Read the Docs build information
Build id: 498953
Project: institute-for-disease-modeling-covasim
Version: latest
Commit: 569d9c762a5b893eb1036a62f86b90a7d151ba88
Date: 2020-12-05T23:23:12.576398Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-12-05T23:23:14.167801Z, end-time: 2020-12-05T23:23:15.892429Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/covasim.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2020-12-05T23:23:16.235537Z, end-time: 2020-12-05T23:23:16.304132Z, 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 569d9c7 update docs numba version

[rtd-command-info] start-time: 2020-12-05T23:23:16.446582Z, end-time: 2020-12-05T23:23:16.503293Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-12-05T23:23:17.751711Z, end-time: 2020-12-05T23:23:21.807271Z, 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-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: 2020-12-05T23:23:21.968271Z, end-time: 2020-12-05T23:23:23.686188Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (20.3.1)

[rtd-command-info] start-time: 2020-12-05T23:23:23.850235Z, end-time: 2020-12-05T23:23:33.134563Z, 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
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=7b3901911f9ac28915992a3b799d720699a2d35558ab11a9ed8b45a2c154492c
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Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.7 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-50.3.2 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2

[rtd-command-info] start-time: 2020-12-05T23:23:33.243964Z, end-time: 2020-12-05T23:23:50.941727Z, duration: 17, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Building wheels for collected packages: optuna, pandocfilters, PrettyTable, pyperclip, pyrsistent, PyYAML
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  Stored in directory: /tmp/pip-ephem-wheel-cache-1ev1zxan/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000
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Successfully built optuna pandocfilters PrettyTable pyperclip pyrsistent PyYAML
Installing collected packages: zipp, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, wcwidth, pyperclip, pbr, nest-asyncio, nbformat, jupyter-client, colorama, async-generator, testpath, stevedore, sqlalchemy, PyYAML, python-editor, PrettyTable, pandocfilters, nbclient, mistune, Mako, jupyterlab-pygments, entrypoints, defusedxml, cmd2, bleach, tqdm, toml, py, pockets, pluggy, nbconvert, llvmlite, joblib, iniconfig, colorlog, cmaes, cliff, alembic, sphinxcontrib-napoleon, pytest, plantweb, optuna, numba, nbsphinx
Successfully installed Mako-1.1.3 PrettyTable-0.7.2 PyYAML-5.3.1 alembic-1.4.3 async-generator-1.10 attrs-20.3.0 bleach-3.2.1 cliff-3.5.0 cmaes-0.7.0 cmd2-1.4.0 colorama-0.4.4 colorlog-4.6.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-3.1.1 iniconfig-1.1.1 ipython-genutils-0.2.0 joblib-0.17.0 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.7.0 jupyterlab-pygments-0.1.2 llvmlite-0.31.0 mistune-0.8.4 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nbsphinx-0.8.0 nest-asyncio-1.4.3 numba-0.48.0 optuna-2.3.0 pandocfilters-1.4.3 pbr-5.5.1 plantweb-1.2.1 pluggy-0.13.1 pockets-0.9.1 py-1.9.0 pyperclip-1.8.1 pyrsistent-0.17.3 pytest-6.1.2 python-editor-1.0.4 pyzmq-20.0.0 sphinxcontrib-napoleon-0.7 sqlalchemy-1.3.20 stevedore-3.3.0 testpath-0.4.4 toml-0.10.2 tornado-6.1 tqdm-4.54.1 traitlets-5.0.5 wcwidth-0.2.5 webencodings-0.5.1 zipp-3.4.0

