Read the Docs build information
Build id: 1149982
Project: institute-for-disease-modeling-covasim
Version: latest
Commit: a3db333f464596e66df5dee1502e7796516eb081
Date: 2022-10-22T20:53:11.288785Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-10-22T20:53:13.390658Z, end-time: 2022-10-22T20:53:16.335376Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/covasim.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-10-22T20:53:16.542900Z, end-time: 2022-10-22T20:53:16.666650Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

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 a3db333f Merge pull request #1396 from amath-idm/rc3.1.4

[rtd-command-info] start-time: 2022-10-22T20:53:16.873361Z, end-time: 2022-10-22T20:53:16.939750Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-10-22T20:53:18.124277Z, end-time: 2022-10-22T20:53:39.537184Z, duration: 21, 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: 2022-10-22T20:53:39.741608Z, end-time: 2022-10-22T20:53:41.707439Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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[rtd-command-info] start-time: 2022-10-22T20:53:41.894642Z, end-time: 2022-10-22T20:53:49.400216Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 setuptools<58.3.0
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Building wheels for collected packages: mock
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Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.9.24 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 pytz-2022.5 readthedocs-sphinx-ext-2.1.9 recommonmark-0.5.0 requests-2.28.1 setuptools-58.2.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.12

[rtd-command-info] start-time: 2022-10-22T20:53:49.632482Z, end-time: 2022-10-22T20:54:08.802095Z, duration: 19, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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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 debugpy-1.6.3 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 executing-1.1.1 fastjsonschema-2.16.2 greenlet-1.1.3.post0 importlib-metadata-4.13.0 importlib-resources-5.10.0 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 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 optuna-3.0.3 pandoc-2.2 pandocfilters-1.5.0 parso-0.8.3 pbr-5.11.0 pexpect-4.8.0 pickleshare-0.7.5 pkgutil-resolve-name-1.3.10 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: 2022-10-22T20:54:09.003842Z, end-time: 2022-10-22T20:54:47.203877Z, duration: 38, 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
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Requirement already satisfied: numpy in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from covasim==3.1.4) (1.19.2)
Collecting numpy
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Collecting statsmodels
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Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from covasim==3.1.4) (3.3.2)
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Collecting sciris>=2.0.1
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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>=2.0.1->covasim==3.1.4) (5.9.3)
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Collecting line-profiler
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Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from matplotlib->covasim==3.1.4) (0.10.0)
Collecting cycler>=0.10
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Collecting contourpy>=1.0.1
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Collecting fonttools>=4.22.0
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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==3.1.4) (9.2.0)
Requirement already satisfied: importlib-metadata in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from numba->covasim==3.1.4) (4.13.0)
Collecting importlib-metadata
  Downloading importlib_metadata-5.0.0-py3-none-any.whl (21 kB)
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==3.1.4) (58.2.0)
Collecting setuptools
  Downloading setuptools-65.5.0-py3-none-any.whl (1.2 MB)
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Collecting llvmlite<0.40,>=0.39.0dev0
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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==3.1.4) (2022.5)
Collecting patsy>=0.5.2
  Downloading patsy-0.5.3-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==3.1.4) (1.16.0)
Collecting gitdb<5,>=4.0.1
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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-3.1.4-py3-none-any.whl size=1631903 sha256=4f01e4abb7bdf8c8719c30ee7ad65206d046323ca8ae4a5707a90a39171f7ba8
  Stored in directory: /tmp/pip-ephem-wheel-cache-z58lf68e/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=89244 sha256=074bc88049e6b69248cf0466d951304549d84db558f3cbd278853b9e26e684ea
  Stored in directory: /tmp/pip-ephem-wheel-cache-z58lf68e/wheels/0b/ca/cd/76ef5e7b99a27c1323a1c4f488b7f2e5b6cbb02f255a396282
  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=83340d860b1ff569d248512858ee86df8f74755a417f6e412b9da8b3d8279181
  Stored in directory: /tmp/pip-ephem-wheel-cache-z58lf68e/wheels/ed/1e/d2/9de96f4ce0c282911c3c839c47cc57895eaddb1f3b2712da76
Successfully built covasim jellyfish memory-profiler
Installing collected packages: line-profiler, xlsxwriter, smmap, setuptools, numpy, memory-profiler, llvmlite, kiwisolver, jsonpickle, jellyfish, importlib-metadata, fonttools, et-xmlfile, dill, cycler, scipy, patsy, pandas, openpyxl, numba, multiprocess, gitdb, contourpy, statsmodels, matplotlib, 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: importlib-metadata
    Found existing installation: importlib-metadata 4.13.0
    Uninstalling importlib-metadata-4.13.0:
      Successfully uninstalled importlib-metadata-4.13.0
  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: scipy
    Found existing installation: scipy 1.8.1
    Uninstalling scipy-1.8.1:
      Successfully uninstalled scipy-1.8.1
  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.
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
seaborn 0.12.1 requires matplotlib!=3.6.1,>=3.1, but you have matplotlib 3.6.1 which is incompatible.
optuna 3.0.3 requires importlib-metadata<5.0.0, but you have importlib-metadata 5.0.0 which is incompatible.
optuna 3.0.3 requires scipy<1.9.0,>=1.7.0, but you have scipy 1.9.3 which is incompatible.
Successfully installed contourpy-1.0.5 covasim-3.1.4 cycler-0.11.0 dill-0.3.5.1 et-xmlfile-1.1.0 fonttools-4.38.0 gitdb-4.0.9 gitpython-3.1.29 importlib-metadata-5.0.0 jellyfish-0.9.0 jsonpickle-2.2.0 kiwisolver-1.4.4 line-profiler-3.5.1 llvmlite-0.39.1 matplotlib-3.6.1 memory-profiler-0.60.0 multiprocess-0.70.13 numba-0.56.3 numpy-1.23.4 openpyxl-3.0.10 pandas-1.5.1 patsy-0.5.3 scipy-1.9.3 sciris-2.0.1 setuptools-65.5.0 smmap-5.0.0 statsmodels-0.13.2 xlsxwriter-3.0.3

