Read the Docs build information
Build id: 411597
Project: institute-for-disease-modeling-covasim
Version: latest
Commit: 017a3b72aa1a0d0c1ff06415212654024efedb62
Date: 2020-09-02T20:38:01.550200Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-09-02T20:38:03.309222Z, end-time: 2020-09-02T20:38:04.714076Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/InstituteforDiseaseModeling/covasim.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-09-02T20:38:05.039176Z, end-time: 2020-09-02T20:38:05.107207Z, 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 017a3b7 update changelog

[rtd-command-info] start-time: 2020-09-02T20:38:05.223495Z, end-time: 2020-09-02T20:38:05.276935Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-09-02T20:38:06.455742Z, end-time: 2020-09-02T20:38:10.286010Z, duration: 3, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-09-02T20:38:10.585484Z, end-time: 2020-09-02T20:38:11.248547Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (20.2.2)

[rtd-command-info] start-time: 2020-09-02T20:38:11.367027Z, end-time: 2020-09-02T20:38:19.237515Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1
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Building wheels for collected packages: mock, future
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=43862da3f232a42816410effbd7f1c175e0b2fe0c26717aed1ab5dc8a241f825
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Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, imagesize, MarkupSafe, Jinja2, certifi, chardet, idna, urllib3, requests, six, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, snowballstemmer, pyparsing, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
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Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 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 urllib3-1.25.10

