpix_ypix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 335--337 []\T1/pcr/m/n/10 getAttributeValues() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 335--337 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 337--339 []\T1/pcr/m/n/10 getIndividualsWithProperty() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 337--339 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 339--341 []\T1/pcr/m/n/10 getNextIndividualSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 339--341 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 341--343 []\T1/pcr/m/n/10 getNextInfectionSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 341--343 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 343--345 []\T1/pcr/m/n/10 getPropertyValues2() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 343--345 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (26.83089pt too wide) in paragraph at lines 349--351 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 359--361 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports.s patial.SpatialNode Underfull \hbox (badness 7308) in paragraph at lines 361--362 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather. WeatherNode prop- Overfull \hbox (6.84114pt too wide) in paragraph at lines 362--364 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata Overfull \hbox (1.47115pt too wide) in paragraph at lines 364--366 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 366--368 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 366--368 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class [36] Underfull \hbox (badness 10000) in paragraph at lines 368--370 []\T1/pcr/m/n/10 InitAgeUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 368--370 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 370--372 []\T1/pcr/m/n/10 InitRiskUniform() \T1/ptm/m/n/10 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382--384 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/pcr/m/n/10 loadInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 384--386 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 392--394 []\T1/pcr/m/n/10 make_config_from_poi() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 392--394 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 394--396 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 394--396 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 396--398 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lines 441--442 []| \T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 445--446 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , [37] Overfull \hbox (2.6225pt too wide) in paragraph at lines 446--447 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileTools\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 447--448 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 448--449 []| \T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 454--456 []\T1/pcr/m/n/10 MortalityRateByAge() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 454--456 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 456--458 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 461--463 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 461--463 \T1/ptm/m/it/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 463--465 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 465--467 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 465--467 \T1/ptm/m/it/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 467--469 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 469--471 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 471--473 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (67.96114pt too wide) in paragraph at lines 474--476 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograp hics.Demographics.Demographics Overfull \hbox (32.8303pt too wide) in paragraph at lines 476--478 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 480--482 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 482--484 []\T1/pcr/m/n/10 node_ID_from_lat_long() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 482--484 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (55.96114pt too wide) in paragraph at lines 484--486 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Demographics.Demographics Overfull \hbox (20.8303pt too wide) in paragraph at lines 486--488 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialrep orts.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 488--490 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 490--491 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather Underfull \hbox (badness 10000) in paragraph at lines 491--493 []\T1/pcr/m/n/10 nodeid_from_lat_lon() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 5802) in paragraph at lines 493--495 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Overfull \hbox (81.59949pt too wide) in paragraph at lines 495--497 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Overfull \hbox (2.8303pt too wide) in paragraph at lines 497--499 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreport s.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 500--501 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weath er.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 501--503 []\T1/pcr/m/n/10 nodes_for_DTK() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 503--505 []\T1/pcr/m/n/10 NoInitialPrevalence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 503--505 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 505--507 []\T1/pcr/m/n/10 NoMigrationHeterogeneity() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 505--507 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 507--509 []\T1/pcr/m/n/10 NoRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 507--509 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 509--511 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (31.71117pt too wide) in paragraph at lines 511--513 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 513--515 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 515--517 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 520--522 []\T1/pcr/m/n/10 printParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 520--522 