Read the Docs build information
Build id: 1018601
Project: institute-for-disease-modeling-covasim
Version: latest
Commit: a8254e04a199f1a54e13af64dc022a47a328c949
Date: 2022-07-19T06:21:48.489725Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-07-19T06:25:54.280404Z, end-time: 2022-07-19T06:25:58.214197Z, 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,192.30.255.113' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-07-19T06:25:58.399776Z, end-time: 2022-07-19T06:25:58.523392Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by 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 a8254e04 Merge pull request #382 from InstituteforDiseaseModeling/dependabot/pip/tests/pillow-9.0.1

[rtd-command-info] start-time: 2022-07-19T06:25:58.824886Z, end-time: 2022-07-19T06:25:58.892849Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-07-19T06:26:00.016025Z, end-time: 2022-07-19T06:26:04.887953Z, duration: 4, exit-code: 0
python3.8 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.8.6'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-07-19T06:26:05.126279Z, end-time: 2022-07-19T06:26:06.953131Z, duration: 1, 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/python3.8/site-packages (22.1.2)
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
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    Uninstalling setuptools-63.2.0:
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[rtd-command-info] start-time: 2022-07-19T06:26:07.129510Z, end-time: 2022-07-19T06:26:33.738612Z, duration: 26, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 setuptools<58.3.0
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Collecting MarkupSafe>=2.0
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Building wheels for collected packages: mock, pillow, future
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=56e06988a3160b48924e21b566b688eb84aa35a1eb157b5f8fc11d16f181fae2
  Stored in directory: /tmp/pip-ephem-wheel-cache-9fk0ltzu/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65
  Building wheel for pillow (setup.py): started
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  Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260169 sha256=d3d49d670e95d0dd94eebaf85093b816d18c58bad1cc70ceba4a9c6bee2631e8
  Stored in directory: /tmp/pip-ephem-wheel-cache-9fk0ltzu/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d
  Building wheel for future (setup.py): started
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  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=1bd5af6fb456bf9f5a3fcda5e8dc7a06937c942d9d85eb92ed698cb4288ff158
  Stored in directory: /tmp/pip-ephem-wheel-cache-9fk0ltzu/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built mock pillow future
Installing collected packages: snowballstemmer, pytz, mock, alabaster, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.1.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 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 urllib3-1.26.10

[rtd-command-info] start-time: 2022-07-19T06:26:33.934578Z, end-time: 2022-07-19T06:26:53.481125Z, duration: 19, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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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, scipy, pyzmq, PyYAML, python-dateutil, pyrsistent, pypandoc, py, psutil, prompt-toolkit, PrettyTable, pockets, plumbum, pluggy, pillow, pexpect, pbr, parso, pandocfilters, nest-asyncio, Mako, jupyterlab-pygments, greenlet, entrypoints, defusedxml, decorator, debugpy, colorlog, cmaes, bleach, autopage, attrs, asttokens, stevedore, stack-data, sqlalchemy, sphinxcontrib-napoleon, pytest, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, importlib-resources, importlib-metadata, cmd2, beautifulsoup4, seaborn, jupyter-client, jsonschema, ipython, cliff, alembic, optuna, nbformat, ipykernel, nbclient, nbconvert, nbsphinx
  Attempting uninstall: python-dateutil
    Found existing installation: python-dateutil 2.8.1
    Not uninstalling python-dateutil at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest
    Can't uninstall 'python-dateutil'. No files were found to uninstall.
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
Successfully installed Mako-1.2.1 PrettyTable-3.3.0 PyYAML-6.0 alembic-1.8.1 asttokens-2.0.5 attrs-21.4.0 autopage-0.5.1 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.1 cliff-3.10.1 cmaes-0.8.2 cmd2-2.4.2 colorlog-6.6.0 debugpy-1.6.2 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 executing-0.8.3 fastjsonschema-2.16.1 greenlet-1.1.2 importlib-metadata-4.12.0 importlib-resources-5.8.0 iniconfig-1.1.1 ipykernel-6.15.1 ipython-8.4.0 jedi-0.18.1 jsonschema-4.7.2 jupyter-client-7.3.4 jupyter-core-4.11.1 jupyterlab-pygments-0.2.2 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.6.6 nbconvert-6.5.0 nbformat-5.4.0 nbsphinx-0.8.9 nest-asyncio-1.5.5 optuna-2.10.1 pandoc-2.2 pandocfilters-1.5.0 parso-0.8.3 pbr-5.9.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.2.0 plantweb-1.2.1 pluggy-1.0.0 plumbum-1.7.2 ply-3.11 pockets-0.9.1 prompt-toolkit-3.0.30 psutil-5.9.1 ptyprocess-0.7.0 pure-eval-0.2.2 py-1.11.0 pypandoc-1.8.1 pyperclip-1.8.2 pyrsistent-0.18.1 pytest-7.1.2 python-dateutil-2.8.2 pyzmq-23.2.0 scipy-1.8.1 seaborn-0.11.2 soupsieve-2.3.2.post1 sphinxcontrib-napoleon-0.7 sqlalchemy-1.4.39 stack-data-0.3.0 stevedore-4.0.0 tinycss2-1.1.1 tomli-2.0.1 tornado-6.2 tqdm-4.64.0 traitlets-5.3.0 wcwidth-0.2.5 webencodings-0.5.1 zipp-3.8.1

