Read the Docs build information
Build id: 1706555
Project: institute-for-disease-modeling-fpsim
Version: latest
Commit: 6d155aba4489c3fcfcf7b8c9c89135c759e0d8d9
Date: 2023-09-07T04:13:13.652361Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-09-07T04:15:14.817277Z, end-time: 2023-09-07T04:15:15.444441Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/fpsim/fpsim.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-09-07T04:15:16.289958Z, end-time: 2023-09-07T04:15:18.085907Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main
From https://github.com/fpsim/fpsim
 * [new tag]         v0.19.2    -> v0.19.2
 * [new tag]         v0.22.0    -> v0.22.0
 * [new tag]         v0.22.1    -> v0.22.1
 * [new tag]         v0.23.0    -> v0.23.0
 * [new tag]         v0.24.0    -> v0.24.0

[rtd-command-info] start-time: 2023-09-07T04:15:18.581744Z, end-time: 2023-09-07T04:15:18.669728Z, 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 6d155ab Pass initial distribution of new attributes to People()

[rtd-command-info] start-time: 2023-09-07T04:15:19.107458Z, end-time: 2023-09-07T04:15:19.164994Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-09-07T04:15:19.606394Z, end-time: 2023-09-07T04:15:19.664367Z, duration: 0, exit-code: 0
cat .readthedocs.yaml
# .readthedocs.yaml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the version of Python and other tools you might need
build:
  os: ubuntu-20.04
  tools:
    python: "3.9"

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

# If using Sphinx, optionally build your docs in additional formats such as PDF
# formats:

# Optionally declare the Python requirements required to build your docs
python:
  install:
    - requirements: docs/requirements.txt
    - method: pip
      path: .

[rtd-command-info] start-time: 2023-09-07T04:15:26.505067Z, end-time: 2023-09-07T04:15:26.587913Z, duration: 0, exit-code: 0
asdf global python 3.9.17


[rtd-command-info] start-time: 2023-09-07T04:15:27.322389Z, end-time: 2023-09-07T04:15:28.258175Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.17.final.0-64 in 615ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-09-07T04:15:28.950582Z, end-time: 2023-09-07T04:15:40.007511Z, duration: 11, 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-fpsim/envs/latest/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (57.4.0)
Collecting setuptools
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Installing collected packages: setuptools, pip
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    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-23.2.1 setuptools-68.2.0

[rtd-command-info] start-time: 2023-09-07T04:15:40.442953Z, end-time: 2023-09-07T04:15:50.677651Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.3
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Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, zipp, urllib3, sphinxcontrib-jsmath, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx, sphinxcontrib-jquery, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.8.0 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.5 sphinx-rtd-theme-1.3.0 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.0.4 zipp-3.16.2

[rtd-command-info] start-time: 2023-09-07T04:15:51.125760Z, end-time: 2023-09-07T04:16:10.701805Z, duration: 19, exit-code: 0
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[rtd-command-info] start-time: 2023-09-07T04:16:11.185095Z, end-time: 2023-09-07T04:16:44.491063Z, duration: 33, exit-code: 0
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Building wheels for collected packages: fpsim
  Building wheel for fpsim (setup.py): started
  Building wheel for fpsim (setup.py): finished with status 'done'
  Created wheel for fpsim: filename=fpsim-0.26.3-py3-none-any.whl size=482837 sha256=6f23bf8e6074fb91f292a31db249201e417b1693c38765e72d3d939800747be6
  Stored in directory: /tmp/pip-ephem-wheel-cache-v7l2n5x3/wheels/54/be/71/b6a93e28e1af4f52153fe34b99119b980ee057025c8abb6ee6
Successfully built fpsim
Installing collected packages: pytz, zstandard, xlsxwriter, tzdata, smmap, pyparsing, numpy, memory-profiler, llvmlite, line-profiler, kiwisolver, jsonpickle, jellyfish, importlib-resources, fonttools, et-xmlfile, dill, cycler, scipy, pyarrow, patsy, pandas, openpyxl, numba, multiprocess, gitdb, contourpy, statsmodels, matplotlib, gitpython, seaborn, sciris, mizani, plotnine, fpsim
  Attempting uninstall: numpy
    Found existing installation: numpy 1.25.2
    Uninstalling numpy-1.25.2:
      Successfully uninstalled numpy-1.25.2
Successfully installed contourpy-1.1.0 cycler-0.11.0 dill-0.3.7 et-xmlfile-1.1.0 fonttools-4.42.1 fpsim-0.26.3 gitdb-4.0.10 gitpython-3.1.34 importlib-resources-6.0.1 jellyfish-1.0.0 jsonpickle-3.0.2 kiwisolver-1.4.5 line-profiler-4.1.1 llvmlite-0.40.1 matplotlib-3.7.2 memory-profiler-0.61.0 mizani-0.9.3 multiprocess-0.70.15 numba-0.57.1 numpy-1.24.4 openpyxl-3.1.2 pandas-2.1.0 patsy-0.5.3 plotnine-0.12.3 pyarrow-13.0.0 pyparsing-3.0.9 pytz-2023.3.post1 scipy-1.11.2 sciris-3.1.0 seaborn-0.12.2 smmap-5.0.0 statsmodels-0.14.0 tzdata-2023.3 xlsxwriter-3.1.2 zstandard-0.21.0