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 524--526 []\T1/pcr/m/n/10 provenance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Overfull \hbox (15.58075pt too wide) in paragraph at lines 529--531 []\T1/pcr/m/n/10 rates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Mig rationFile.MigrationFile Overfull \hbox (1.84042pt too wide) in paragraph at lines 531--532 []\T1/pcr/m/n/10 read() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.dtkFileTools\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 533--535 []\T1/pcr/m/n/10 recurser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 533--535 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 535--537 []\T1/pcr/m/n/10 removeIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 535--537 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 removeNumberIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 537--539 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), [38] Overfull \hbox (56.83089pt too wide) in paragraph at lines 539--541 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 541--543 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 543--545 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 545--547 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Overfull \hbox (4.77174pt too wide) in paragraph at lines 547--549 []\T1/pcr/m/n/10 res_in_degrees \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demogr aphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 553--555 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 555--557 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 557--559 []\T1/pcr/m/n/10 serialized_dtk_to_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 557--559 \T1/ptm/m/it/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 559--561 []\T1/pcr/m/n/10 SerializedPopulation \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 559--561 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 561--563 []\T1/pcr/m/n/10 SerialObject \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 563--565 []\T1/pcr/m/n/10 set_age_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 563--565 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 565--567 []\T1/pcr/m/n/10 set_age_simple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 565--567 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 567--569 []\T1/pcr/m/n/10 set_boxcar_seasonal() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 567--569 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 569--571 []\T1/pcr/m/n/10 set_demog_distributions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 569--571 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in 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graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 579--581 []\T1/pcr/m/n/10 set_risk_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 579--581 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Overfull \hbox (16.62106pt too wide) in paragraph at lines 581--583 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_t o_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 583--585 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 583--585 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 585--587 []\T1/pcr/m/n/10 set_static_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 585--587 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 587--589 []\T1/pcr/m/n/10 set_suscept_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 587--589 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 589--591 []\T1/pcr/m/n/10 set_suscept_simple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 589--591 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 591--593 []\T1/pcr/m/n/10 setAttribute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 591--593 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 593--595 []\T1/pcr/m/n/10 setAttributes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 593--595 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 595--597 []\T1/pcr/m/n/10 SetDefaultFromTemplate() Overfull \hbox (34.06111pt too wide) in paragraph at lines 595--597 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 597--599 []\T1/pcr/m/n/10 SetDefaultIndividualAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 597--599 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 599--601 []\T1/pcr/m/n/10 SetDefaultIndividualProperties() Overfull \hbox (34.06111pt too wide) in paragraph at lines 599--601 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 601--603 []\T1/pcr/m/n/10 SetDefaultNodeAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 601--603 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 603--605 []\T1/pcr/m/n/10 SetDefaultProperties() Overfull \hbox (34.06111pt too wide) in paragraph at lines 603--605 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 605--607 []\T1/pcr/m/n/10 SetDefaultPropertiesFertMort() Overfull \hbox (34.06111pt too wide) in paragraph at lines 605--607 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 607--609 []\T1/pcr/m/n/10 SetIndividualAttributtsWithFertMort() Overfull \hbox (34.06111pt too wide) in paragraph at lines 607--609 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 609--611 []\T1/pcr/m/n/10 setIndividualPropertyInfections() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (25.39023pt too wide) in paragraph at lines 609--611 \T1/ptm/m/it/10 mod-ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 611--613 []\T1/pcr/m/n/10 SetMinimalNodeAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 611--613 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 613--615 []\T1/pcr/m/n/10 SetNodeDefaultFromTemplate() Overfull \hbox (34.06111pt too wide) in paragraph at lines 613--615 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 615--617 []\T1/pcr/m/n/10 SetOverdispersion() Overfull \hbox (34.06111pt too wide) 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paragraph at lines 635--637 []\T1/pcr/m/n/10 start_time() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (91.05998pt too wide) in paragraph at lines 637--639 []\T1/pcr/m/n/10 STATIC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.D emographicsGenerator.DemographicsType Overfull \hbox (44.83089pt too wide) in paragraph at lines 639--641 []\T1/pcr/m/n/10 step_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (13.71117pt too wide) in paragraph at lines 641--643 []\T1/pcr/m/n/10 step_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelre ports.channels.Header Overfull \hbox (50.83089pt too wide) in paragraph at lines 648--650 []\T1/pcr/m/n/10 time_stamp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (19.71117pt too wide) in paragraph at lines 650--652 []\T1/pcr/m/n/10 time_stamp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr 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(\T1/ptm/m/it/10 emod_api.examples.spatial_ report.Coordinate [40] [41]) (./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/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emod-api.pdf (45 pages, 217995 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. 