[rtd-command-info] start-time: 2022-07-19T06:26:53.674329Z, end-time: 2022-07-19T06:27:18.264940Z, duration: 24, 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/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from covasim==3.1.3) (1.19.2)
Collecting numpy
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Collecting numba
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  Downloading pandas-1.4.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
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Collecting statsmodels
  Downloading statsmodels-0.13.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
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Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from covasim==3.1.3) (3.3.2)
Collecting matplotlib
  Downloading matplotlib-3.5.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.3 MB)
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Collecting sciris>=1.3.3
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Collecting jsonpickle
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Collecting openpyxl
  Downloading openpyxl-3.0.10-py2.py3-none-any.whl (242 kB)
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Collecting line-profiler
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Collecting jellyfish
  Downloading jellyfish-0.9.0.tar.gz (132 kB)
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  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting memory-profiler
  Downloading memory_profiler-0.60.0.tar.gz (38 kB)
  Preparing metadata (setup.py): started
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Collecting gitpython
  Downloading GitPython-3.1.27-py3-none-any.whl (181 kB)
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Collecting ansicolors
  Downloading ansicolors-1.1.8-py2.py3-none-any.whl (13 kB)
Collecting xlsxwriter
  Downloading XlsxWriter-3.0.3-py3-none-any.whl (149 kB)
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Requirement already satisfied: psutil in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sciris>=1.3.3->covasim==3.1.3) (5.9.1)
Collecting multiprocess
  Downloading multiprocess-0.70.13-py38-none-any.whl (131 kB)
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Collecting fonttools>=4.22.0
  Downloading fonttools-4.34.4-py3-none-any.whl (944 kB)
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Requirement already satisfied: python-dateutil>=2.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from matplotlib->covasim==3.1.3) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from matplotlib->covasim==3.1.3) (1.2.0)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.4-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB)
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Requirement already satisfied: pillow>=6.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from matplotlib->covasim==3.1.3) (9.2.0)
Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from matplotlib->covasim==3.1.3) (0.10.0)
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from matplotlib->covasim==3.1.3) (3.0.9)
Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from matplotlib->covasim==3.1.3) (21.3)
Collecting numpy
  Downloading numpy-1.22.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.9 MB)
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Collecting llvmlite<0.39,>=0.38.0rc1
  Downloading llvmlite-0.38.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from numba->covasim==3.1.3) (58.2.0)
Collecting setuptools
  Downloading setuptools-63.2.0-py3-none-any.whl (1.2 MB)
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Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from pandas->covasim==3.1.3) (2022.1)
Collecting patsy>=0.5.2
  Downloading patsy-0.5.2-py2.py3-none-any.whl (233 kB)
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Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from patsy>=0.5.2->statsmodels->covasim==3.1.3) (1.16.0)
Collecting gitdb<5,>=4.0.1
  Downloading gitdb-4.0.9-py3-none-any.whl (63 kB)
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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-3.1.3-py3-none-any.whl size=1636189 sha256=9c8542bfe7e58e5365f3c56ae54ddf1a84c49d180890438ca2bb7e5179d02bd0
  Stored in directory: /tmp/pip-ephem-wheel-cache-fhl9rvyt/wheels/8e/0a/d8/1c91b2c2d1243047ecfeb611d13b952f1fa6c0034752c6cb05
  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-cp38-cp38-linux_x86_64.whl size=89238 sha256=ba1ce496d919fad9ae63f0551e22146fe42114c7214ca24dfde20d0978d4c567
  Stored in directory: /tmp/pip-ephem-wheel-cache-fhl9rvyt/wheels/f1/c7/3c/4c83132de76359e3a429fd09c08995945ca96c5290a41651d3
  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=31284 sha256=2b46f5911770fbcc7cb3f9ad31a02399fccc2052e647493c87c1a004b4e3359c
  Stored in directory: /tmp/pip-ephem-wheel-cache-fhl9rvyt/wheels/01/ca/8b/b518dd2aef69635ad6fcab87069c9c52f355a2e9c5d4c02da9
Successfully built covasim jellyfish memory-profiler
Installing collected packages: line-profiler, ansicolors, xlsxwriter, smmap, setuptools, numpy, memory-profiler, llvmlite, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, patsy, pandas, 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: numpy
    Found existing installation: numpy 1.19.2
    Not uninstalling numpy at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest
    Can't uninstall 'numpy'. No files were found to uninstall.
  Attempting uninstall: kiwisolver
    Found existing installation: kiwisolver 1.2.0
    Not uninstalling kiwisolver at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest
    Can't uninstall 'kiwisolver'. No files were found to uninstall.
  Attempting uninstall: cycler
    Found existing installation: cycler 0.10.0
    Not uninstalling cycler at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest
    Can't uninstall 'cycler'. No files were found to uninstall.
  Attempting uninstall: pandas
    Found existing installation: pandas 1.1.3
    Not uninstalling pandas at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest
    Can't uninstall 'pandas'. No files were found to uninstall.
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.3.2
    Not uninstalling matplotlib at /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest
    Can't uninstall 'matplotlib'. No files were found to uninstall.
Successfully installed ansicolors-1.1.8 covasim-3.1.3 cycler-0.11.0 dill-0.3.5.1 et-xmlfile-1.1.0 fonttools-4.34.4 gitdb-4.0.9 gitpython-3.1.27 jellyfish-0.9.0 jsonpickle-2.2.0 kiwisolver-1.4.4 line-profiler-3.5.1 llvmlite-0.38.1 matplotlib-3.5.2 memory-profiler-0.60.0 multiprocess-0.70.13 numba-0.55.2 numpy-1.22.4 openpyxl-3.0.10 pandas-1.4.3 patsy-0.5.2 sciris-1.3.3 setuptools-63.2.0 smmap-5.0.0 statsmodels-0.13.2 xlsxwriter-3.0.3

