Read the Docs build information
Build id: 524701
Project: institute-for-disease-modeling-emod-api
Version: latest
Commit: bdd63a360352208657f94e18bb6a3ad641f08fa7
Date: 2021-01-07T03:52:59.060932Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-01-07T03:53:00.659218Z, end-time: 2021-01-07T03:53:01.648770Z, 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: 2021-01-07T03:53:02.385613Z, end-time: 2021-01-07T03:53:02.565734Z, 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 bdd63a3 No longer pass in the (empty) list of implicit config functions. (#172)

[rtd-command-info] start-time: 2021-01-07T03:53:02.780058Z, end-time: 2021-01-07T03:53:02.833279Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-01-07T03:53:04.204427Z, end-time: 2021-01-07T03:53:08.408884Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-01-07T03:53:08.646951Z, end-time: 2021-01-07T03:53:10.502544Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (20.3.3)

[rtd-command-info] start-time: 2021-01-07T03:53:10.677163Z, end-time: 2021-01-07T03:53:20.028987Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
Collecting commonmark==0.8.1
  Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB)
Collecting docutils==0.14
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Collecting mock==1.0.1
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Collecting pillow==5.4.1
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Collecting recommonmark==0.5.0
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Collecting setuptools==41.0.1
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=705b821ec90a14f1ac315a06bfdcc5e29307c0576fb26caaf51268e7c24ac0e5
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  Building wheel for future (setup.py): finished with status 'done'
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  Stored in directory: /tmp/pip-ephem-wheel-cache-mi4_w6gq/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.3 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.5 readthedocs-sphinx-ext-2.1.2 recommonmark-0.5.0 requests-2.25.1 setuptools-51.1.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2

[rtd-command-info] start-time: 2021-01-07T03:53:20.467110Z, end-time: 2021-01-07T03:53:27.174305Z, duration: 6, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
Requirement already satisfied: pandas in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (1.1.3)
Requirement already satisfied: scipy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 5)) (1.5.3)
Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 8)) (3.3.2)
Collecting numpy==1.19.3
  Downloading numpy-1.19.3-cp37-cp37m-manylinux2010_x86_64.whl (14.9 MB)
Collecting geopy
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Collecting geographiclib<2,>=1.49
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Collecting lz4
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Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (2020.12.5)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (1.2.0)
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Requirement already satisfied: python-dateutil>=2.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 8)) (2.8.1)
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Collecting pillow>=6.2.0
  Downloading Pillow-8.1.0-cp37-cp37m-manylinux1_x86_64.whl (2.2 MB)
Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 4)) (2020.5)
Collecting pyproj
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Collecting shapely
  Downloading Shapely-1.7.1-cp37-cp37m-manylinux1_x86_64.whl (1.0 MB)
Building wheels for collected packages: pyyaml
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44620 sha256=d1a8e23ca0744260680d2b283bc62b2322f1cd89c4f67ceb9893be6ba1a9fcc3
  Stored in directory: /tmp/pip-ephem-wheel-cache-o8o52hbg/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653
Successfully built pyyaml
Installing collected packages: pillow, numpy, geographiclib, shapely, pyyaml, pyproj, lz4, geopy
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
  Attempting uninstall: numpy
    Found existing installation: numpy 1.19.2
    Not uninstalling numpy at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest
    Can't uninstall 'numpy'. No files were found to uninstall.
Successfully installed geographiclib-1.50 geopy-2.1.0 lz4-3.1.1 numpy-1.19.3 pillow-8.1.0 pyproj-3.0.0.post1 pyyaml-5.3.1 shapely-1.7.1

[rtd-command-info] start-time: 2021-01-07T03:53:27.761828Z, end-time: 2021-01-07T03:53:34.225929Z, duration: 6, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple
Collecting plantweb~=1.2.1
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Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (1.15.0)
Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (0.14)
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Collecting pygit2~=1.2.1
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Collecting sphinx~=3.2.1
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Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (20.8)
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Building wheels for collected packages: docopt, wrapt
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Successfully built docopt wrapt
Installing collected packages: wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pycparser, sphinx, pyjwt, pockets, docopt, deprecated, cffi, cached-property, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, PyGithub, pygit2, py-make, plantweb
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed PyGithub-1.54.1 cached-property-1.5.2 cffi-1.14.4 deprecated-1.2.10 docopt-0.6.2 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.20 pygit2-1.2.1 pyjwt-1.7.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.16 sphinxcontrib-qthelp-1.0.3 wrapt-1.12.1

