Read the Docs build information
Build id: 424762
Project: institute-for-disease-modeling-emod-tuberculosis
Version: latest
Commit: db2edbe6c70488e4aeb4935d0a1a66c8dfa6a01d
Date: 2020-09-17T21:03:47.308853Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-09-17T21:03:57.167962Z, end-time: 2020-09-17T21:04:11.636901Z, duration: 14, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/Documentation.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2020-09-17T21:04:12.537733Z, end-time: 2020-09-17T21:04:12.990295Z, 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 db2edbe6 Merge pull request #1154 from JSchripsema-IDM/rtd_w_lauren

[rtd-command-info] start-time: 2020-09-17T21:04:13.140043Z, end-time: 2020-09-17T21:04:13.202262Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-09-17T21:04:14.665280Z, end-time: 2020-09-17T21:04:18.855675Z, duration: 4, 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-emod-tuberculosis/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-09-17T21:04:19.543709Z, end-time: 2020-09-17T21:04:20.245404Z, 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-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (20.2.3)

[rtd-command-info] start-time: 2020-09-17T21:04:20.357437Z, end-time: 2020-09-17T21:04:28.730028Z, duration: 8, 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
Collecting Pygments==2.3.1
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Collecting docutils==0.14
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Collecting mock==1.0.1
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Collecting pillow==5.4.1
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Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting packaging
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Collecting snowballstemmer>=1.1
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Collecting requests>=2.0.0
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Collecting Jinja2>=2.3
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Collecting certifi>=2017.4.17
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Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
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Collecting MarkupSafe>=0.23
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Collecting pytz>=2015.7
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=555ab3335546f6bc829a3040b5d2c5a0b01b11416eb7872c2eabd6258b90e87f
  Stored in directory: /tmp/pip-ephem-wheel-cache-b8lsq0n9/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=4f3368cfaebbb5dc7f1ee3f19984c30471367a00bb9f34f2124563e877b58737
  Stored in directory: /tmp/pip-ephem-wheel-cache-b8lsq0n9/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pyparsing, packaging, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, snowballstemmer, idna, chardet, certifi, urllib3, requests, MarkupSafe, Jinja2, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 50.3.0
    Uninstalling setuptools-50.3.0:
      Successfully uninstalled setuptools-50.3.0
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10

[rtd-command-info] start-time: 2020-09-17T21:04:28.963059Z, end-time: 2020-09-17T21:04:33.998787Z, duration: 5, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Collecting sphinx-rtd-theme~=0.5.0
  Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 MB)
Collecting sphinxcontrib-napoleon~=0.7
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Collecting sphinx~=3.2.0
  Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB)
Collecting plantweb~=1.2.1
  Downloading plantweb-1.2.1-py3-none-any.whl (20 kB)
Collecting numpy~=1.19.1
  Downloading numpy-1.19.2-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB)
Collecting numpydoc~=1.0.0
  Downloading numpydoc-1.0.0-py3-none-any.whl (47 kB)
Collecting pockets>=0.3
  Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB)
Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r requirements.txt (line 2)) (1.15.0)
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.4)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.11.2)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.3.1)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.8.0)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (20.4)
Collecting sphinxcontrib-jsmath
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (41.0.1)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.0.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.2.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.7.12)
Collecting sphinxcontrib-htmlhelp
  Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB)
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  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.14)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.24.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.1)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.1)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.4.7)
Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.6.20)
Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-tuberculosis/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.25.10)
Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-applehelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, numpy, numpydoc
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed numpy-1.19.2 numpydoc-1.0.0 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