[rtd-command-info] start-time: 2022-10-22T20:54:48.921048Z, end-time: 2022-10-22T20:54:48.982442Z, 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': 'main',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'main',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'main',
    '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': 'a3db333f',
}

# 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/1149982/'

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: 2022-10-22T20:54:49.199514Z, end-time: 2022-10-22T20:59:13.872085Z, duration: 264, 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 3.1.4 (2022-10-22) — © 2020-2022 by IDM


Building Jupyter notebooks with build option: auto


loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 46 source files that are out of date
updating environment: 46 added, 0 changed, 0 removed
reading sources... [  2%] conduct
reading sources... [  4%] contributing
reading sources... [  6%] covasim.analysis
reading sources... [  8%] covasim.base
reading sources... [ 10%] covasim.data
reading sources... [ 13%] covasim.data.country_age_data
reading sources... [ 15%] covasim.data.household_size_data
reading sources... [ 17%] covasim.data.loaders
reading sources... [ 19%] covasim.data.state_age_data
reading sources... [ 21%] covasim.defaults
reading sources... [ 23%] covasim.immunity
reading sources... [ 26%] covasim.interventions
reading sources... [ 28%] covasim.misc
reading sources... [ 30%] covasim.parameters
reading sources... [ 32%] covasim.people
reading sources... [ 34%] covasim.plotting
reading sources... [ 36%] covasim.population
reading sources... [ 39%] covasim.requirements
reading sources... [ 41%] covasim.run
reading sources... [ 43%] covasim.settings
reading sources... [ 45%] covasim.sim
reading sources... [ 47%] covasim.utils
reading sources... [ 50%] covasim.version
reading sources... [ 52%] data
reading sources... [ 54%] faq
reading sources... [ 56%] glossary
reading sources... [ 58%] index
reading sources... [ 60%] modules
reading sources... [ 63%] overview
reading sources... [ 65%] papers
reading sources... [ 67%] parameters
reading sources... [ 69%] style
reading sources... [ 71%] tutorials
reading sources... [ 73%] tutorials/README
reading sources... [ 76%] tutorials/tut_advanced
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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... [ 78%] 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... [ 80%] 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... [ 82%] tutorials/tut_deployment
reading sources... [ 84%] tutorials/tut_immunity
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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)
reading sources... [ 89%] tutorials/tut_intro
/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... [ 91%] tutorials/tut_people
/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... [ 93%] tutorials/tut_plotting
/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 91, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 112, in preprocess_cell
    cell = self.execute_cell(cell, index, store_history=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nest_asyncio.py", line 90, in run_until_complete
    return f.result()
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/futures.py", line 178, in result
    raise self._exception
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/tasks.py", line 280, in __step
    result = coro.send(None)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 1019, in async_execute_cell
    await self._check_raise_for_error(cell, cell_index, exec_reply)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 913, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
sim.plot(style='seaborn-whitegrid')
------------------

