Read the Docs build information
Build id: 501649
Project: institute-for-disease-modeling-emod-api
Version: latest
Commit: 8415f94fbde98d70c15b13842934c61eeaaf1156
Date: 2020-12-08T20:18:53.502429Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-12-08T20:18:54.975566Z, end-time: 2020-12-08T20:18:56.067699Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emod-api.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2020-12-08T20:18:56.577281Z, end-time: 2020-12-08T20:18:56.728097Z, 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 <new-branch-name>

HEAD is now at 8415f94 Fixes build breaks in #163 (#164)

[rtd-command-info] start-time: 2020-12-08T20:18:56.913449Z, end-time: 2020-12-08T20:18:56.965656Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-12-08T20:18:58.432138Z, end-time: 2020-12-08T20:19:04.310387Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-12-08T20:19:04.424999Z, end-time: 2020-12-08T20:19:06.111518Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (20.3.1)

[rtd-command-info] start-time: 2020-12-08T20:19:06.221229Z, end-time: 2020-12-08T20:19:15.220171Z, 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 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
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Building wheels for collected packages: mock, future
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Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.3 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-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-20.7 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-51.0.0 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2

[rtd-command-info] start-time: 2020-12-08T20:19:15.504526Z, end-time: 2020-12-08T20:19:21.506615Z, duration: 6, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Building wheels for collected packages: pyyaml
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Successfully built pyyaml
Installing collected packages: pillow, numpy, geographiclib, shapely, pyyaml, pyproj, lz4, geopy
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
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  Attempting uninstall: numpy
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    Not uninstalling numpy at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest
    Can't uninstall 'numpy'. No files were found to uninstall.
Successfully installed geographiclib-1.50 geopy-2.0.0 lz4-3.1.1 numpy-1.19.3 pillow-8.0.1 pyproj-3.0.0.post1 pyyaml-5.3.1 shapely-1.7.1

[rtd-command-info] start-time: 2020-12-08T20:19:21.743184Z, end-time: 2020-12-08T20:19:28.367863Z, duration: 6, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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  Stored in directory: /tmp/pip-ephem-wheel-cache-f831fe9w/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=71027 sha256=8016eb7d21c5be2d2d0def76d8f63ac6095b39a4e2815d1ff1dd484b319df668
  Stored in directory: /tmp/pip-ephem-wheel-cache-f831fe9w/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6
Successfully built docopt wrapt
Installing collected packages: urllib3, wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, requests, pycparser, sphinx, pyjwt, pockets, docopt, deprecated, cffi, cached-property, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, PyGithub, pygit2, py-make, plantweb
  Attempting uninstall: urllib3
    Found existing installation: urllib3 1.26.2
    Uninstalling urllib3-1.26.2:
      Successfully uninstalled urllib3-1.26.2
  Attempting uninstall: requests
    Found existing installation: requests 2.25.0
    Uninstalling requests-2.25.0:
      Successfully uninstalled requests-2.25.0
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed PyGithub-1.54 cached-property-1.5.2 cffi-1.14.4 deprecated-1.2.10 docopt-0.6.2 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.20 pygit2-1.2.1 pyjwt-1.7.1 requests-2.24.0 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.16 sphinxcontrib-qthelp-1.0.3 urllib3-1.25.11 wrapt-1.12.1

