Read the Docs build information
Build id: 1956201
Project: institute-for-disease-modeling-hpvsim
Version: latest
Commit: 133a13a577ba01de6266078a41a2266ed5c519e4
Date: 2024-01-17T19:25:43.472016Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-01-17T19:25:57.407530Z, end-time: 2024-01-17T19:25:58.033054Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/InstituteforDiseaseModeling/hpvsim.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-01-17T19:25:58.101620Z, end-time: 2024-01-17T19:25:59.761344Z, 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/InstituteforDiseaseModeling/hpvsim
 * [new tag]         v0.3.7     -> v0.3.7
 * [new tag]         v0.4.0     -> v0.4.0
 * [new tag]         v0.4.16    -> v0.4.16
 * [new tag]         v0.4.5     -> v0.4.5
 * [new tag]         v1.0.0     -> v1.0.0
 * [new tag]         v1.1.1     -> v1.1.1
 * [new tag]         v1.2.0     -> v1.2.0
 * [new tag]         v1.2.2     -> v1.2.2
 * [new tag]         v1.2.3     -> v1.2.3
 * [new tag]         v1.2.4     -> v1.2.4
 * [new tag]         v1.2.5     -> v1.2.5
 * [new tag]         v1.2.6     -> v1.2.6
 * [new tag]         v1.2.7     -> v1.2.7

[rtd-command-info] start-time: 2024-01-17T19:25:59.897917Z, end-time: 2024-01-17T19:25:59.973251Z, 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 133a13a Merge pull request #643 from amath-idm/rc2.0.0

[rtd-command-info] start-time: 2024-01-17T19:26:00.052448Z, end-time: 2024-01-17T19:26:00.116393Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2024-01-17T19:26:00.189238Z, end-time: 2024-01-17T19:26:00.246387Z, 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: 2024-01-17T19:26:05.622714Z, end-time: 2024-01-17T19:26:05.695108Z, duration: 0, exit-code: 0
asdf global python 3.9.18


[rtd-command-info] start-time: 2024-01-17T19:26:06.085849Z, end-time: 2024-01-17T19:26:07.364203Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.18.final.0-64 in 915ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/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==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-01-17T19:26:07.437497Z, end-time: 2024-01-17T19:26:18.777655Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (23.1)
Collecting pip
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (67.6.1)
Collecting setuptools
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-23.3.2 setuptools-69.0.3

[rtd-command-info] start-time: 2024-01-17T19:26:18.848450Z, end-time: 2024-01-17T19:26:28.095386Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx)
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Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.3 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.1.0 zipp-3.17.0

[rtd-command-info] start-time: 2024-01-17T19:26:28.175073Z, end-time: 2024-01-17T19:27:13.657230Z, duration: 45, 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: 2024-01-17T19:27:13.748408Z, end-time: 2024-01-17T19:27:28.179415Z, duration: 14, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .
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  Stored in directory: /tmp/pip-ephem-wheel-cache-mmv8z2ql/wheels/51/35/6f/df976332f8d726e8d5b6219b83a0569f551e10d63ed39a50fb
Successfully built hpvsim
Installing collected packages: zstandard, xlsxwriter, smmap, scipy, memory-profiler, line-profiler, jsonpickle, jellyfish, et-xmlfile, dill, openpyxl, multiprocess, gitdb, gitpython, sciris, hpvsim
Successfully installed dill-0.3.7 et-xmlfile-1.1.0 gitdb-4.0.11 gitpython-3.1.41 hpvsim-2.0.0 jellyfish-1.0.3 jsonpickle-3.0.2 line-profiler-4.1.2 memory-profiler-0.61.0 multiprocess-0.70.15 openpyxl-3.1.2 scipy-1.11.4 sciris-3.1.2 smmap-5.0.1 xlsxwriter-3.1.9 zstandard-0.22.0

[rtd-command-info] start-time: 2024-01-17T19:27:28.757299Z, end-time: 2024-01-17T19:27:28.819290Z, 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 hpvsim as hpv

# Set environment
os.environ['SPHINX_BUILD'] = 'True' # This is used so cv.options.set('jupyter') doesn't reset the Matplotlib renderer
os.environ['HPVSIM_WARNINGS'] = 'error' # Don't let warnings pass in the tutorials
os.environ['PYDEVD_DISABLE_FILE_VALIDATION'] = '1' # Suppress harmless warning in documentation build
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 "hpvsim 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',
    'IPython.sphinxext.ipython_console_highlighting'  # Temporary fix for https://github.com/spatialaudio/nbsphinx/issues/687
]

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 = 'HPVsim'
copyright = f'2022 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for {project} version {hpv.__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 = hpv.__version__
release = hpv.__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/hpvsim/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/hpvsim/en/latest'

