Read the Docs build information
Build id: 407969
Project: institute-for-disease-modeling-synthpops-test
Version: latest
Commit: 82c36eec3d7adf62bfede3e9716605d2e512b2ef
Date: 2020-08-28T21:23:46.427783Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-08-28T21:23:47.932968Z, end-time: 2020-08-28T21:23:52.287607Z, duration: 4, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/JSchripsema-IDM/synthpops-2.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-08-28T21:23:52.727899Z, end-time: 2020-08-28T21:23:53.977175Z, duration: 1, exit-code: 0
git checkout --force origin/rtd
Note: checking out 'origin/rtd'.

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 82c36ee added fail_on_warning flag to YAML and updates to generate-api code to fix warnings seen on RTD build

[rtd-command-info] start-time: 2020-08-28T21:23:54.101443Z, end-time: 2020-08-28T21:23:54.150371Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-08-28T21:23:55.926797Z, end-time: 2020-08-28T21:23:59.696215Z, 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-synthpops-test/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-08-28T21:23:59.952665Z, end-time: 2020-08-28T21:24:00.594606Z, 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-synthpops-test/envs/latest/lib/python3.7/site-packages (20.2.2)

[rtd-command-info] start-time: 2020-08-28T21:24:00.846460Z, end-time: 2020-08-28T21:24:08.782561Z, 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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Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, pytz, babel, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, certifi, chardet, urllib3, idna, requests, MarkupSafe, Jinja2, imagesize, pyparsing, six, 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: 2020-08-28T21:24:09.044490Z, end-time: 2020-08-28T21:24:11.861168Z, duration: 2, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.1.4)
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Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-qthelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb
  Attempting uninstall: sphinx
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Successfully installed plantweb-1.2.1 pockets-0.9.1 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

