Read the Docs build information
Build id: 1611863
Project: institute-for-disease-modeling-covasim
Version: v3.0.3
Commit: 531c449271bb40020d384b31b7484daa14d73035
Date: 2023-07-20T20:31:12.922768Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-07-20T20:34:02.543076Z, end-time: 2023-07-20T20:34:08.210272Z, duration: 5, 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: 2023-07-20T20:34:08.441994Z, end-time: 2023-07-20T20:34:08.549641Z, duration: 0, exit-code: 0
git checkout --force 531c449271bb40020d384b31b7484daa14d73035
Note: switching to '531c449271bb40020d384b31b7484daa14d73035'.

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 531c4492 update tutorial

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git clean -d -f -f


[rtd-command-info] start-time: 2023-07-20T20:34:09.074482Z, end-time: 2023-07-20T20:34:09.210862Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Build documentation in the docs/ directory with Sphinx
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true

# Build documentation with MkDocs
#mkdocs:
#  configuration: mkdocs.yml

# Optionally build your docs in additional formats such as PDF
formats:
  - htmlzip
  - pdf

# Optionally set the version of Python and requirements required to build your docs
python:
  version: 3.8
  install:
    - requirements: docs/requirements.txt
    - method: pip
      path: .
  system_packages: true
    
# Optionally rank topics in search results, between -10 (lower) and 10 (higher).
# 0 is normal rank, not no rank

search:
  ranking:
    index.html: 3
    modules.html: 2

[rtd-command-info] start-time: 2023-07-20T20:34:11.781878Z, end-time: 2023-07-20T20:34:30.596498Z, duration: 18, exit-code: 0
python3.8 -mvirtualenv --system-site-packages $READTHEDOCS_VIRTUALENV_PATH
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/v3.0.3/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-07-20T20:34:30.848485Z, end-time: 2023-07-20T20:34:32.422679Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages (23.2)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages (68.0.0)

[rtd-command-info] start-time: 2023-07-20T20:34:32.745933Z, end-time: 2023-07-20T20:34:42.082331Z, duration: 9, 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<2.3 jinja2<3.1.0 setuptools
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Building wheels for collected packages: mock
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Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, setuptools, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 setuptools-68.0.0 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 urllib3-2.0.4

[rtd-command-info] start-time: 2023-07-20T20:34:42.347167Z, end-time: 2023-07-20T20:34:59.406156Z, duration: 17, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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[rtd-command-info] start-time: 2023-07-20T20:34:59.656711Z, end-time: 2023-07-20T20:35:30.530870Z, duration: 30, exit-code: 0
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Building wheels for collected packages: covasim
  Building wheel for covasim (setup.py): started
  Building wheel for covasim (setup.py): finished with status 'done'
  Created wheel for covasim: filename=covasim-3.0.3-py3-none-any.whl size=201112 sha256=a141848316720048db4dadafb10743441cea108cfcd7efe1526c90b302777b8a
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Successfully built covasim
Installing collected packages: zstandard, zipp, xlsxwriter, xlrd, smmap, numpy, memory-profiler, llvmlite, line-profiler, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, scipy, patsy, pandas, openpyxl, multiprocess, importlib-resources, gitdb, contourpy, statsmodels, numba, matplotlib, gitpython, sciris, covasim
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Successfully installed contourpy-1.1.0 covasim-3.0.3 dill-0.3.6 et-xmlfile-1.1.0 fonttools-4.41.0 gitdb-4.0.10 gitpython-3.1.32 importlib-resources-6.0.0 jellyfish-1.0.0 jsonpickle-3.0.1 line-profiler-4.0.3 llvmlite-0.40.1 matplotlib-3.7.2 memory-profiler-0.61.0 multiprocess-0.70.14 numba-0.57.1 numpy-1.24.4 openpyxl-3.1.2 pandas-2.0.3 patsy-0.5.3 scipy-1.10.1 sciris-3.0.0 smmap-5.0.0 statsmodels-0.14.0 xlrd-1.2.0 xlsxwriter-3.1.2 zipp-3.16.2 zstandard-0.21.0