[rtd-command-info] start-time: 2020-12-05T23:23:51.046556Z, end-time: 2020-12-05T23:24:03.320785Z, duration: 12, 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: manifest_maker: MANIFEST.in, line 5: '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/settings.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/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
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/settings.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/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/settings.py to settings.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__.misc.cpython-37: module references __file__
creating dist
creating 'dist/covasim-2.0.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing covasim-2.0.0-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/covasim-2.0.0-py3.7.egg
Extracting covasim-2.0.0-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 2.0.0 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-2.0.0-py3.7.egg
Processing dependencies for covasim==2.0.0
Searching for sciris>=1.0.0
Reading https://pypi.org/simple/sciris/
Downloading https://files.pythonhosted.org/packages/4d/c6/a61bf5405a640fa42d8897b795bfb04ab1eb406e07e2d72c1b44cce6f651/sciris-1.0.0-py3-none-any.whl#sha256=42b04033ceb5ee0c09617ffa83f7bb63c511b06ecbe40b142f1c44844fd37a24
Best match: sciris 1.0.0
Processing sciris-1.0.0-py3-none-any.whl
Installing sciris-1.0.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sciris-1.0.0-py3.7.egg/EGG-INFO/requires.txt
Adding sciris 1.0.0 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/sciris-1.0.0-py3.7.egg
Searching for statsmodels
Reading https://pypi.org/simple/statsmodels/
Downloading https://files.pythonhosted.org/packages/93/97/67bf20df36a88ce8dd84828f83453b91177e1ff0abd8c92f2e0a47782689/statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=588c0f7e29403161ca952dcdad3d67970583742e9f11f66c7c5b08ac97a0408c
Best match: statsmodels 0.12.1
Processing statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl
Installing statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/statsmodels-0.12.1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding statsmodels 0.12.1 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/statsmodels-0.12.1-py3.7-linux-x86_64.egg
Searching for xlsxwriter
Reading https://pypi.org/simple/xlsxwriter/
Downloading https://files.pythonhosted.org/packages/6b/41/bf1aae04932d1eaffee1fc5f8b38ca47bbbf07d765129539bc4bcce1ce0c/XlsxWriter-1.3.7-py2.py3-none-any.whl#sha256=b807c2d3e379bf6a925f472955beef3e07495c1bac708640696876e68675b49b
Best match: XlsxWriter 1.3.7
Processing XlsxWriter-1.3.7-py2.py3-none-any.whl
Installing XlsxWriter-1.3.7-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding XlsxWriter 1.3.7 to easy-install.pth file
Installing vba_extract.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/XlsxWriter-1.3.7-py3.7.egg
Searching for xlrd
Reading https://pypi.org/simple/xlrd/
Downloading https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl#sha256=e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde
Best match: xlrd 1.2.0
Processing xlrd-1.2.0-py2.py3-none-any.whl
Installing xlrd-1.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding xlrd 1.2.0 to easy-install.pth file
Installing runxlrd.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/xlrd-1.2.0-py3.7.egg
Searching for psutil
Reading https://pypi.org/simple/psutil/
Downloading https://files.pythonhosted.org/packages/33/e0/82d459af36bda999f82c7ea86c67610591cf5556168f48fd6509e5fa154d/psutil-5.7.3.tar.gz#sha256=af73f7bcebdc538eda9cc81d19db1db7bf26f103f91081d780bbacfcb620dee2
Best match: psutil 5.7.3
Processing psutil-5.7.3.tar.gz