[rtd-command-info] start-time: 2020-08-28T21:24:12.724521Z, end-time: 2020-08-28T21:24:34.504767Z, duration: 21, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating synthpops.egg-info
writing synthpops.egg-info/PKG-INFO
writing dependency_links to synthpops.egg-info/dependency_links.txt
writing requirements to synthpops.egg-info/requires.txt
writing top-level names to synthpops.egg-info/top_level.txt
writing manifest file 'synthpops.egg-info/SOURCES.txt'
reading manifest file 'synthpops.egg-info/SOURCES.txt'
writing manifest file 'synthpops.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/synthpops
copying synthpops/contact_networks_industries.py -> build/lib/synthpops
copying synthpops/read_write.py -> build/lib/synthpops
copying synthpops/__init__.py -> build/lib/synthpops
copying synthpops/base.py -> build/lib/synthpops
copying synthpops/school_modules.py -> build/lib/synthpops
copying synthpops/data_distributions.py -> build/lib/synthpops
copying synthpops/config.py -> build/lib/synthpops
copying synthpops/sampling.py -> build/lib/synthpops
copying synthpops/version.py -> build/lib/synthpops
copying synthpops/long_term_care_facilities.py -> build/lib/synthpops
copying synthpops/api.py -> build/lib/synthpops
copying synthpops/contacts.py -> build/lib/synthpops
copying synthpops/contact_networks.py -> build/lib/synthpops
copying synthpops/plot_tools.py -> build/lib/synthpops
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/contact_networks_industries.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/read_write.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/__init__.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/base.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/school_modules.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/data_distributions.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/config.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/sampling.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/version.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/long_term_care_facilities.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/api.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/contacts.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/contact_networks.py -> build/bdist.linux-x86_64/egg/synthpops
copying build/lib/synthpops/plot_tools.py -> build/bdist.linux-x86_64/egg/synthpops
byte-compiling build/bdist.linux-x86_64/egg/synthpops/contact_networks_industries.py to contact_networks_industries.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/read_write.py to read_write.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/base.py to base.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/school_modules.py to school_modules.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/data_distributions.py to data_distributions.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/config.py to config.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/sampling.py to sampling.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/version.py to version.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/long_term_care_facilities.py to long_term_care_facilities.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/api.py to api.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/contacts.py to contacts.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/contact_networks.py to contact_networks.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/synthpops/plot_tools.py to plot_tools.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying synthpops.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying synthpops.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying synthpops.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying synthpops.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying synthpops.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
synthpops.__pycache__.config.cpython-37: module references __file__
creating dist
creating 'dist/synthpops-1.0.0-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 synthpops-1.0.0-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/synthpops-1.0.0-py3.7.egg
Extracting synthpops-1.0.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding synthpops 1.0.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/synthpops-1.0.0-py3.7.egg
Processing dependencies for synthpops==1.0.0
Searching for pydot
Reading https://pypi.org/simple/pydot/
Downloading https://files.pythonhosted.org/packages/33/d1/b1479a770f66d962f545c2101630ce1d5592d90cb4f083d38862e93d16d2/pydot-1.4.1-py2.py3-none-any.whl#sha256=67be714300c78fda5fd52f79ec994039e3f76f074948c67b5ff539b433ad354f
Best match: pydot 1.4.1
Processing pydot-1.4.1-py2.py3-none-any.whl
Installing pydot-1.4.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/pydot-1.4.1-py3.7.egg/EGG-INFO/requires.txt
Adding pydot 1.4.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/pydot-1.4.1-py3.7.egg
Searching for graphviz
Reading https://pypi.org/simple/graphviz/
Downloading https://files.pythonhosted.org/packages/62/dc/9dd6a6b9b8977248e165e075b109eea6e8eac71faa28ca378c3d98e54fbe/graphviz-0.14.1-py2.py3-none-any.whl#sha256=088562ef6e3dad5e8dde9389caf4a84f768e65dcaa08238cfcdf36d2b30ccf61
Best match: graphviz 0.14.1
Processing graphviz-0.14.1-py2.py3-none-any.whl
Installing graphviz-0.14.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/graphviz-0.14.1-py3.7.egg/EGG-INFO/requires.txt
Adding graphviz 0.14.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/graphviz-0.14.1-py3.7.egg
Searching for seaborn
Reading https://pypi.org/simple/seaborn/