[rtd-command-info] start-time: 2023-07-20T20:35:34.448800Z, end-time: 2023-07-20T20:35:34.513422Z, 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

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',
    'css_files': [
        '_static/theme_overrides.css'
    ]
}
# 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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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': "v3.0.3",
    'version_slug': "v3.0.3",
    '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/"),
    ("v3.1.4", "/en/v3.1.4/"),
    ("v3.1.3", "/en/v3.1.3/"),
    ("v3.1.2", "/en/v3.1.2/"),
    ("v3.1.1", "/en/v3.1.1/"),
    ("v3.1.0", "/en/v3.1.0/"),
    ("v3.0.7", "/en/v3.0.7/"),
    ("v3.0.6", "/en/v3.0.6/"),
    ("v3.0.5", "/en/v3.0.5/"),
    ("v3.0.4", "/en/v3.0.4/"),
    ("v3.0.3", "/en/v3.0.3/"),
    ("v3.0.2", "/en/v3.0.2/"),
    ("v3.0.1", "/en/v3.0.1/"),
    ("v3.0.0", "/en/v3.0.0/"),
    ("v2.1.2", "/en/v2.1.2/"),
    ("v2.1.1", "/en/v2.1.1/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-covasim',
    'name': u'covasim',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'G-SVDSQH04EM',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'covasim',
    'github_version': 'v3.0.3',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'v3.0.3',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'v3.0.3',
    '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': 'G-SVDSQH04EM',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '531c4492',
}

# 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():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
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 'tag' == '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/1611863/'

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: 2023-07-20T20:35:34.735339Z, end-time: 2023-07-20T20:36:22.447763Z, duration: 47, exit-code: 2
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v1.8.6
Matplotlib is building the font cache; this may take a moment.
Covasim 3.0.3 (2021-05-17) — © 2021 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/v3.0.3/lib/python3.8/site-packages/jupyter_client/localinterfaces.py:54: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  ret = f(**kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/jupyter_client/localinterfaces.py:54: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  ret = f(**kwargs)

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/nbsphinx/__init__.py", line 618, in parse
    rststring, resources = exporter.from_notebook_node(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/nbsphinx/__init__.py", line 397, in from_notebook_node
    nb, resources = pp.preprocess(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 100, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 121, 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/v3.0.3/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
    return loop.run_until_complete(inner)
  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/v3.0.3/lib/python3.8/site-packages/nbclient/client.py", line 1058, 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/v3.0.3/lib/python3.8/site-packages/nbclient/client.py", line 914, 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:
------------------
import numpy as np
import covasim as cv
cv.options.set(dpi=100, show=False, close=True, verbose=0) # Standard options for Jupyter notebook

# Create the first sim
orig_sim = cv.Sim(pop_type='hybrid', n_days=120, label='Default hybrid population')
orig_sim.initialize() # Initialize the population

# Create the second sim
sim = orig_sim.copy()

# Define the new layer, 'transport'
n_people = len(sim.people)
n_contacts_per_person = 0.5
n_contacts = int(n_contacts_per_person*n_people)
contacts_p1 = cv.choose(max_n=n_people, n=n_contacts)
contacts_p2 = cv.choose(max_n=n_people, n=n_contacts)
beta = np.ones(n_contacts)
layer = cv.Layer(p1=contacts_p1, p2=contacts_p2, beta=beta) # Create the new layer

# Add this layer in and re-initialize the sim
sim.people.contacts.add_layer(transport=layer)
sim.reset_layer_pars() # Automatically add layer 'q' to the parameters using default values
sim.initialize() # Reinitialize
sim.label = f'Transport layer with {n_contacts_per_person} contacts/person'

# Run and compare
msim = cv.MultiSim([orig_sim, sim])
msim.run()
msim.plot()
------------------

----- stdout -----
Covasim 3.0.3 (2021-05-17) — © 2021 by IDM
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/base.py:358: FutureWarning: sc.day() argument "start_day" has been deprecated as of v1.2.2; use "start_date" instead
  return sc.day(day, *args, start_day=self['start_day'])
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/base.py:358: FutureWarning: sc.day() argument "start_day" has been deprecated as of v1.2.2; use "start_date" instead
  return sc.day(day, *args, start_day=self['start_day'])
------------------