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Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 916--916 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 916--916 \T1/ptm/m/it/10 tion_column_name: [9] Overfull \hbox (54.94496pt too wide) in paragraph at lines 931--932 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [10] Underfull \hbox (badness 10000) in paragraph at lines 979--979 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 979--979 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 979--979 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 979--979 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 979--979 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 994--995 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [11] Overfull \hbox (6.3048pt too wide) in paragraph at lines 1050--1050 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 1050--1050 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 1050--1050 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 1056--1056 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 1062--1062 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 1062--1062 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 1068--1068 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 1068--1068 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [12] Underfull \hbox (badness 10000) in paragraph at lines 1141--1143 []\T1/ptm/m/n/10 json ob-ject aka python dict that can be di-rectly passed to D e-mo-graph- Overfull \hbox (25.80493pt too wide) in paragraph at lines 1179--1179 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Overfull \hbox (46.30493pt too wide) in paragraph at lines 1185--1185 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (42.23488pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 mean- Overfull \hbox (44.91478pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 AgeAt- Overfull \hbox (28.90492pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 In- Overfull \hbox (32.23474pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 fec- Overfull \hbox (58.0548pt too wide) in paragraph at lines 1185--1185 \T1/ptm/m/it/10 tion=2.5\T1/pcr/m/n/10 ) Overfull \hbox (55.80493pt too wide) in paragraph at lines 1191--1191 []\T1/ptm/m/it/10 demog\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1197--1197 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (88.30493pt too wide) in paragraph at lines 1229--1229 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Crude- Overfull \hbox (124.88449pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 BirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 1229--1229 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 \T1/ptm/m/it/10 start=100\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1235--1235 \T1/ptm/m/it/10 end=330\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fac- [13] Underfull \hbox (badness 10000) in paragraph at lines 1238--1241 []\T1/ptm/m/n/10 Requires con-fig en-ables in-fec-tiv-ity scal-ing: e.g.: `En-a ble_Infectivity_Scaling': 1, `En- Overfull \hbox (22.9045pt too wide) in paragraph at lines 1322--1322 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1328--1328 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1328--1328 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1334--1334 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1363--1364 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from [14] Underfull \hbox (badness 10000) in paragraph at lines 1383--1383 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu-tion\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1384--1385 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1411--1411 []\T1/ptm/m/it/10 demog\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1411--1411 \T1/ptm/m/it/10 fn\T1/ptm/m/n/10 , [15] Underfull \hbox (badness 10000) in paragraph at lines 1481--1481 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (28.70406pt too wide) in paragraph at lines 1481--1481 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Overfull \hbox (34.70406pt too wide) in paragraph at lines 1507--1507 \T1/ptm/m/it/10 use_existing=False\T1/pcr/m/n/10 ) Overfull \hbox (19.2944pt too wide) in paragraph at lines 1557--1557 []\T1/ptm/m/it/10 filename_format\T1/ptm/m/n/10 , Overfull \hbox (3.61461pt too wide) in paragraph at lines 1557--1557 \T1/ptm/m/it/10 core_idx=0\T1/pcr/m/n/10 ) [16] [17] Underfull \hbox (badness 10000) in paragraph at lines 1684--1684 \T1/ptm/m/it/10 ef-fi-cacy=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1694--1694 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- Underfull \hbox (badness 10000) in paragraph at lines 1712--1712 []\T1/ptm/m/it/10 pop=1000000.