[rtd-command-info] start-time: 2020-09-02T20:38:19.340686Z, end-time: 2020-09-02T20:39:05.653327Z, duration: 46, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets->-r requirements.txt (line 11)) (20.4)
Building wheels for collected packages: fire, dill, memory-profiler, psutil, mpld3, retrying, termcolor, et-xmlfile, tornado, pyrsistent, pandocfilters
  Building wheel for fire (setup.py): started
  Building wheel for fire (setup.py): finished with status 'done'
  Created wheel for fire: filename=fire-0.3.1-py2.py3-none-any.whl size=111005 sha256=82882ef27a83cb05c7893c3f32ed0b376fafc00eb2d5b327e10bb69826075edb
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  Created wheel for dill: filename=dill-0.3.2-py3-none-any.whl size=78912 sha256=092c4aa26bae8bfc9e3e9967a6d4f2da92e96615247ec4eb2d2a506ffc9cdf14
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  Building wheel for memory-profiler (setup.py): started
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  Created wheel for memory-profiler: filename=memory_profiler-0.57.0-py3-none-any.whl size=28993 sha256=03198b32edf8d0f9c534dd9018f3a27813e1018dcce42727acb27188358b6ad0
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/0c/84/4a/8afc0620ec149b2c0a4ed08b021e3a2dc7063fa08e1fcb40c8
  Building wheel for psutil (setup.py): started
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  Created wheel for psutil: filename=psutil-5.7.2-cp37-cp37m-linux_x86_64.whl size=283658 sha256=5333b520bf66beeeb73f24861aaec4840668c350c8e670908e9910c6429f422f
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/2d/43/97/00701864a7bee6d9e1a52dd682537dcbf1d013d0e2e6f0c1f1
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  Created wheel for mpld3: filename=mpld3-0.5.1-py3-none-any.whl size=364063 sha256=fbacf17a250f9a97ebd07ff5d70a15a4d47f531a5ab53b47d24ae5563aee02cc
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  Created wheel for retrying: filename=retrying-1.3.3-py3-none-any.whl size=11429 sha256=7fdc84468918b290919ee3c797a7e9c713c61f3bb28270a87cbaf363bf2a251e
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/f9/8d/8d/f6af3f7f9eea3553bc2fe6d53e4b287dad18b06a861ac56ddf
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  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4830 sha256=b5dd44c6e194f98e51e30d534c5486b9e1dc32fea7ae49cd13c48df3571d1713
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
  Building wheel for et-xmlfile (setup.py): started
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  Created wheel for et-xmlfile: filename=et_xmlfile-1.0.1-py3-none-any.whl size=8917 sha256=fee2b9ec9e2a05b6676afa1c83acc9fc03bf5d8a4f89135b9e3b594f69e0f6e3
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/e2/bd/55/048b4fd505716c4c298f42ee02dffd9496bb6d212b266c7f31
  Building wheel for tornado (setup.py): started
  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.4-cp37-cp37m-linux_x86_64.whl size=428561 sha256=d325cf0ea8048929b402facb417feda6b97ecba5f6f46014afb381ed6badd918
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/7d/14/fa/d88fb5da77d813ea0ffca38a2ab2a052874e9e1142bad0b348
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  Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp37-cp37m-linux_x86_64.whl size=116012 sha256=8507e84c1a070f20c5f9349a41d1fb3cb507b8f0b34df0d652e896bb3d54f054
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/22/52/11/f0920f95c23ed7d2d0b05f2b7b2f4509e87a20cfe8ea43d987
  Building wheel for pandocfilters (setup.py): started
  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7855 sha256=a318c0f6940070e153d993cb7a5575a9bb596a7f0c2be11fc42d2cbbcc43b0c4
  Stored in directory: /tmp/pip-ephem-wheel-cache-yt8i06jx/wheels/63/99/01/9fe785b86d1e091a6b2a61e06ddb3d8eb1bc9acae5933d4740
Successfully built fire dill memory-profiler psutil mpld3 retrying termcolor et-xmlfile tornado pyrsistent pandocfilters
Installing collected packages: numpy, python-dateutil, pandas, scipy, kiwisolver, cycler, pillow, matplotlib, patsy, statsmodels, llvmlite, numba, jellyfish, dill, xlsxwriter, xlrd, decorator, wcwidth, prompt-toolkit, ptyprocess, pexpect, backcall, parso, jedi, ipython-genutils, traitlets, pickleshare, ipython, line-profiler, psutil, memory-profiler, zipp, importlib-metadata, jsonpickle, smmap, gitdb, gitpython, jdcal, et-xmlfile, openpyexcel, sciris, redis, vine, billiard, amqp, kombu, celery, cachelib, werkzeug, itsdangerous, click, flask, flask-session, zope.interface, constantly, PyHamcrest, incremental, attrs, Automat, hyperlink, twisted, sqlalchemy, flask-login, pyasn1, pycparser, cffi, cryptography, pyasn1-modules, service-identity, mpld3, scirisweb, gunicorn, retrying, plotly, pyrsistent, jsonschema, jupyter-core, nbformat, tornado, pyzmq, jupyter-client, ipykernel, argon2-cffi, Send2Trash, mistune, webencodings, bleach, defusedxml, pandocfilters, testpath, entrypoints, nbconvert, terminado, prometheus-client, notebook, widgetsnbextension, ipywidgets, termcolor, fire
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
Successfully installed Automat-20.2.0 PyHamcrest-2.0.2 Send2Trash-1.5.0 amqp-2.6.1 argon2-cffi-20.1.0 attrs-20.1.0 backcall-0.2.0 billiard-3.6.3.0 bleach-3.1.5 cachelib-0.1.1 celery-4.4.7 cffi-1.14.2 click-7.1.2 constantly-15.1.0 cryptography-3.1 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 dill-0.3.2 entrypoints-0.3 et-xmlfile-1.0.1 fire-0.3.1 flask-1.1.2 flask-login-0.5.0 flask-session-0.3.2 gitdb-4.0.5 gitpython-3.1.7 gunicorn-20.0.4 hyperlink-20.0.1 importlib-metadata-1.7.0 incremental-17.5.0 ipykernel-5.3.4 ipython-7.18.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 itsdangerous-1.1.0 jdcal-1.4.1 jedi-0.17.2 jellyfish-0.8.2 jsonpickle-1.4.1 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.6.3 kiwisolver-1.2.0 kombu-4.6.11 line-profiler-3.0.2 llvmlite-0.31.0 matplotlib-3.3.1 memory-profiler-0.57.0 mistune-0.8.4 mpld3-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 notebook-6.1.3 numba-0.48.0 numpy-1.19.1 openpyexcel-2.5.14 pandas-1.1.1 pandocfilters-1.4.2 parso-0.7.1 patsy-0.5.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-7.2.0 plotly-4.9.0 prometheus-client-0.8.0 prompt-toolkit-3.0.7 psutil-5.7.2 ptyprocess-0.6.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pycparser-2.20 pyrsistent-0.16.0 python-dateutil-2.8.1 pyzmq-19.0.2 redis-2.10.6 retrying-1.3.3 scipy-1.5.2 sciris-0.17.4 scirisweb-0.17.0 service-identity-18.1.0 smmap-3.0.4 sqlalchemy-1.3.19 statsmodels-0.12.0 termcolor-1.1.0 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 traitlets-5.0.2 twisted-20.3.0 vine-1.3.0 wcwidth-0.2.5 webencodings-0.5.1 werkzeug-1.0.1 widgetsnbextension-3.5.1 xlrd-1.2.0 xlsxwriter-1.3.3 zipp-3.1.0 zope.interface-5.1.0