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[1], line 30
     28 msim = cv.MultiSim([orig_sim, sim])
     29 msim.run()
---> 30 msim.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/run.py:532, in MultiSim.plot(self, to_plot, inds, plot_sims, color_by_sim, max_sims, colors, labels, alpha_range, plot_args, show_args, **kwargs)
    530         # Actually plot
    531         merged_plot_args = sc.mergedicts({'alpha':alphas[s]}, plot_args) # Need a new variable to avoid overwriting
--> 532         fig = sim.plot(fig=fig, to_plot=to_plot, colors=colors[s], labels=merged_labels, plot_args=merged_plot_args, show_args=merged_show_args, **kwargs)
    534 return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/sim.py:1303, in Sim.plot(self, *args, **kwargs)
   1249 def plot(self, *args, **kwargs):
   1250     '''
   1251     Plot the results of a single simulation.
   1252 
   (...)
   1301     New in version 2.1.0: argument passing, date_args, and mpl_args
   1302     '''
-> 1303     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1304     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/plotting.py:381, 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, mpl_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    378 ''' Plot the results of a single simulation -- see Sim.plot() for documentation '''
    380 # Handle inputs
--> 381 args = handle_args(fig_args=fig_args, plot_args=plot_args, scatter_args=scatter_args, axis_args=axis_args, fill_args=fill_args,
    382                    legend_args=legend_args, show_args=show_args, date_args=date_args, mpl_args=mpl_args, **kwargs)
    383 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 fig, figs = create_figs(args, sep_figs, fig, ax)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/plotting.py:57, in handle_args(fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, mpl_args, **kwargs)
     55 args.legend  = sc.mergedicts(defaults.legend,  legend_args)
     56 args.date    = sc.mergedicts(defaults.date,    fill_args)
---> 57 args.show    = sc.mergedicts(defaults.show,    show_args)
     58 args.mpl     = sc.mergedicts(defaults.mpl,     mpl_args)
     60 # If unused keyword arguments remain, raise an error

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/sciris/sc_utils.py:1319, in mergedicts(_strict, _overwrite, _copy, _sameclass, _die, *args, **kwargs)
   1317         if arg is not None and _die: # pragma: no cover
   1318             errormsg = f'Could not handle argument {a} of {type(arg)}: expecting dict or None'
-> 1319             raise TypeError(errormsg)
   1321 if _copy:
   1322     outputdict = dcp(outputdict, die=_die)

TypeError: Could not handle argument 1 of <class 'bool'>: expecting dict or None


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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/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/v3.0.3/lib/python3.8/site-packages/nbsphinx/__init__.py", line 625, in parse
    raise NotebookError('\n'.join(lines))
nbsphinx.NotebookError: CellExecutionError in tutorials/tut_advanced.ipynb:
------------------
import numpy as np
import covasim as cv
cv.options.set(dpi=100, show=False, close=True, verbose=0) # Standard options for Jupyter notebook

# Create the first sim
orig_sim = cv.Sim(pop_type='hybrid', n_days=120, label='Default hybrid population')
orig_sim.initialize() # Initialize the population

# Create the second sim
sim = orig_sim.copy()

# Define the new layer, 'transport'
n_people = len(sim.people)
n_contacts_per_person = 0.5
n_contacts = int(n_contacts_per_person*n_people)
contacts_p1 = cv.choose(max_n=n_people, n=n_contacts)
contacts_p2 = cv.choose(max_n=n_people, n=n_contacts)
beta = np.ones(n_contacts)
layer = cv.Layer(p1=contacts_p1, p2=contacts_p2, beta=beta) # Create the new layer

# Add this layer in and re-initialize the sim
sim.people.contacts.add_layer(transport=layer)
sim.reset_layer_pars() # Automatically add layer 'q' to the parameters using default values
sim.initialize() # Reinitialize
sim.label = f'Transport layer with {n_contacts_per_person} contacts/person'

