Read the Docs build information
Build id: 1149997
Project: institute-for-disease-modeling-covasim
Version: latest
Commit: 05a554f8cc772c53fa5cd6f87a39ba20d669df37
Date: 2022-10-22T21:25:53.816714Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-10-22T21:32:44.170012Z, end-time: 2022-10-22T21:32:47.092260Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/covasim.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-10-22T21:32:47.341245Z, end-time: 2022-10-22T21:32:47.467832Z, duration: 0, exit-code: 0
git checkout --force origin/fix-readthedocs
Note: switching to 'origin/fix-readthedocs'.

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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 05a554f8 change python version

[rtd-command-info] start-time: 2022-10-22T21:32:47.671491Z, end-time: 2022-10-22T21:32:47.745608Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-10-22T21:32:52.890289Z, end-time: 2022-10-22T21:32:52.974462Z, duration: 0, exit-code: 0
asdf global python 3.9.13


[rtd-command-info] start-time: 2022-10-22T21:32:53.493290Z, end-time: 2022-10-22T21:32:54.472469Z, duration: 0, exit-code: 0
python -mvirtualenv --system-site-packages 
created virtual environment CPython3.9.13.final.0-64 in 673ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest, clear=False, no_vcs_ignore=False, global=True)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2022-10-22T21:32:54.749891Z, end-time: 2022-10-22T21:33:05.857569Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Downloading pip-22.3-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (57.4.0)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-22.3 setuptools-58.2.0

[rtd-command-info] start-time: 2022-10-22T21:33:06.078262Z, end-time: 2022-10-22T21:33:15.056933Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 setuptools<58.3.0
Collecting pillow
  Downloading Pillow-9.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 50.7 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 241.5 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 118.5 MB/s eta 0:00:00
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 174.8 MB/s eta 0:00:00
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 146.0 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.2
  Downloading readthedocs_sphinx_ext-2.1.9-py2.py3-none-any.whl (11 kB)
Collecting jinja2<3.1.0
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 241.9 MB/s eta 0:00:00
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 279.3 MB/s eta 0:00:00
Collecting docutils>=0.11
  Downloading docutils-0.19-py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 276.1 MB/s eta 0:00:00
Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 166.3 MB/s eta 0:00:00
Collecting packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 193.0 MB/s eta 0:00:00
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 192.1 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.13.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 269.1 MB/s eta 0:00:00
Collecting requests>=2.0.0
  Downloading requests-2.28.1-py3-none-any.whl (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 206.3 MB/s eta 0:00:00
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 269.2 MB/s eta 0:00:00
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting pytz>=2015.7
  Downloading pytz-2022.5-py2.py3-none-any.whl (500 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 500.7/500.7 kB 262.8 MB/s eta 0:00:00
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.12-py2.py3-none-any.whl (140 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.4/140.4 kB 223.9 MB/s eta 0:00:00
Collecting charset-normalizer<3,>=2
  Downloading charset_normalizer-2.1.1-py3-none-any.whl (39 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2022.9.24-py3-none-any.whl (161 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 161.1/161.1 kB 243.6 MB/s eta 0:00:00
Collecting idna<4,>=2.5
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 209.0 MB/s eta 0:00:00
Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 231.8 MB/s eta 0:00:00
Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 233.1 MB/s eta 0:00:00
Building wheels for collected packages: mock
  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=23772 sha256=11db1ac567f259f980f49ea561fa60f51f4b81a755add34e019ef85602f9a212
  Stored in directory: /tmp/pip-ephem-wheel-cache-pbzn7d3p/wheels/95/5a/42/6d69898ad0ccd6d30cf1ea4ae71db699e0c7bef2294dc557a5
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.9.24 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 pytz-2022.5 readthedocs-sphinx-ext-2.1.9 recommonmark-0.5.0 requests-2.28.1 setuptools-58.2.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.12