[rtd-command-info] start-time: 2021-01-07T03:53:34.389415Z, end-time: 2021-01-07T03:53:35.159768Z, duration: 0, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating emod_api.egg-info
writing emod_api.egg-info/PKG-INFO
writing dependency_links to emod_api.egg-info/dependency_links.txt
writing requirements to emod_api.egg-info/requires.txt
writing top-level names to emod_api.egg-info/top_level.txt
writing manifest file 'emod_api.egg-info/SOURCES.txt'
reading manifest file 'emod_api.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'emod_api/tests/data/*'
warning: no directories found matching 'emod_api/dtk_tools/serialization/test-data/*'
writing manifest file 'emod_api.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/examples
copying examples/serialized_file_mc_to_sc.py -> build/lib/examples
copying examples/intervention_from_schema.py -> build/lib/examples
copying examples/__init__.py -> build/lib/examples
copying examples/weather_file.py -> build/lib/examples
copying examples/insetchart.py -> build/lib/examples
copying examples/write_config_from_default_and_params.py -> build/lib/examples
copying examples/default_from_schema.py -> build/lib/examples
copying examples/some_config_i_found.py -> build/lib/examples
copying examples/spatial_report.py -> build/lib/examples
creating build/lib/emod_api
copying emod_api/campaign.py -> build/lib/emod_api
copying emod_api/schema_to_class.py -> build/lib/emod_api
copying emod_api/__init__.py -> build/lib/emod_api
copying emod_api/__main__.py -> build/lib/emod_api
creating build/lib/emod_api/serialization
copying emod_api/serialization/CensusAndModPop.py -> build/lib/emod_api/serialization
copying emod_api/serialization/SerializedPopulation.py -> build/lib/emod_api/serialization
copying emod_api/serialization/dtkFileTools.py -> build/lib/emod_api/serialization
copying emod_api/serialization/__init__.py -> build/lib/emod_api/serialization
copying emod_api/serialization/__main__.py -> build/lib/emod_api/serialization
copying emod_api/serialization/dtkFileSupport.py -> build/lib/emod_api/serialization
copying emod_api/serialization/dtkFileUtility.py -> build/lib/emod_api/serialization
creating build/lib/emod_api/tabularoutput
copying emod_api/tabularoutput/__init__.py -> build/lib/emod_api/tabularoutput
copying emod_api/tabularoutput/__main__.py -> build/lib/emod_api/tabularoutput
creating build/lib/emod_api/schema
copying emod_api/schema/get_schema.py -> build/lib/emod_api/schema
copying emod_api/schema/__init__.py -> build/lib/emod_api/schema
copying emod_api/schema/dtk_post_process_schema.py -> build/lib/emod_api/schema
copying emod_api/schema/__main__.py -> build/lib/emod_api/schema
creating build/lib/emod_api/channelreports
copying emod_api/channelreports/__init__.py -> build/lib/emod_api/channelreports
copying emod_api/channelreports/channels.py -> build/lib/emod_api/channelreports
copying emod_api/channelreports/__main__.py -> build/lib/emod_api/channelreports
creating build/lib/emod_api/config
copying emod_api/config/from_overrides.py -> build/lib/emod_api/config
copying emod_api/config/schema_to_config.py -> build/lib/emod_api/config
copying emod_api/config/dtk_pre_process_adhocevents.py -> build/lib/emod_api/config
copying emod_api/config/from_poi_and_binary.py -> build/lib/emod_api/config
copying emod_api/config/default_from_schema_no_validation.py -> build/lib/emod_api/config
copying emod_api/config/dtk_post_process_adhocevents.py -> build/lib/emod_api/config
copying emod_api/config/__init__.py -> build/lib/emod_api/config
copying emod_api/config/default_from_schema.py -> build/lib/emod_api/config
copying emod_api/config/from_schema.py -> build/lib/emod_api/config
copying emod_api/config/__main__.py -> build/lib/emod_api/config
copying emod_api/config/dtk_pre_process_w5ml.py -> build/lib/emod_api/config
creating build/lib/emod_api/weather
copying emod_api/weather/__init__.py -> build/lib/emod_api/weather
copying emod_api/weather/weather.py -> build/lib/emod_api/weather
copying emod_api/weather/__main__.py -> build/lib/emod_api/weather
creating build/lib/emod_api/interventions
copying emod_api/interventions/__init__.py -> build/lib/emod_api/interventions
copying emod_api/interventions/outbreak.py -> build/lib/emod_api/interventions
copying emod_api/interventions/utils.py -> build/lib/emod_api/interventions
copying emod_api/interventions/import_pressure.py -> build/lib/emod_api/interventions
copying emod_api/interventions/__main__.py -> build/lib/emod_api/interventions
copying emod_api/interventions/simple_vaccine.py -> build/lib/emod_api/interventions
creating build/lib/emod_api/migration
copying emod_api/migration/__init__.py -> build/lib/emod_api/migration
copying emod_api/migration/Migration.py -> build/lib/emod_api/migration
copying emod_api/migration/__main__.py -> build/lib/emod_api/migration
creating build/lib/emod_api/spatialreports
copying emod_api/spatialreports/__init__.py -> build/lib/emod_api/spatialreports
copying emod_api/spatialreports/spatial.py -> build/lib/emod_api/spatialreports