# Run and compare
msim = cv.MultiSim([orig_sim, sim])
msim.run()
msim.plot()
------------------

----- stdout -----
Covasim 3.0.3 (2021-05-17) — © 2021 by IDM
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/base.py:358: FutureWarning: sc.day() argument "start_day" has been deprecated as of v1.2.2; use "start_date" instead
  return sc.day(day, *args, start_day=self['start_day'])
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/base.py:358: FutureWarning: sc.day() argument "start_day" has been deprecated as of v1.2.2; use "start_date" instead
  return sc.day(day, *args, start_day=self['start_day'])
------------------

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[1], line 30
     28 msim = cv.MultiSim([orig_sim, sim])
     29 msim.run()
---> 30 msim.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/run.py:532, in MultiSim.plot(self, to_plot, inds, plot_sims, color_by_sim, max_sims, colors, labels, alpha_range, plot_args, show_args, **kwargs)
    530         # Actually plot
    531         merged_plot_args = sc.mergedicts({'alpha':alphas[s]}, plot_args) # Need a new variable to avoid overwriting
--> 532         fig = sim.plot(fig=fig, to_plot=to_plot, colors=colors[s], labels=merged_labels, plot_args=merged_plot_args, show_args=merged_show_args, **kwargs)
    534 return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/sim.py:1303, in Sim.plot(self, *args, **kwargs)
   1249 def plot(self, *args, **kwargs):
   1250     '''
   1251     Plot the results of a single simulation.
   1252 
   (...)
   1301     New in version 2.1.0: argument passing, date_args, and mpl_args
   1302     '''
-> 1303     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1304     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/plotting.py:381, 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, mpl_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    378 ''' Plot the results of a single simulation -- see Sim.plot() for documentation '''
    380 # Handle inputs
--> 381 args = handle_args(fig_args=fig_args, plot_args=plot_args, scatter_args=scatter_args, axis_args=axis_args, fill_args=fill_args,
    382                    legend_args=legend_args, show_args=show_args, date_args=date_args, mpl_args=mpl_args, **kwargs)
    383 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 fig, figs = create_figs(args, sep_figs, fig, ax)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/plotting.py:57, in handle_args(fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, mpl_args, **kwargs)
     55 args.legend  = sc.mergedicts(defaults.legend,  legend_args)
     56 args.date    = sc.mergedicts(defaults.date,    fill_args)
---> 57 args.show    = sc.mergedicts(defaults.show,    show_args)
     58 args.mpl     = sc.mergedicts(defaults.mpl,     mpl_args)
     60 # If unused keyword arguments remain, raise an error

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/sciris/sc_utils.py:1319, in mergedicts(_strict, _overwrite, _copy, _sameclass, _die, *args, **kwargs)
   1317         if arg is not None and _die: # pragma: no cover
   1318             errormsg = f'Could not handle argument {a} of {type(arg)}: expecting dict or None'
-> 1319             raise TypeError(errormsg)
   1321 if _copy:
   1322     outputdict = dcp(outputdict, die=_die)

TypeError: Could not handle argument 1 of <class 'bool'>: expecting dict or None

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

    nbsphinx_allow_errors = True


Notebook error:
CellExecutionError in tutorials/tut_advanced.ipynb:
------------------
import numpy as np
import covasim as cv
cv.options.set(dpi=100, show=False, close=True, verbose=0) # Standard options for Jupyter notebook

# Create the first sim
orig_sim = cv.Sim(pop_type='hybrid', n_days=120, label='Default hybrid population')
orig_sim.initialize() # Initialize the population

# Create the second sim
sim = orig_sim.copy()

# Define the new layer, 'transport'
n_people = len(sim.people)
n_contacts_per_person = 0.5
n_contacts = int(n_contacts_per_person*n_people)
contacts_p1 = cv.choose(max_n=n_people, n=n_contacts)
contacts_p2 = cv.choose(max_n=n_people, n=n_contacts)
beta = np.ones(n_contacts)
layer = cv.Layer(p1=contacts_p1, p2=contacts_p2, beta=beta) # Create the new layer