[rtd-command-info] start-time: 2020-09-02T20:39:05.776755Z, end-time: 2020-09-02T20:39:10.625554Z, duration: 4, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting sphinx-rtd-theme~=0.5.0
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Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 2)) (1.15.0)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
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  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.11.2)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.24.0)
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Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (20.4)
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Collecting toml
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Collecting py>=1.8.2
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Collecting pluggy<1.0,>=0.12
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Requirement already satisfied: attrs>=17.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from pytest->-r docs/requirements.txt (line 5)) (20.1.0)
Collecting more-itertools>=4.0.0
  Downloading more_itertools-8.5.0-py3-none-any.whl (44 kB)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.1.1)
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Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2020.6.20)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2020.1)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.4.7)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->-r docs/requirements.txt (line 5)) (3.1.0)
Installing collected packages: sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, iniconfig, toml, py, pluggy, more-itertools, pytest
  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 iniconfig-1.0.1 more-itertools-8.5.0 plantweb-1.2.1 pluggy-0.13.1 pockets-0.9.1 py-1.9.0 pytest-6.0.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3 toml-0.10.1

[rtd-command-info] start-time: 2020-09-02T20:39:11.209338Z, end-time: 2020-09-02T20:39:12.630813Z, duration: 1, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating covasim.egg-info
writing covasim.egg-info/PKG-INFO
writing dependency_links to covasim.egg-info/dependency_links.txt
writing requirements to covasim.egg-info/requires.txt
writing top-level names to covasim.egg-info/top_level.txt
writing manifest file 'covasim.egg-info/SOURCES.txt'
reading manifest file 'covasim.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: manifest_maker: MANIFEST.in, line 3: 'recursive-include' expects <dir> <pattern1> <pattern2> ...

warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
writing manifest file 'covasim.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/covasim
copying covasim/run.py -> build/lib/covasim
copying covasim/people.py -> build/lib/covasim
copying covasim/analysis.py -> build/lib/covasim
copying covasim/parameters.py -> build/lib/covasim
copying covasim/misc.py -> build/lib/covasim
copying covasim/defaults.py -> build/lib/covasim
copying covasim/__init__.py -> build/lib/covasim
copying covasim/base.py -> build/lib/covasim
copying covasim/interventions.py -> build/lib/covasim
copying covasim/version.py -> build/lib/covasim
copying covasim/utils.py -> build/lib/covasim
copying covasim/population.py -> build/lib/covasim
copying covasim/requirements.py -> build/lib/covasim
copying covasim/sim.py -> build/lib/covasim
copying covasim/plotting.py -> build/lib/covasim
creating build/lib/covasim/data
copying covasim/data/loaders.py -> build/lib/covasim/data
copying covasim/data/household_size_data.py -> build/lib/covasim/data
copying covasim/data/__init__.py -> build/lib/covasim/data
copying covasim/data/state_age_data.py -> build/lib/covasim/data
copying covasim/data/country_age_data.py -> build/lib/covasim/data
creating build/lib/covasim/webapp
copying covasim/webapp/cova_app.py -> build/lib/covasim/webapp
copying covasim/webapp/__init__.py -> build/lib/covasim/webapp
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/run.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/people.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/analysis.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/parameters.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/misc.py -> build/bdist.linux-x86_64/egg/covasim
creating build/bdist.linux-x86_64/egg/covasim/data
copying build/lib/covasim/data/loaders.py -> build/bdist.linux-x86_64/egg/covasim/data
copying build/lib/covasim/data/household_size_data.py -> build/bdist.linux-x86_64/egg/covasim/data
copying build/lib/covasim/data/__init__.py -> build/bdist.linux-x86_64/egg/covasim/data
copying build/lib/covasim/data/state_age_data.py -> build/bdist.linux-x86_64/egg/covasim/data
copying build/lib/covasim/data/country_age_data.py -> build/bdist.linux-x86_64/egg/covasim/data
copying build/lib/covasim/defaults.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/__init__.py -> build/bdist.linux-x86_64/egg/covasim
creating build/bdist.linux-x86_64/egg/covasim/webapp
copying build/lib/covasim/webapp/cova_app.py -> build/bdist.linux-x86_64/egg/covasim/webapp
copying build/lib/covasim/webapp/__init__.py -> build/bdist.linux-x86_64/egg/covasim/webapp
copying build/lib/covasim/base.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/interventions.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/version.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/utils.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/population.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/requirements.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/sim.py -> build/bdist.linux-x86_64/egg/covasim
copying build/lib/covasim/plotting.py -> build/bdist.linux-x86_64/egg/covasim
byte-compiling build/bdist.linux-x86_64/egg/covasim/run.py to run.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/people.py to people.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/analysis.py to analysis.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/parameters.py to parameters.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/misc.py to misc.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/data/loaders.py to loaders.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/data/household_size_data.py to household_size_data.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/data/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/data/state_age_data.py to state_age_data.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/data/country_age_data.py to country_age_data.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/defaults.py to defaults.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/webapp/cova_app.py to cova_app.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/webapp/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/base.py to base.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/interventions.py to interventions.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/version.py to version.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/population.py to population.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/requirements.py to requirements.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/sim.py to sim.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/covasim/plotting.py to plotting.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying covasim.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying covasim.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying covasim.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying covasim.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying covasim.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
covasim.__pycache__.interventions.cpython-37: module MAY be using inspect.getouterframes
covasim.__pycache__.interventions.cpython-37: module MAY be using inspect.trace
covasim.__pycache__.misc.cpython-37: module references __file__
covasim.__pycache__.misc.cpython-37: module MAY be using inspect.getouterframes
covasim.webapp.__pycache__.cova_app.cpython-37: module references __file__
creating dist
creating 'dist/covasim-1.5.3-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 covasim-1.5.3-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/covasim-1.5.3-py3.7.egg
Extracting covasim-1.5.3-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding covasim 1.5.3 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/covasim-1.5.3-py3.7.egg
Processing dependencies for covasim==1.5.3
Searching for fire==0.3.1
Best match: fire 0.3.1
Adding fire 0.3.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for ipywidgets==7.5.1
Best match: ipywidgets 7.5.1
Adding ipywidgets 7.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for plotly==4.9.0
Best match: plotly 4.9.0
Adding plotly 4.9.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for gunicorn==20.0.4
Best match: gunicorn 20.0.4
Adding gunicorn 20.0.4 to easy-install.pth file
Installing gunicorn script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for scirisweb==0.17.0
Best match: scirisweb 0.17.0
Adding scirisweb 0.17.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for sciris==0.17.4
Best match: sciris 0.17.4
Adding sciris 0.17.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for numba==0.48.0
Best match: numba 0.48.0
Adding numba 0.48.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for statsmodels==0.12.0
Best match: statsmodels 0.12.0
Adding statsmodels 0.12.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for matplotlib==3.3.1
Best match: matplotlib 3.3.1
Adding matplotlib 3.3.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.5.2
Best match: scipy 1.5.2
Adding scipy 1.5.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pandas==1.1.1