[rtd-command-info] start-time: 2023-09-07T04:16:50.175936Z, end-time: 2023-09-07T04:16:50.224101Z, 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 fpsim as fp

# Set environment
os.environ['SPHINX_BUILD'] = 'True' # This is used so cv.options.set('jupyter') doesn't reset the Matplotlib renderer
os.environ['FPSIM_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 "fp_analysis" 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 = 'FPsim'
copyright = f'2022 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for {project} version {fp.__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 versions
version = fp.__version__
release = fp.__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/fpsim/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/fpsim/en/latest'

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

# -- 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, 'fpsim-docs.tex', 'fpsim',
     '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, 'fpsim-docs', 'fpsim',
     [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, 'fpsim-docs', 'fpsim',
     author, 'Institute for Disease Modeling', 'How to use the FPsim model for family planning simulations.',
     'Miscellaneous'),
]

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

intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
                       'covasim': ('https://docs.idmod.org/projects/covasim/en/latest/', 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')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    '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/"),
    ("v0.24.0", "/en/v0.24.0/"),
    ("v0.23.0", "/en/v0.23.0/"),
    ("v0.22.1", "/en/v0.22.1/"),
    ("v0.22.0", "/en/v0.22.0/"),
    ("v0.19.2", "/en/v0.19.2/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-fpsim',
    'name': u'fpsim',
    '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': 'fpsim',
    'proxied_api_host': '/_',
    'github_repo': 'fpsim',
    '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': 'G-SVDSQH04EM',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '6d155aba',
}

# 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 '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-fpsim/builds/1706555/'

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: 2023-09-07T04:16:50.765033Z, end-time: 2023-09-07T04:17:13.380409Z, duration: 22, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.5
Matplotlib is building the font cache; this may take a moment.


Building Jupyter notebooks with build option: auto


making output directory... done
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 26 source files that are out of date
updating environment: [new config] 26 added, 0 changed, 0 removed
reading sources... [  4%] fpsim.analyzers
reading sources... [  8%] fpsim.base
reading sources... [ 12%] fpsim.calibration
reading sources... [ 15%] fpsim.defaults
reading sources... [ 19%] fpsim.experiment
reading sources... [ 23%] fpsim.interventions
reading sources... [ 27%] fpsim.locations
reading sources... [ 31%] fpsim.locations.calibrate_manual
reading sources... [ 35%] fpsim.locations.ethiopia
reading sources... [ 38%] fpsim.locations.kenya
reading sources... [ 42%] fpsim.locations.senegal
reading sources... [ 46%] fpsim.parameters
reading sources... [ 50%] fpsim.scenarios
reading sources... [ 54%] fpsim.settings
reading sources... [ 58%] fpsim.sim
reading sources... [ 62%] fpsim.utils
reading sources... [ 65%] fpsim.version
reading sources... [ 69%] index
reading sources... [ 73%] modules
reading sources... [ 77%] overview
reading sources... [ 81%] tutorials
reading sources... [ 85%] tutorials/README
reading sources... [ 88%] tutorials/T1_intro
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/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-fpsim/envs/latest/lib/python3.9/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)
WARNING: autodoc: failed to import module 'calibrate_manual' from module 'fpsim.locations'; the following exception was raised:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/ext/autodoc/importer.py", line 65, in import_module
    return importlib.import_module(modname)
  File "/home/docs/.asdf/installs/python/3.9.17/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/locations/calibrate_manual.py", line 62, in <module>
    os.mkdir(f'./{country}/figs')
FileNotFoundError: [Errno 2] No such file or directory: './ethiopia/figs'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/ext/autodoc/importer.py", line 90, in import_object
    module = import_module(modname, warningiserror=warningiserror)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/ext/autodoc/importer.py", line 69, in import_module
    raise ImportError(exc, traceback.format_exc()) from exc
ImportError: (FileNotFoundError(2, 'No such file or directory'), 'Traceback (most recent call last):\n  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/ext/autodoc/importer.py", line 65, in import_module\n    return importlib.import_module(modname)\n  File "/home/docs/.asdf/installs/python/3.9.17/lib/python3.9/importlib/__init__.py", line 127, in import_module\n    return _bootstrap._gcd_import(name[level:], package, level)\n  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import\n  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load\n  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked\n  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked\n  File "<frozen importlib._bootstrap_external>", line 850, in exec_module\n  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed\n  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/locations/calibrate_manual.py", line 62, in <module>\n    os.mkdir(f\'./{country}/figs\')\nFileNotFoundError: [Errno 2] No such file or directory: \'./ethiopia/figs\'\n')