copying emod_api/spatialreports/__main__.py -> build/lib/emod_api/spatialreports
creating build/lib/emod_api/demographics
copying emod_api/demographics/DemographicsGenerator.py -> build/lib/emod_api/demographics
copying emod_api/demographics/demographics_utils.py -> build/lib/emod_api/demographics
copying emod_api/demographics/__init__.py -> build/lib/emod_api/demographics
copying emod_api/demographics/grid_construction.py -> build/lib/emod_api/demographics
copying emod_api/demographics/DemographicsTemplates.py -> build/lib/emod_api/demographics
copying emod_api/demographics/Demographics.py -> build/lib/emod_api/demographics
copying emod_api/demographics/__main__.py -> build/lib/emod_api/demographics
copying emod_api/demographics/BaseInputFile.py -> build/lib/emod_api/demographics
copying emod_api/demographics/DemographicsInputDataParsers.py -> build/lib/emod_api/demographics
copying emod_api/demographics/Node.py -> build/lib/emod_api/demographics
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/serialized_file_mc_to_sc.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/intervention_from_schema.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/__init__.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/weather_file.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/insetchart.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/write_config_from_default_and_params.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/default_from_schema.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/some_config_i_found.py -> build/bdist.linux-x86_64/egg/examples
copying build/lib/examples/spatial_report.py -> build/bdist.linux-x86_64/egg/examples
creating build/bdist.linux-x86_64/egg/emod_api
creating build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/CensusAndModPop.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/SerializedPopulation.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/dtkFileTools.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/dtkFileSupport.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
copying build/lib/emod_api/serialization/dtkFileUtility.py -> build/bdist.linux-x86_64/egg/emod_api/serialization
creating build/bdist.linux-x86_64/egg/emod_api/tabularoutput
copying build/lib/emod_api/tabularoutput/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput
copying build/lib/emod_api/tabularoutput/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput
creating build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/get_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/dtk_post_process_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/schema/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/schema
copying build/lib/emod_api/campaign.py -> build/bdist.linux-x86_64/egg/emod_api
copying build/lib/emod_api/schema_to_class.py -> build/bdist.linux-x86_64/egg/emod_api
copying build/lib/emod_api/__init__.py -> build/bdist.linux-x86_64/egg/emod_api
creating build/bdist.linux-x86_64/egg/emod_api/channelreports
copying build/lib/emod_api/channelreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports
copying build/lib/emod_api/channelreports/channels.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports
copying build/lib/emod_api/channelreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports
creating build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/from_overrides.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/schema_to_config.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/dtk_pre_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/from_poi_and_binary.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/default_from_schema_no_validation.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/dtk_post_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/default_from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/config
copying build/lib/emod_api/config/dtk_pre_process_w5ml.py -> build/bdist.linux-x86_64/egg/emod_api/config
creating build/bdist.linux-x86_64/egg/emod_api/weather
copying build/lib/emod_api/weather/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/weather
copying build/lib/emod_api/weather/weather.py -> build/bdist.linux-x86_64/egg/emod_api/weather
copying build/lib/emod_api/weather/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/weather
creating build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/utils.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/import_pressure.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
copying build/lib/emod_api/interventions/simple_vaccine.py -> build/bdist.linux-x86_64/egg/emod_api/interventions
creating build/bdist.linux-x86_64/egg/emod_api/migration
copying build/lib/emod_api/migration/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/migration
copying build/lib/emod_api/migration/Migration.py -> build/bdist.linux-x86_64/egg/emod_api/migration
copying build/lib/emod_api/migration/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/migration
creating build/bdist.linux-x86_64/egg/emod_api/spatialreports
