Read the Docs build information Build id: 1224869 Project: institute-for-disease-modeling-fpsim Version: latest Commit: 3212dd7979ecc3696e1d60e5ff03628c10e8c60a Date: 2022-12-15T22:41:22.384307Z State: finished Success: True [rtd-command-info] start-time: 2022-12-15T22:41:24.613415Z, end-time: 2022-12-15T22:41:25.659950Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/fpsim/fpsim.git . Cloning into '.'... [rtd-command-info] start-time: 2022-12-15T22:41:25.863928Z, end-time: 2022-12-15T22:41:25.963955Z, 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 3212dd7 Merge pull request #73 from fpsim/method-mix-kenya [rtd-command-info] start-time: 2022-12-15T22:41:26.189620Z, end-time: 2022-12-15T22:41:26.247559Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-12-15T22:41:31.653744Z, end-time: 2022-12-15T22:41:31.759630Z, duration: 0, exit-code: 0 asdf global python 3.9.15 [rtd-command-info] start-time: 2022-12-15T22:41:32.262821Z, end-time: 2022-12-15T22:41:33.227096Z, duration: 0, exit-code: 0 python -mvirtualenv --system-site-packages created virtual environment CPython3.9.15.final.0-64 in 669ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest, clear=False, no_vcs_ignore=False, global=True) 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: 2022-12-15T22:41:33.434216Z, end-time: 2022-12-15T22:41:42.898258Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-22.3.1-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools<58.3.0 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<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools, pip Attempting uninstall: setuptools 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-22.3.1 setuptools-58.2.0 [rtd-command-info] start-time: 2022-12-15T22:41:43.135781Z, end-time: 2022-12-15T22:41:55.328909Z, duration: 12, 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 sphinx-rtd-theme readthedocs-sphinx-ext<2.3 setuptools<58.3.0 Collecting pillow Downloading Pillow-9.3.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 60.6 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 160.5 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): 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eta 0:00:00 Collecting importlib-metadata>=4.8 Downloading importlib_metadata-5.1.0-py3-none-any.whl (21 kB) Collecting Pygments>=2.12 Downloading Pygments-2.13.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 153.2 MB/s eta 0:00:00 Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 159.6 MB/s eta 0:00:00 Collecting pytz>=2015.7 Downloading pytz-2022.6-py2.py3-none-any.whl (498 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 498.1/498.1 kB 156.2 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.11.0-py3-none-any.whl (6.6 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting certifi>=2017.4.17 Downloading certifi-2022.12.7-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 143.0 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 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sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.11.0 certifi-2022.12.7 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 importlib-metadata-5.1.0 mock-1.0.1 packaging-22.0 pillow-9.3.0 pytz-2022.6 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.1 setuptools-58.2.0 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.1.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-1.26.13 zipp-3.11.0 [rtd-command-info] start-time: 2022-12-15T22:41:55.544633Z, end-time: 2022-12-15T22:42:17.950118Z, duration: 22, 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beautifulsoup4, nbformat, jupyter-client, ipython, cliff, alembic, optuna, nbclient, ipykernel, nbconvert, nbsphinx Attempting uninstall: importlib-metadata Found existing installation: importlib-metadata 5.1.0 Uninstalling importlib-metadata-5.1.0: Successfully uninstalled importlib-metadata-5.1.0 Successfully installed Mako-1.2.4 PrettyTable-3.5.0 PyYAML-6.0 alembic-1.9.0 asttokens-2.2.1 attrs-22.1.0 autopage-0.5.1 