[rtd-command-info] start-time: 2020-12-08T20:19:28.482807Z, end-time: 2020-12-08T20:19:29.227708Z, duration: 0, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating emod_api.egg-info
writing emod_api.egg-info/PKG-INFO
writing dependency_links to emod_api.egg-info/dependency_links.txt
writing requirements to emod_api.egg-info/requires.txt
writing top-level names to emod_api.egg-info/top_level.txt
writing manifest file 'emod_api.egg-info/SOURCES.txt'
reading manifest file 'emod_api.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'emod_api/tests/data/*'
warning: no directories found matching 'emod_api/dtk_tools/serialization/test-data/*'
writing manifest file 'emod_api.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/examples
copying examples/serialized_file_mc_to_sc.py -> build/lib/examples
copying examples/intervention_from_schema.py -> build/lib/examples
copying examples/__init__.py -> build/lib/examples
copying examples/weather_file.py -> build/lib/examples
copying examples/insetchart.py -> build/lib/examples
copying examples/write_config_from_default_and_params.py -> build/lib/examples
copying examples/default_from_schema.py -> build/lib/examples
copying examples/some_config_i_found.py -> build/lib/examples
copying examples/spatial_report.py -> build/lib/examples
creating build/lib/emod_api
copying emod_api/campaign.py -> build/lib/emod_api
copying emod_api/schema_to_class.py -> build/lib/emod_api
copying emod_api/__init__.py -> build/lib/emod_api
copying emod_api/__main__.py -> build/lib/emod_api
creating build/lib/emod_api/serialization
copying emod_api/serialization/CensusAndModPop.py -> build/lib/emod_api/serialization
copying emod_api/serialization/SerializedPopulation.py -> build/lib/emod_api/serialization
copying emod_api/serialization/dtkFileTools.py -> build/lib/emod_api/serialization
copying emod_api/serialization/__init__.py -> build/lib/emod_api/serialization
copying emod_api/serialization/__main__.py -> build/lib/emod_api/serialization
copying emod_api/serialization/dtkFileSupport.py -> build/lib/emod_api/serialization
copying emod_api/serialization/dtkFileUtility.py -> build/lib/emod_api/serialization
creating build/lib/emod_api/tabularoutput
copying emod_api/tabularoutput/__init__.py -> build/lib/emod_api/tabularoutput
copying emod_api/tabularoutput/__main__.py -> build/lib/emod_api/tabularoutput
creating build/lib/emod_api/schema
copying emod_api/schema/get_schema.py -> build/lib/emod_api/schema
copying emod_api/schema/__init__.py -> build/lib/emod_api/schema
copying emod_api/schema/dtk_post_process_schema.py -> build/lib/emod_api/schema
copying emod_api/schema/__main__.py -> build/lib/emod_api/schema
creating build/lib/emod_api/channelreports
copying emod_api/channelreports/__init__.py -> build/lib/emod_api/channelreports
copying emod_api/channelreports/channels.py -> build/lib/emod_api/channelreports
copying emod_api/channelreports/__main__.py -> build/lib/emod_api/channelreports
creating build/lib/emod_api/config
copying emod_api/config/from_overrides.py -> build/lib/emod_api/config
copying emod_api/config/schema_to_config.py -> build/lib/emod_api/config
copying emod_api/config/dtk_pre_process_adhocevents.py -> build/lib/emod_api/config
copying emod_api/config/from_poi_and_binary.py -> build/lib/emod_api/config
copying emod_api/config/default_from_schema_no_validation.py -> build/lib/emod_api/config
copying emod_api/config/dtk_post_process_adhocevents.py -> build/lib/emod_api/config
copying emod_api/config/__init__.py -> build/lib/emod_api/config
copying emod_api/config/default_from_schema.py -> build/lib/emod_api/config
copying emod_api/config/from_schema.py -> build/lib/emod_api/config
copying emod_api/config/__main__.py -> build/lib/emod_api/config
copying emod_api/config/dtk_pre_process_w5ml.py -> build/lib/emod_api/config
creating build/lib/emod_api/weather
copying emod_api/weather/__init__.py -> build/lib/emod_api/weather
copying emod_api/weather/weather.py -> build/lib/emod_api/weather
copying emod_api/weather/__main__.py -> build/lib/emod_api/weather
creating build/lib/emod_api/interventions
copying emod_api/interventions/__init__.py -> build/lib/emod_api/interventions
copying emod_api/interventions/outbreak.py -> build/lib/emod_api/interventions
copying emod_api/interventions/import_pressure.py -> build/lib/emod_api/interventions
copying emod_api/interventions/__main__.py -> build/lib/emod_api/interventions
copying emod_api/interventions/simple_vaccine.py -> build/lib/emod_api/interventions
creating build/lib/emod_api/migration
copying emod_api/migration/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/grid_construction.py -> build/lib/emod_api/demographics
copying emod_api/demographics/DemographicsTemplates.py -> build/lib/emod_api/demographics
copying emod_api/demographics/Demographics.py -> build/lib/emod_api/demographics
copying emod_api/demographics/__main__.py -> build/lib/emod_api/demographics
copying emod_api/demographics/BaseInputFile.py -> build/lib/emod_api/demographics
copying emod_api/demographics/DemographicsInputDataParsers.py -> build/lib/emod_api/demographics
copying emod_api/demographics/Node.py -> build/lib/emod_api/demographics
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/serialized_file_mc_to_sc.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/intervention_from_schema.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/__init__.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/weather_file.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/insetchart.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/write_config_from_default_and_params.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/default_from_schema.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/some_config_i_found.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/spatial_report.py -> build/bdist.linux-x86_64/egg/examples
creating build/bdist.linux-x86_64/egg/emod_api
creating build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/CensusAndModPop.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/SerializedPopulation.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/dtkFileTools.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/dtkFileSupport.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/dtkFileUtility.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
creating build/bdist.linux-x86_64/egg/emod_api/tabularoutput
copying build/lib/emod_api/tabularoutput/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput
copying build/lib/emod_api/tabularoutput/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput
creating build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/get_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/dtk_post_process_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/campaign.py -> build/bdist.linux-x86_64/egg/emod_api