[rtd-command-info] start-time: 2022-10-22T21:33:15.362916Z, end-time: 2022-10-22T21:33:46.215528Z, duration: 30, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting pytest
  Downloading pytest-7.1.3-py3-none-any.whl (298 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.2/298.2 kB 13.0 MB/s eta 0:00:00
Requirement already satisfied: sphinx-rtd-theme in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3)
Collecting sphinxcontrib-napoleon
  Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB)
Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from -r docs/requirements.txt (line 4)) (1.8.6)
Collecting plantweb
  Downloading plantweb-1.2.1-py3-none-any.whl (20 kB)
Collecting ipykernel
  Downloading ipykernel-6.16.1-py3-none-any.whl (138 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 138.5/138.5 kB 252.1 MB/s eta 0:00:00
Collecting nbsphinx
  Downloading nbsphinx-0.8.9-py3-none-any.whl (25 kB)
Collecting pandoc
  Downloading pandoc-2.2.tar.gz (29 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pypandoc
  Downloading pypandoc-1.9-py3-none-any.whl (20 kB)
Collecting optuna
  Downloading optuna-3.0.3-py3-none-any.whl (348 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 348.5/348.5 kB 61.5 MB/s eta 0:00:00
Collecting seaborn
  Downloading seaborn-0.12.1-py3-none-any.whl (288 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 255.3 MB/s eta 0:00:00
Collecting pluggy<2.0,>=0.12
  Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB)
Collecting iniconfig
  Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting tomli>=1.0.0
  Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting py>=1.8.2
  Downloading py-1.11.0-py2.py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.7/98.7 kB 216.4 MB/s eta 0:00:00
Collecting attrs>=19.2.0
  Downloading attrs-22.1.0-py2.py3-none-any.whl (58 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.8/58.8 kB 214.2 MB/s eta 0:00:00
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from pytest->-r docs/requirements.txt (line 1)) (21.3)
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-covasim/envs/latest/lib/python3.9/site-packages (from sphinxcontrib-napoleon->-r docs/requirements.txt (line 3)) (1.16.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (0.7.12)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (1.4.1)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.2.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (58.2.0)
Requirement already satisfied: docutils<0.18,>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (0.17.1)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.13.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.10.3)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (3.0.3)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (1.2.4)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.28.1)
Collecting psutil
  Downloading psutil-5.9.3-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (291 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 291.4/291.4 kB 256.1 MB/s eta 0:00:00
Collecting pyzmq>=17
  Downloading pyzmq-24.0.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 153.5 MB/s eta 0:00:00
Collecting tornado>=6.1
  Downloading tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (423 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 424.0/424.0 kB 262.3 MB/s eta 0:00:00
Collecting jupyter-client>=6.1.12
  Downloading jupyter_client-7.4.3-py3-none-any.whl (132 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.2/132.2 kB 243.2 MB/s eta 0:00:00
Collecting ipython>=7.23.1
  Downloading ipython-8.5.0-py3-none-any.whl (752 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 752.0/752.0 kB 268.2 MB/s eta 0:00:00
Collecting nest-asyncio
  Downloading nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)
Collecting matplotlib-inline>=0.1
  Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
Collecting debugpy>=1.0
  Downloading debugpy-1.6.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 254.7 MB/s eta 0:00:00
Collecting traitlets>=5.1.0
  Downloading traitlets-5.5.0-py3-none-any.whl (107 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 107.4/107.4 kB 223.9 MB/s eta 0:00:00
Collecting nbformat
  Downloading nbformat-5.7.0-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.1/77.1 kB 206.9 MB/s eta 0:00:00
Collecting nbconvert!=5.4
  Downloading nbconvert-7.2.2-py3-none-any.whl (271 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 271.6/271.6 kB 253.2 MB/s eta 0:00:00
Collecting plumbum
  Downloading plumbum-1.8.0-py3-none-any.whl (117 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.5/117.5 kB 234.6 MB/s eta 0:00:00
Collecting ply
  Downloading ply-3.11-py2.py3-none-any.whl (49 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.6/49.6 kB 209.6 MB/s eta 0:00:00
Collecting scipy<1.9.0,>=1.7.0
  Downloading scipy-1.8.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (42.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.2/42.2 MB 203.5 MB/s eta 0:00:00
Collecting colorlog
  Downloading colorlog-6.7.0-py2.py3-none-any.whl (11 kB)