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

# -- 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, 'hpvsim-docs.tex', 'HPVsim',
     '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, 'hpvsim-docs', 'HPVsim',
     [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, 'hpvsim-docs', 'HVPsim',
     author, 'Institute for Disease Modeling', 'How to use HPVsim to simulate HPV transmission.',
     '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),
                       'fpsim': ('https://docs.idmod.org/projects/fpsim/en/latest', None),
                       'sciris': ('https://sciris.readthedocs.io/en/latest/', None)
                       }

# Configure nbsphinx
nbsphinx_kernel_name = "python"
nbsphinx_timeout = 180 # 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/"),
    ("v2.0.0", "/en/v2.0.0/"),
    ("v1.2.7", "/en/v1.2.7/"),
    ("v1.2.6", "/en/v1.2.6/"),
    ("v1.2.5", "/en/v1.2.5/"),
    ("v1.2.4", "/en/v1.2.4/"),
    ("v1.2.3", "/en/v1.2.3/"),
    ("v1.2.2", "/en/v1.2.2/"),
    ("v1.2.0", "/en/v1.2.0/"),
    ("v1.1.1", "/en/v1.1.1/"),
    ("v1.0.0", "/en/v1.0.0/"),
    ("v0.4.16", "/en/v0.4.16/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-hpvsim',
    'name': u'hpvsim',
    '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': 'hpvsim',
    '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': '133a13a5',
}

# 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-hpvsim/builds/1956201/'

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: 2024-01-17T19:27:28.886445Z, end-time: 2024-01-17T19:34:15.608719Z, duration: 406, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
HPVsim 2.0.0 (2023-11-29) — © 2023 by IDM
HPVsim data: at least one file missing: {'metadata': False, 'age_dist': False, 'birth': False, 'death': False, 'life_expectancy': False}


————————————————————————————————————
Downloading preprocessed HPVsim data
————————————————————————————————————

Note: this automatic download only happens once, when HPVsim is first run.


Downloading 1 URL(s)...
Downloading https://github.com/amath-idm/hpvsim_data/blob/main/hpvsim_data_v1.3.zip?raw=true...
Saving to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.3.zip.zip...
Time to download https://github.com/amath-idm/hpvsim_data/blob/main/hpvsim_data_v1.3.zip?raw=true: 2.37 s
Time to download 1 URLs: 2.37 s
Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.3.zip.zip"

Data downloaded.


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 33 source files that are out of date
updating environment: [new config] 33 added, 0 changed, 0 removed
reading sources... [  3%] hpvsim.analysis
reading sources... [  6%] hpvsim.base
reading sources... [  9%] hpvsim.calibration
reading sources... [ 12%] hpvsim.data
reading sources... [ 15%] hpvsim.data.downloaders
reading sources... [ 18%] hpvsim.data.loaders
reading sources... [ 21%] hpvsim.defaults
reading sources... [ 24%] hpvsim.hiv
reading sources... [ 27%] hpvsim.immunity
reading sources... [ 30%] hpvsim.interventions
reading sources... [ 33%] hpvsim.misc
reading sources... [ 36%] hpvsim.parameters
reading sources... [ 39%] hpvsim.people
reading sources... [ 42%] hpvsim.plotting
reading sources... [ 45%] hpvsim.population
reading sources... [ 48%] hpvsim.run
reading sources... [ 52%] hpvsim.settings
reading sources... [ 55%] hpvsim.sim
reading sources... [ 58%] hpvsim.utils
reading sources... [ 61%] hpvsim.version
reading sources... [ 64%] index
reading sources... [ 67%] modules
reading sources... [ 70%] overview
reading sources... [ 73%] tutorials
reading sources... [ 76%] tutorials/README
reading sources... [ 79%] tutorials/tut_analyzers
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: 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-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: 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-hpvsim/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.5).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
reading sources... [ 82%] tutorials/tut_calibration
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
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reading sources... [ 85%] tutorials/tut_interventions
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  ret = f(**kwargs)
reading sources... [ 88%] tutorials/tut_intro
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
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reading sources... [ 91%] tutorials/tut_people
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
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reading sources... [ 94%] tutorials/tut_plotting
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
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reading sources... [ 97%] tutorials/tut_running
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long)
  ret = f(**kwargs)
reading sources... [100%] whats-new
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:20: ERROR: Content block expected for the "raw" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:20: ERROR: Content block expected for the "raw" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:20: ERROR: Content block expected for the "raw" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:20: ERROR: Content block expected for the "raw" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:20: ERROR: Content block expected for the "raw" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:22: ERROR: Content block expected for the "raw" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/tutorials/tut_analyzers.ipynb:20: ERROR: Content block expected for the "raw" directive; none found.
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