Read the Docs build information
Build id: 1149991
Project: institute-for-disease-modeling-covasim
Version: latest
Commit: 384713fdf8497a603a83fb6740e111bec2abd71a
Date: 2022-10-22T21:18:00.814921Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-10-22T21:18:03.569723Z, end-time: 2022-10-22T21:18:06.712282Z, duration: 3, 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: 2022-10-22T21:18:06.920902Z, end-time: 2022-10-22T21:18:07.061316Z, 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 384713fd update readthedocs config

[rtd-command-info] start-time: 2022-10-22T21:18:07.249452Z, end-time: 2022-10-22T21:18:07.321074Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-10-22T21:18:12.482390Z, end-time: 2022-10-22T21:18:13.168915Z, duration: 0, exit-code: 0
asdf global python 3.9.13


[rtd-command-info] start-time: 2022-10-22T21:18:14.094882Z, end-time: 2022-10-22T21:18:15.480945Z, duration: 1, exit-code: 0
python -mvirtualenv 
created virtual environment CPython3.9.13.final.0-64 in 682ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  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: 2022-10-22T21:18:15.689136Z, end-time: 2022-10-22T21:18:26.582401Z, duration: 10, 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: 2022-10-22T21:18:26.847537Z, end-time: 2022-10-22T21:18:34.971639Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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
Collecting pillow
  Downloading Pillow-9.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 53.1 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 157.9 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 124.2 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 157.7 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 149.9 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 135.2 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 155.0 MB/s eta 0:00:00
Collecting Pygments>=2.0
  Downloading Pygments-2.13.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 177.9 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 sphinx<2) (58.2.0)
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 232.9 MB/s eta 0:00:00
Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 261.2 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 159.6 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 213.3 MB/s eta 0:00:00
Collecting packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 198.8 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 261.8 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 247.0 MB/s eta 0:00:00
Collecting certifi>=2017.4.17
  Downloading certifi-2022.9.24-py3-none-any.whl (161 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 161.1/161.1 kB 256.7 MB/s eta 0:00:00
Collecting charset-normalizer<3,>=2
  Downloading charset_normalizer-2.1.1-py3-none-any.whl (39 kB)
Collecting idna<4,>=2.5
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 200.8 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 217.9 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 219.7 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=185e9f715dc4235358b8ea9d0e1c34b6e253c82e511aa57e45ba9bec4d7638b5
  Stored in directory: /tmp/pip-ephem-wheel-cache-13p3g0lc/wheels/95/5a/42/6d69898ad0ccd6d30cf1ea4ae71db699e0c7bef2294dc557a5
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, urllib3, sphinxcontrib-serializinghtml, six, 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 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: 2022-10-22T21:18:35.208767Z, end-time: 2022-10-22T21:19:06.210699Z, duration: 31, 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 11.3 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 248.1 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 50.3 MB/s eta 0:00:00
Collecting seaborn
  Downloading seaborn-0.12.1-py3-none-any.whl (288 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 264.3 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 attrs>=19.2.0
  Downloading attrs-22.1.0-py2.py3-none-any.whl (58 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.8/58.8 kB 204.9 MB/s eta 0:00:00
Collecting iniconfig
  Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting py>=1.8.2
  Downloading py-1.11.0-py2.py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.7/98.7 kB 234.0 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 tomli>=1.0.0
  Downloading tomli-2.0.1-py3-none-any.whl (12 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)
Collecting pockets>=0.3
  Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB)
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: 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: 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: 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: 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)
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: 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: 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: 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: 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)
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 231.6 MB/s eta 0:00:00
Collecting matplotlib-inline>=0.1
  Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
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 141.1 MB/s eta 0:00:00
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 245.2 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 277.3 MB/s eta 0:00:00
Collecting nest-asyncio
  Downloading nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)
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 262.3 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 237.4 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 208.9 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 246.3 MB/s eta 0:00:00
Collecting nbformat
  Downloading nbformat-5.7.0-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.1/77.1 kB 202.3 MB/s eta 0:00:00
Collecting plumbum
  Downloading plumbum-1.8.0-py3-none-any.whl (117 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.5/117.5 kB 237.3 MB/s eta 0:00:00
Collecting ply
  Downloading ply-3.11-py2.py3-none-any.whl (49 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.6/49.6 kB 195.6 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 172.5 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 272.1 MB/s eta 0:00:00