Collecting cliff
  Downloading cliff-4.0.0-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 81.0/81.0 kB 204.5 MB/s eta 0:00:00
Collecting numpy
  Downloading numpy-1.23.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 207.9 MB/s eta 0:00:00
Collecting PyYAML
  Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 661.8/661.8 kB 275.3 MB/s eta 0:00:00
Collecting sqlalchemy>=1.3.0
  Downloading SQLAlchemy-1.4.42-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 272.0 MB/s eta 0:00:00
Collecting alembic>=1.5.0
  Downloading alembic-1.8.1-py3-none-any.whl (209 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.8/209.8 kB 259.0 MB/s eta 0:00:00
Collecting cmaes>=0.8.2
  Downloading cmaes-0.8.2-py3-none-any.whl (15 kB)
Collecting tqdm
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 194.3 MB/s eta 0:00:00
Collecting importlib-metadata<5.0.0
  Downloading importlib_metadata-4.13.0-py3-none-any.whl (23 kB)
Collecting pandas>=0.25
  Downloading pandas-1.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 204.0 MB/s eta 0:00:00
Collecting matplotlib!=3.6.1,>=3.1
  Downloading matplotlib-3.6.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.8/11.8 MB 206.6 MB/s eta 0:00:00
Collecting Mako
  Downloading Mako-1.2.3-py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.7/78.7 kB 235.6 MB/s eta 0:00:00
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from babel!=2.0,>=1.3->sphinx->-r docs/requirements.txt (line 4)) (2022.5)
Collecting zipp>=0.5
  Downloading zipp-3.9.0-py3-none-any.whl (5.8 kB)
Collecting decorator
  Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting stack-data
  Downloading stack_data-0.5.1-py3-none-any.whl (24 kB)
Collecting prompt-toolkit<3.1.0,>3.0.1
  Downloading prompt_toolkit-3.0.31-py3-none-any.whl (382 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 382.3/382.3 kB 269.1 MB/s eta 0:00:00
Collecting pickleshare
  Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting pexpect>4.3
  Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.0/59.0 kB 222.0 MB/s eta 0:00:00
Collecting jedi>=0.16
  Downloading jedi-0.18.1-py2.py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 269.5 MB/s eta 0:00:00
Collecting backcall
  Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from Jinja2>=2.3->sphinx->-r docs/requirements.txt (line 4)) (2.1.1)
Collecting entrypoints
  Downloading entrypoints-0.4-py3-none-any.whl (5.3 kB)
Collecting python-dateutil>=2.8.2
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 239.1 MB/s eta 0:00:00
Collecting jupyter-core>=4.9.2
  Downloading jupyter_core-4.11.2-py3-none-any.whl (88 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.5/88.5 kB 160.1 MB/s eta 0:00:00
Collecting fonttools>=4.22.0
  Downloading fonttools-4.38.0-py3-none-any.whl (965 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 265.1 MB/s eta 0:00:00
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting contourpy>=1.0.1
  Downloading contourpy-1.0.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (296 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 296.3/296.3 kB 264.1 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.4-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 270.2 MB/s eta 0:00:00
Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn->-r docs/requirements.txt (line 11)) (3.0.9)
Requirement already satisfied: pillow>=6.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn->-r docs/requirements.txt (line 11)) (9.2.0)
Collecting pandocfilters>=1.4.1
  Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB)
Collecting jupyterlab-pygments
  Downloading jupyterlab_pygments-0.2.2-py2.py3-none-any.whl (21 kB)
Collecting beautifulsoup4
  Downloading beautifulsoup4-4.11.1-py3-none-any.whl (128 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 128.2/128.2 kB 234.3 MB/s eta 0:00:00
Collecting defusedxml
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Collecting nbclient>=0.5.0
  Downloading nbclient-0.7.0-py3-none-any.whl (71 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 71.9/71.9 kB 220.8 MB/s eta 0:00:00
Collecting mistune<3,>=2.0.3
  Downloading mistune-2.0.4-py2.py3-none-any.whl (24 kB)
Collecting bleach
  Downloading bleach-5.0.1-py3-none-any.whl (160 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.9/160.9 kB 260.5 MB/s eta 0:00:00
Collecting tinycss2
  Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB)
Collecting jsonschema>=2.6
  Downloading jsonschema-4.16.0-py3-none-any.whl (83 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.1/83.1 kB 219.8 MB/s eta 0:00:00
Collecting fastjsonschema
  Downloading fastjsonschema-2.16.2-py3-none-any.whl (22 kB)
Requirement already satisfied: charset-normalizer<3,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (2.1.1)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (2022.9.24)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (1.26.12)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from requests>=2.0.0->sphinx->-r docs/requirements.txt (line 4)) (3.4)
Collecting greenlet!=0.4.17