copying build/lib/emod_api/schema_to_class.py -> build/bdist.linux-x86_64/egg/emod_api
copying build/lib/emod_api/__init__.py -> build/bdist.linux-x86_64/egg/emod_api
creating build/bdist.linux-x86_64/egg/emod_api/channelreports
copying build/lib/emod_api/channelreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports
copying build/lib/emod_api/channelreports/channels.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports
copying build/lib/emod_api/channelreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports
creating build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/from_overrides.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/schema_to_config.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/dtk_pre_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/from_poi_and_binary.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/default_from_schema_no_validation.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/dtk_post_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/default_from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/dtk_pre_process_w5ml.py -> build/bdist.linux-x86_64/egg/emod_api/config
creating build/bdist.linux-x86_64/egg/emod_api/weather
copying build/lib/emod_api/weather/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/weather
copying build/lib/emod_api/weather/weather.py -> build/bdist.linux-x86_64/egg/emod_api/weather
copying build/lib/emod_api/weather/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/weather
creating build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/import_pressure.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/simple_vaccine.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
creating build/bdist.linux-x86_64/egg/emod_api/migration
copying build/lib/emod_api/migration/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/grid_construction.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/Demographics.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/BaseInputFile.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/DemographicsInputDataParsers.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/Node.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
byte-compiling build/bdist.linux-x86_64/egg/examples/serialized_file_mc_to_sc.py to serialized_file_mc_to_sc.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/intervention_from_schema.py to intervention_from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/weather_file.py to weather_file.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/insetchart.py to insetchart.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/write_config_from_default_and_params.py to write_config_from_default_and_params.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/default_from_schema.py to default_from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/some_config_i_found.py to some_config_i_found.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/spatial_report.py to spatial_report.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/CensusAndModPop.py to CensusAndModPop.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/SerializedPopulation.py to SerializedPopulation.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileTools.py to dtkFileTools.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileSupport.py to dtkFileSupport.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileUtility.py to dtkFileUtility.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/get_schema.py to get_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/dtk_post_process_schema.py to dtk_post_process_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/campaign.py to campaign.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema_to_class.py to schema_to_class.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/channels.py to channels.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_overrides.py to from_overrides.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/schema_to_config.py to schema_to_config.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_adhocevents.py to dtk_pre_process_adhocevents.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_poi_and_binary.py to from_poi_and_binary.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema_no_validation.py to default_from_schema_no_validation.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_post_process_adhocevents.py to dtk_post_process_adhocevents.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema.py to default_from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_schema.py to from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_w5ml.py to dtk_pre_process_w5ml.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/weather.py to weather.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/outbreak.py to outbreak.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/import_pressure.py to import_pressure.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/simple_vaccine.py to simple_vaccine.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/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/grid_construction.py to grid_construction.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Demographics.py to Demographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/BaseInputFile.py to BaseInputFile.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsInputDataParsers.py to DemographicsInputDataParsers.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Node.py to Node.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
emod_api.config.__pycache__.from_poi_and_binary.cpython-37: module references __file__
emod_api.serialization.__pycache__.dtkFileTools.cpython-37: module references __file__
emod_api.serialization.__pycache__.dtkFileUtility.cpython-37: module references __file__
examples.__pycache__.insetchart.cpython-37: module references __file__
examples.__pycache__.spatial_report.cpython-37: module references __file__
examples.__pycache__.weather_file.cpython-37: module references __file__
creating dist
creating 'dist/emod_api-1.4.0-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-1.4.0-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-1.4.0-py3.7.egg
Extracting emod_api-1.4.0-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 1.4.0 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-1.4.0-py3.7.egg
Processing dependencies for emod-api==1.4.0
Searching for geopy==2.0.0
Best match: geopy 2.0.0
Adding geopy 2.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for matplotlib==3.3.2
Best match: matplotlib 3.3.2
Adding matplotlib 3.3.2 to easy-install.pth file