Best match: pandas 1.1.1
Adding pandas 1.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for numpy==1.19.1
Best match: numpy 1.19.1
Adding numpy 1.19.1 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for termcolor==1.1.0
Best match: termcolor 1.1.0
Adding termcolor 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/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-covasim/envs/latest/lib/python3.7/site-packages
Searching for widgetsnbextension==3.5.1
Best match: widgetsnbextension 3.5.1
Adding widgetsnbextension 3.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for ipykernel==5.3.4
Best match: ipykernel 5.3.4
Adding ipykernel 5.3.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for nbformat==5.0.7
Best match: nbformat 5.0.7
Adding nbformat 5.0.7 to easy-install.pth file
Installing jupyter-trust script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for ipython==7.18.1
Best match: ipython 7.18.1
Adding ipython 7.18.1 to easy-install.pth file
Installing iptest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing iptest3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for traitlets==5.0.2
Best match: traitlets 5.0.2
Adding traitlets 5.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for retrying==1.3.3
Best match: retrying 1.3.3
Adding retrying 1.3.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for setuptools==41.0.1
Best match: setuptools 41.0.1
Adding setuptools 41.0.1 to easy-install.pth file
Installing easy_install script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing easy_install-3.6 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for decorator==4.4.2
Best match: decorator 4.4.2
Adding decorator 4.4.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for service-identity==18.1.0
Best match: service-identity 18.1.0
Adding service-identity 18.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Flask==1.1.2
Best match: Flask 1.1.2
Adding Flask 1.1.2 to easy-install.pth file
Installing flask script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Werkzeug==1.0.1
Best match: Werkzeug 1.0.1
Adding Werkzeug 1.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for celery==4.4.7
Best match: celery 4.4.7
Adding celery 4.4.7 to easy-install.pth file
Installing celery script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for mpld3==0.5.1
Best match: mpld3 0.5.1
Adding mpld3 0.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for SQLAlchemy==1.3.19
Best match: SQLAlchemy 1.3.19
Adding SQLAlchemy 1.3.19 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/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-covasim/envs/latest/lib/python3.7/site-packages
Searching for redis==2.10.6
Best match: redis 2.10.6
Adding redis 2.10.6 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Twisted==20.3.0
Best match: Twisted 20.3.0
Adding Twisted 20.3.0 to easy-install.pth file
Installing cftp script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing ckeygen script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing conch script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing mailmail script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing pyhtmlizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing tkconch script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing trial script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing twist script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing twistd script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Flask-Session==0.3.2
Best match: Flask-Session 0.3.2
Adding Flask-Session 0.3.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pyasn1==0.4.8
Best match: pyasn1 0.4.8
Adding pyasn1 0.4.8 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Flask-Login==0.5.0
Best match: Flask-Login 0.5.0
Adding Flask-Login 0.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for GitPython==3.1.7
Best match: GitPython 3.1.7
Adding GitPython 3.1.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for requests==2.24.0
Best match: requests 2.24.0
Adding requests 2.24.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for XlsxWriter==1.3.3
Best match: XlsxWriter 1.3.3
Adding XlsxWriter 1.3.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for openpyexcel==2.5.14
Best match: openpyexcel 2.5.14
Adding openpyexcel 2.5.14 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for memory-profiler==0.57.0
Best match: memory-profiler 0.57.0
Adding memory-profiler 0.57.0 to easy-install.pth file
Installing mprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for dill==0.3.2
Best match: dill 0.3.2
Adding dill 0.3.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for line-profiler==3.0.2
Best match: line-profiler 3.0.2
Adding line-profiler 3.0.2 to easy-install.pth file
Installing kernprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jellyfish==0.8.2
Best match: jellyfish 0.8.2
Adding jellyfish 0.8.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for psutil==5.7.2
Best match: psutil 5.7.2
Adding psutil 5.7.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for xlrd==1.2.0
Best match: xlrd 1.2.0
Adding xlrd 1.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jsonpickle==1.4.1
Best match: jsonpickle 1.4.1
Adding jsonpickle 1.4.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for llvmlite==0.31.0
Best match: llvmlite 0.31.0
Adding llvmlite 0.31.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for patsy==0.5.1
Best match: patsy 0.5.1
Adding patsy 0.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Pillow==7.2.0
Best match: Pillow 7.2.0
Adding Pillow 7.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
Adding python-dateutil 2.8.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for kiwisolver==1.2.0
Best match: kiwisolver 1.2.0
Adding kiwisolver 1.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for certifi==2020.6.20
Best match: certifi 2020.6.20
Adding certifi 2020.6.20 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for cycler==0.10.0
Best match: cycler 0.10.0
Adding cycler 0.10.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pytz==2020.1
Best match: pytz 2020.1
Adding pytz 2020.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for notebook==6.1.3
Best match: notebook 6.1.3
Adding notebook 6.1.3 to easy-install.pth file
Installing jupyter-bundlerextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-nbextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-notebook script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-serverextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for tornado==6.0.4
Best match: tornado 6.0.4
Adding tornado 6.0.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jupyter-client==6.1.7
Best match: jupyter-client 6.1.7
Adding jupyter-client 6.1.7 to easy-install.pth file
Installing jupyter-kernel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-kernelspec script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-run script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for ipython-genutils==0.2.0
Best match: ipython-genutils 0.2.0
Adding ipython-genutils 0.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jsonschema==3.2.0