Downloading https://files.pythonhosted.org/packages/c7/e6/54aaaafd0b87f51dfba92ba73da94151aa3bc179e5fe88fc5dfb3038e860/seaborn-0.10.1-py3-none-any.whl#sha256=c901ce494541fb4714cfa7db79d0232dc3f4c4dfd3f273bacf17816084df5b53
Best match: seaborn 0.10.1
Processing seaborn-0.10.1-py3-none-any.whl
Installing seaborn-0.10.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/seaborn-0.10.1-py3.7.egg/EGG-INFO/requires.txt
Adding seaborn 0.10.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/seaborn-0.10.1-py3.7.egg
Searching for cmasher
Reading https://pypi.org/simple/cmasher/
Downloading https://files.pythonhosted.org/packages/80/51/0a289443380bc697b522b286d845c87092341f228772dc3092b6004a5725/cmasher-1.5.1-py3-none-any.whl#sha256=0e9c4948408e166af8a7fc302cfab6fa78590c413f1dc6b8106e28ddc6770c46
Best match: cmasher 1.5.1
Processing cmasher-1.5.1-py3-none-any.whl
Installing cmasher-1.5.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/cmasher-1.5.1-py3.7.egg/EGG-INFO/requires.txt
Adding cmasher 1.5.1 to easy-install.pth file
Installing cmr script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/cmasher-1.5.1-py3.7.egg
Searching for cmocean
Reading https://pypi.org/simple/cmocean/
Downloading https://files.pythonhosted.org/packages/48/02/d0f19b00b252fd972e3daec05be73aa811091528f21b90442a15d6a96d89/cmocean-2.0-py3-none-any.whl#sha256=1753f004d84d21c89e76106b2f56e2847808951b2373843bece4dcf532e1a91f
Best match: cmocean 2.0
Processing cmocean-2.0-py3-none-any.whl
Installing cmocean-2.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/cmocean-2.0-py3.7.egg/EGG-INFO/requires.txt
Adding cmocean 2.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/cmocean-2.0-py3.7.egg
Searching for networkx
Reading https://pypi.org/simple/networkx/
Downloading https://files.pythonhosted.org/packages/9b/cd/dc52755d30ba41c60243235460961fc28022e5b6731f16c268667625baea/networkx-2.5-py3-none-any.whl#sha256=8c5812e9f798d37c50570d15c4a69d5710a18d77bafc903ee9c5fba7454c616c
Best match: networkx 2.5
Processing networkx-2.5-py3-none-any.whl
Installing networkx-2.5-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/networkx-2.5-py3.7.egg/EGG-INFO/requires.txt
Adding networkx 2.5 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/networkx-2.5-py3.7.egg
Searching for numba==0.48.0
Reading https://pypi.org/simple/numba/
Downloading https://files.pythonhosted.org/packages/f6/10/d30ccbcbc7b19c96b228f86be82619c5f86c88344e5f492a6c93cce2439f/numba-0.48.0-1-cp37-cp37m-manylinux1_x86_64.whl#sha256=467564f72a30abaf55d55b30998818b34c10fd85cbcfa505a1c67cbd09d79a96
Best match: numba 0.48.0
Processing numba-0.48.0-1-cp37-cp37m-manylinux1_x86_64.whl
Installing numba-0.48.0-1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/numba-0.48.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding numba 0.48.0 to easy-install.pth file
Installing numba script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin
Installing pycc script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/numba-0.48.0-py3.7-linux-x86_64.egg
Searching for pandas
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/61/ed/10112535645ad7afd26c3b9defd20a32d9e42340b19c4f73ff26ccad06ee/pandas-1.1.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=84c101d0f7bbf0d9f1be9a2f29f6fcc12415442558d067164e50a56edfb732b4
Best match: pandas 1.1.1
Processing pandas-1.1.1-cp37-cp37m-manylinux1_x86_64.whl
Installing pandas-1.1.1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/pandas-1.1.1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding pandas 1.1.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/pandas-1.1.1-py3.7-linux-x86_64.egg
Searching for scipy
Reading https://pypi.org/simple/scipy/
Downloading https://files.pythonhosted.org/packages/65/f9/f7a7e5009711579c72da2725174825e5056741bf4001815d097eef1b2e17/scipy-1.5.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=eecf40fa87eeda53e8e11d265ff2254729d04000cd40bae648e76ff268885d66
Best match: scipy 1.5.2
Processing scipy-1.5.2-cp37-cp37m-manylinux1_x86_64.whl
Installing scipy-1.5.2-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/scipy-1.5.2-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding scipy 1.5.2 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/scipy-1.5.2-py3.7-linux-x86_64.egg
Searching for numpy
Reading https://pypi.org/simple/numpy/
Downloading https://files.pythonhosted.org/packages/3d/d1/90cd7e0b27ee86d77f5386d38b74520486100286d50772377791b6ef22ff/numpy-1.19.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=1bc0145999e8cb8aed9d4e65dd8b139adf1919e521177f198529687dbf613065
Best match: numpy 1.19.1
Processing numpy-1.19.1-cp37-cp37m-manylinux1_x86_64.whl
Installing numpy-1.19.1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
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-synthpops-test/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/numpy-1.19.1-py3.7-linux-x86_64.egg
Searching for matplotlib
Reading https://pypi.org/simple/matplotlib/
Downloading https://files.pythonhosted.org/packages/f1/b9/712584f12f840968a14969a1fe298ffdeaa9c4b484b3bfd973c74c4a481d/matplotlib-3.3.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=636c6330a7dcb18bac114dbeaff314fbbb0c11682f9a9601de69a50e331d18d7
Best match: matplotlib 3.3.1
Processing matplotlib-3.3.1-cp37-cp37m-manylinux1_x86_64.whl
Installing matplotlib-3.3.1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/matplotlib-3.3.1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding matplotlib 3.3.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/matplotlib-3.3.1-py3.7-linux-x86_64.egg
Searching for sciris>=0.16.5
Reading https://pypi.org/simple/sciris/