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-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/ext/autodoc/importer.py", line 65, in import_module
    return importlib.import_module(modname)
  File "/home/docs/.asdf/installs/python/3.9.17/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/locations/calibrate_manual.py", line 62, in <module>
    os.mkdir(f'./{country}/figs')
FileNotFoundError: [Errno 2] No such file or directory: './ethiopia/figs'


Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/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-fpsim/envs/latest/lib/python3.9/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-fpsim/envs/latest/lib/python3.9/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-fpsim/envs/latest/lib/python3.9/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-fpsim/envs/latest/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
    return loop.run_until_complete(inner)
  File "/home/docs/.asdf/installs/python/3.9.17/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
    return future.result()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/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-fpsim/envs/latest/lib/python3.9/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 fpsim as fp

sim = fp.Sim()
sim.run()
fig = sim.plot()
------------------

----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/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
------------------

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/base.py:73, in ParsObj.__getitem__(self, key)
     72 try:
---> 73     return self.pars[key]
     74 except:

KeyError: 'urban_prop'

During handling of the above exception, another exception occurred:

KeyNotFoundError                          Traceback (most recent call last)
Cell In[1], line 4
      1 import fpsim as fp
      3 sim = fp.Sim()
----> 4 sim.run()
      5 fig = sim.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1368, in Sim.run(self, verbose)
   1366 if verbose is None:
   1367     verbose = self['verbose']
-> 1368 self.initialize()
   1369 if self.already_run:
   1370     errormsg = 'Cannot re-run an already run sim; please recreate or copy prior to a run'

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1043, in Sim.initialize(self, force)
   1041     fpu.set_seed(self['seed'])
   1042     self.init_results()
-> 1043     self.init_people()
   1044 return self

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1231, in Sim.init_people(self, output, **kwargs)
   1229 def init_people(self, output=False, **kwargs):
   1230     ''' Create the people '''
-> 1231     p = sc.objdict(self.make_people(n=int(self['n_agents'])))
   1232     self.people = People(pars=self.pars, age=p.age, sex=p.sex, method=p.method, barrier=p.barrier, debut_age=p.debut_age, fertile=p.fertile,
   1233                          urban=p.urban, partnered=p.partnered, paid_employment=p.paid_employment, sexual_autonomy=p.sexual_autonomy,
   1234                          control_over_wages=p.control_over_wages)
   1235     return

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1221, in Sim.make_people(self, n, age, sex, method, debut_age)
   1219 debut_age = self['debut_age']['ages'][fpu.n_multinomial(self['debut_age']['probs'], n)]
   1220 fertile = fpu.n_binomial(1 - self['primary_infertility'], n)
-> 1221 urban = self.initialize_urban(n, self['urban_prop'])
   1222 empowerment_dict = self.initialize_empowerment(n, age, sex)
   1223 partnered = self.initialize_partnered(n, age, sex)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/base.py:77, in ParsObj.__getitem__(self, key)
     75 all_keys = '\n'.join(list(self.pars.keys()))
     76 errormsg = f'Key "{key}" not found; available keys:\n{all_keys}'
---> 77 raise sc.KeyNotFoundError(errormsg)