Best match: jsonschema 3.2.0
Adding jsonschema 3.2.0 to easy-install.pth file
Installing jsonschema script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jupyter-core==4.6.3
Best match: jupyter-core 4.6.3
Adding jupyter-core 4.6.3 to easy-install.pth file
Installing jupyter script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-migrate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing jupyter-troubleshoot script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for backcall==0.2.0
Best match: backcall 0.2.0
Adding backcall 0.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Pygments==2.3.1
Best match: Pygments 2.3.1
Adding Pygments 2.3.1 to easy-install.pth file
Installing pygmentize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pickleshare==0.7.5
Best match: pickleshare 0.7.5
Adding pickleshare 0.7.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jedi==0.17.2
Best match: jedi 0.17.2
Adding jedi 0.17.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pexpect==4.8.0
Best match: pexpect 4.8.0
Adding pexpect 4.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for prompt-toolkit==3.0.7
Best match: prompt-toolkit 3.0.7
Adding prompt-toolkit 3.0.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for attrs==20.1.0
Best match: attrs 20.1.0
Adding attrs 20.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pyasn1-modules==0.2.8
Best match: pyasn1-modules 0.2.8
Adding pyasn1-modules 0.2.8 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for cryptography==3.1
Best match: cryptography 3.1
Adding cryptography 3.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for itsdangerous==1.1.0
Best match: itsdangerous 1.1.0
Adding itsdangerous 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Jinja2==2.11.2
Best match: Jinja2 2.11.2
Adding Jinja2 2.11.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for click==7.1.2
Best match: click 7.1.2
Adding click 7.1.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for billiard==3.6.3.0
Best match: billiard 3.6.3.0
Adding billiard 3.6.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for vine==1.3.0
Best match: vine 1.3.0
Adding vine 1.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for kombu==4.6.11
Best match: kombu 4.6.11
Adding kombu 4.6.11 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for incremental==17.5.0
Best match: incremental 17.5.0
Adding incremental 17.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for zope.interface==5.1.0
Best match: zope.interface 5.1.0
Adding zope.interface 5.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Automat==20.2.0
Best match: Automat 20.2.0
Adding Automat 20.2.0 to easy-install.pth file
Installing automat-visualize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for hyperlink==20.0.1
Best match: hyperlink 20.0.1
Adding hyperlink 20.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for constantly==15.1.0
Best match: constantly 15.1.0
Adding constantly 15.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for PyHamcrest==2.0.2
Best match: PyHamcrest 2.0.2
Adding PyHamcrest 2.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for cachelib==0.1.1
Best match: cachelib 0.1.1
Adding cachelib 0.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for gitdb==4.0.5
Best match: gitdb 4.0.5
Adding gitdb 4.0.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for chardet==3.0.4
Best match: chardet 3.0.4
Adding chardet 3.0.4 to easy-install.pth file
Installing chardetect script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for urllib3==1.25.10
Best match: urllib3 1.25.10
Adding urllib3 1.25.10 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for idna==2.10
Best match: idna 2.10
Adding idna 2.10 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for jdcal==1.4.1
Best match: jdcal 1.4.1
Adding jdcal 1.4.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for et-xmlfile==1.0.1
Best match: et-xmlfile 1.0.1
Adding et-xmlfile 1.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for importlib-metadata==1.7.0
Best match: importlib-metadata 1.7.0
Adding importlib-metadata 1.7.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for prometheus-client==0.8.0
Best match: prometheus-client 0.8.0
Adding prometheus-client 0.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for terminado==0.8.3
Best match: terminado 0.8.3
Adding terminado 0.8.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for Send2Trash==1.5.0
Best match: Send2Trash 1.5.0
Adding Send2Trash 1.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for nbconvert==5.6.1
Best match: nbconvert 5.6.1
Adding nbconvert 5.6.1 to easy-install.pth file
Installing jupyter-nbconvert script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pyzmq==19.0.2
Best match: pyzmq 19.0.2
Adding pyzmq 19.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for argon2-cffi==20.1.0
Best match: argon2-cffi 20.1.0
Adding argon2-cffi 20.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pyrsistent==0.16.0
Best match: pyrsistent 0.16.0
Adding pyrsistent 0.16.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for parso==0.7.1
Best match: parso 0.7.1
Adding parso 0.7.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for ptyprocess==0.6.0
Best match: ptyprocess 0.6.0
Adding ptyprocess 0.6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for wcwidth==0.2.5
Best match: wcwidth 0.2.5
Adding wcwidth 0.2.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for cffi==1.14.2
Best match: cffi 1.14.2
Adding cffi 1.14.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for MarkupSafe==1.1.1
Best match: MarkupSafe 1.1.1
Adding MarkupSafe 1.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for amqp==2.6.1
Best match: amqp 2.6.1
Adding amqp 2.6.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for smmap==3.0.4
Best match: smmap 3.0.4
Adding smmap 3.0.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for zipp==3.1.0
Best match: zipp 3.1.0
Adding zipp 3.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pandocfilters==1.4.2
Best match: pandocfilters 1.4.2
Adding pandocfilters 1.4.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for defusedxml==0.6.0
Best match: defusedxml 0.6.0
Adding defusedxml 0.6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for mistune==0.8.4
Best match: mistune 0.8.4
Adding mistune 0.8.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for bleach==3.1.5
Best match: bleach 3.1.5
Adding bleach 3.1.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for entrypoints==0.3
Best match: entrypoints 0.3
Adding entrypoints 0.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for testpath==0.4.4
Best match: testpath 0.4.4
Adding testpath 0.4.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for pycparser==2.20
Best match: pycparser 2.20
Adding pycparser 2.20 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for packaging==20.4
Best match: packaging 20.4
Adding packaging 20.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Searching for webencodings==0.5.1
Best match: webencodings 0.5.1
Adding webencodings 0.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for covasim==1.5.3