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for pyproj==3.0.0.post1
Best match: pyproj 3.0.0.post1
Adding pyproj 3.0.0.post1 to easy-install.pth file
Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for Shapely==1.7.1
Best match: Shapely 1.7.1
Adding Shapely 1.7.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.5.3
Best match: scipy 1.5.3
scipy 1.5.3 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for pandas==1.1.3
Best match: pandas 1.1.3
pandas 1.1.3 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for PyYAML==5.3.1
Best match: PyYAML 5.3.1
Adding PyYAML 5.3.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for lz4==3.1.1
Best match: lz4 3.1.1
Adding lz4 3.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for numpy==1.19.3
Best match: numpy 1.19.3
Adding numpy 1.19.3 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for geographiclib==1.50
Best match: geographiclib 1.50
Adding geographiclib 1.50 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for cycler==0.10.0
Best match: cycler 0.10.0
cycler 0.10.0 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for kiwisolver==1.2.0
Best match: kiwisolver 1.2.0
kiwisolver 1.2.0 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for pyparsing==2.4.7
Best match: pyparsing 2.4.7
Adding pyparsing 2.4.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
python-dateutil 2.8.1 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for Pillow==8.0.1
Best match: Pillow 8.0.1
Adding Pillow 8.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for certifi==2020.12.5
Best match: certifi 2020.12.5
Adding certifi 2020.12.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for pytz==2020.4
Best match: pytz 2020.4
Adding pytz 2020.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Searching for six==1.15.0
Best match: six 1.15.0
Adding six 1.15.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for emod-api==1.4.0