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 num_nodes=100\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1712--1712 \T1/ptm/m/it/10 mig_factor=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 frac_rural=0.3\T 1/ptm/m/n/10 , [18] Overfull \hbox (24.70302pt too wide) in paragraph at lines 1796--1796 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1880--1880 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1880--1880 \T1/ptm/m/it/10 num- Overfull \hbox (9.63463pt too wide) in paragraph at lines 1880--1880 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1892--1892 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1892--1892 \T1/ptm/m/it/10 num- Underfull \hbox (badness 10000) in paragraph at lines 1892--1892 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1892--1892 \T1/ptm/m/it/10 prop-er-ties\T1/ptm/m/n/10 , [19] Overfull \hbox (45.96484pt too wide) in paragraph at lines 1898--1898 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Overfull \hbox (22.35486pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 in- Overfull \hbox (22.35486pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 di- Overfull \hbox (26.7948pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 vid- Overfull \hbox (43.74474pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 ual_idx\T1/ptm/m/n/10 , Overfull \hbox (58.84471pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 prop_value\T1/ptm/m/n/10 , Overfull \hbox (29.57497pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 han- Overfull \hbox (29.46484pt too wide) in paragraph at lines 1898--1898 \T1/ptm/m/it/10 dle\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1904--1904 []\T1/ptm/m/it/10 prop_values\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1904--1904 \T1/ptm/m/it/10 node\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1919--1919 []\T1/ptm/m/it/10 attribute\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 fil- Underfull \hbox (badness 10000) in paragraph at lines 1919--1919 \T1/ptm/m/it/10 ter_fct=>\T1/pcr/m/n/10 ) Overfull \hbox (28.96484pt too wide) in paragraph at lines 1953--1953 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , Overfull \hbox (10.35486pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 in- Overfull \hbox (14.23474pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 fec- Overfull \hbox (17.3048pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 tion\T1/ptm/m/n/10 , Overfull \hbox (55.52435pt too wide) in paragraph at lines 1953--1953 \T1/ptm/m/it/10 fct=>\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 []\T1/ptm/m/it/10 suid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 kwargs={}\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 copy_ind=None\T1/ptm/m/n/10 , [20] Underfull \hbox (badness 10000) in paragraph at lines 1981--1981 []\T1/ptm/m/it/10 name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 1987--1987 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Overfull \hbox (5.06378pt too wide) in paragraph at lines 1987--1987 \T1/ptm/m/it/10 rentlevel=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 dtk.nodes\TS1/ptm/m /it/10 '\T1/pcr/m/n/10 ) Underfull \hbox (badness 6493) in paragraph at lines 2085--2085 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2085--2085 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2085--2085 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : [21] Underfull \hbox (badness 10000) in paragraph at lines 2201--2201 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2201--2201 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2201--2201 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2201--2201 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2201--2201 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2215--2215 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2215--2215 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2215--2215 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2215--2215 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2215--2215 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2237--2237 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2237--2237 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2237--2237 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2237--2237 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2237--2237 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , [22] Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 2259--2259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 2259--2259 \T1/ptm/m/it/10 06 18:44:46 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 2259--2259 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2322--2322 \T1/ptm/m/it/10 List[int] = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data: Underfull \hbox (badness 10000) in paragraph at lines 2322--2322 \T1/ptm/m/it/10 numpy.array = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start: [23] [24] [25] [26] Underfull \hbox (badness 10000) in paragraph at lines 2744--2746 []\T1/ptm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 2747--2749 []\T1/ptm/m/n/10 python -m [27] [28] Chapter 2. [29] [30] Overfull \hbox (66.6225pt too wide) in paragraph at lines 2799--2800 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/1 0 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2800--2801 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2801--2802 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2810--2811 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2811--2812 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 2812--2813 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2813--2814 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2817--2818 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2821--2822 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2823--2824 []\T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2828--2829 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2834--2835 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2835--2836 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , [31] (./institute-for-disease-modeling-emod-api.ind [32] Overfull \hbox (30.30013pt too wide) in paragraph at lines 9--11 []\T1/pcr/m/n/10 add() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.seri alization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 11--13 []\T1/pcr/m/n/10 AddAgeDependentTransmission() Overfull \hbox (34.06111pt too wide) in paragraph at lines 11--13 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/pcr/m/n/10 AddIndividualPropertyAndHINT() Overfull \hbox (34.06111pt too wide) in paragraph at lines 13--15 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Overfull \hbox (123.59949pt too wide) in paragraph at lines 15--17 []\T1/pcr/m/n/10 addInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serial