# Add this layer in and re-initialize the sim
sim.people.contacts.add_layer(transport=layer)
sim.reset_layer_pars() # Automatically add layer 'q' to the parameters using default values
sim.initialize() # Reinitialize
sim.label = f'Transport layer with {n_contacts_per_person} contacts/person'

# Run and compare
msim = cv.MultiSim([orig_sim, sim])
msim.run()
msim.plot()
------------------

----- stdout -----
Covasim 3.0.3 (2021-05-17) \u2014 \xa9 2021 by IDM
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/base.py:358: FutureWarning: sc.day() argument "start_day" has been deprecated as of v1.2.2; use "start_date" instead
  return sc.day(day, *args, start_day=self['start_day'])
----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/base.py:358: FutureWarning: sc.day() argument "start_day" has been deprecated as of v1.2.2; use "start_date" instead
  return sc.day(day, *args, start_day=self['start_day'])
------------------

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[1], line 30
     28 msim = cv.MultiSim([orig_sim, sim])
     29 msim.run()
---> 30 msim.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/run.py:532, in MultiSim.plot(self, to_plot, inds, plot_sims, color_by_sim, max_sims, colors, labels, alpha_range, plot_args, show_args, **kwargs)
    530         # Actually plot
    531         merged_plot_args = sc.mergedicts({'alpha':alphas[s]}, plot_args) # Need a new variable to avoid overwriting
--> 532         fig = sim.plot(fig=fig, to_plot=to_plot, colors=colors[s], labels=merged_labels, plot_args=merged_plot_args, show_args=merged_show_args, **kwargs)
    534 return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/sim.py:1303, in Sim.plot(self, *args, **kwargs)
   1249 def plot(self, *args, **kwargs):
   1250     '''
   1251     Plot the results of a single simulation.
   1252 
   (...)
   1301     New in version 2.1.0: argument passing, date_args, and mpl_args
   1302     '''
-> 1303     fig = cvplt.plot_sim(sim=self, *args, **kwargs)
   1304     return fig

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/plotting.py:381, 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, mpl_args, n_cols, grid, commaticks, setylim, log_scale, colors, labels, do_show, sep_figs, fig, ax, **kwargs)
    378 ''' Plot the results of a single simulation -- see Sim.plot() for documentation '''
    380 # Handle inputs
--> 381 args = handle_args(fig_args=fig_args, plot_args=plot_args, scatter_args=scatter_args, axis_args=axis_args, fill_args=fill_args,
    382                    legend_args=legend_args, show_args=show_args, date_args=date_args, mpl_args=mpl_args, **kwargs)
    383 to_plot, n_cols, n_rows = handle_to_plot('sim', to_plot, n_cols, sim=sim)
    384 fig, figs = create_figs(args, sep_figs, fig, ax)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/covasim/plotting.py:57, in handle_args(fig_args, plot_args, scatter_args, axis_args, fill_args, legend_args, date_args, show_args, mpl_args, **kwargs)
     55 args.legend  = sc.mergedicts(defaults.legend,  legend_args)
     56 args.date    = sc.mergedicts(defaults.date,    fill_args)
---> 57 args.show    = sc.mergedicts(defaults.show,    show_args)
     58 args.mpl     = sc.mergedicts(defaults.mpl,     mpl_args)
     60 # If unused keyword arguments remain, raise an error

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/v3.0.3/lib/python3.8/site-packages/sciris/sc_utils.py:1319, in mergedicts(_strict, _overwrite, _copy, _sameclass, _die, *args, **kwargs)
   1317         if arg is not None and _die: # pragma: no cover
   1318             errormsg = f'Could not handle argument {a} of {type(arg)}: expecting dict or None'
-> 1319             raise TypeError(errormsg)
   1321 if _copy:
   1322     outputdict = dcp(outputdict, die=_die)

TypeError: Could not handle argument 1 of <class 'bool'>: expecting dict or None

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

    nbsphinx_allow_errors = True