[rtd-command-info] start-time: 2020-12-08T20:19:30.858936Z, end-time: 2020-12-08T20:19:30.927712Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Sphinx Demo docs build configuration file, created by
# sphinx-quickstart on Fri Aug 26 16:52:16 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# docs root, use os.path.abspath to make it absolute, like shown here.
#
import os
import subprocess
import sys
import sphinx_rtd_theme
import configparser

if sys.platform in ["linux", "darwin"]:
    subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
else:
    subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))


# -- General configuration ------------------------------------------------

# If your docs needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.mathjax',
    'sphinx.ext.githubpages',
    'sphinx.ext.autodoc',
    'sphinxcontrib.napoleon',
    'sphinx.ext.todo',
    'plantweb.directive',
    'sphinxcontrib.programoutput'
]

plantuml = 'plantweb'

autodoc_default_options = {
    'member-order': 'bysource',
    'members': None,
    'exclude-members': '__all__'
}

autodoc_mock_imports = ['emod_api.dtk_tools']

napoleon_google_docstring = True
# napoleon_numpy_docstring = True

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The encoding of source files.
#
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'EMOD-API'
copyright = u'2020, Bill & Melinda Gates Foundation. All rights reserved.'
author = u'Institute for Disease Modeling'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
#current_path = os.path.dirname(__file__)
#version_path = os.path.join(current_path, '..', '.bumpversion.cfg')
#config = configparser.ConfigParser()
#config.read(version_path)

#version = config['bumpversion']['current_version']
# The full version, including alpha/beta/rc tags.
# release = u'1.0'

# The language for content autogenerated by Sphinx. Refer to docs
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
# today = ''
#
# Else, today_fmt is used as the format for a strftime call.
#
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False

# RST epilog is added to the end of every topic. Useful for replace
# directives to use across the docset.

rst_epilog = "\n.. include:: /variables.txt"

# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the docs for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# docs.
# #
# html_theme_options = {
# }

# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# The name for this set of Sphinx documents.
# "<project> v<release> 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 <link> 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",
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    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
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    ("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',
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    'bitbucket_repo': 'None',
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    '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,
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    'docsearch_disabled': False,
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    'global_analytics_code': 'UA-17997319-2',
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}




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:
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    latex_elements_rtd = {
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    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2020-12-08T20:19:31.256947Z, end-time: 2020-12-08T20:20:00.838730Z, 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 48 source files that are out of date
updating environment: [new config] 48 added, 0 changed, 0 removed
reading sources... [  2%] emod_api
reading sources... [  4%] emod_api.campaign
reading sources... [  6%] emod_api.channelreports
reading sources... [  8%] emod_api.channelreports.channels
reading sources... [ 10%] emod_api.config
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reading sources... [ 27%] emod_api.config.from_schema
reading sources... [ 29%] emod_api.config.schema_to_config
emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema.
reading sources... [ 31%] emod_api.demographics
reading sources... [ 33%] emod_api.demographics.BaseInputFile
reading sources... [ 35%] emod_api.demographics.Demographics
Matplotlib is building the font cache; this may take a moment.
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reading sources... [ 72%] emod_api.serialization
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reading sources... [ 77%] emod_api.serialization.SerializedPopulation
reading sources... [ 79%] emod_api.serialization.dtkFileSupport
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reading sources... [ 85%] emod_api.spatialreports
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reading sources... [ 89%] emod_api.tabularoutput
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reading sources... [ 93%] emod_api.weather.weather
reading sources... [ 95%] emod_api_index
reading sources... [ 97%] glossary
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  2%] emod_api
writing output... [  4%] emod_api.campaign
writing output... [  6%] emod_api.channelreports
writing output... [  8%] emod_api.channelreports.channels
writing output... [ 10%] emod_api.config
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writing output... [ 14%] emod_api.config.default_from_schema_no_validation
writing output... [ 16%] emod_api.config.dtk_post_process_adhocevents
writing output... [ 18%] emod_api.config.dtk_pre_process_adhocevents
writing output... [ 20%] emod_api.config.dtk_pre_process_w5ml
writing output... [ 22%] emod_api.config.from_overrides
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writing output... [ 95%] emod_api_index
writing output... [ 97%] glossary
writing output... [100%] index

generating indices...  genindex py-modindexdone
writing additional pages...  search opensearchdone
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
  return f(*args, **kwds)