Downloading https://files.pythonhosted.org/packages/00/41/b9d322d413080daff10aef2309a14f37342f7e1e50f3adf1db0573fee7dc/sciris-0.17.4-py3-none-any.whl#sha256=6baaa7d7cf0def872f624bdcf0525c02ab1a5a48a2a9adca4f4f91d47f61e626
Best match: sciris 0.17.4
Processing sciris-0.17.4-py3-none-any.whl
Installing sciris-0.17.4-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sciris-0.17.4-py3.7.egg/EGG-INFO/requires.txt
Adding sciris 0.17.4 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sciris-0.17.4-py3.7.egg
Searching for e13tools>=0.9.4
Reading https://pypi.org/simple/e13tools/
Downloading https://files.pythonhosted.org/packages/ec/5e/a254c1be9583eaa78402e97cf250d60114a47e518d823ae955f7b72b732f/e13tools-0.9.4-py3-none-any.whl#sha256=1deaf40d1f91152f8fbf1c7a4d7d5409cf902a22a19f8564bcfae50e14bc0596
Best match: e13tools 0.9.4
Processing e13tools-0.9.4-py3-none-any.whl
Installing e13tools-0.9.4-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/e13tools-0.9.4-py3.7.egg/EGG-INFO/requires.txt
Adding e13tools 0.9.4 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/e13tools-0.9.4-py3.7.egg
Searching for colorspacious>=1.1.0
Reading https://pypi.org/simple/colorspacious/
Downloading https://files.pythonhosted.org/packages/ab/a1/318b9aeca7b9856410ededa4f52d6f82174d1a41e64bdd70d951e532675a/colorspacious-1.1.2-py2.py3-none-any.whl#sha256=c78befa603cea5dccb332464e7dd29e96469eebf6cd5133029153d1e69e3fd6f
Best match: colorspacious 1.1.2
Processing colorspacious-1.1.2-py2.py3-none-any.whl
Installing colorspacious-1.1.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/colorspacious-1.1.2-py3.7.egg/EGG-INFO/requires.txt
Adding colorspacious 1.1.2 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/colorspacious-1.1.2-py3.7.egg
Searching for decorator>=4.3.0
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-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/decorator-4.4.2-py3.7.egg
Searching for llvmlite<0.32.0,>=0.31.0dev0
Reading https://pypi.org/simple/llvmlite/
Downloading https://files.pythonhosted.org/packages/a0/10/d02c0ac683fc47ecda3426249509cf771d748b6a2c0e9d5ebbee76a7b80a/llvmlite-0.31.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=81fc9ac6682a41f53bca113a8f97959b92728112f91714e850a72dc6d9dd8ced
Best match: llvmlite 0.31.0
Processing llvmlite-0.31.0-cp37-cp37m-manylinux1_x86_64.whl
Installing llvmlite-0.31.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding llvmlite 0.31.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/llvmlite-0.31.0-py3.7-linux-x86_64.egg
Searching for python-dateutil>=2.7.3
Reading https://pypi.org/simple/python-dateutil/
Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl#sha256=75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a
Best match: python-dateutil 2.8.1
Processing python_dateutil-2.8.1-py2.py3-none-any.whl
Installing python_dateutil-2.8.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/python_dateutil-2.8.1-py3.7.egg/EGG-INFO/requires.txt
Adding python-dateutil 2.8.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/python_dateutil-2.8.1-py3.7.egg
Searching for pillow>=6.2.0
Reading https://pypi.org/simple/pillow/
Downloading https://files.pythonhosted.org/packages/e8/f2/6722dd0c22e3a143ac792ccb2424924ac72af4adea756b1165b4cad50da7/Pillow-7.2.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=52125833b070791fcb5710fabc640fc1df07d087fc0c0f02d3661f76c23c5b8b
Best match: Pillow 7.2.0
Processing Pillow-7.2.0-cp37-cp37m-manylinux1_x86_64.whl
Installing Pillow-7.2.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding Pillow 7.2.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/Pillow-7.2.0-py3.7-linux-x86_64.egg
Searching for kiwisolver>=1.0.1
Reading https://pypi.org/simple/kiwisolver/
Downloading https://files.pythonhosted.org/packages/31/b9/6202dcae729998a0ade30e80ac00f616542ef445b088ec970d407dfd41c0/kiwisolver-1.2.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=603162139684ee56bcd57acc74035fceed7dd8d732f38c0959c8bd157f913fec
Best match: kiwisolver 1.2.0
Processing kiwisolver-1.2.0-cp37-cp37m-manylinux1_x86_64.whl
Installing kiwisolver-1.2.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding kiwisolver 1.2.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/kiwisolver-1.2.0-py3.7-linux-x86_64.egg
Searching for cycler>=0.10
Reading https://pypi.org/simple/cycler/
Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl#sha256=1d8a5ae1ff6c5cf9b93e8811e581232ad8920aeec647c37316ceac982b08cb2d
Best match: cycler 0.10.0
Processing cycler-0.10.0-py2.py3-none-any.whl
Installing cycler-0.10.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/cycler-0.10.0-py3.7.egg/EGG-INFO/requires.txt
Adding cycler 0.10.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/cycler-0.10.0-py3.7.egg
Searching for xlsxwriter
Reading https://pypi.org/simple/xlsxwriter/
Downloading https://files.pythonhosted.org/packages/2b/98/17875723b6814fc4d0fc03f0997ee00de2dbd78cf195e2ec3f2c9c789d40/XlsxWriter-1.3.3-py2.py3-none-any.whl#sha256=88ab71d464e8f6c3923335cc92d6035260aa9e7c8b27fcbb3a5bc07e2c671d22
Best match: XlsxWriter 1.3.3
Processing XlsxWriter-1.3.3-py2.py3-none-any.whl
Installing XlsxWriter-1.3.3-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding XlsxWriter 1.3.3 to easy-install.pth file
Installing vba_extract.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/XlsxWriter-1.3.3-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-synthpops-test/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-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz#sha256=90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb
Best match: psutil 5.7.2
Processing psutil-5.7.2.tar.gz