copying build/lib/emod_api/spatialreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports
copying build/lib/emod_api/spatialreports/spatial.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports
copying build/lib/emod_api/spatialreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports
copying build/lib/emod_api/__main__.py -> build/bdist.linux-x86_64/egg/emod_api
creating build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/DemographicsGenerator.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/demographics_utils.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/grid_construction.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/Demographics.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/BaseInputFile.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/DemographicsInputDataParsers.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
copying build/lib/emod_api/demographics/Node.py -> build/bdist.linux-x86_64/egg/emod_api/demographics
byte-compiling build/bdist.linux-x86_64/egg/examples/serialized_file_mc_to_sc.py to serialized_file_mc_to_sc.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/intervention_from_schema.py to intervention_from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/weather_file.py to weather_file.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/insetchart.py to insetchart.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/write_config_from_default_and_params.py to write_config_from_default_and_params.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/default_from_schema.py to default_from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/some_config_i_found.py to some_config_i_found.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/examples/spatial_report.py to spatial_report.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/CensusAndModPop.py to CensusAndModPop.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/SerializedPopulation.py to SerializedPopulation.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileTools.py to dtkFileTools.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileSupport.py to dtkFileSupport.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileUtility.py to dtkFileUtility.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/get_schema.py to get_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/dtk_post_process_schema.py to dtk_post_process_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/campaign.py to campaign.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema_to_class.py to schema_to_class.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/channels.py to channels.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_overrides.py to from_overrides.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/schema_to_config.py to schema_to_config.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_adhocevents.py to dtk_pre_process_adhocevents.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_poi_and_binary.py to from_poi_and_binary.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema_no_validation.py to default_from_schema_no_validation.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_post_process_adhocevents.py to dtk_post_process_adhocevents.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema.py to default_from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_schema.py to from_schema.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_w5ml.py to dtk_pre_process_w5ml.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/weather.py to weather.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/outbreak.py to outbreak.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/import_pressure.py to import_pressure.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/simple_vaccine.py to simple_vaccine.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/Migration.py to Migration.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/spatial.py to spatial.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsGenerator.py to DemographicsGenerator.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/demographics_utils.py to demographics_utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/grid_construction.py to grid_construction.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Demographics.py to Demographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/BaseInputFile.py to BaseInputFile.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsInputDataParsers.py to DemographicsInputDataParsers.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Node.py to Node.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emod_api.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
  File "build/bdist.linux-x86_64/egg/emod_api/demographics/Demographics.py", line 57
    def from_synth_pop(tot_pop=1e6, num_nodes=100, frac_rural=0.3, id_ref="from_synth_pop");
                                                                                           ^
SyntaxError: invalid syntax