Collecting cliff
  Downloading cliff-4.0.0-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 81.0/81.0 kB 207.8 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 174.3 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 261.9 MB/s eta 0:00:00
Collecting colorlog
  Downloading colorlog-6.7.0-py2.py3-none-any.whl (11 kB)
Collecting importlib-metadata<5.0.0
  Downloading importlib_metadata-4.13.0-py3-none-any.whl (23 kB)
Collecting tqdm
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 222.0 MB/s eta 0:00:00
Collecting cmaes>=0.8.2
  Downloading cmaes-0.8.2-py3-none-any.whl (15 kB)
Collecting alembic>=1.5.0
  Downloading alembic-1.8.1-py3-none-any.whl (209 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.8/209.8 kB 260.2 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 181.2 MB/s eta 0:00:00
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 161.6 MB/s eta 0:00:00
Collecting Mako
  Downloading Mako-1.2.3-py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.7/78.7 kB 208.6 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 jedi>=0.16
  Downloading jedi-0.18.1-py2.py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 273.7 MB/s eta 0:00:00
Collecting stack-data
  Downloading stack_data-0.5.1-py3-none-any.whl (24 kB)
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 209.3 MB/s eta 0:00:00
Collecting backcall
  Downloading backcall-0.2.0-py2.py3-none-any.whl (11 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 270.8 MB/s eta 0:00:00
Collecting decorator
  Downloading decorator-5.1.1-py3-none-any.whl (9.1 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 python-dateutil>=2.8.2
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 262.7 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 244.1 MB/s eta 0:00:00
Collecting entrypoints
  Downloading entrypoints-0.4-py3-none-any.whl (5.3 kB)
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 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 270.8 MB/s eta 0:00:00
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.38.0-py3-none-any.whl (965 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 272.7 MB/s eta 0:00:00
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 262.7 MB/s eta 0:00:00
Collecting jupyterlab-pygments
  Downloading jupyterlab_pygments-0.2.2-py2.py3-none-any.whl (21 kB)
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 236.8 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 218.1 MB/s eta 0:00:00
Collecting beautifulsoup4
  Downloading beautifulsoup4-4.11.1-py3-none-any.whl (128 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 128.2/128.2 kB 252.7 MB/s eta 0:00:00
Collecting tinycss2
  Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB)
Collecting pandocfilters>=1.4.1
  Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB)
Collecting fastjsonschema
  Downloading fastjsonschema-2.16.2-py3-none-any.whl (22 kB)
Collecting jsonschema>=2.6
  Downloading jsonschema-4.16.0-py3-none-any.whl (83 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.1/83.1 kB 212.8 MB/s eta 0:00:00
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: 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)
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: 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)
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 248.1 MB/s eta 0:00:00
Collecting PrettyTable>=0.7.2
  Downloading prettytable-3.4.1-py3-none-any.whl (26 kB)
Collecting autopage>=0.4.0
  Downloading autopage-0.5.1-py3-none-any.whl (29 kB)
Collecting cmd2>=1.0.0
  Downloading cmd2-2.4.2-py3-none-any.whl (147 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.1/147.1 kB 250.8 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 190.8 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 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 wcwidth>=0.1.7
  Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
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 231.0 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 233.0 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 246.9 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 pure-eval
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting executing
  Downloading executing-1.1.1-py2.py3-none-any.whl (22 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=995d66b68e56a751688cd462c27d23ad6e9520037b174cc1060d669e1f3faf04
  Stored in directory: /tmp/pip-ephem-wheel-cache-ys7d9uwb/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=1ad92c5ece25f9a3c10cd9e42437ce847b4d4d106cf8d62e2ceeffd7eeb6c224
  Stored in directory: /tmp/pip-ephem-wheel-cache-ys7d9uwb/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: 2022-10-22T21:19:07.934572Z, end-time: 2022-10-22T21:19:07.997442Z, 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': '384713fd',
}

# 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/1149991/'

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: 2022-10-22T21:19:08.205229Z, end-time: 2022-10-22T21:19:08.621274Z, duration: 0, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.6

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/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/checkouts/latest/docs/conf.py", line 19, in <module>
    import covasim as cv
ModuleNotFoundError: No module named 'covasim'

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 300, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/config.py", line 203, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/config.py", line 380, in eval_config_file
    raise ConfigError(msg % traceback.format_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-covasim/envs/latest/lib/python3.9/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/checkouts/latest/docs/conf.py", line 19, in <module>
    import covasim as cv
ModuleNotFoundError: No module named 'covasim'


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-covasim/envs/latest/lib/python3.9/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.9/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/checkouts/latest/docs/conf.py", line 19, in <module>
    import covasim as cv
ModuleNotFoundError: No module named 'covasim'