[rtd-command-info] start-time: 2020-09-02T20:39:14.198065Z, end-time: 2020-09-02T20:39:14.267919Z, duration: 0, exit-code: 0
cat docs/conf.py
# Sphinx Demo documentation 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
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import subprocess
import sys
import sphinx_rtd_theme

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

# Rename "covasim package" to "API reference"
filename = 'modules.rst' # This must match the Makefile
with open(filename) as f: # Read exitsting file
    lines = f.readlines()
lines[0] = "API reference\n" # Blast away the existing heading and replace with this
lines[1] = "=============\n" # Ensure the heading is the right length
with open(filename, "w") as f: # Write new file
    f.writelines(lines)


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

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

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

plantuml = 'plantweb'

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

autodoc_mock_imports = []


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'


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

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = 'Covasim'
copyright = '2020, Bill & Melinda Gates Foundation. All rights reserved.'
author = '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.
import covasim
version = covasim.__version__
# The full version, including alpha/beta/rc tags.
# release = '1.0'

# The language for content autogenerated by Sphinx. Refer to documentation
# 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']

# suppress warnings for multiple possible Python references in the namespace
# suppress_warnings = ['ref.python']

# 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 documentation 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
# documentation.
# #
# 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> documentation" by default.
#
# html_title = '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 documentation.
#
# 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 = 'Covasim'

# -- 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': '%XeLaTeX packages'
                '\\usepackage{xltxtra}'
                '\\usepackage{fontspec} %%Font package'
                '\\usepackage{xunicode}'
                '%%Select fonts'
                '\\setmainfont[Mapping=tex-text]{nimbusserif}'
                '\\setsansfont[Mapping=tex-text]{nimbussans}'
                '\\setmonofont{nimbusmono}',

    # 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, 'covasim-docs.tex', 'Covasim',
     '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, 'covasim-docs', 'Covasim',
     [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, 'covasim-docs', 'Covasim',
     author, 'Institute for Disease Modeling', 'How to use IDM-Tools 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/covasim/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/covasim/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-covasim',
    'name': u'covasim',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://docs.idmod.org/projects/covasim/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': 'covasim',
    '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': '017a3b72',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

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

[rtd-command-info] start-time: 2020-09-02T20:39:14.416363Z, end-time: 2020-09-02T20:39:29.161764Z, duration: 14, exit-code: 0
python sphinx-build -T -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.2.1
Covasim 1.5.3 (2020-09-01) — © 2020 by IDM
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 30 source files that are out of date
updating environment: [new config] 30 added, 0 changed, 0 removed
reading sources... [  3%] conduct
reading sources... [  6%] contributing
reading sources... [ 10%] covasim.analysis
reading sources... [ 13%] covasim.base
reading sources... [ 16%] covasim.data
reading sources... [ 20%] covasim.data.country_age_data
reading sources... [ 23%] covasim.data.household_size_data
reading sources... [ 26%] covasim.data.loaders
reading sources... [ 30%] covasim.data.state_age_data
reading sources... [ 33%] covasim.defaults
reading sources... [ 36%] covasim.interventions
reading sources... [ 40%] covasim.misc
reading sources... [ 43%] covasim.parameters
reading sources... [ 46%] covasim.people
reading sources... [ 50%] covasim.plotting
reading sources... [ 53%] covasim.population
reading sources... [ 56%] covasim.requirements
reading sources... [ 60%] covasim.run
reading sources... [ 63%] covasim.sim
reading sources... [ 66%] covasim.utils
reading sources... [ 70%] covasim.version
reading sources... [ 73%] covasim.webapp
reading sources... [ 76%] covasim.webapp.cova_app
reading sources... [ 80%] data
reading sources... [ 83%] docker
reading sources... [ 86%] index
reading sources... [ 90%] modules
reading sources... [ 93%] parameters
reading sources... [ 96%] webapp
reading sources... [100%] whatsnew

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  3%] conduct
writing output... [  6%] contributing
writing output... [ 10%] covasim.analysis
writing output... [ 13%] covasim.base
writing output... [ 16%] covasim.data
writing output... [ 20%] covasim.data.country_age_data
writing output... [ 23%] covasim.data.household_size_data
writing output... [ 26%] covasim.data.loaders
writing output... [ 30%] covasim.data.state_age_data
writing output... [ 33%] covasim.defaults
writing output... [ 36%] covasim.interventions
writing output... [ 40%] covasim.misc
writing output... [ 43%] covasim.parameters
writing output... [ 46%] covasim.people
writing output... [ 50%] covasim.plotting
writing output... [ 53%] covasim.population
writing output... [ 56%] covasim.requirements
writing output... [ 60%] covasim.run
writing output... [ 63%] covasim.sim
writing output... [ 66%] covasim.utils
writing output... [ 70%] covasim.version
writing output... [ 73%] covasim.webapp
writing output... [ 76%] covasim.webapp.cova_app
writing output... [ 80%] data
writing output... [ 83%] docker
writing output... [ 86%] index
writing output... [ 90%] modules
writing output... [ 93%] parameters
writing output... [ 96%] webapp
writing output... [100%] whatsnew