Writing /tmp/easy_install-l2fgvsv5/psutil-5.7.3/setup.cfg
Running psutil-5.7.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-l2fgvsv5/psutil-5.7.3/egg-dist-tmp-utp__6o6
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/psutil-5.7.3-py3.7-linux-x86_64.egg
Extracting psutil-5.7.3-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding psutil 5.7.3 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/psutil-5.7.3-py3.7-linux-x86_64.egg
Searching for openpyexcel>=2.5
Reading https://pypi.org/simple/openpyexcel/
Downloading https://files.pythonhosted.org/packages/32/e1/722047fae7a46b658d7fa038cf5b952fbbb150c3c8a31012e4fb76eba27d/openpyexcel-2.5.14-py2.py3-none-any.whl#sha256=f18f4efadbc25a26870885f342e14b6cd6862ca1f4b8195b394fc2681ccdbaab
Best match: openpyexcel 2.5.14
Processing openpyexcel-2.5.14-py2.py3-none-any.whl
Installing openpyexcel-2.5.14-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/openpyexcel-2.5.14-py3.7.egg/EGG-INFO/requires.txt
Adding openpyexcel 2.5.14 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/openpyexcel-2.5.14-py3.7.egg
Searching for multiprocess
Reading https://pypi.org/simple/multiprocess/
Downloading https://files.pythonhosted.org/packages/db/20/458ac043a57322365ac2ed86a911bf7598fc2e49bccb3f94ea810fbb6b9b/multiprocess-0.70.11.1-py37-none-any.whl#sha256=164c77448e357ebee0dc6abc7ee8c823e40e295e629a5fc6d31725109a3a7ee9
Best match: multiprocess 0.70.11.1
Processing multiprocess-0.70.11.1-py37-none-any.whl
Installing multiprocess-0.70.11.1-py37-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/multiprocess-0.70.11.1-py3.7.egg/EGG-INFO/requires.txt
Adding multiprocess 0.70.11.1 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/multiprocess-0.70.11.1-py3.7.egg
Searching for memory-profiler
Reading https://pypi.org/simple/memory-profiler/
Downloading https://files.pythonhosted.org/packages/8f/fd/d92b3295657f8837e0177e7b48b32d6651436f0293af42b76d134c3bb489/memory_profiler-0.58.0.tar.gz#sha256=01385ac0fec944fcf7969814ec4406c6d8a9c66c079d09276723c5a7680f44e5
Best match: memory-profiler 0.58.0
Processing memory_profiler-0.58.0.tar.gz
Writing /tmp/easy_install-_iz350ej/memory_profiler-0.58.0/setup.cfg
Running memory_profiler-0.58.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-_iz350ej/memory_profiler-0.58.0/egg-dist-tmp-e6p6ibf2
warning: no files found matching 'mprof.bat'
zip_safe flag not set; analyzing archive contents...
__pycache__.memory_profiler.cpython-37: module MAY be using inspect.getsourcefile
__pycache__.memory_profiler.cpython-37: module MAY be using inspect.stack
__pycache__.memory_profiler.cpython-37: module MAY be using inspect.trace
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/memory_profiler-0.58.0-py3.7.egg
Extracting memory_profiler-0.58.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding memory-profiler 0.58.0 to easy-install.pth file
Installing mprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/memory_profiler-0.58.0-py3.7.egg
Searching for line-profiler
Reading https://pypi.org/simple/line-profiler/
Downloading https://files.pythonhosted.org/packages/fb/89/cb7787463c0bc676d3200d278d26a732ce4921ba5efce6eb8e1fc29b6fff/line_profiler-3.1.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=2b937d8b207cee753d175cc65907901bd9ccadfe20ff2038df9aeae2eafcba6b
Best match: line-profiler 3.1.0
Processing line_profiler-3.1.0-cp37-cp37m-manylinux1_x86_64.whl
Installing line_profiler-3.1.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/line_profiler-3.1.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding line-profiler 3.1.0 to easy-install.pth file
Installing kernprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/line_profiler-3.1.0-py3.7-linux-x86_64.egg
Searching for jsonpickle