[rtd-command-info] start-time: 2022-07-19T06:27:19.806022Z, end-time: 2022-07-19T06:27:19.867170Z, 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__

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# 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': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-87656833-3',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'a8254e04',
}

# 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/1018601/'

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: 2022-07-19T06:27:20.051959Z, end-time: 2022-07-19T06:30:34.112317Z, duration: 194, exit-code: 2
python -m sphinx -T -E -W --keep-going -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 3.1.3 (2022-07-19) — © 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 44 source files that are out of date
updating environment: 44 added, 0 changed, 0 removed
reading sources... [  2%] conduct
reading sources... [  4%] contributing
reading sources... [  6%] covasim.analysis
reading sources... [  9%] covasim.base
reading sources... [ 11%] covasim.data
reading sources... [ 13%] covasim.data.country_age_data
reading sources... [ 15%] covasim.data.household_size_data
reading sources... [ 18%] covasim.data.loaders
reading sources... [ 20%] covasim.data.state_age_data
reading sources... [ 22%] covasim.defaults
reading sources... [ 25%] covasim.immunity
reading sources... [ 27%] covasim.interventions
reading sources... [ 29%] covasim.misc
reading sources... [ 31%] covasim.parameters
reading sources... [ 34%] covasim.people
reading sources... [ 36%] covasim.plotting
reading sources... [ 38%] covasim.population
reading sources... [ 40%] covasim.requirements
reading sources... [ 43%] covasim.run
reading sources... [ 45%] covasim.settings
reading sources... [ 47%] covasim.sim
reading sources... [ 50%] covasim.utils
reading sources... [ 52%] covasim.version
reading sources... [ 54%] data
reading sources... [ 56%] faq
reading sources... [ 59%] glossary
reading sources... [ 61%] index
reading sources... [ 63%] modules
reading sources... [ 65%] overview
reading sources... [ 68%] parameters
reading sources... [ 70%] tutorials
reading sources... [ 72%] tutorials/README
reading sources... [ 75%] tutorials/tut_advanced
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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... [ 77%] tutorials/tut_analyzers
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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... [ 79%] tutorials/tut_calibration
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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... [ 81%] tutorials/tut_deployment
reading sources... [ 84%] tutorials/tut_immunity
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/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/python3.8/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)):
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/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/python3.8/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/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 89, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 110, 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/python3.8/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/python3.8/site-packages/nbclient/util.py", line 60, in just_run
    return loop.run_until_complete(coro)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
    return future.result()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 1025, 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/python3.8/site-packages/nbclient/client.py", line 919, 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:
------------------
# Plot intervention
protect = msim.sims[1].get_intervention(protect_elderly) # Find intervention by type
protect.plot()
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Input In [12], in <cell line: 2>()
      1 # Plot intervention
----> 2 protect = msim.sims[1].get_intervention(protect_elderly) # Find intervention by type
      3 protect.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/base.py:852, in BaseSim.get_intervention(self, label, partial, first, die)
    828 def get_intervention(self, label=None, partial=False, first=False, die=True):
    829     '''
    830     Like get_interventions(), find the matching intervention(s) by label,
    831     index, or type. If more than one intervention matches, return the last
   (...)
    850         tp = sim.get_intervention(first=True)
    851     '''
--> 852     return self._get_ia('interventions', label=label, partial=partial, first=first, die=die, as_inds=False, as_list=False)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/base.py:794, in BaseSim._get_ia(self, which, label, partial, as_list, as_inds, die, first)
    792 if die:
    793     errormsg = f'No {which} matching "{label}" were found'
--> 794     raise ValueError(errormsg)
    795 else:
    796     output = None