ization.SerializedPopulation.SerializedPopulation Overfull \hbox (8.17026pt too wide) in paragraph at lines 17--19 \T1/ptm/m/it/10 ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 19--21 []\T1/pcr/m/n/10 AddSeasonalForcing() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 19--21 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 AgeStructureUNWPP() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 21--23 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (37.49991pt too wide) in paragraph at lines 23--25 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Contents Overfull \hbox (32.4899pt too wide) in paragraph at lines 25--27 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (7.95116pt too wide) in paragraph at lines 27--29 \T1/ptm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 29--31 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 33--35 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 35--37 []\T1/pcr/m/n/10 apply_to_defaults_or_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 35--37 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 37--39 []\T1/pcr/m/n/10 arcsec_to_deg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 37--39 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 39--41 []\T1/pcr/m/n/10 as_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (41.61118pt too wide) in paragraph at lines 41--43 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Channel Overfull \hbox (37.71117pt too wide) in paragraph at lines 43--45 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 54--56 []\T1/pcr/m/n/10 BaseInputFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 54--56 \T1/ptm/m/it/10 emod_api.demographics.BaseInputFile\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 56--57 []\T1/pcr/m/n/10 basicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 58--60 []\T1/pcr/m/n/10 byte_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/pcr/m/n/10 changeSusceptibility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 63--65 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (68.83089pt too wide) in paragraph at lines 66--68 []\T1/pcr/m/n/10 channel_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 68--70 []\T1/pcr/m/n/10 ChannelReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (38.83089pt too wide) in paragraph at lines 70--72 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Overfull \hbox (29.59027pt too wide) in paragraph at lines 72--74 []\T1/pcr/m/n/10 chunk_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 74--76 []\T1/pcr/m/n/10 chunk_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile [33] Overfull \hbox (36.91025pt too wide) in paragraph at lines 78--80 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.EllZeeFour Overfull \hbox (21.29066pt too wide) in paragraph at lines 80--82 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Snappy Overfull \hbox (50.91016pt too wide) in paragraph at lines 82--84 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 84--86 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 86--88 []\T1/pcr/m/n/10 compressed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 88--90 []\T1/pcr/m/n/10 compression() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 90--92 []\T1/pcr/m/n/10 ConstantMortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 90--92 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (46.65079pt too wide) in paragraph at lines 92--94 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 94--95 []\T1/pcr/m/n/10 Coordinate \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 95--97 []\T1/pcr/m/n/10 createIndividual() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 95--97 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (12.84114pt too wide) in paragraph at lines 97--99 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Metadata Overfull \hbox (7.47115pt too wide) in paragraph at lines 99--101 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 106--108 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports .spatial.SpatialNode Underfull \hbox (badness 10000) in paragraph at lines 112--114 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 112--114 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 114--116 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 114--116 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/pcr/m/n/10 date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 118--119 []\T1/pcr/m/n/10 decode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (10.77174pt too wide) in paragraph at lines 119--121 []\T1/pcr/m/n/10 default_density \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 121--123 []\T1/pcr/m/n/10 default_population Underfull \hbox (badness 10000) in paragraph at lines 121--123 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node at- Underfull \hbox (badness 7291) in paragraph at lines 123--125 []\T1/pcr/m/n/10 DefaultSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 123--125 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 125--127 []\T1/pcr/m/n/10 Demographics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 125--127 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 127--129 []\T1/pcr/m/n/10 DemographicsGenerator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 127--129 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 129--131 []\T1/pcr/m/n/10 DemographicsType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 129--131 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/pcr/m/n/10 dtk_to_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (56.83089pt too wide) in paragraph at lines 133--135 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 135--137 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/pcr/m/n/10 DtkFile.Contents \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 DtkFile.Objects \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 142--144 []\T1/pcr/m/n/10 DtkFileV1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 DtkFileV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/pcr/m/n/10 DtkFileV2.NodesV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 148--150 []\T1/pcr/m/n/10 DtkFileV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 