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.1 cliff-4.1.0 cmaes-0.9.0 cmd2-2.4.2 colorlog-6.7.0 comm-0.1.2 debugpy-1.6.4 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 exceptiongroup-1.0.4 executing-1.2.0 fastjsonschema-2.16.2 greenlet-2.0.1 importlib-metadata-4.13.0 iniconfig-1.1.1 ipykernel-6.19.2 ipython-8.7.0 jedi-0.18.2 jsonschema-4.17.3 jupyter-client-7.4.8 jupyter-core-5.1.0 jupyterlab-pygments-0.2.2 matplotlib-inline-0.1.6 mistune-2.0.4 nbclient-0.7.2 nbconvert-7.2.6 nbformat-5.7.0 nbsphinx-0.8.10 nest-asyncio-1.5.6 numpy-1.23.5 optuna-3.0.4 pandoc-2.3 pandocfilters-1.5.0 parso-0.8.3 pbr-5.11.0 pexpect-4.8.0 pickleshare-0.7.5 pluggy-1.0.0 plumbum-1.8.0 ply-3.11 pockets-0.9.1 prompt-toolkit-3.0.36 psutil-5.9.4 ptyprocess-0.7.0 pure-eval-0.2.2 pypandoc-1.10 pyperclip-1.8.2 pyrsistent-0.19.2 pytest-7.2.0 python-dateutil-2.8.2 pyzmq-24.0.1 scipy-1.8.1 soupsieve-2.3.2.post1 sphinxcontrib-napoleon-0.7 sqlalchemy-1.4.45 stack-data-0.6.2 stevedore-4.1.1 tinycss2-1.2.1 tomli-2.0.1 tornado-6.2 tqdm-4.64.1 traitlets-5.7.1 wcwidth-0.2.5 webencodings-0.5.1 [rtd-command-info] start-time: 2022-12-15T22:42:18.184518Z, end-time: 2022-12-15T22:42:48.094019Z, duration: 29, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir . 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sha256=ef2a839bd6ac380d79bf62945cbb8fe09ce4b9a745d00506996cce1ef035053d Stored in directory: /tmp/pip-ephem-wheel-cache-1gps5gi0/wheels/54/be/71/b6a93e28e1af4f52153fe34b99119b980ee057025c8abb6ee6 Building wheel for jellyfish (setup.py): started Building wheel for jellyfish (setup.py): finished with status 'done' Created wheel for jellyfish: filename=jellyfish-0.9.0-cp39-cp39-linux_x86_64.whl size=102040 sha256=cc33e51b39dc3fcd386a966e5b5c24e5cc8beeda81a1f17697bba3f3fbf64613 Stored in directory: /tmp/pip-ephem-wheel-cache-1gps5gi0/wheels/a1/38/09/217f100d5ba4e37ff47b0da300ad91e165f1c9ddafcdb6838a Successfully built fpsim jellyfish Installing collected packages: palettable, xlsxwriter, smmap, setuptools, pyparsing, pyarrow, patsy, memory-profiler, llvmlite, line-profiler, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, contourpy, pandas, openpyxl, numba, multiprocess, matplotlib, gitdb, statsmodels, seaborn, mizani, gitpython, sciris, plotnine, fpsim Attempting uninstall: setuptools Found existing installation: setuptools 58.2.0 Uninstalling setuptools-58.2.0: Successfully uninstalled setuptools-58.2.0 Successfully installed contourpy-1.0.6 cycler-0.11.0 dill-0.3.6 et-xmlfile-1.1.0 fonttools-4.38.0 fpsim-0.21.1 gitdb-4.0.10 gitpython-3.1.29 jellyfish-0.9.0 jsonpickle-3.0.0 kiwisolver-1.4.4 line-profiler-4.0.2 llvmlite-0.39.1 matplotlib-3.6.2 memory-profiler-0.61.0 mizani-0.8.1 multiprocess-0.70.14 numba-0.56.4 openpyxl-3.0.10 palettable-3.3.0 pandas-1.5.2 patsy-0.5.3 plotnine-0.10.1 pyarrow-10.0.1 pyparsing-3.0.9 sciris-2.0.4 seaborn-0.12.1 setuptools-65.6.3 smmap-5.0.0 statsmodels-0.13.5 xlsxwriter-3.0.3 [rtd-command-info] start-time: 2022-12-15T22:42:49.811783Z, end-time: 2022-12-15T22:42:49.876851Z, 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 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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("v0.19.2", "/en/v0.19.2/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/fpsim/en/latest/pdf/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-fpsim', 'name': u'fpsim', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/fpsim/en/latest/', 'analytics_code': 'UA-87656833-3', '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': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '3212dd79', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-fpsim/builds/1224869/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2022-12-15T22:42:50.058831Z, end-time: 2022-12-15T22:44:15.020120Z, duration: 84, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v5.3.0 Building Jupyter notebooks with build option: auto making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 24 source files that are out of date updating environment: [new config] 24 added, 0 changed, 0 removed reading sources... 