  Downloading greenlet-1.1.3.post0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (154 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.4/154.4 kB 243.2 MB/s eta 0:00:00
Collecting stevedore>=2.0.1
  Downloading stevedore-4.1.0-py3-none-any.whl (50 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.0/50.0 kB 197.9 MB/s eta 0:00:00
Collecting autopage>=0.4.0
  Downloading autopage-0.5.1-py3-none-any.whl (29 kB)
Collecting PrettyTable>=0.7.2
  Downloading prettytable-3.4.1-py3-none-any.whl (26 kB)
Collecting cmd2>=1.0.0
  Downloading cmd2-2.4.2-py3-none-any.whl (147 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.1/147.1 kB 253.4 MB/s eta 0:00:00
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sphinxcontrib-websupport->sphinx->-r docs/requirements.txt (line 4)) (1.1.5)
Collecting wcwidth>=0.1.7
  Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Collecting pyperclip>=1.6
  Downloading pyperclip-1.8.2.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting parso<0.9.0,>=0.8.0
  Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 237.6 MB/s eta 0:00:00
Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0
  Downloading pyrsistent-0.18.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (115 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 115.6/115.6 kB 215.3 MB/s eta 0:00:00
Collecting ptyprocess>=0.5
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Collecting pbr!=2.1.0,>=2.0.0
  Downloading pbr-5.11.0-py2.py3-none-any.whl (112 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 112.6/112.6 kB 222.1 MB/s eta 0:00:00
Collecting soupsieve>1.2
  Downloading soupsieve-2.3.2.post1-py3-none-any.whl (37 kB)
Collecting webencodings
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting executing
  Downloading executing-1.1.1-py2.py3-none-any.whl (22 kB)
Collecting pure-eval
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting asttokens
  Downloading asttokens-2.0.8-py2.py3-none-any.whl (23 kB)
Building wheels for collected packages: pandoc, pyperclip
  Building wheel for pandoc (setup.py): started
  Building wheel for pandoc (setup.py): finished with status 'done'
  Created wheel for pandoc: filename=pandoc-2.2-py3-none-any.whl size=29558 sha256=f4261a5a92fe07f08004e985c7d74ac77888b6fb86bf7b613f8c83d9420a9a73
  Stored in directory: /tmp/pip-ephem-wheel-cache-kelo0oph/wheels/ad/8d/02/e3b447114344b0286e1ade33509e9e402915a4c1854d20500c
  Building wheel for pyperclip (setup.py): started
  Building wheel for pyperclip (setup.py): finished with status 'done'
  Created wheel for pyperclip: filename=pyperclip-1.8.2-py3-none-any.whl size=11136 sha256=38b42aec7b146aa6df969129d65c1d96a73220bb50fad8604e0c1c48bc4738c1
  Stored in directory: /tmp/pip-ephem-wheel-cache-kelo0oph/wheels/23/12/dd/067d543d895c9036459c68b02a9dcd66c7aad675ef90cbd3ab
Successfully built pandoc pyperclip
Installing collected packages: webencodings, wcwidth, pyperclip, pure-eval, ptyprocess, ply, pickleshare, mistune, iniconfig, fastjsonschema, executing, backcall, zipp, traitlets, tqdm, tornado, tomli, tinycss2, soupsieve, pyzmq, PyYAML, python-dateutil, pyrsistent, pypandoc, py, psutil, prompt-toolkit, PrettyTable, pockets, plumbum, pluggy, pexpect, pbr, parso, pandocfilters, numpy, nest-asyncio, Mako, kiwisolver, jupyterlab-pygments, greenlet, fonttools, entrypoints, defusedxml, decorator, debugpy, cycler, colorlog, bleach, autopage, attrs, asttokens, stevedore, stack-data, sqlalchemy, sphinxcontrib-napoleon, scipy, pytest, plantweb, pandoc, pandas, matplotlib-inline, jupyter-core, jsonschema, jedi, importlib-metadata, contourpy, cmd2, cmaes, beautifulsoup4, nbformat, matplotlib, jupyter-client, ipython, cliff, alembic, seaborn, optuna, nbclient, ipykernel, nbconvert, nbsphinx
Successfully installed Mako-1.2.3 PrettyTable-3.4.1 PyYAML-6.0 alembic-1.8.1 asttokens-2.0.8 attrs-22.1.0 autopage-0.5.1 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.1 cliff-4.0.0 cmaes-0.8.2 cmd2-2.4.2 colorlog-6.7.0 contourpy-1.0.5 cycler-0.11.0 debugpy-1.6.3 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 executing-1.1.1 fastjsonschema-2.16.2 fonttools-4.38.0 greenlet-1.1.3.post0 importlib-metadata-4.13.0 iniconfig-1.1.1 ipykernel-6.16.1 ipython-8.5.0 jedi-0.18.1 jsonschema-4.16.0 jupyter-client-7.4.3 jupyter-core-4.11.2 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 matplotlib-3.6.0 matplotlib-inline-0.1.6 mistune-2.0.4 nbclient-0.7.0 nbconvert-7.2.2 nbformat-5.7.0 nbsphinx-0.8.9 nest-asyncio-1.5.6 numpy-1.23.4 optuna-3.0.3 pandas-1.5.1 pandoc-2.2 pandocfilters-1.5.0 parso-0.8.3 pbr-5.11.0 pexpect-4.8.0 pickleshare-0.7.5 plantweb-1.2.1 pluggy-1.0.0 plumbum-1.8.0 ply-3.11 pockets-0.9.1 prompt-toolkit-3.0.31 psutil-5.9.3 ptyprocess-0.7.0 pure-eval-0.2.2 py-1.11.0 pypandoc-1.9 pyperclip-1.8.2 pyrsistent-0.18.1 pytest-7.1.3 python-dateutil-2.8.2 pyzmq-24.0.1 scipy-1.8.1 seaborn-0.12.1 soupsieve-2.3.2.post1 sphinxcontrib-napoleon-0.7 sqlalchemy-1.4.42 stack-data-0.5.1 stevedore-4.1.0 tinycss2-1.2.1 tomli-2.0.1 tornado-6.2 tqdm-4.64.1 traitlets-5.5.0 wcwidth-0.2.5 webencodings-0.5.1 zipp-3.9.0