150--152 []\T1/pcr/m/n/10 DtkFileV3.NodesV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 152--154 []\T1/pcr/m/n/10 DtkFileV4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 154--156 []\T1/pcr/m/n/10 DtkHeader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 156--157 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\T1/pcr/m/n/10 duplicate_nodeID_check() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 161--163 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/pcr/m/n/10 EllZeeFour \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [34] Overfull \hbox (64.1225pt too wide) in paragraph at lines 180--181 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 182--183 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 184--185 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (10.1225pt too wide) in paragraph at lines 202--203 []\T1/pcr/m/n/10 emod_api.demographics.demographics_utils Overfull \hbox (28.1225pt too wide) in paragraph at lines 204--205 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 206--207 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 208--209 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (22.1225pt too wide) in paragraph at lines 216--217 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc Overfull \hbox (4.1225pt too wide) in paragraph at lines 238--239 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 252--253 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 264--266 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 264--266 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.demographics.DemographicsTe mplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 266--268 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 272--274 []\T1/pcr/m/n/10 fill_nodes_legacy() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 272--274 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (4.62106pt too wide) in paragraph at lines 274--276 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict [35] Overfull \hbox (36.30013pt too wide) in paragraph at lines 276--278 []\T1/pcr/m/n/10 find() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 278--280 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (81.59949pt too wide) in paragraph at lines 280--282 []\T1/pcr/m/n/10 flush() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 284--286 []\T1/pcr/m/n/10 from_csv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 284--286 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 288--290 []\T1/pcr/m/n/10 from_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 288--290 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.w eather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 292--294 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 292--294 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 294--296 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 294--296 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 296--298 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 296--298 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 298--300 []\T1/pcr/m/n/10 from_synth_pop() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 300--302 []\T1/pcr/m/n/10 fromBasicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 300--302 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 302--304 []\T1/pcr/m/n/10 FullRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 302--304 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 307--309 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (80.97084pt too wide) in paragraph at lines 309--311 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.BaseInputFile.BaseInputFile Overfull \hbox (85.96114pt too wide) in paragraph at lines 311--313 []\T1/pcr/m/n/10 generate_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 313--315 []\T1/pcr/m/n/10 generate_headers() Overfull \hbox (29.07082pt too wide) in paragraph at lines 313--315 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.BaseInputFile.BaseInputFi le Underfull \hbox (badness 10000) in paragraph at lines 315--317 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 315--317 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (173.87039pt too wide) in paragraph at lines 317--319 []\T1/pcr/m/n/10 generate_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 319--321 []\T1/pcr/m/n/10 generatePopulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 319--321 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 321--323 []\T1/pcr/m/n/10 get_class_with_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Overfull \hbox (62.64088pt too wide) in paragraph at lines 323--325 \T1/ptm/m/it/10 mod-ule emod_api.config.default_from_schema_no_validation\T1/pt m/m/n/10 ), Overfull \hbox (55.96114pt too wide) in paragraph at lines 325--327 []\T1/pcr/m/n/10 get_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 327--329 []\T1/pcr/m/n/10 get_node_ids_from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 327--329 \T1/ptm/m/it/10 emod_api.demographics.Demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 329--331 []\T1/pcr/m/n/10 get_node_pops_from_params() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (105.59949pt too wide) in paragraph at lines 331--333 []\T1/pcr/m/n/10 get_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializa tion.SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 333--335 []\T1/pcr/m/n/10 get_xpix_ypix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 335--337 []\T1/pcr/m/n/10 getAttributeValues() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 335--337 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 337--339 []\T1/pcr/m/n/10 getIndividualsWithProperty() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 337--339 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 339--341 []\T1/pcr/m/n/10 getNextIndividualSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 339--341 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 341--343 []\T1/pcr/m/n/10 getNextInfectionSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 341--343 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 343--345 []\T1/pcr/m/n/10 getPropertyValues2() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 