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(./institute-for-disease-modeling-fpsim.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-fpsim.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r .enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} Output written on institute-for-disease-modeling-fpsim.pdf (65 pages, 436815 by tes). Transcript written on institute-for-disease-modeling-fpsim.log. Latexmk: Index file 'institute-for-disease-modeling-fpsim.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-fpsim.ind' from line 'No file institute-for-disease-modeling-fpsim.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-fpsim.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-fpsim.pdf' Latexmk: List of undefined refs and citations: Reference `fpsim.analyzers:module-fpsim.analyzers' on page 61 undefined on input line 7392 Reference `fpsim.base:module-fpsim.base' on page 61 undefined on input line 7393 Reference `fpsim.calibration:module-fpsim.calibration' on page 61 undefined on input line 7394 Reference `fpsim.defaults:module-fpsim.defaults' on page 61 undefined on input line 7395 Reference `fpsim.experiment:module-fpsim.experiment' on page 61 undefined on input line 7396 Reference `fpsim.interventions:module-fpsim.interventions' on page 61 undefined on input line 7397 Reference `fpsim.locations.kenya:module-fpsim.locations.kenya' on page 61 undefined on input line 7399 Reference `fpsim.locations.senegal:module-fpsim.locations.senegal' on page 61 undefined on input line 7400 Reference `fpsim.locations:module-fpsim.locations' on page 61 undefined on input line 7398 Reference `fpsim.parameters:module-fpsim.parameters' on page 61 undefined on input line 7401 Reference `fpsim.scenarios:module-fpsim.scenarios' on page 61 undefined on input line 7402 Reference `fpsim.settings:module-fpsim.settings' on page 61 undefined on input line 7403 Reference `fpsim.sim:module-fpsim.sim' on page 61 undefined on input line 7404 Reference `fpsim.utils:module-fpsim.utils' on page 61 undefined on input line 7405 Reference `fpsim.version:module-fpsim.version' on page 61 undefined on input line 7406 Reference `modules:module-fpsim' on page 61 undefined on input line 7391 Rule 'makeindex institute-for-disease-modeling-fpsim.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-fpsim.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-fpsim.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-fpsim.ind" "institute-for-disease-modeling-fpsim.idx"' ------------ === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-fpsim.idx'... This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-fpsim.idx....done (285 entries accepted, 0 rejected). Sorting entries.....done (2445 comparisons). Generating output file institute-for-disease-modeling-fpsim.ind....done (377 lines written, 0 warnings). Output written in institute-for-disease-modeling-fpsim.ind. Transcript written in institute-for-disease-modeling-fpsim.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-fpsim.aux' 'institute-for-disease-modeling-fpsim.ind' 'institute-for-disease-modeling-fpsim.out' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-fpsim" "fpsim-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4] [5] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [6] Underfull \vbox (badness 10000) detected at line 695 Underfull \vbox (badness 10000) detected at line 695 [7] [8 <./tutorials_T1_intro_2_2.pdf>] [9] ! Package inputenc Error: Unicode character ☠ (U+2620) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.891 ...20; results: b=68914 ☠=11805 pop=62232) Overfull \vbox (1.8739pt too high) detected at line 997 [10] ! Package inputenc Error: Unicode character ☠ (U+2620) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1021 ...0; results: b=68914 ☠=11805 pop=62232) [11] Underfull \vbox (badness 10000) detected at line 1124 [12] ! 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