Reading https://pypi.org/simple/jsonpickle/
Downloading https://files.pythonhosted.org/packages/ee/d5/1cc282dc23346a43aab461bf2e8c36593aacd34242bee1a13fa750db0cfe/jsonpickle-1.4.2-py2.py3-none-any.whl#sha256=2ac5863099864c63d7f0c367af5e512c94f3384977dd367f2eae5f2303f7b92c
Best match: jsonpickle 1.4.2
Processing jsonpickle-1.4.2-py2.py3-none-any.whl
Installing jsonpickle-1.4.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jsonpickle-1.4.2-py3.7.egg/EGG-INFO/requires.txt
Adding jsonpickle 1.4.2 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/jsonpickle-1.4.2-py3.7.egg
Searching for jellyfish
Reading https://pypi.org/simple/jellyfish/
Downloading https://files.pythonhosted.org/packages/04/3f/d03cb056f407ef181a45569255348457b1a0915fc4eb23daeceb930a68a4/jellyfish-0.8.2.tar.gz#sha256=a499741401512d05bbd3556e448e960bc908eba3879fb73d450e8e91566a030b
Best match: jellyfish 0.8.2
Processing jellyfish-0.8.2.tar.gz
Writing /tmp/easy_install-l8838oqt/jellyfish-0.8.2/setup.cfg
Running jellyfish-0.8.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-l8838oqt/jellyfish-0.8.2/egg-dist-tmp-8a8poc7m
warning: no previously-included files matching '.git' found anywhere in distribution
cjellyfish/soundex.c: In function ‘soundex’:
cjellyfish/soundex.c:8:10: warning: ‘c’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     char c, prev;
          ^
cjellyfish/porter.c: In function ‘m’:
cjellyfish/porter.c:127:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if (! cons(z, i)) break; i++;
       ^~
cjellyfish/porter.c:127:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       if (! cons(z, i)) break; i++;
                                ^
cjellyfish/porter.c: In function ‘step4’:
cjellyfish/porter.c:339:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (ends(z, 4, "ence")) break; return;
                 ^~
cjellyfish/porter.c:339:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
                 if (ends(z, 4, "ence")) break; return;
                                                ^~~~~~
cjellyfish/porter.c:343:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (ends(z, 4, "ible")) break; return;
                 ^~
cjellyfish/porter.c:343:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
                 if (ends(z, 4, "ible")) break; return;
                                                ^~~~~~
cjellyfish/porter.c:347:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (ends(z, 3, "ent")) break; return;
                 ^~
cjellyfish/porter.c:347:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
                 if (ends(z, 3, "ent")) break; return;
                                               ^~~~~~
cjellyfish/porter.c:349:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (ends(z, 2, "ou")) break; return;
                 ^~
cjellyfish/porter.c:349:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
                 if (ends(z, 2, "ou")) break; return;
                                              ^~~~~~
cjellyfish/porter.c:353:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (ends(z, 3, "iti")) break; return;
                 ^~
cjellyfish/porter.c:353:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
                 if (ends(z, 3, "iti")) break; return;
                                               ^~~~~~
zip_safe flag not set; analyzing archive contents...
jellyfish.__pycache__.cjellyfish.cpython-37: module references __file__
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jellyfish-0.8.2-py3.7-linux-x86_64.egg
Extracting jellyfish-0.8.2-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding jellyfish 0.8.2 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/jellyfish-0.8.2-py3.7-linux-x86_64.egg
Searching for gitpython