343--345 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (26.83089pt too wide) in paragraph at lines 349--351 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 359--361 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports.s patial.SpatialNode Underfull \hbox (badness 7308) in paragraph at lines 361--362 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather. WeatherNode prop- Overfull \hbox (6.84114pt too wide) in paragraph at lines 362--364 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata Overfull \hbox (1.47115pt too wide) in paragraph at lines 364--366 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 366--368 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 366--368 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class [36] Underfull \hbox (badness 10000) in paragraph at lines 368--370 []\T1/pcr/m/n/10 InitAgeUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 368--370 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 370--372 []\T1/pcr/m/n/10 InitRiskUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 370--372 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 372--374 []\T1/pcr/m/n/10 InitSusceptConstant() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 372--374 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (20.8303pt too wide) in paragraph at lines 374--376 []\T1/pcr/m/n/10 interval() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialrep orts.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 380--382 []\T1/pcr/m/n/10 lat_lon_from_nodeid() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 382--384 []\T1/pcr/m/n/10 load_default_config_as_rod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (31.30106pt too wide) in paragraph at lines 382--384 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/pcr/m/n/10 loadInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 384--386 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 392--394 []\T1/pcr/m/n/10 make_config_from_poi() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 392--394 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 394--396 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 394--396 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 396--398 []\T1/pcr/m/n/10 make_config_from_poi_and_config_file() Overfull \hbox (16.3614pt too wide) in paragraph at lines 396--398 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 398--400 []\T1/pcr/m/n/10 make_config_from_poi_and_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (3.35153pt too wide) in paragraph at lines 398--400 \T1/ptm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 401--402 []\T1/pcr/m/n/10 metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather Underfull \hbox (badness 10000) in paragraph at lines 403--405 []\T1/pcr/m/n/10 MigrationFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (2.6225pt too wide) in paragraph at lines 411--412 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 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lines 456--458 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 461--463 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 461--463 \T1/ptm/m/it/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 463--465 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 465--467 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 465--467 \T1/ptm/m/it/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 467--469 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 469--471 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 471--473 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (67.96114pt too wide) in paragraph at lines 474--476 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograp hics.Demographics.Demographics Overfull \hbox (32.8303pt too wide) in paragraph at lines 476--478 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 480--482 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 482--484 []\T1/pcr/m/n/10 node_ID_from_lat_long() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 482--484 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (55.96114pt too wide) in paragraph at lines 484--486 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Demographics.Demographics Overfull \hbox (20.8303pt too wide) in paragraph at lines 486--488 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialrep orts.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 488--490 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 490--491 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather Underfull \hbox (badness 10000) in paragraph at lines 491--493 []\T1/pcr/m/n/10 nodeid_from_lat_lon() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 5802) in paragraph at lines 493--495 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 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Underfull \hbox (badness 10000) in paragraph at lines 505--507 []\T1/pcr/m/n/10 NoMigrationHeterogeneity() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 505--507 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 507--509 []\T1/pcr/m/n/10 NoRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 507--509 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 509--511 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (31.71117pt too wide) in paragraph at lines 511--513 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 513--515 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 515--517 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 520--522 []\T1/pcr/m/n/10 printParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 520--522 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 524--526 []\T1/pcr/m/n/10 provenance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Overfull \hbox (15.58075pt too wide) in paragraph at lines 529--531 []\T1/pcr/m/n/10 rates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.Mig rationFile.MigrationFile Overfull \hbox (1.84042pt too wide) in paragraph at lines 531--532 []\T1/pcr/m/n/10 read() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.dtkFileTools\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 533--535 []\T1/pcr/m/n/10 recurser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 533--535 