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-1.4.7-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-1.4.7-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-1.4.7-py3.7.egg
Extracting emod_api-1.4.7-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 1.4.7 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-1.4.7-py3.7.egg
Processing dependencies for emod-api==1.4.7
Searching for geopy==2.1.0
Best match: geopy 2.1.0
Adding geopy 2.1.0 to easy-install.pth file

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

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
python-dateutil 2.8.1 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for Pillow==8.1.0
Best match: Pillow 8.1.0
Adding Pillow 8.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/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==2020.5
Best match: pytz 2020.5
Adding pytz 2020.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/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==1.4.7
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.7-py3.7.egg/emod_api/demographics/Demographics.py", line 57
    def from_synth_pop(tot_pop=1e6, num_nodes=100, frac_rural=0.3, id_ref="from_synth_pop");
                                                                                           ^
SyntaxError: invalid syntax

[rtd-command-info] start-time: 2021-01-07T03:53:36.757132Z, end-time: 2021-01-07T03:53:36.831225Z, 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",
    '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': 'bdd63a36',
}




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: 2021-01-07T03:53:37.001011Z, end-time: 2021-01-07T03:53:55.977563Z, duration: 18, exit-code: 1
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
reading sources... [ 12%] emod_api.config.default_from_schema
reading sources... [ 14%] emod_api.config.default_from_schema_no_validation
reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents
reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents
reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml
reading sources... [ 22%] emod_api.config.from_overrides
reading sources... [ 25%] emod_api.config.from_poi_and_binary
reading sources... [ 27%] emod_api.config.from_schema
reading sources... [ 29%] emod_api.config.schema_to_config
emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema.
reading sources... [ 31%] emod_api.demographics
reading sources... [ 33%] emod_api.demographics.BaseInputFile
reading sources... [ 35%] emod_api.demographics.Demographics
reading sources... [ 37%] emod_api.demographics.DemographicsGenerator
reading sources... [ 39%] emod_api.demographics.DemographicsInputDataParsers
reading sources... [ 41%] emod_api.demographics.DemographicsTemplates
reading sources... [ 43%] emod_api.demographics.Node
reading sources... [ 45%] emod_api.demographics.demographics_utils
reading sources... [ 47%] emod_api.demographics.grid_construction
reading sources... [ 50%] emod_api.interventions
reading sources... [ 52%] emod_api.interventions.import_pressure
reading sources... [ 54%] emod_api.interventions.outbreak
reading sources... [ 56%] emod_api.interventions.simple_vaccine
reading sources... [ 58%] emod_api.interventions.utils
reading sources... [ 60%] emod_api.migration
reading sources... [ 62%] emod_api.migration.Migration
reading sources... [ 64%] emod_api.schema
reading sources... [ 66%] emod_api.schema.dtk_post_process_schema
reading sources... [ 68%] emod_api.schema.get_schema
reading sources... [ 70%] emod_api.schema_to_class
reading sources... [ 72%] emod_api.serialization
reading sources... [ 75%] emod_api.serialization.CensusAndModPop
reading sources... [ 77%] emod_api.serialization.SerializedPopulation
reading sources... [ 79%] emod_api.serialization.dtkFileSupport
reading sources... [ 81%] emod_api.serialization.dtkFileTools
reading sources... [ 83%] emod_api.serialization.dtkFileUtility
reading sources... [ 85%] emod_api.spatialreports
reading sources... [ 87%] emod_api.spatialreports.spatial
reading sources... [ 89%] emod_api.tabularoutput
reading sources... [ 91%] emod_api.weather
reading sources... [ 93%] emod_api.weather.weather
reading sources... [ 95%] emod_api_index
reading sources... [ 97%] glossary
reading sources... [100%] index

/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: autodoc: failed to import module 'Demographics' from module 'emod_api.demographics'; the following exception was raised:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 66, in import_module
    return importlib.import_module(modname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 724, in exec_module
  File "<frozen importlib._bootstrap_external>", line 860, in get_code
  File "<frozen importlib._bootstrap_external>", line 791, in source_to_code
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.7-py3.7.egg/emod_api/demographics/Demographics.py", line 57
    def from_synth_pop(tot_pop=1e6, num_nodes=100, frac_rural=0.3, id_ref="from_synth_pop");
                                                                                           ^
SyntaxError: invalid syntax