Reading https://pypi.org/simple/gitpython/
Downloading https://files.pythonhosted.org/packages/24/d1/a7f8fe3df258549b303415157328bfcc63e9b11d06a7ad7a3327f3d32606/GitPython-3.1.11-py3-none-any.whl#sha256=6eea89b655917b500437e9668e4a12eabdcf00229a0df1762aabd692ef9b746b
Best match: GitPython 3.1.11
Processing GitPython-3.1.11-py3-none-any.whl
Installing GitPython-3.1.11-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/GitPython-3.1.11-py3.7.egg/EGG-INFO/requires.txt
Adding GitPython 3.1.11 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/GitPython-3.1.11-py3.7.egg
Searching for dill
Reading https://pypi.org/simple/dill/
Downloading https://files.pythonhosted.org/packages/52/d6/79f40d230895fa1ce3b6af0d22e0ac79c65175dc069c194b79cc8e05a033/dill-0.3.3-py2.py3-none-any.whl#sha256=78370261be6ea49037ace8c17e0b7dd06d0393af6513cc23f9b222d9367ce389
Best match: dill 0.3.3
Processing dill-0.3.3-py2.py3-none-any.whl
Installing dill-0.3.3-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/dill-0.3.3-py3.7.egg/EGG-INFO/requires.txt
Adding dill 0.3.3 to easy-install.pth file
Installing undill script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin
Installing get_objgraph script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/dill-0.3.3-py3.7.egg
Searching for patsy>=0.5
Reading https://pypi.org/simple/patsy/
Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl#sha256=5465be1c0e670c3a965355ec09e9a502bf2c4cbe4875e8528b0221190a8a5d40
Best match: patsy 0.5.1
Processing patsy-0.5.1-py2.py3-none-any.whl
Installing patsy-0.5.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/patsy-0.5.1-py3.7.egg/EGG-INFO/requires.txt
Adding patsy 0.5.1 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/patsy-0.5.1-py3.7.egg
Searching for jdcal
Reading https://pypi.org/simple/jdcal/
Downloading https://files.pythonhosted.org/packages/f0/da/572cbc0bc582390480bbd7c4e93d14dc46079778ed915b505dc494b37c57/jdcal-1.4.1-py2.py3-none-any.whl#sha256=1abf1305fce18b4e8aa248cf8fe0c56ce2032392bc64bbd61b5dff2a19ec8bba
Best match: jdcal 1.4.1
Processing jdcal-1.4.1-py2.py3-none-any.whl
Installing jdcal-1.4.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding jdcal 1.4.1 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/jdcal-1.4.1-py3.7.egg
Searching for et-xmlfile
Reading https://pypi.org/simple/et-xmlfile/
Downloading https://files.pythonhosted.org/packages/22/28/a99c42aea746e18382ad9fb36f64c1c1f04216f41797f2f0fa567da11388/et_xmlfile-1.0.1.tar.gz#sha256=614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b
Best match: et-xmlfile 1.0.1
Processing et_xmlfile-1.0.1.tar.gz
Writing /tmp/easy_install-0al57qlb/et_xmlfile-1.0.1/setup.cfg
Running et_xmlfile-1.0.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-0al57qlb/et_xmlfile-1.0.1/egg-dist-tmp-r1c4tiwa
zip_safe flag not set; analyzing archive contents...
et_xmlfile.tests.__pycache__.common_imports.cpython-37: module references __file__
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/et_xmlfile-1.0.1-py3.7.egg
Extracting et_xmlfile-1.0.1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding et-xmlfile 1.0.1 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/et_xmlfile-1.0.1-py3.7.egg
Searching for IPython
Reading https://pypi.org/simple/IPython/
Downloading https://files.pythonhosted.org/packages/e0/c7/1c91a71b413c82cd4c49fb8b6676f6135650cd2cca2745a96bd84a56166c/ipython-7.19.0-py3-none-any.whl#sha256=c987e8178ced651532b3b1ff9965925bfd445c279239697052561a9ab806d28f
Best match: ipython 7.19.0
Processing ipython-7.19.0-py3-none-any.whl
Installing ipython-7.19.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/ipython-7.19.0-py3.7.egg/EGG-INFO/requires.txt
Adding ipython 7.19.0 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