[rtd-command-info] start-time: 2022-10-22T21:33:46.507053Z, end-time: 2022-10-22T21:34:12.267163Z, duration: 25, exit-code: 0
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .
Processing /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/checkouts/latest
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from covasim==3.1.4) (1.23.4)
Collecting numba
  Downloading numba-0.56.3-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 67.0 MB/s eta 0:00:00
Requirement already satisfied: pandas in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from covasim==3.1.4) (1.5.1)
Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from covasim==3.1.4) (1.8.1)
Collecting scipy
  Downloading scipy-1.9.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (33.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.8/33.8 MB 195.7 MB/s eta 0:00:00
Collecting statsmodels
  Downloading statsmodels-0.13.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.9/9.9 MB 206.4 MB/s eta 0:00:00
Requirement already satisfied: matplotlib in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from covasim==3.1.4) (3.6.0)
Collecting matplotlib
  Downloading matplotlib-3.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.8/11.8 MB 193.2 MB/s eta 0:00:00
Collecting sciris>=2.0.1
  Downloading sciris-2.0.1-py3-none-any.whl (180 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 180.1/180.1 kB 266.8 MB/s eta 0:00:00
Collecting jsonpickle
  Downloading jsonpickle-2.2.0-py2.py3-none-any.whl (39 kB)
Collecting multiprocess
  Downloading multiprocess-0.70.13-py39-none-any.whl (132 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.3/132.3 kB 248.4 MB/s eta 0:00:00
Collecting memory-profiler
  Downloading memory_profiler-0.60.0.tar.gz (38 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: pyyaml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sciris>=2.0.1->covasim==3.1.4) (6.0)
Collecting jellyfish
  Downloading jellyfish-0.9.0.tar.gz (132 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.6/132.6 kB 224.4 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting line-profiler
  Downloading line_profiler-3.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (70 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 70.8/70.8 kB 186.9 MB/s eta 0:00:00
Collecting openpyxl
  Downloading openpyxl-3.0.10-py2.py3-none-any.whl (242 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 242.1/242.1 kB 256.0 MB/s eta 0:00:00
Collecting gitpython
  Downloading GitPython-3.1.29-py3-none-any.whl (182 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 182.5/182.5 kB 230.5 MB/s eta 0:00:00
Collecting dill
  Downloading dill-0.3.5.1-py2.py3-none-any.whl (95 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 95.8/95.8 kB 234.7 MB/s eta 0:00:00
Collecting xlsxwriter
  Downloading XlsxWriter-3.0.3-py3-none-any.whl (149 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 150.0/150.0 kB 241.7 MB/s eta 0:00:00
Requirement already satisfied: psutil in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from sciris>=2.0.1->covasim==3.1.4) (5.9.3)
Requirement already satisfied: cycler>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (0.11.0)
Requirement already satisfied: pillow>=6.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (9.2.0)
Requirement already satisfied: contourpy>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (1.0.5)
Requirement already satisfied: python-dateutil>=2.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (2.8.2)
Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (21.3)
Requirement already satisfied: fonttools>=4.22.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (1.4.4)
Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from matplotlib->covasim==3.1.4) (3.0.9)
Collecting llvmlite<0.40,>=0.39.0dev0
  Downloading llvmlite-0.39.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.6/34.6 MB 204.3 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from numba->covasim==3.1.4) (58.2.0)
Collecting setuptools
  Downloading setuptools-65.5.0-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 272.1 MB/s eta 0:00:00
Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from pandas->covasim==3.1.4) (2022.5)
Collecting patsy>=0.5.2
  Downloading patsy-0.5.3-py2.py3-none-any.whl (233 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.8/233.8 kB 245.8 MB/s eta 0:00:00
Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages (from patsy>=0.5.2->statsmodels->covasim==3.1.4) (1.16.0)
Collecting gitdb<5,>=4.0.1
  Downloading gitdb-4.0.9-py3-none-any.whl (63 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.1/63.1 kB 221.1 MB/s eta 0:00:00
Collecting et-xmlfile
  Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Collecting smmap<6,>=3.0.1
  Downloading smmap-5.0.0-py3-none-any.whl (24 kB)
Building wheels for collected packages: covasim, jellyfish, memory-profiler
  Building wheel for covasim (setup.py): started
  Building wheel for covasim (setup.py): finished with status 'done'
  Created wheel for covasim: filename=covasim-3.1.4-py3-none-any.whl size=1631903 sha256=6663e788f88ae6da24138108621c76975dbca4a6ad6fc89d08080a9831f6ee5e
  Stored in directory: /tmp/pip-ephem-wheel-cache-5a5l22ew/wheels/47/88/46/fbd9fe4897d2ee7c348589195791d23c63897c8ab5b36306d1
  Building wheel for jellyfish (setup.py): started
  Building wheel for jellyfish (setup.py): finished with status 'done'
  Created wheel for jellyfish: filename=jellyfish-0.9.0-cp39-cp39-linux_x86_64.whl size=102030 sha256=414de022be72b5789dd63905af0d085b9bd276b6ff7534e7a5b242fe8e58bc42
  Stored in directory: /tmp/pip-ephem-wheel-cache-5a5l22ew/wheels/a1/38/09/217f100d5ba4e37ff47b0da300ad91e165f1c9ddafcdb6838a
  Building wheel for memory-profiler (setup.py): started
  Building wheel for memory-profiler (setup.py): finished with status 'done'
  Created wheel for memory-profiler: filename=memory_profiler-0.60.0-py3-none-any.whl size=31285 sha256=0ce5a7f483caa7793a33ebff272c25b24282b2a58955fd357e4e1e7dd3d3fcaa
  Stored in directory: /tmp/pip-ephem-wheel-cache-5a5l22ew/wheels/08/18/6c/20a49338c318cc9b43db94223b398a4f438ef4aabc0f785e9f
Successfully built covasim jellyfish memory-profiler
Installing collected packages: line-profiler, xlsxwriter, smmap, setuptools, scipy, patsy, memory-profiler, llvmlite, jsonpickle, jellyfish, et-xmlfile, dill, openpyxl, numba, multiprocess, matplotlib, gitdb, statsmodels, gitpython, sciris, covasim
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.2.0
    Uninstalling setuptools-58.2.0:
      Successfully uninstalled setuptools-58.2.0
  Attempting uninstall: scipy
    Found existing installation: scipy 1.8.1
    Uninstalling scipy-1.8.1:
      Successfully uninstalled scipy-1.8.1
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.6.0
    Uninstalling matplotlib-3.6.0:
      Successfully uninstalled matplotlib-3.6.0
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
seaborn 0.12.1 requires matplotlib!=3.6.1,>=3.1, but you have matplotlib 3.6.1 which is incompatible.
optuna 3.0.3 requires scipy<1.9.0,>=1.7.0, but you have scipy 1.9.3 which is incompatible.
Successfully installed covasim-3.1.4 dill-0.3.5.1 et-xmlfile-1.1.0 gitdb-4.0.9 gitpython-3.1.29 jellyfish-0.9.0 jsonpickle-2.2.0 line-profiler-3.5.1 llvmlite-0.39.1 matplotlib-3.6.1 memory-profiler-0.60.0 multiprocess-0.70.13 numba-0.56.3 openpyxl-3.0.10 patsy-0.5.3 scipy-1.9.3 sciris-2.0.1 setuptools-65.5.0 smmap-5.0.0 statsmodels-0.13.2 xlsxwriter-3.0.3