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 535--537 []\T1/pcr/m/n/10 removeIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 535--537 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 removeNumberIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 537--539 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), [38] Overfull \hbox (56.83089pt too wide) in paragraph at lines 539--541 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 541--543 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 543--545 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 545--547 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Overfull \hbox (4.77174pt too wide) in paragraph at lines 547--549 []\T1/pcr/m/n/10 res_in_degrees \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demogr aphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 553--555 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 555--557 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 557--559 []\T1/pcr/m/n/10 serialized_dtk_to_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 557--559 \T1/ptm/m/it/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 559--561 []\T1/pcr/m/n/10 SerializedPopulation \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 559--561 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 561--563 []\T1/pcr/m/n/10 SerialObject \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 563--565 []\T1/pcr/m/n/10 set_age_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 563--565 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 565--567 []\T1/pcr/m/n/10 set_age_simple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 565--567 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 567--569 []\T1/pcr/m/n/10 set_boxcar_seasonal() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 567--569 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 569--571 []\T1/pcr/m/n/10 set_demog_distributions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 569--571 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 571--573 []\T1/pcr/m/n/10 set_growing_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 571--573 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 573--575 []\T1/pcr/m/n/10 set_immune_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 573--575 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 575--577 []\T1/pcr/m/n/10 set_init_prev() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 575--577 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (173.87039pt too wide) in paragraph at lines 577--579 []\T1/pcr/m/n/10 set_resolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 579--581 []\T1/pcr/m/n/10 set_risk_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 579--581 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Overfull \hbox (16.62106pt too wide) in paragraph at lines 581--583 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_t o_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 583--585 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 583--585 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 585--587 []\T1/pcr/m/n/10 set_static_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 585--587 \T1/ptm/m/it/10 emod_api.demographics.demographics_utils\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 587--589 []\T1/pcr/m/n/10 set_suscept_complex() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 587--589 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 589--591 []\T1/pcr/m/n/10 set_suscept_simple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 589--591 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 591--593 []\T1/pcr/m/n/10 setAttribute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 591--593 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 593--595 []\T1/pcr/m/n/10 setAttributes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 593--595 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 595--597 []\T1/pcr/m/n/10 SetDefaultFromTemplate() Overfull \hbox (34.06111pt too wide) in paragraph at lines 595--597 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 597--599 []\T1/pcr/m/n/10 SetDefaultIndividualAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 597--599 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 599--601 []\T1/pcr/m/n/10 SetDefaultIndividualProperties() Overfull \hbox (34.06111pt too wide) in paragraph at lines 599--601 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 601--603 []\T1/pcr/m/n/10 SetDefaultNodeAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 601--603 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 603--605 []\T1/pcr/m/n/10 SetDefaultProperties() Overfull \hbox (34.06111pt too wide) in paragraph at lines 603--605 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 605--607 []\T1/pcr/m/n/10 SetDefaultPropertiesFertMort() Overfull \hbox (34.06111pt too wide) in paragraph at lines 605--607 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 607--609 []\T1/pcr/m/n/10 SetIndividualAttributtsWithFertMort() Overfull \hbox (34.06111pt too wide) in paragraph at lines 607--609 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 609--611 []\T1/pcr/m/n/10 setIndividualPropertyInfections() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (25.39023pt too wide) in paragraph at lines 609--611 \T1/ptm/m/it/10 mod-ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 611--613 []\T1/pcr/m/n/10 SetMinimalNodeAttributes() Overfull \hbox (34.06111pt too wide) in paragraph at lines 611--613 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 613--615 []\T1/pcr/m/n/10 SetNodeDefaultFromTemplate() Overfull \hbox (34.06111pt too wide) in paragraph at lines 613--615 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Demographics.Demographics Underfull \hbox (badness 10000) in paragraph at lines 615--617 []\T1/pcr/m/n/10 SetOverdispersion() Overfull \hbox (34.06111pt too wide) 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(\T1/ptm/m/it/10 emod_api.examples.spatial_ report.Coordinate [40] [41]) (./institute-for-disease-modeling-emod-api.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emod-api.pdf (45 pages, 218062 bytes). 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