Writing /tmp/easy_install-r4zku73x/psutil-5.7.2/setup.cfg
Running psutil-5.7.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-r4zku73x/psutil-5.7.2/egg-dist-tmp-_opv22ba
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/psutil-5.7.2-py3.7-linux-x86_64.egg
Extracting psutil-5.7.2-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding psutil 5.7.2 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/psutil-5.7.2-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-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/openpyexcel-2.5.14-py3.7.egg
Searching for memory-profiler
Reading https://pypi.org/simple/memory-profiler/
Downloading https://files.pythonhosted.org/packages/f4/03/175d380294b2333b9b79c2f2aa235eb90ee95e3ddef644497a9455404312/memory_profiler-0.57.0.tar.gz#sha256=23b196f91ea9ac9996e30bfab1e82fecc30a4a1d24870e81d1e81625f786a2c3
Best match: memory-profiler 0.57.0
Processing memory_profiler-0.57.0.tar.gz
Writing /tmp/easy_install-doo53uwp/memory_profiler-0.57.0/setup.cfg
Running memory_profiler-0.57.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-doo53uwp/memory_profiler-0.57.0/egg-dist-tmp-jiam4pke
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-synthpops-test/envs/latest/lib/python3.7/site-packages/memory_profiler-0.57.0-py3.7.egg
Extracting memory_profiler-0.57.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
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-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/memory_profiler-0.57.0-py3.7.egg
Searching for line-profiler
Reading https://pypi.org/simple/line-profiler/
Downloading https://files.pythonhosted.org/packages/a3/c7/8c3af643c203c1e481043caca821dce9cb0b14e1cbff20e06d117be2713c/line_profiler-3.0.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=e095430561ae8166d698a02ec9c08a30a7018baceda423e8919e390e0ba9acda
Best match: line-profiler 3.0.2
Processing line_profiler-3.0.2-cp37-cp37m-manylinux1_x86_64.whl
Installing line_profiler-3.0.2-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/line_profiler-3.0.2-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
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-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/line_profiler-3.0.2-py3.7-linux-x86_64.egg
Searching for jsonpickle
Reading https://pypi.org/simple/jsonpickle/
Downloading https://files.pythonhosted.org/packages/af/ca/4fee219cc4113a5635e348ad951cf8a2e47fed2e3342312493f5b73d0007/jsonpickle-1.4.1-py2.py3-none-any.whl#sha256=8919c166bac0574e3d74425c7559434062002d9dfc0ac2afa6dc746ba4a19439
Best match: jsonpickle 1.4.1
Processing jsonpickle-1.4.1-py2.py3-none-any.whl
Installing jsonpickle-1.4.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/jsonpickle-1.4.1-py3.7.egg/EGG-INFO/requires.txt
Adding jsonpickle 1.4.1 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/jsonpickle-1.4.1-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-8z4ynm4v/jellyfish-0.8.2/setup.cfg
Running jellyfish-0.8.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8z4ynm4v/jellyfish-0.8.2/egg-dist-tmp-s853vw_9
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-synthpops-test/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-synthpops-test/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-synthpops-test/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/f9/1e/a45320cab182bf1c8656107b3d4c042e659742822fc6bff150d769a984dd/GitPython-3.1.7-py3-none-any.whl#sha256=fa3b92da728a457dd75d62bb5f3eb2816d99a7fe6c67398e260637a40e3fafb5
Best match: GitPython 3.1.7
Processing GitPython-3.1.7-py3-none-any.whl
Installing GitPython-3.1.7-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/GitPython-3.1.7-py3.7.egg/EGG-INFO/requires.txt
Adding GitPython 3.1.7 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/GitPython-3.1.7-py3.7.egg
Searching for dill
Reading https://pypi.org/simple/dill/
Downloading https://files.pythonhosted.org/packages/e2/96/518a8ea959a734b70d2e95fef98bcbfdc7adad1c1e5f5dd9148c835205a5/dill-0.3.2.zip#sha256=6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e
Best match: dill 0.3.2
Processing dill-0.3.2.zip
Writing /tmp/easy_install-o1roy5qk/dill-0.3.2/setup.cfg
Running dill-0.3.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-o1roy5qk/dill-0.3.2/egg-dist-tmp-tjwr99hw
no previously-included directories found matching '.git'
no previously-included directories found matching '.coverage'
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/dill-0.3.2-py3.7.egg
Extracting dill-0.3.2-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding dill 0.3.2 to easy-install.pth file
Installing undill script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin
Installing get_objgraph script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/dill-0.3.2-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-synthpops-test/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-synthpops-test/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-13w5vu0m/et_xmlfile-1.0.1/setup.cfg
Running et_xmlfile-1.0.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-13w5vu0m/et_xmlfile-1.0.1/egg-dist-tmp-6wcbco5o
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-synthpops-test/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-synthpops-test/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-synthpops-test/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/a4/43/fd8ea01774d50f4008ec6c6a3788dd33b966c3177ebcb1fb46cbae6b849e/ipython-7.18.0-py3-none-any.whl#sha256=73c61ebcc30baadf600b870c3a38b96d6e5ae8dde5ef5425b8aab75dc9a9a602
Best match: ipython 7.18.0
Processing ipython-7.18.0-py3-none-any.whl