[rtd-command-info] start-time: 2022-10-22T21:34:14.141615Z, end-time: 2022-10-22T21:34:14.209703Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config


# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import subprocess
import sys
import sphinx_rtd_theme
from datetime import datetime
import covasim as cv

# Set environment
os.environ['SPHINX_BUILD'] = 'True' # This is used so cv.options.set('jupyter') doesn't reset the Matplotlib renderer
os.environ['COVASIM_WARNINGS'] = 'error' # Don't let warnings pass in the tutorials
on_rtd = os.environ.get('READTHEDOCS') == 'True'

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

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


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

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

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.mathjax',
    'sphinx.ext.githubpages',
    'sphinx.ext.autodoc',
    'sphinx.ext.napoleon',
    'sphinx.ext.todo',
    'sphinx.ext.viewcode',  # Add a link to the Python source code for classes, functions etc.
    'nbsphinx',
]

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

autodoc_mock_imports = []


napoleon_google_docstring = True

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

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
source_suffix = '.rst'
master_doc = 'index'

# General information about the project.
project = 'Covasim'
copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for Covasim version {cv.__version__}.\n'
author = 'Institute for Disease Modeling'

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

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

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

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False

# RST epilog is added to the end of every topic. Useful for replace
# directives to use across the docset.
rst_epilog = "\n.. include:: /variables.txt"

# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'

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


html_logo = "images/IDM_white.png"
html_favicon = "images/favicon.ico"

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

html_context = {
    'rtd_url': 'https://docs.idmod.org/projects/covasim/en/latest',
    'theme_vcs_pageview_mode': 'edit'
}
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#
if not on_rtd:
    html_extra_path = ['robots.txt']

# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
html_last_updated_fmt = '%Y-%b-%d'


# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
html_show_sphinx = False

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
html_use_opensearch = 'docs.idmod.org/projects/covasim/en/latest'

# Output file base name for HTML help builder.
htmlhelp_basename = 'Covasim'

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

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    # 'papersize': 'letterpaper',
    # The font size ('10pt', '11pt' or '12pt').
    # 'pointsize': '10pt',
    # Additional stuff for the LaTeX preamble.
    'preamble': '%XeLaTeX packages'
                '\\usepackage{xltxtra}'
                '\\usepackage{fontspec} %%Font package'
                '\\usepackage{xunicode}'
                '%%Select fonts'
                '\\setmainfont[Mapping=tex-text]{nimbusserif}'
                '\\setsansfont[Mapping=tex-text]{nimbussans}'
                '\\setmonofont{nimbusmono}',

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

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

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

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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'covasim-docs', 'Covasim',
     [author], 1)
]

# If true, show URL addresses after external links.
#
man_show_urls = True

# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'covasim-docs', 'Covasim',
     author, 'Institute for Disease Modeling', 'How to use IDM-Tools for disease simulations.',
     'Miscellaneous'),
]

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

# Configure nbsphinx
nbsphinx_kernel_name = "python"
nbsphinx_timeout = 90 # Time in seconds; use -1 for no timeout
nbsphinx_execute_arguments = [
    "--InlineBackend.figure_formats={'svg', 'pdf'}",
    "--InlineBackend.rc=figure.dpi=96",
]

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




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/covasim/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/covasim/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-covasim',
    'name': u'covasim',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://docs.idmod.org/projects/covasim/en/latest/',
    'analytics_code': 'UA-87656833-3',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'covasim',
    'github_version': 'fix-readthedocs',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'fix-readthedocs',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'fix-readthedocs',
    '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': '05a554f8',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-covasim/builds/1149997/'

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: 2022-10-22T21:34:14.436895Z, end-time: 2022-10-22T21:38:16.502382Z, duration: 242, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.6
Matplotlib is building the font cache; this may take a moment.
Covasim 3.1.4 (2022-10-22) — © 2020-2022 by IDM


Building Jupyter notebooks with build option: auto


loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 46 source files that are out of date
updating environment: 46 added, 0 changed, 0 removed
reading sources... [  2%] conduct
reading sources... [  4%] contributing
reading sources... [  6%] covasim.analysis
reading sources... [  8%] covasim.base
reading sources... [ 10%] covasim.data
reading sources... [ 13%] covasim.data.country_age_data
reading sources... [ 15%] covasim.data.household_size_data
reading sources... [ 17%] covasim.data.loaders
reading sources... [ 19%] covasim.data.state_age_data
reading sources... [ 21%] covasim.defaults
reading sources... [ 23%] covasim.immunity
reading sources... [ 26%] covasim.interventions
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
reading sources... [ 28%] covasim.misc
reading sources... [ 30%] covasim.parameters
reading sources... [ 32%] covasim.people
reading sources... [ 34%] covasim.plotting
reading sources... [ 36%] covasim.population
reading sources... [ 39%] covasim.requirements
reading sources... [ 41%] covasim.run
reading sources... [ 43%] covasim.settings
reading sources... [ 45%] covasim.sim
reading sources... [ 47%] covasim.utils
reading sources... [ 50%] covasim.version
reading sources... [ 52%] data
reading sources... [ 54%] faq
reading sources... [ 56%] glossary
reading sources... [ 58%] index
reading sources... [ 60%] modules
reading sources... [ 63%] overview
reading sources... [ 65%] papers
reading sources... [ 67%] parameters
reading sources... [ 69%] style
reading sources... [ 71%] tutorials
reading sources... [ 73%] tutorials/README
reading sources... [ 76%] tutorials/tut_advanced
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 78%] tutorials/tut_analyzers
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 80%] tutorials/tut_calibration
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 82%] tutorials/tut_deployment
reading sources... [ 84%] tutorials/tut_immunity
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 86%] tutorials/tut_interventions
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 89%] tutorials/tut_intro
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 91%] tutorials/tut_people
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)
reading sources... [ 93%] tutorials/tut_plotting
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:265: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  warn("Unexpected error discovering local network interfaces: %s" % e)