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/ipython-7.19.0-py3.7.egg
Searching for gitdb<5,>=4.0.1
Reading https://pypi.org/simple/gitdb/
Downloading https://files.pythonhosted.org/packages/48/11/d1800bca0a3bae820b84b7d813ad1eff15a48a64caea9c823fc8c1b119e8/gitdb-4.0.5-py3-none-any.whl#sha256=91f36bfb1ab7949b3b40e23736db18231bf7593edada2ba5c3a174a7b23657ac
Best match: gitdb 4.0.5
Processing gitdb-4.0.5-py3-none-any.whl
Installing gitdb-4.0.5-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/gitdb-4.0.5-py3.7.egg/EGG-INFO/requires.txt
Adding gitdb 4.0.5 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/gitdb-4.0.5-py3.7.egg
Searching for prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
Reading https://pypi.org/simple/prompt-toolkit/
Downloading https://files.pythonhosted.org/packages/8a/aa/198e6a857e83ea8b711a6ae0c37717c0eb1b23ff52e3732a644fcd389cb3/prompt_toolkit-3.0.8-py3-none-any.whl#sha256=7debb9a521e0b1ee7d2fe96ee4bd60ef03c6492784de0547337ca4433e46aa63
Best match: prompt-toolkit 3.0.8
Processing prompt_toolkit-3.0.8-py3-none-any.whl
Installing prompt_toolkit-3.0.8-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/prompt_toolkit-3.0.8-py3.7.egg/EGG-INFO/requires.txt
Adding prompt-toolkit 3.0.8 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/prompt_toolkit-3.0.8-py3.7.egg
Searching for pickleshare
Reading https://pypi.org/simple/pickleshare/
Downloading https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl#sha256=9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56
Best match: pickleshare 0.7.5
Processing pickleshare-0.7.5-py2.py3-none-any.whl
Installing pickleshare-0.7.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding pickleshare 0.7.5 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/pickleshare-0.7.5-py3.7.egg
Searching for pexpect>4.3
Reading https://pypi.org/simple/pexpect/
Downloading https://files.pythonhosted.org/packages/39/7b/88dbb785881c28a102619d46423cb853b46dbccc70d3ac362d99773a78ce/pexpect-4.8.0-py2.py3-none-any.whl#sha256=0b48a55dcb3c05f3329815901ea4fc1537514d6ba867a152b581d69ae3710937
Best match: pexpect 4.8.0
Processing pexpect-4.8.0-py2.py3-none-any.whl
Installing pexpect-4.8.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/pexpect-4.8.0-py3.7.egg/EGG-INFO/requires.txt
Adding pexpect 4.8.0 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/pexpect-4.8.0-py3.7.egg
Searching for jedi>=0.10
Reading https://pypi.org/simple/jedi/
Downloading https://files.pythonhosted.org/packages/c3/d4/36136b18daae06ad798966735f6c3fb96869c1be9f8245d2a8f556e40c36/jedi-0.17.2-py2.py3-none-any.whl#sha256=98cc583fa0f2f8304968199b01b6b4b94f469a1f4a74c1560506ca2a211378b5
Best match: jedi 0.17.2
Processing jedi-0.17.2-py2.py3-none-any.whl
Installing jedi-0.17.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jedi-0.17.2-py3.7.egg/EGG-INFO/requires.txt
Adding jedi 0.17.2 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/jedi-0.17.2-py3.7.egg
Searching for decorator
Reading https://pypi.org/simple/decorator/
Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760
Best match: decorator 4.4.2
Processing decorator-4.4.2-py2.py3-none-any.whl
Installing decorator-4.4.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding decorator 4.4.2 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/decorator-4.4.2-py3.7.egg
Searching for backcall
Reading https://pypi.org/simple/backcall/
Downloading https://files.pythonhosted.org/packages/4c/1c/ff6546b6c12603d8dd1070aa3c3d273ad4c07f5771689a7b69a550e8c951/backcall-0.2.0-py2.py3-none-any.whl#sha256=fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255
Best match: backcall 0.2.0
Processing backcall-0.2.0-py2.py3-none-any.whl
Installing backcall-0.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding backcall 0.2.0 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/backcall-0.2.0-py3.7.egg
Searching for smmap<4,>=3.0.1
Reading https://pypi.org/simple/smmap/
Downloading https://files.pythonhosted.org/packages/b0/9a/4d409a6234eb940e6a78dfdfc66156e7522262f5f2fecca07dc55915952d/smmap-3.0.4-py2.py3-none-any.whl#sha256=54c44c197c819d5ef1991799a7e30b662d1e520f2ac75c9efbeb54a742214cf4
Best match: smmap 3.0.4
Processing smmap-3.0.4-py2.py3-none-any.whl
Installing smmap-3.0.4-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding smmap 3.0.4 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/smmap-3.0.4-py3.7.egg
Searching for ptyprocess>=0.5
Reading https://pypi.org/simple/ptyprocess/
Downloading https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl#sha256=d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f
Best match: ptyprocess 0.6.0
Processing ptyprocess-0.6.0-py2.py3-none-any.whl
Installing ptyprocess-0.6.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
Adding ptyprocess 0.6.0 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/ptyprocess-0.6.0-py3.7.egg
Searching for parso<0.8.0,>=0.7.0
Reading https://pypi.org/simple/parso/
Downloading https://files.pythonhosted.org/packages/93/d1/e635bdde32890db5aeb2ffbde17e74f68986305a4466b0aa373b861e3f00/parso-0.7.1-py2.py3-none-any.whl#sha256=97218d9159b2520ff45eb78028ba8b50d2bc61dcc062a9682666f2dc4bd331ea
Best match: parso 0.7.1
Processing parso-0.7.1-py2.py3-none-any.whl
Installing parso-0.7.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/parso-0.7.1-py3.7.egg/EGG-INFO/requires.txt
Adding parso 0.7.1 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/parso-0.7.1-py3.7.egg
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 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 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 numpy==1.19.2
Best match: numpy 1.19.2
numpy 1.19.2 is already the active version in easy-install.pth
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for requests==2.25.0
Best match: requests 2.25.0
Adding requests 2.25.0 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 setuptools==50.3.2
Best match: setuptools 50.3.2
Adding setuptools 50.3.2 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-3.8 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 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 Pillow==8.0.0
Best match: Pillow 8.0.0
Pillow 8.0.0 is already the active version in easy-install.pth