Installing ipython-7.18.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/ipython-7.18.0-py3.7.egg/EGG-INFO/requires.txt
Adding ipython 7.18.0 to easy-install.pth file
Installing iptest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin
Installing iptest3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin
Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin
Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/ipython-7.18.0-py3.7.egg
Searching for importlib-metadata
Reading https://pypi.org/simple/importlib-metadata/
Downloading https://files.pythonhosted.org/packages/8e/58/cdea07eb51fc2b906db0968a94700866fc46249bdc75cac23f9d13168929/importlib_metadata-1.7.0-py2.py3-none-any.whl#sha256=dc15b2969b4ce36305c51eebe62d418ac7791e9a157911d58bfb1f9ccd8e2070
Best match: importlib-metadata 1.7.0
Processing importlib_metadata-1.7.0-py2.py3-none-any.whl
Installing importlib_metadata-1.7.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/importlib_metadata-1.7.0-py3.7.egg/EGG-INFO/requires.txt
Adding importlib-metadata 1.7.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/importlib_metadata-1.7.0-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-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/gitdb-4.0.5-py3.7.egg
Searching for traitlets>=4.2
Reading https://pypi.org/simple/traitlets/
Downloading https://files.pythonhosted.org/packages/d0/c1/020d36d000db4b3451882e16bed27f32e94145fba55567cbfd39c9c8fc8e/traitlets-5.0.0rc2-py3-none-any.whl#sha256=d56e45db33a0f37ffa3cc4cfa439fc09ed2906e228d0f28310fcd42a19facdce
Best match: traitlets 5.0.0rc2
Processing traitlets-5.0.0rc2-py3-none-any.whl
Installing traitlets-5.0.0rc2-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/traitlets-5.0.0rc2-py3.7.egg/EGG-INFO/requires.txt
Adding traitlets 5.0.0rc2 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/traitlets-5.0.0rc2-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/72/65/a3ef98b56d57a6d0a04cea5810ecbf3700a225d296ca298b3442dddebb42/prompt_toolkit-3.0.6-py3-none-any.whl#sha256=683397077a64cd1f750b71c05afcfc6612a7300cb6932666531e5a54f38ea564
Best match: prompt-toolkit 3.0.6
Processing prompt_toolkit-3.0.6-py3-none-any.whl
Installing prompt_toolkit-3.0.6-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/prompt_toolkit-3.0.6-py3.7.egg/EGG-INFO/requires.txt
Adding prompt-toolkit 3.0.6 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/prompt_toolkit-3.0.6-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-synthpops-test/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-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/pexpect-4.8.0-py3.7.egg
Searching for jedi>=0.16
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-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/jedi-0.17.2-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-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/backcall-0.2.0-py3.7.egg
Searching for zipp>=0.5
Reading https://pypi.org/simple/zipp/
Downloading https://files.pythonhosted.org/packages/b2/34/bfcb43cc0ba81f527bc4f40ef41ba2ff4080e047acb0586b56b3d017ace4/zipp-3.1.0-py3-none-any.whl#sha256=aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b
Best match: zipp 3.1.0
Processing zipp-3.1.0-py3-none-any.whl
Installing zipp-3.1.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/zipp-3.1.0-py3.7.egg/EGG-INFO/requires.txt
Adding zipp 3.1.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/zipp-3.1.0-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-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/smmap-3.0.4-py3.7.egg
Searching for ipython-genutils
Reading https://pypi.org/simple/ipython-genutils/
Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl#sha256=72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8
Best match: ipython-genutils 0.2.0
Processing ipython_genutils-0.2.0-py2.py3-none-any.whl
Installing ipython_genutils-0.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding ipython-genutils 0.2.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/ipython_genutils-0.2.0-py3.7.egg
Searching for wcwidth
Reading https://pypi.org/simple/wcwidth/
Downloading https://files.pythonhosted.org/packages/59/7c/e39aca596badaf1b78e8f547c807b04dae603a433d3e7a7e04d67f2ef3e5/wcwidth-0.2.5-py2.py3-none-any.whl#sha256=beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784
Best match: wcwidth 0.2.5
Processing wcwidth-0.2.5-py2.py3-none-any.whl
Installing wcwidth-0.2.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Adding wcwidth 0.2.5 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/wcwidth-0.2.5-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-synthpops-test/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-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/envs/latest/lib/python3.7/site-packages/parso-0.7.1-py3.7.egg
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-synthpops-test/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-synthpops-test/envs/latest/bin
Installing easy_install-3.6 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/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-synthpops-test/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-synthpops-test/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-synthpops-test/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-synthpops-test/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-synthpops-test/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-synthpops-test/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/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-synthpops-test/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for synthpops==1.0.0