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbsphinx.py", line 1043, in parse
    rststring, resources = exporter.from_notebook_node(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbsphinx.py", line 853, in from_notebook_node
    nb, resources = pp.preprocess(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 91, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 112, in preprocess_cell
    cell = self.execute_cell(cell, index, store_history=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbclient/util.py", line 85, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbclient/util.py", line 60, in just_run
    return loop.run_until_complete(coro)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nest_asyncio.py", line 90, in run_until_complete
    return f.result()
  File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/asyncio/tasks.py", line 256, in __step
    result = coro.send(None)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbclient/client.py", line 1019, in async_execute_cell
    await self._check_raise_for_error(cell, cell_index, exec_reply)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbclient/client.py", line 913, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
sim.plot(style='seaborn-whitegrid')
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In [11], line 1
----> 1 sim.plot(style='seaborn-whitegrid')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/sim.py:1331, in Sim.plot(self, *args, **kwargs)
   1264 def plot(self, *args, **kwargs):
   1265     '''
   1266     Plot the results of a single simulation.
   1267 
   (...)
   1329     | New in version 3.1.2: updated date arguments; mpl_args renamed style_args
   1330     '''
-> 1331     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1332     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/plotting.py:385, in plot_sim(to_plot, sim, do_save, fig_path, fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, style_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    382 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 # Do the plotting
--> 385 with cvo.with_style(args.style):
    386     fig, figs = create_figs(args, sep_figs, fig, ax)
    387     variant_keys = sim.result_keys('variant')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/settings.py:515, in Options.with_style(self, style_args, use, **kwargs)
    513 # Handle style, overwiting existing
    514 style = kwargs.pop('style', None)
--> 515 rc = self._handle_style(style, reset=False)
    517 def pop_keywords(sourcekeys, rckey):
    518     ''' Helper function to handle input arguments '''

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/settings.py:471, in Options._handle_style(self, style, reset, copy)
    469     else:
    470         errormsg = f'Style "{style}"; not found; options are "covasim" (default), "simple", plus:\n{sc.newlinejoin(pl.style.available)}'
--> 471         raise ValueError(errormsg)
    472 if reset:
    473     self.rc = rc

ValueError: Style "seaborn-whitegrid"; not found; options are "covasim" (default), "simple", plus:
Solarize_Light2
_classic_test_patch
_mpl-gallery
_mpl-gallery-nogrid
bmh
classic
dark_background
fast
fivethirtyeight
ggplot
grayscale
seaborn-v0_8
seaborn-v0_8-bright
seaborn-v0_8-colorblind
seaborn-v0_8-dark
seaborn-v0_8-dark-palette
seaborn-v0_8-darkgrid
seaborn-v0_8-deep
seaborn-v0_8-muted
seaborn-v0_8-notebook
seaborn-v0_8-paper
seaborn-v0_8-pastel
seaborn-v0_8-poster
seaborn-v0_8-talk
seaborn-v0_8-ticks
seaborn-v0_8-white
seaborn-v0_8-whitegrid
tableau-colorblind10
ValueError: Style "seaborn-whitegrid"; not found; options are "covasim" (default), "simple", plus:
Solarize_Light2
_classic_test_patch
_mpl-gallery
_mpl-gallery-nogrid
bmh
classic
dark_background
fast
fivethirtyeight
ggplot
grayscale
seaborn-v0_8
seaborn-v0_8-bright
seaborn-v0_8-colorblind
seaborn-v0_8-dark
seaborn-v0_8-dark-palette
seaborn-v0_8-darkgrid
seaborn-v0_8-deep
seaborn-v0_8-muted
seaborn-v0_8-notebook
seaborn-v0_8-paper
seaborn-v0_8-pastel
seaborn-v0_8-poster
seaborn-v0_8-talk
seaborn-v0_8-ticks
seaborn-v0_8-white
seaborn-v0_8-whitegrid
tableau-colorblind10


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/cmd/build.py", line 304, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/application.py", line 341, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 345, in build_update
    self.build(to_build,
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 360, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 468, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 490, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 534, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/io.py", line 318, in read_doc
    pub.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/docutils/core.py", line 217, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/nbsphinx.py", line 1050, in parse
    raise NotebookError('\n'.join(lines))
nbsphinx.NotebookError: CellExecutionError in tutorials/tut_plotting.ipynb:
------------------
sim.plot(style='seaborn-whitegrid')
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In [11], line 1
----> 1 sim.plot(style='seaborn-whitegrid')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/sim.py:1331, in Sim.plot(self, *args, **kwargs)
   1264 def plot(self, *args, **kwargs):
   1265     '''
   1266     Plot the results of a single simulation.
   1267 
   (...)
   1329     | New in version 3.1.2: updated date arguments; mpl_args renamed style_args
   1330     '''
-> 1331     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1332     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/plotting.py:385, in plot_sim(to_plot, sim, do_save, fig_path, fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, style_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    382 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 # Do the plotting
--> 385 with cvo.with_style(args.style):
    386     fig, figs = create_figs(args, sep_figs, fig, ax)
    387     variant_keys = sim.result_keys('variant')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/settings.py:515, in Options.with_style(self, style_args, use, **kwargs)
    513 # Handle style, overwiting existing
    514 style = kwargs.pop('style', None)
--> 515 rc = self._handle_style(style, reset=False)
    517 def pop_keywords(sourcekeys, rckey):
    518     ''' Helper function to handle input arguments '''