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

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

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

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for 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 pytz==2020.4
Best match: pytz 2020.4
Adding pytz 2020.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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 urllib3==1.26.2
Best match: urllib3 1.26.2
Adding urllib3 1.26.2 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 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 importlib-metadata==3.1.1
Best match: importlib-metadata 3.1.1
Adding importlib-metadata 3.1.1 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 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 traitlets==5.0.5
Best match: traitlets 5.0.5
Adding traitlets 5.0.5 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 Pygments==2.7.2
Best match: Pygments 2.7.2
Adding Pygments 2.7.2 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 zipp==3.4.0
Best match: zipp 3.4.0
Adding zipp 3.4.0 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 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 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
Finished processing dependencies for covasim==2.0.0

[rtd-command-info] start-time: 2020-12-05T23:24:04.719251Z, end-time: 2020-12-05T23:24:04.790750Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config


# 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

on_rtd = os.environ.get('READTHEDOCS') == 'True'

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.mathjax',
    'sphinx.ext.githubpages',
    'sphinx.ext.autodoc',
    'sphinx.ext.napoleon',
    'sphinx.ext.todo',
    'sphinx.ext.viewcode',  # Add a link to the Python source code for classes, functions etc.
    'plantweb.directive',
    'nbsphinx',
]

plantuml = 'plantweb'

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

autodoc_mock_imports = []


napoleon_google_docstring = True

# Configure autosummary
autosummary_generate = True  # Turn on sphinx.ext.autosummary
autoclass_content = "both"  # Add __init__ doc (ie. params) to class summaries
html_show_sourcelink = False  # Remove 'view source code' from top of page (for html, not python)
autodoc_member_order = 'bysource' # Keep original ordering
add_module_names = False  # NB, does not work
autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes

# 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'
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 as cv
version = cv.__version__
# The full version, including alpha/beta/rc tags.
release = cv.__version__

# 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']


pygments_style = 'sphinx'

# 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'

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


html_logo = "images/IDM_white.png"
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 = {
    'rtd_url': 'https://docs.idmod.org/projects/covasim/en/latest',
    'theme_vcs_pageview_mode': 'edit',
    '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.
#
if not on_rtd:
    html_extra_path = ['robots.txt']

# 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 = 'Y%-%b-%d'


# 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 = 'docs.idmod.org/projects/covasim/en/latest'

# 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

# -- 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'),
]

# Example configuration for intersphinx: refer to the Python standard library.
# intersphinx_mapping = {'https://docs.python.org/': None}