[rtd-command-info] start-time: 2020-08-28T21:24:35.644645Z, end-time: 2020-08-28T21:24:35.717816Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# 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__)))

# -- 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', '.md']
source_suffix = '.rst'

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

# The master toctree document.
master_doc = 'index'

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

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = u''
# The full version, including alpha/beta/rc tags.
# release = u'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']

# 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 = u'Sphinx Demo v1.0'

# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
html_logo = "images/IDM_white.png"

# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
html_favicon = "images/favicon.ico"

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']

html_context = {
    'css_files': [
        '_static/theme_overrides.css'
        ]
}
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the 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 = 'SynthPops'

# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'synthpops-docs.tex', u'SynthPops',
     u'Institute for Disease Modeling', 'manual'),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#
# latex_use_parts = False

# If true, show page references after internal links.
#
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
#
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
#
# latex_appendices = []

# It false, will not define \strong, \code,     itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True

# If false, no module index is generated.
#
# latex_domain_indices = True


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'synthpops-docs', u'SynthPops',
     [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, 'synthpops-docs', u'SynthPops',
     author, 'Institute for Disease Modeling', 'How to use SynthPops for creating synthetic populations.',
     '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/synthpops/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/synthpops/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-synthpops-test',
    'name': u'synthpops',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://docs.idmod.org/projects/synthpops/en/latest/',
    'analytics_code': 'UA-87656833-3',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'JSchripsema-IDM',
    'proxied_api_host': '/_',
    'github_repo': 'synthpops-2',
    'github_version': 'rtd',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'rtd',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'rtd',
    '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': '82c36eec',
}




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: 2020-08-28T21:24:35.862668Z, end-time: 2020-08-28T21:24:36.227006Z, duration: 0, exit-code: 2
python sphinx-build -T -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.2.1
rm: cannot remove 'synthpops_index.rst': No such file or directory
rm: cannot remove 'modules.rst': No such file or directory
make: *** [generate-api] Error 1

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 89, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/conf.py", line 25, in <module>
    subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', 'generate-api']' returned non-zero exit status 2.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 279, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 218, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 174, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 332, in eval_config_file
    raise ConfigError(msg % traceback.format_exc()) from exc
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 89, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/conf.py", line 25, in <module>
    subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', 'generate-api']' returned non-zero exit status 2.


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 89, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/conf.py", line 25, in <module>
    subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', 'generate-api']' returned non-zero exit status 2.