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/settings.py:471, in Options._handle_style(self, style, reset, copy)
    469     else:
    470         errormsg = f'Style "{style}"; not found; options are "covasim" (default), "simple", plus:\n{sc.newlinejoin(pl.style.available)}'
--> 471         raise ValueError(errormsg)
    472 if reset:
    473     self.rc = rc

ValueError: Style "seaborn-whitegrid"; not found; options are "covasim" (default), "simple", plus:
Solarize_Light2
_classic_test_patch
_mpl-gallery
_mpl-gallery-nogrid
bmh
classic
dark_background
fast
fivethirtyeight
ggplot
grayscale
seaborn-v0_8
seaborn-v0_8-bright
seaborn-v0_8-colorblind
seaborn-v0_8-dark
seaborn-v0_8-dark-palette
seaborn-v0_8-darkgrid
seaborn-v0_8-deep
seaborn-v0_8-muted
seaborn-v0_8-notebook
seaborn-v0_8-paper
seaborn-v0_8-pastel
seaborn-v0_8-poster
seaborn-v0_8-talk
seaborn-v0_8-ticks
seaborn-v0_8-white
seaborn-v0_8-whitegrid
tableau-colorblind10
ValueError: Style "seaborn-whitegrid"; not found; options are "covasim" (default), "simple", plus:
Solarize_Light2
_classic_test_patch
_mpl-gallery
_mpl-gallery-nogrid
bmh
classic
dark_background
fast
fivethirtyeight
ggplot
grayscale
seaborn-v0_8
seaborn-v0_8-bright
seaborn-v0_8-colorblind
seaborn-v0_8-dark
seaborn-v0_8-dark-palette
seaborn-v0_8-darkgrid
seaborn-v0_8-deep
seaborn-v0_8-muted
seaborn-v0_8-notebook
seaborn-v0_8-paper
seaborn-v0_8-pastel
seaborn-v0_8-poster
seaborn-v0_8-talk
seaborn-v0_8-ticks
seaborn-v0_8-white
seaborn-v0_8-whitegrid
tableau-colorblind10

You can ignore this error by setting the following in conf.py:

    nbsphinx_allow_errors = True


Notebook error:
CellExecutionError in tutorials/tut_plotting.ipynb:
------------------
sim.plot(style='seaborn-whitegrid')
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In [11], line 1
----> 1 sim.plot(style='seaborn-whitegrid')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/sim.py:1331, in Sim.plot(self, *args, **kwargs)
   1264 def plot(self, *args, **kwargs):
   1265     '''
   1266     Plot the results of a single simulation.
   1267 
   (...)
   1329     | New in version 3.1.2: updated date arguments; mpl_args renamed style_args
   1330     '''
-> 1331     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1332     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/plotting.py:385, in plot_sim(to_plot, sim, do_save, fig_path, fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, style_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    382 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 # Do the plotting
--> 385 with cvo.with_style(args.style):
    386     fig, figs = create_figs(args, sep_figs, fig, ax)
    387     variant_keys = sim.result_keys('variant')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/settings.py:515, in Options.with_style(self, style_args, use, **kwargs)
    513 # Handle style, overwiting existing
    514 style = kwargs.pop('style', None)
--> 515 rc = self._handle_style(style, reset=False)
    517 def pop_keywords(sourcekeys, rckey):
    518     ''' Helper function to handle input arguments '''

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/covasim/settings.py:471, in Options._handle_style(self, style, reset, copy)
    469     else:
    470         errormsg = f'Style "{style}"; not found; options are "covasim" (default), "simple", plus:\n{sc.newlinejoin(pl.style.available)}'
--> 471         raise ValueError(errormsg)
    472 if reset:
    473     self.rc = rc

ValueError: Style "seaborn-whitegrid"; not found; options are "covasim" (default), "simple", plus:
Solarize_Light2
_classic_test_patch
_mpl-gallery
_mpl-gallery-nogrid
bmh
classic
dark_background
fast
fivethirtyeight
ggplot
grayscale
seaborn-v0_8
seaborn-v0_8-bright
seaborn-v0_8-colorblind
seaborn-v0_8-dark
seaborn-v0_8-dark-palette
seaborn-v0_8-darkgrid
seaborn-v0_8-deep
seaborn-v0_8-muted
seaborn-v0_8-notebook
seaborn-v0_8-paper
seaborn-v0_8-pastel
seaborn-v0_8-poster
seaborn-v0_8-talk
seaborn-v0_8-ticks
seaborn-v0_8-white
seaborn-v0_8-whitegrid
tableau-colorblind10
ValueError: Style "seaborn-whitegrid"; not found; options are "covasim" (default), "simple", plus:
Solarize_Light2
_classic_test_patch
_mpl-gallery
_mpl-gallery-nogrid
bmh
classic
dark_background
fast
fivethirtyeight
ggplot
grayscale
seaborn-v0_8
seaborn-v0_8-bright
seaborn-v0_8-colorblind
seaborn-v0_8-dark
seaborn-v0_8-dark-palette
seaborn-v0_8-darkgrid
seaborn-v0_8-deep
seaborn-v0_8-muted
seaborn-v0_8-notebook
seaborn-v0_8-paper
seaborn-v0_8-pastel
seaborn-v0_8-poster
seaborn-v0_8-talk
seaborn-v0_8-ticks
seaborn-v0_8-white
seaborn-v0_8-whitegrid
tableau-colorblind10

You can ignore this error by setting the following in conf.py:

    nbsphinx_allow_errors = True