WARNING: autodoc: failed to import module 'DemographicsGenerator' from module 'emod_api.demographics'; the following exception was raised:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 66, in import_module
    return importlib.import_module(modname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.7-py3.7.egg/emod_api/demographics/DemographicsGenerator.py", line 15, in <module>
    from emod_api.demographics.Demographics import Demographics
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.7-py3.7.egg/emod_api/demographics/Demographics.py", line 57
    def from_synth_pop(tot_pop=1e6, num_nodes=100, frac_rural=0.3, id_ref="from_synth_pop");
                                                                                           ^
SyntaxError: invalid syntax

WARNING: autodoc: failed to import module 'Migration' from module 'emod_api.migration'; the following exception was raised:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 66, in import_module
    return importlib.import_module(modname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.7-py3.7.egg/emod_api/migration/Migration.py", line 12, in <module>
    import emod_api.demographics.Demographics as Demog
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-1.4.7-py3.7.egg/emod_api/demographics/Demographics.py", line 57
    def from_synth_pop(tot_pop=1e6, num_nodes=100, frac_rural=0.3, id_ref="from_synth_pop");
                                                                                           ^
SyntaxError: invalid syntax

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  2%] emod_api
writing output... [  4%] emod_api.campaign
writing output... [  6%] emod_api.channelreports
writing output... [  8%] emod_api.channelreports.channels
writing output... [ 10%] emod_api.config
writing output... [ 12%] emod_api.config.default_from_schema
writing output... [ 14%] emod_api.config.default_from_schema_no_validation
writing output... [ 16%] emod_api.config.dtk_post_process_adhocevents
writing output... [ 18%] emod_api.config.dtk_pre_process_adhocevents
writing output... [ 20%] emod_api.config.dtk_pre_process_w5ml
writing output... [ 22%] emod_api.config.from_overrides
writing output... [ 25%] emod_api.config.from_poi_and_binary
writing output... [ 27%] emod_api.config.from_schema
writing output... [ 29%] emod_api.config.schema_to_config
writing output... [ 31%] emod_api.demographics
writing output... [ 33%] emod_api.demographics.BaseInputFile
writing output... [ 35%] emod_api.demographics.Demographics
writing output... [ 37%] emod_api.demographics.DemographicsGenerator
writing output... [ 39%] emod_api.demographics.DemographicsInputDataParsers
writing output... [ 41%] emod_api.demographics.DemographicsTemplates
writing output... [ 43%] emod_api.demographics.Node
writing output... [ 45%] emod_api.demographics.demographics_utils
writing output... [ 47%] emod_api.demographics.grid_construction
writing output... [ 50%] emod_api.interventions
writing output... [ 52%] emod_api.interventions.import_pressure
writing output... [ 54%] emod_api.interventions.outbreak
writing output... [ 56%] emod_api.interventions.simple_vaccine
writing output... [ 58%] emod_api.interventions.utils
writing output... [ 60%] emod_api.migration
writing output... [ 62%] emod_api.migration.Migration
writing output... [ 64%] emod_api.schema
writing output... [ 66%] emod_api.schema.dtk_post_process_schema
writing output... [ 68%] emod_api.schema.get_schema
writing output... [ 70%] emod_api.schema_to_class
writing output... [ 72%] emod_api.serialization
writing output... [ 75%] emod_api.serialization.CensusAndModPop
writing output... [ 77%] emod_api.serialization.SerializedPopulation
writing output... [ 79%] emod_api.serialization.dtkFileSupport
writing output... [ 81%] emod_api.serialization.dtkFileTools
writing output... [ 83%] emod_api.serialization.dtkFileUtility
writing output... [ 85%] emod_api.spatialreports
writing output... [ 87%] emod_api.spatialreports.spatial
writing output... [ 89%] emod_api.tabularoutput
writing output... [ 91%] emod_api.weather
writing output... [ 93%] emod_api.weather.weather
writing output... [ 95%] emod_api_index
writing output... [ 97%] glossary
writing output... [100%] index

generating indices...  genindex py-modindexdone
writing additional pages...  search opensearchdone
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 3 warnings.
Updating searchtools for Read the Docs search...