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

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/sim.py:1331, in Sim.plot(self, *args, **kwargs)
   1264 def plot(self, *args, **kwargs):
   1265     '''
   1266     Plot the results of a single simulation.
   1267 
   (...)
   1329     | New in version 3.1.2: updated date arguments; mpl_args renamed style_args
   1330     '''
-> 1331     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1332     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/plotting.py:385, in plot_sim(to_plot, sim, do_save, fig_path, fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, style_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    382 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 # Do the plotting
--> 385 with cvo.with_style(args.style):
    386     fig, figs = create_figs(args, sep_figs, fig, ax)
    387     variant_keys = sim.result_keys('variant')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/settings.py:515, in Options.with_style(self, style_args, use, **kwargs)
    513 # Handle style, overwiting existing
    514 style = kwargs.pop('style', None)
--> 515 rc = self._handle_style(style, reset=False)
    517 def pop_keywords(sourcekeys, rckey):
    518     ''' Helper function to handle input arguments '''

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/settings.py:471, in Options._handle_style(self, style, reset, copy)
    469     else:
    470         errormsg = f'Style "{style}"; not found; options are "covasim" (default), "simple", plus:\n{sc.newlinejoin(pl.style.available)}'
--> 471         raise ValueError(errormsg)
    472 if reset:
    473     self.rc = rc

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


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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_plotting.ipynb:
------------------
sim.plot(style='seaborn-whitegrid')
------------------

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

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/sim.py:1331, in Sim.plot(self, *args, **kwargs)
   1264 def plot(self, *args, **kwargs):
   1265     '''
   1266     Plot the results of a single simulation.
   1267 
   (...)
   1329     | New in version 3.1.2: updated date arguments; mpl_args renamed style_args
   1330     '''
-> 1331     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1332     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/plotting.py:385, in plot_sim(to_plot, sim, do_save, fig_path, fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, style_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    382 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 # Do the plotting
--> 385 with cvo.with_style(args.style):
    386     fig, figs = create_figs(args, sep_figs, fig, ax)
    387     variant_keys = sim.result_keys('variant')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/settings.py:515, in Options.with_style(self, style_args, use, **kwargs)
    513 # Handle style, overwiting existing
    514 style = kwargs.pop('style', None)
--> 515 rc = self._handle_style(style, reset=False)
    517 def pop_keywords(sourcekeys, rckey):
    518     ''' Helper function to handle input arguments '''

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/settings.py:471, in Options._handle_style(self, style, reset, copy)
    469     else:
    470         errormsg = f'Style "{style}"; not found; options are "covasim" (default), "simple", plus:\n{sc.newlinejoin(pl.style.available)}'
--> 471         raise ValueError(errormsg)
    472 if reset:
    473     self.rc = rc

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

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

    nbsphinx_allow_errors = True


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

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

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/sim.py:1331, in Sim.plot(self, *args, **kwargs)
   1264 def plot(self, *args, **kwargs):
   1265     '''
   1266     Plot the results of a single simulation.
   1267 
   (...)
   1329     | New in version 3.1.2: updated date arguments; mpl_args renamed style_args
   1330     '''
-> 1331     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1332     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/plotting.py:385, in plot_sim(to_plot, sim, do_save, fig_path, fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, style_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    382 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 # Do the plotting
--> 385 with cvo.with_style(args.style):
    386     fig, figs = create_figs(args, sep_figs, fig, ax)
    387     variant_keys = sim.result_keys('variant')

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/settings.py:515, in Options.with_style(self, style_args, use, **kwargs)
    513 # Handle style, overwiting existing
    514 style = kwargs.pop('style', None)
--> 515 rc = self._handle_style(style, reset=False)
    517 def pop_keywords(sourcekeys, rckey):
    518     ''' Helper function to handle input arguments '''

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim/settings.py:471, in Options._handle_style(self, style, reset, copy)
    469     else:
    470         errormsg = f'Style "{style}"; not found; options are "covasim" (default), "simple", plus:\n{sc.newlinejoin(pl.style.available)}'
--> 471         raise ValueError(errormsg)
    472 if reset:
    473     self.rc = rc

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

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

    nbsphinx_allow_errors = True