[rtd-command-info] start-time: 2020-12-08T20:20:01.102947Z, end-time: 2020-12-08T20:20:06.437011Z, duration: 5, exit-code: 0
python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v3.2.1
rm: cannot remove 'modules.rst': No such file or directory
make: [generate-api] Error 1 (ignored)
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: [new config] 48 added, 0 changed, 0 removed
reading sources... [  2%] emod_api
reading sources... [  4%] emod_api.campaign
reading sources... [  6%] emod_api.channelreports
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reading sources... [ 10%] emod_api.config
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reading sources... [ 14%] emod_api.config.default_from_schema_no_validation
reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents
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reading sources... [ 27%] emod_api.config.from_schema
reading sources... [ 29%] emod_api.config.schema_to_config
emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema.
reading sources... [ 31%] emod_api.demographics
reading sources... [ 33%] emod_api.demographics.BaseInputFile
reading sources... [ 35%] emod_api.demographics.Demographics
reading sources... [ 37%] emod_api.demographics.DemographicsGenerator
reading sources... [ 39%] emod_api.demographics.DemographicsInputDataParsers
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reading sources... [ 43%] emod_api.demographics.Node
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reading sources... [ 97%] glossary
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.BaseInputFile emod_api.demographics.Demographics emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics_utils emod_api.demographics.grid_construction emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.migration emod_api.migration.Migration emod_api.migration.MigrationFile emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.CensusAndModPop emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary done
writing... done
writing additional files...  opensearchdone
copying static files... ... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.
Updating searchtools for Read the Docs search... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
  return f(*args, **kwds)

[rtd-command-info] start-time: 2020-12-08T20:20:06.598435Z, end-time: 2020-12-08T20:20:11.884641Z, duration: 5, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v3.2.1
rm: cannot remove 'modules.rst': No such file or directory
make: [generate-api] Error 1 (ignored)
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: [new config] 48 added, 0 changed, 0 removed
reading sources... [  2%] emod_api
reading sources... [  4%] emod_api.campaign
reading sources... [  6%] emod_api.channelreports
reading sources... [  8%] emod_api.channelreports.channels
reading sources... [ 10%] emod_api.config
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reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents
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reading sources... [ 27%] emod_api.config.from_schema
reading sources... [ 29%] emod_api.config.schema_to_config
emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema.
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reading sources... [ 45%] emod_api.demographics.demographics_utils
reading sources... [ 47%] emod_api.demographics.grid_construction
reading sources... [ 50%] emod_api.interventions
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reading sources... [ 64%] emod_api.schema
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reading sources... [ 68%] emod_api.schema.get_schema
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reading sources... [ 89%] emod_api.tabularoutput
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reading sources... [ 93%] emod_api.weather.weather
reading sources... [ 95%] emod_api_index
reading sources... [ 97%] glossary
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing emod-api-docs.tex... index emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.BaseInputFile emod_api.demographics.Demographics emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics_utils emod_api.demographics.grid_construction emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.migration emod_api.migration.Migration emod_api.migration.MigrationFile emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.CensusAndModPop emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary 
resolving references...
done
writing... done
copying TeX support files... copying TeX support files...
done
build succeeded.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
  return f(*args, **kwds)
WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/checkouts/latest/docs/_build/latex/_static/searchtools.js

[rtd-command-info] start-time: 2020-12-08T20:20:12.152843Z, end-time: 2020-12-08T20:20:12.208162Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2020-12-08T20:20:12.331981Z, end-time: 2020-12-08T20:20:14.343652Z, 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, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, <GEN1> chunk 1.
Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, <GEN2> chunk 1.
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
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Chapter 1.

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[]\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder(

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[7]
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Chapter 1.

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ok=s2c.ReadOnlyDict) os.remove( ^^Pde-

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[5]
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[]\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 ,
[6]
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[]\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder(

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\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 ,

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tm/m/it/10 '\T1/ptm/m/n/10 ,

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'\T1/ptm/m/it/10 Gridded

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Chapter 2.
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Chapter 1.

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[]\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder(

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[25] [26] [27] [28]
Chapter 2.
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Transcript written on institute-for-disease-modeling-emod-api.log.
Latexmk: Index file 'institute-for-disease-modeling-emod-api.idx' was written
Latexmk: 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'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Errors, in force_mode: so I tried finishing targets

[rtd-command-info] start-time: 2020-12-08T20:20:14.644721Z, end-time: 2020-12-08T20:20:14.700690Z, duration: 0, exit-code: 0
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