ValueError: No interventions matching "<class '__main__.protect_elderly'>" were found
ValueError: No interventions matching "<class '__main__.protect_elderly'>" were found


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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/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/python3.8/site-packages/nbsphinx.py", line 1050, in parse
    raise NotebookError('\n'.join(lines))
nbsphinx.NotebookError: CellExecutionError in tutorials/tut_interventions.ipynb:
------------------
# Plot intervention
protect = msim.sims[1].get_intervention(protect_elderly) # Find intervention by type
protect.plot()
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Input In [12], in <cell line: 2>()
      1 # Plot intervention
----> 2 protect = msim.sims[1].get_intervention(protect_elderly) # Find intervention by type
      3 protect.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/base.py:852, in BaseSim.get_intervention(self, label, partial, first, die)
    828 def get_intervention(self, label=None, partial=False, first=False, die=True):
    829     '''
    830     Like get_interventions(), find the matching intervention(s) by label,
    831     index, or type. If more than one intervention matches, return the last
   (...)
    850         tp = sim.get_intervention(first=True)
    851     '''
--> 852     return self._get_ia('interventions', label=label, partial=partial, first=first, die=die, as_inds=False, as_list=False)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/base.py:794, in BaseSim._get_ia(self, which, label, partial, as_list, as_inds, die, first)
    792 if die:
    793     errormsg = f'No {which} matching "{label}" were found'
--> 794     raise ValueError(errormsg)
    795 else:
    796     output = None

ValueError: No interventions matching "<class '__main__.protect_elderly'>" were found
ValueError: No interventions matching "<class '__main__.protect_elderly'>" were found

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

    nbsphinx_allow_errors = True


Notebook error:
CellExecutionError in tutorials/tut_interventions.ipynb:
------------------
# Plot intervention
protect = msim.sims[1].get_intervention(protect_elderly) # Find intervention by type
protect.plot()
------------------

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Input In [12], in <cell line: 2>()
      1 # Plot intervention
----> 2 protect = msim.sims[1].get_intervention(protect_elderly) # Find intervention by type
      3 protect.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/base.py:852, in BaseSim.get_intervention(self, label, partial, first, die)
    828 def get_intervention(self, label=None, partial=False, first=False, die=True):
    829     '''
    830     Like get_interventions(), find the matching intervention(s) by label,
    831     index, or type. If more than one intervention matches, return the last
   (...)
    850         tp = sim.get_intervention(first=True)
    851     '''
--> 852     return self._get_ia('interventions', label=label, partial=partial, first=first, die=die, as_inds=False, as_list=False)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/base.py:794, in BaseSim._get_ia(self, which, label, partial, as_list, as_inds, die, first)
    792 if die:
    793     errormsg = f'No {which} matching "{label}" were found'
--> 794     raise ValueError(errormsg)
    795 else:
    796     output = None

ValueError: No interventions matching "<class '__main__.protect_elderly'>" were found
ValueError: No interventions matching "<class '__main__.protect_elderly'>" were found

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

    nbsphinx_allow_errors = True