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

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2020-09-02T20:39:29.323037Z, end-time: 2020-09-02T20:39:38.051201Z, duration: 8, 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
Covasim 1.5.3 (2020-09-01) — © 2020 by IDM
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] 30 added, 0 changed, 0 removed
reading sources... [  3%] conduct
reading sources... [  6%] contributing
reading sources... [ 10%] covasim.analysis
reading sources... [ 13%] covasim.base
reading sources... [ 16%] covasim.data
reading sources... [ 20%] covasim.data.country_age_data
reading sources... [ 23%] covasim.data.household_size_data
reading sources... [ 26%] covasim.data.loaders
reading sources... [ 30%] covasim.data.state_age_data
reading sources... [ 33%] covasim.defaults
reading sources... [ 36%] covasim.interventions
reading sources... [ 40%] covasim.misc
reading sources... [ 43%] covasim.parameters
reading sources... [ 46%] covasim.people
reading sources... [ 50%] covasim.plotting
reading sources... [ 53%] covasim.population
reading sources... [ 56%] covasim.requirements
reading sources... [ 60%] covasim.run
reading sources... [ 63%] covasim.sim
reading sources... [ 66%] covasim.utils
reading sources... [ 70%] covasim.version
reading sources... [ 73%] covasim.webapp
reading sources... [ 76%] covasim.webapp.cova_app
reading sources... [ 80%] data
reading sources... [ 83%] docker
reading sources... [ 86%] index
reading sources... [ 90%] modules
reading sources... [ 93%] parameters
reading sources... [ 96%] webapp
reading sources... [100%] whatsnew

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... parameters whatsnew contributing conduct webapp docker data modules covasim.data covasim.data.country_age_data covasim.data.household_size_data covasim.data.loaders covasim.data.state_age_data covasim.webapp covasim.webapp.cova_app covasim.analysis covasim.base covasim.defaults covasim.interventions covasim.misc covasim.parameters covasim.people covasim.plotting covasim.population covasim.requirements covasim.run covasim.sim covasim.utils covasim.version done
writing... done
writing additional files...  opensearchdone
copying static files... ... done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.

[rtd-command-info] start-time: 2020-09-02T20:39:38.453718Z, end-time: 2020-09-02T20:39:47.299326Z, duration: 8, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v3.2.1
Covasim 1.5.3 (2020-09-01) — © 2020 by IDM
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] 30 added, 0 changed, 0 removed
reading sources... [  3%] conduct
reading sources... [  6%] contributing
reading sources... [ 10%] covasim.analysis
reading sources... [ 13%] covasim.base
reading sources... [ 16%] covasim.data
reading sources... [ 20%] covasim.data.country_age_data
reading sources... [ 23%] covasim.data.household_size_data
reading sources... [ 26%] covasim.data.loaders
reading sources... [ 30%] covasim.data.state_age_data
reading sources... [ 33%] covasim.defaults
reading sources... [ 36%] covasim.interventions
reading sources... [ 40%] covasim.misc
reading sources... [ 43%] covasim.parameters
reading sources... [ 46%] covasim.people
reading sources... [ 50%] covasim.plotting
reading sources... [ 53%] covasim.population
reading sources... [ 56%] covasim.requirements
reading sources... [ 60%] covasim.run
reading sources... [ 63%] covasim.sim
reading sources... [ 66%] covasim.utils
reading sources... [ 70%] covasim.version
reading sources... [ 73%] covasim.webapp
reading sources... [ 76%] covasim.webapp.cova_app
reading sources... [ 80%] data
reading sources... [ 83%] docker
reading sources... [ 86%] index
reading sources... [ 90%] modules
reading sources... [ 93%] parameters
reading sources... [ 96%] webapp
reading sources... [100%] whatsnew

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing covasim-docs.tex... index parameters whatsnew contributing conduct webapp docker data modules covasim.data covasim.data.country_age_data covasim.data.household_size_data covasim.data.loaders covasim.data.state_age_data covasim.webapp covasim.webapp.cova_app covasim.analysis covasim.base covasim.defaults covasim.interventions covasim.misc covasim.parameters covasim.people covasim.plotting covasim.population covasim.requirements covasim.run covasim.sim covasim.utils covasim.version 
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).

[rtd-command-info] start-time: 2020-09-02T20:39:47.595508Z, end-time: 2020-09-02T20:39:47.655064Z, 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'" );
}

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[1] [2]
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[][][]$\T1/ptm/m/n/10 https : / / population . un . org / household / exceldata
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