KeyNotFoundError: Key "urban_prop" not found; available keys:
location
n_agents
scaled_pop
start_year
end_year
timestep
method_timestep
seed
verbose
track_switching
track_as
method_age
age_limit_fecundity
max_age
switch_frequency
end_first_tri
preg_dur_low
preg_dur_high
postpartum_dur
breastfeeding_dur_mu
breastfeeding_dur_beta
max_lam_dur
short_int
low_age_short_int
high_age_short_int
abortion_prob
twins_prob
LAM_efficacy
maternal_mortality_factor
fecundity_var_low
fecundity_var_high
high_parity
high_parity_nonuse
primary_infertility
exposure_factor
restrict_method_use
mcpr_growth_rate
mcpr_max
mcpr_norm_year
filenames
age_pyramid
age_mortality
maternal_mortality
infant_mortality
miscarriage_rates
stillbirth_rate
age_fecundity
fecundity_ratio_nullip
lactational_amenorrhea
sexual_activity
sexual_activity_pp
debut_age
exposure_age
exposure_parity
spacing_pref
methods
barriers
mortality_probs
interventions
analyzers


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-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/cmd/build.py", line 298, in build_main
    app.build(args.force_all, args.filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/application.py", line 355, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 293, in build_update
    self.build(to_build,
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 313, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 420, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 441, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 498, in read_doc
    publisher.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/docutils/core.py", line 217, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/sphinx/io.py", line 105, in read
    self.parse()
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 625, in parse
    raise NotebookError('\n'.join(lines))
nbsphinx.NotebookError: CellExecutionError in tutorials/T1_intro.ipynb:
------------------
import fpsim as fp

sim = fp.Sim()
sim.run()
fig = sim.plot()
------------------

----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/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
------------------

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/base.py:73, in ParsObj.__getitem__(self, key)
     72 try:
---> 73     return self.pars[key]
     74 except:

KeyError: 'urban_prop'

During handling of the above exception, another exception occurred:

KeyNotFoundError                          Traceback (most recent call last)
Cell In[1], line 4
      1 import fpsim as fp
      3 sim = fp.Sim()
----> 4 sim.run()
      5 fig = sim.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1368, in Sim.run(self, verbose)
   1366 if verbose is None:
   1367     verbose = self['verbose']
-> 1368 self.initialize()
   1369 if self.already_run:
   1370     errormsg = 'Cannot re-run an already run sim; please recreate or copy prior to a run'

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1043, in Sim.initialize(self, force)
   1041     fpu.set_seed(self['seed'])
   1042     self.init_results()
-> 1043     self.init_people()
   1044 return self

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1231, in Sim.init_people(self, output, **kwargs)
   1229 def init_people(self, output=False, **kwargs):
   1230     ''' Create the people '''
-> 1231     p = sc.objdict(self.make_people(n=int(self['n_agents'])))
   1232     self.people = People(pars=self.pars, age=p.age, sex=p.sex, method=p.method, barrier=p.barrier, debut_age=p.debut_age, fertile=p.fertile,
   1233                          urban=p.urban, partnered=p.partnered, paid_employment=p.paid_employment, sexual_autonomy=p.sexual_autonomy,
   1234                          control_over_wages=p.control_over_wages)
   1235     return

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1221, in Sim.make_people(self, n, age, sex, method, debut_age)
   1219 debut_age = self['debut_age']['ages'][fpu.n_multinomial(self['debut_age']['probs'], n)]
   1220 fertile = fpu.n_binomial(1 - self['primary_infertility'], n)
-> 1221 urban = self.initialize_urban(n, self['urban_prop'])
   1222 empowerment_dict = self.initialize_empowerment(n, age, sex)
   1223 partnered = self.initialize_partnered(n, age, sex)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/base.py:77, in ParsObj.__getitem__(self, key)
     75 all_keys = '\n'.join(list(self.pars.keys()))
     76 errormsg = f'Key "{key}" not found; available keys:\n{all_keys}'
---> 77 raise sc.KeyNotFoundError(errormsg)