# Configure nbsphinx
nbsphinx_kernel_name = "python"
nbsphinx_timeout = 60 # Time in seconds; use -1 for no timeout
nbsphinx_execute_arguments = [
    "--InlineBackend.figure_formats={'svg', 'pdf'}",
    "--InlineBackend.rc=figure.dpi=96",
]

# Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs
nb_ex_default = ['auto', 'never'][0]
nb_ex = os.getenv('NBSPHINX_EXECUTE')
if not nb_ex: nb_ex = nb_ex_default
print(f'\n\nBuilding Jupyter notebooks with build option: {nb_ex}\n\n')
nbsphinx_execute = nb_ex




###########################################################################
#          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': [
    ("latest", "/en/latest/"),
    ],
    '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': '569d9c76',
}




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: 2020-12-05T23:24:04.939761Z, end-time: 2020-12-05T23:25:13.573305Z, duration: 68, exit-code: 2
python sphinx-build -T -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
Matplotlib is building the font cache; this may take a moment.
Covasim 2.0.0 (2020-12-05) — © 2020 by IDM


Building Jupyter notebooks with build option: auto


loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 40 source files that are out of date
updating environment: 40 added, 0 changed, 0 removed
reading sources... [  2%] conduct
reading sources... [  5%] contributing
reading sources... [  7%] covasim.analysis
reading sources... [ 10%] covasim.base
reading sources... [ 12%] covasim.data
reading sources... [ 15%] covasim.data.country_age_data
reading sources... [ 17%] covasim.data.household_size_data
reading sources... [ 20%] covasim.data.loaders
reading sources... [ 22%] covasim.data.state_age_data
reading sources... [ 25%] covasim.defaults
reading sources... [ 27%] covasim.interventions
reading sources... [ 30%] covasim.misc
reading sources... [ 32%] covasim.parameters
reading sources... [ 35%] covasim.people
reading sources... [ 37%] covasim.plotting
reading sources... [ 40%] covasim.population
reading sources... [ 42%] covasim.requirements
reading sources... [ 45%] covasim.run
reading sources... [ 47%] covasim.settings
reading sources... [ 50%] covasim.sim
reading sources... [ 52%] covasim.utils
reading sources... [ 55%] covasim.version
reading sources... [ 57%] data
reading sources... [ 60%] faq
reading sources... [ 62%] glossary
reading sources... [ 65%] index
reading sources... [ 67%] modules
reading sources... [ 70%] overview
reading sources... [ 72%] parameters
reading sources... [ 75%] tutorials/README
reading sources... [ 77%] tutorials/t1
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client/localinterfaces.py:247: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 1021, in parse
    rststring, resources = exporter.from_notebook_node(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 832, in from_notebook_node
    nb, resources = pp.preprocess(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 79, in preprocess
    self.execute()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbclient/client.py", line 524, in async_execute
    async with self.async_setup_kernel(**kwargs):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/async_generator/_util.py", line 34, in __aenter__
    return await self._agen.asend(None)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbclient/client.py", line 482, in async_setup_kernel
    await self.async_start_new_kernel(**kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbclient/client.py", line 394, in async_start_new_kernel
    await ensure_async(self.km.start_kernel(extra_arguments=self.extra_arguments, **kwargs))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbclient/util.py", line 85, in ensure_async
    result = await obj
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client/manager.py", line 571, in start_kernel
    kernel_cmd, kw = self.pre_start_kernel(**kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client/manager.py", line 262, in pre_start_kernel
    kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client/manager.py", line 181, in format_kernel_cmd
    cmd = self.kernel_spec.argv + extra_arguments
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client/manager.py", line 87, in kernel_spec
    self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client/kernelspec.py", line 235, in get_kernel_spec
    raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: No such kernel named python3

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 304, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 341, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 347, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 360, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 468, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 490, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 534, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sphinx/io.py", line 318, in read_doc
    pub.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 1032, in parse
    str(e))
nbsphinx.NotebookError: NoSuchKernel in tutorials/t1.ipynb:
No such kernel named python3

Notebook error:
NoSuchKernel in tutorials/t1.ipynb:
No such kernel named python3