KeyNotFoundError: Key "urban_prop" not found; available keys:
location
n_agents
scaled_pop
start_year
end_year
timestep
method_timestep
seed
verbose
track_switching
track_as
method_age
age_limit_fecundity
max_age
switch_frequency
end_first_tri
preg_dur_low
preg_dur_high
postpartum_dur
breastfeeding_dur_mu
breastfeeding_dur_beta
max_lam_dur
short_int
low_age_short_int
high_age_short_int
abortion_prob
twins_prob
LAM_efficacy
maternal_mortality_factor
fecundity_var_low
fecundity_var_high
high_parity
high_parity_nonuse
primary_infertility
exposure_factor
restrict_method_use
mcpr_growth_rate
mcpr_max
mcpr_norm_year
filenames
age_pyramid
age_mortality
maternal_mortality
infant_mortality
miscarriage_rates
stillbirth_rate
age_fecundity
fecundity_ratio_nullip
lactational_amenorrhea
sexual_activity
sexual_activity_pp
debut_age
exposure_age
exposure_parity
spacing_pref
methods
barriers
mortality_probs
interventions
analyzers

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

    nbsphinx_allow_errors = True


Notebook error:
CellExecutionError in tutorials/T1_intro.ipynb:
------------------
import fpsim as fp

sim = fp.Sim()
sim.run()
fig = sim.plot()
------------------

----- stderr -----
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/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
------------------

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/base.py:73, in ParsObj.__getitem__(self, key)
     72 try:
---> 73     return self.pars[key]
     74 except:

KeyError: 'urban_prop'

During handling of the above exception, another exception occurred:

KeyNotFoundError                          Traceback (most recent call last)
Cell In[1], line 4
      1 import fpsim as fp
      3 sim = fp.Sim()
----> 4 sim.run()
      5 fig = sim.plot()

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1368, in Sim.run(self, verbose)
   1366 if verbose is None:
   1367     verbose = self['verbose']
-> 1368 self.initialize()
   1369 if self.already_run:
   1370     errormsg = 'Cannot re-run an already run sim; please recreate or copy prior to a run'

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1043, in Sim.initialize(self, force)
   1041     fpu.set_seed(self['seed'])
   1042     self.init_results()
-> 1043     self.init_people()
   1044 return self

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1231, in Sim.init_people(self, output, **kwargs)
   1229 def init_people(self, output=False, **kwargs):
   1230     ''' Create the people '''
-> 1231     p = sc.objdict(self.make_people(n=int(self['n_agents'])))
   1232     self.people = People(pars=self.pars, age=p.age, sex=p.sex, method=p.method, barrier=p.barrier, debut_age=p.debut_age, fertile=p.fertile,
   1233                          urban=p.urban, partnered=p.partnered, paid_employment=p.paid_employment, sexual_autonomy=p.sexual_autonomy,
   1234                          control_over_wages=p.control_over_wages)
   1235     return

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/sim.py:1221, in Sim.make_people(self, n, age, sex, method, debut_age)
   1219 debut_age = self['debut_age']['ages'][fpu.n_multinomial(self['debut_age']['probs'], n)]
   1220 fertile = fpu.n_binomial(1 - self['primary_infertility'], n)
-> 1221 urban = self.initialize_urban(n, self['urban_prop'])
   1222 empowerment_dict = self.initialize_empowerment(n, age, sex)
   1223 partnered = self.initialize_partnered(n, age, sex)

File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/fpsim/base.py:77, in ParsObj.__getitem__(self, key)
     75 all_keys = '\n'.join(list(self.pars.keys()))
     76 errormsg = f'Key "{key}" not found; available keys:\n{all_keys}'
---> 77 raise sc.KeyNotFoundError(errormsg)

KeyNotFoundError: Key "urban_prop" not found; available keys:
location
n_agents
scaled_pop
start_year
end_year
timestep
method_timestep
seed
verbose
track_switching
track_as
method_age
age_limit_fecundity
max_age
switch_frequency
end_first_tri
preg_dur_low
preg_dur_high
postpartum_dur
breastfeeding_dur_mu
breastfeeding_dur_beta
max_lam_dur
short_int
low_age_short_int
high_age_short_int
abortion_prob
twins_prob
LAM_efficacy
maternal_mortality_factor
fecundity_var_low
fecundity_var_high
high_parity
high_parity_nonuse
primary_infertility
exposure_factor
restrict_method_use
mcpr_growth_rate
mcpr_max
mcpr_norm_year
filenames
age_pyramid
age_mortality
maternal_mortality
infant_mortality
miscarriage_rates
stillbirth_rate
age_fecundity
fecundity_ratio_nullip
lactational_amenorrhea
sexual_activity
sexual_activity_pp
debut_age
exposure_age
exposure_parity
spacing_pref
methods
barriers
mortality_probs
interventions
analyzers

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

    nbsphinx_allow_errors = True