Read the Docs build information Build id: 1290632 Project: institute-for-disease-modeling-fpsim Version: latest Commit: fdb20f5ff3498116230b953e4d4228b7b29f72de Date: 2023-02-08T16:14:23.880311Z State: finished Success: True [rtd-command-info] start-time: 2023-02-08T16:14:25.829500Z, end-time: 2023-02-08T16:14:26.910536Z, 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: 2023-02-08T16:14:27.204173Z, end-time: 2023-02-08T16:14:27.296983Z, 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 fdb20f5 Merge pull request #113 from fpsim/add-weights-to-matrix [rtd-command-info] start-time: 2023-02-08T16:14:27.550462Z, end-time: 2023-02-08T16:14:27.644198Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-02-08T16:14:32.961701Z, end-time: 2023-02-08T16:14:33.038806Z, duration: 0, exit-code: 0 asdf global python 3.9.15 [rtd-command-info] start-time: 2023-02-08T16:14:33.521451Z, end-time: 2023-02-08T16:14:34.544626Z, duration: 1, exit-code: 0 python -mvirtualenv --system-site-packages $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.15.final.0-64 in 685ms 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: 2023-02-08T16:14:34.779466Z, end-time: 2023-02-08T16:14:45.460793Z, duration: 10, 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-23.0-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-23.0 setuptools-58.2.0 [rtd-command-info] start-time: 2023-02-08T16:14:45.653234Z, end-time: 2023-02-08T16:14:58.883793Z, duration: 13, 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-9.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 63.8 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 170.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started 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/tmp/pip-ephem-wheel-cache-6dir1hug/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, charset-normalizer, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, certifi, babel, alabaster, sphinxcontrib-jquery, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.0.0 mock-1.0.1 packaging-23.0 pillow-9.4.0 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 setuptools-58.2.0 snowballstemmer-2.2.0 sphinx-6.1.3 sphinx-rtd-theme-1.2.0 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jquery-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-1.26.14 zipp-3.12.1 [rtd-command-info] start-time: 2023-02-08T16:14:59.067722Z, end-time: 2023-02-08T16:15:18.519913Z, duration: 19, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pytest Downloading pytest-7.2.1-py3-none-any.whl (317 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 317.1/317.1 kB 12.0 MB/s eta 0:00:00 Requirement already satisfied: sphinx-rtd-theme in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from -r docs/requirements.txt (line 2)) (1.2.0) Collecting sphinxcontrib-napoleon Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Requirement already satisfied: sphinx in 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packages: pandoc Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.3-py3-none-any.whl size=33288 sha256=3fcdd0e5be3f069abf4b57da8f6261ebe3b9aec21fcae68b322a92758c67a726 Stored in directory: /tmp/pip-ephem-wheel-cache-frlemv5d/wheels/69/e6/a1/1daa96d919c9e09a71473649b717b8da286f3f8d7719d1cfc5 Successfully built pandoc Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, ply, pickleshare, mistune, fastjsonschema, executing, backcall, typing-extensions, traitlets, tqdm, tornado, tomli, tinycss2, soupsieve, pyzmq, PyYAML, python-dateutil, pyrsistent, pypandoc, psutil, prompt-toolkit, pockets, plumbum, pluggy, pexpect, parso, pandocfilters, numpy, nest-asyncio, Mako, jupyterlab-pygments, iniconfig, greenlet, exceptiongroup, defusedxml, decorator, debugpy, colorlog, bleach, attrs, asttokens, stack-data, sqlalchemy, sphinxcontrib-napoleon, pytest, pandoc, 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python-dateutil-2.8.2 pyzmq-25.0.0 soupsieve-2.3.2.post1 sphinxcontrib-napoleon-0.7 sqlalchemy-2.0.2 stack-data-0.6.2 tinycss2-1.2.1 tomli-2.0.1 tornado-6.2 tqdm-4.64.1 traitlets-5.9.0 typing-extensions-4.4.0 wcwidth-0.2.6 webencodings-0.5.1 [rtd-command-info] start-time: 2023-02-08T16:15:18.775362Z, end-time: 2023-02-08T16:16:04.834453Z, duration: 46, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir . 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sha256=80902d76cc67c4bb9b0e35a1da0e747863ff4acc15b094d612066d411b5ca90c Stored in directory: /tmp/pip-ephem-wheel-cache-pu7lbiuk/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=102029 sha256=2e540e6a42a162a42b906c1ed0fefa78f9b6a9e6511d8a582ae783788cf9626f Stored in directory: /tmp/pip-ephem-wheel-cache-pu7lbiuk/wheels/a6/28/ba/284e37010e5d3aeed5e45345b58ab8683f97bdce46c9e147f9 Successfully built fpsim jellyfish Installing collected packages: palettable, zstandard, xlsxwriter, smmap, setuptools, pyparsing, numpy, memory-profiler, llvmlite, line-profiler, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, scipy, pyarrow, patsy, pandas, openpyxl, numba, multiprocess, gitdb, contourpy, statsmodels, matplotlib, gitpython, seaborn, sciris, mizani, plotnine, fpsim Attempting uninstall: setuptools Found existing installation: setuptools 58.2.0 Uninstalling setuptools-58.2.0: Successfully uninstalled setuptools-58.2.0 Attempting uninstall: numpy Found existing installation: numpy 1.24.2 Uninstalling numpy-1.24.2: Successfully uninstalled numpy-1.24.2 Successfully installed contourpy-1.0.7 cycler-0.11.0 dill-0.3.6 et-xmlfile-1.1.0 fonttools-4.38.0 fpsim-0.22.1 gitdb-4.0.10 gitpython-3.1.30 jellyfish-0.9.0 jsonpickle-3.0.1 kiwisolver-1.4.4 line-profiler-4.0.2 llvmlite-0.39.1 matplotlib-3.6.3 memory-profiler-0.61.0 mizani-0.8.1 multiprocess-0.70.14 numba-0.56.4 numpy-1.23.5 openpyxl-3.1.0 palettable-3.3.0 pandas-1.5.3 patsy-0.5.3 plotnine-0.10.1 pyarrow-11.0.0 pyparsing-3.0.9 scipy-1.10.0 sciris-2.1.0 seaborn-0.12.2 setuptools-67.2.0 smmap-5.0.0 statsmodels-0.13.5 xlsxwriter-3.0.8 zstandard-0.19.0 [rtd-command-info] start-time: 2023-02-08T16:16:06.652220Z, end-time: 2023-02-08T16:16:06.712718Z, 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: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "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/"), ("v0.22.0", "/en/v0.22.0/"), ("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': 'fdb20f5f', } # 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/1290632/' 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: 2023-02-08T16:16:06.963276Z, end-time: 2023-02-08T16:18:54.270773Z, duration: 167, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . ../_readthedocs/html Running Sphinx v6.1.3 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 24 source files that are out of date updating environment: [new config] 24 added, 0 changed, 0 removed reading sources... [ 4%] fpsim.analyzers reading sources... [ 8%] fpsim.base reading sources... [ 12%] fpsim.calibration reading sources... [ 16%] fpsim.defaults reading sources... [ 20%] fpsim.experiment reading sources... [ 25%] fpsim.interventions reading sources... [ 29%] fpsim.locations reading sources... [ 33%] fpsim.locations.kenya reading sources... [ 37%] fpsim.locations.senegal reading sources... [ 41%] fpsim.parameters reading sources... [ 45%] fpsim.scenarios reading sources... [ 50%] fpsim.settings reading sources... [ 54%] fpsim.sim reading sources... [ 58%] fpsim.utils reading sources... [ 62%] fpsim.version reading sources... [ 66%] index reading sources... 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[100%] whatsnew generating indices... genindex py-modindex done copying linked files... copying notebooks ... [ 33%] tutorials/T1_intro.ipynb copying notebooks ... [ 66%] tutorials/T2_scenarios.ipynb copying notebooks ... [100%] tutorials/T3_scenarios_plotting.ipynb highlighting module code... [ 9%] fpsim.analyzers highlighting module code... [ 18%] fpsim.base highlighting module code... [ 27%] fpsim.calibration highlighting module code... [ 36%] fpsim.experiment highlighting module code... [ 45%] fpsim.interventions highlighting module code... [ 54%] fpsim.locations.kenya highlighting module code... [ 63%] fpsim.locations.senegal highlighting module code... [ 72%] fpsim.parameters highlighting module code... [ 81%] fpsim.scenarios highlighting module code... [ 90%] fpsim.sim highlighting module code... [100%] fpsim.utils writing additional pages... search opensearch done copying images... [ 25%] _build/doctrees/nbsphinx/tutorials_T1_intro_2_2.svg copying images... [ 50%] _build/doctrees/nbsphinx/tutorials_T1_intro_13_0.svg copying images... [ 75%] _build/doctrees/nbsphinx/tutorials_T1_intro_13_1.svg copying images... [100%] _build/doctrees/nbsphinx/tutorials_T1_intro_13_2.svg copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded, 5 warnings. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2023-02-08T16:18:54.592351Z, end-time: 2023-02-08T16:20:10.925923Z, duration: 76, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . ../_readthedocs/pdf Running Sphinx v6.1.3 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 [latex]: all documents updating environment: [new config] 24 added, 0 changed, 0 removed reading sources... 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[ 87%] 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:264: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) warn("Unexpected error discovering local network interfaces: %s" % e) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:264: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) warn("Unexpected error discovering local network interfaces: %s" % e) reading sources... [ 91%] tutorials/T2_scenarios reading sources... [ 95%] tutorials/T3_scenarios_plotting reading sources... [100%] whatsnew /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/latest/docs/tutorials.rst:3: WARNING: toctree contains reference to nonexisting document 'tutorials/T2_plotting' ../CHANGELOG.rst:14: ERROR: Unknown target name: "https://github.com/fpsim/fpsim/pull/113>". ../CHANGELOG.rst:20: ERROR: Unknown target name: "https://github.com/fpsim/fpsim/pull/109>". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/latest/docs/tutorials/T2_scenarios.ipynb: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/latest/docs/tutorials/T3_scenarios_plotting.ipynb: WARNING: document isn't included in any toctree done processing fpsim-docs.tex... index overview tutorials tutorials/T1_intro whatsnew modules fpsim.locations fpsim.locations.kenya fpsim.locations.senegal fpsim.analyzers fpsim.base fpsim.calibration fpsim.defaults fpsim.experiment fpsim.interventions fpsim.parameters fpsim.scenarios fpsim.settings fpsim.sim fpsim.utils fpsim.version resolving references... done writing... done copying images... [ 25%] _build/doctrees/nbsphinx/tutorials_T1_intro_2_2.pdf copying images... [ 50%] _build/doctrees/nbsphinx/tutorials_T1_intro_13_0.pdf copying images... [ 75%] _build/doctrees/nbsphinx/tutorials_T1_intro_13_1.pdf copying images... [100%] _build/doctrees/nbsphinx/tutorials_T1_intro_13_2.pdf copying TeX support files... copying TeX support files... done WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/latest/_readthedocs/pdf/_static/searchtools.js build succeeded, 6 warnings. The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2023-02-08T16:20:11.322171Z, end-time: 2023-02-08T16:20:11.380682Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2023-02-08T16:20:11.600412Z, end-time: 2023-02-08T16:20:34.053539Z, duration: 22, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-fpsim -interaction=nonstopmode Use of uninitialized value in concatenation (.) or string at (eval 13) line 1, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 13) line 2, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 13) line 3, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 13) line 4, chunk 1. Subroutine makeglo redefined at (eval 14) line 7, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 14) line 1, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 14) line 2, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 14) line 3, chunk 1. Use of uninitialized value in concatenation (.) or string at (eval 14) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67. Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 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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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 7445 Reference `fpsim.base:module-fpsim.base' on page 61 undefined on input line 7446 Reference `fpsim.calibration:module-fpsim.calibration' on page 61 undefined on input line 7447 Reference `fpsim.defaults:module-fpsim.defaults' on page 61 undefined on input line 7448 Reference `fpsim.experiment:module-fpsim.experiment' on page 61 undefined on input line 7449 Reference `fpsim.interventions:module-fpsim.interventions' on page 61 undefined on input line 7450 Reference `fpsim.locations.kenya:module-fpsim.locations.kenya' on page 61 undefined on input line 7452 Reference `fpsim.locations.senegal:module-fpsim.locations.senegal' on page 61 undefined on input line 7453 Reference `fpsim.locations:module-fpsim.locations' on page 61 undefined on input line 7451 Reference `fpsim.parameters:module-fpsim.parameters' on page 61 undefined on input line 7454 Reference `fpsim.scenarios:module-fpsim.scenarios' on page 61 undefined on input line 7455 Reference `fpsim.settings:module-fpsim.settings' on page 61 undefined on input line 7456 Reference `fpsim.sim:module-fpsim.sim' on page 61 undefined on input line 7457 Reference `fpsim.utils:module-fpsim.utils' on page 61 undefined on input line 7458 Reference `fpsim.version:module-fpsim.version' on page 61 undefined on input line 7459 Reference `modules:module-fpsim' on page 61 undefined on input line 7444 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'... 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (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 (70 pages, 478722 by tes). Transcript written on institute-for-disease-modeling-fpsim.log. Latexmk: Index file 'institute-for-disease-modeling-fpsim.idx' was written Latexmk: References changed. 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Type H for immediate help. ... l.1958 ...sults: b=69,541 ☠=11,920 pop=62,630)}} ^^M [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/qtm/m/n/10 Pa-ram-e-ter names made more con-sis-tent, e.g. \T1/txtt/m/n/1 0 exposure_correction $\OMS/cmsy/m/n/10 !$ \T1/txtt/m/n/10 exposure_factor\T1/q tm/m/n/10 , [24] Underfull \hbox (badness 10000) in paragraph at lines 2198--2200 \T1/qtm/m/n/10 re-named \T1/txtt/m/n/10 sim[\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 m ethods\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 raw \TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 annual\TS 1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 18[]25\TS1/t xtt/m/n/10 '\T1/txtt/m/n/10 ]\T1/qtm/m/n/10 ; \T1/txtt/m/n/10 sim[\TS1/txtt/m/n /10 '\T1/txtt/m/n/10 methods\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/1 0 '\T1/txtt/m/n/10 probs\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\ T1/txtt/m/n/10 18[]25\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ] Underfull \hbox (badness 10000) in paragraph at lines 2198--2200 \T1/qtm/m/n/10 has been re-named \T1/txtt/m/n/10 sim[\TS1/txtt/m/n/10 '\T1/txtt /m/n/10 methods\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m /n/10 adjusted\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/ n/10 annual\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/n/1 0 18[]25\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 ]\T1/qtm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 2198--2200 \T1/txtt/m/n/10 sim[\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 methods_postpartum\TS1/tx tt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 probs1to6\TS1/tx tt/m/n/10 '\T1/txtt/m/n/10 ][\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 18[]25\TS1/txtt/ m/n/10 '\T1/txtt/m/n/10 ] \T1/qtm/m/n/10 has been re-named Underfull \hbox (badness 10000) in paragraph at lines 2206--2208 []\T1/qtm/m/n/10 Var-i-ous other meth-ods were re-named for clar-ity (e.g. \T1/ txtt/m/n/10 maternal_mortality() $\OMS/cmsy/m/n/10 !$ [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] Underfull \hbox (badness 10000) in paragraph at lines 3679--3682 \T1/qtm/m/n/10 Ei-ther a json file at ^^Psim_output/total_results.json^^Q or a csv file for each state at [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 5064) in paragraph at lines 4886--4888 []\T1/txtt/bx/n/10 custom \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 dict\T1/qtm/m/n/10 ) ^^U a cus-tom dic-tio-nary of ad-di-tional data to fit; for-mat is e.g. [42] [43] [44] [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 5665--5668 \T1/qtm/m/n/10 pars.update_method_eff(`Injectables', 0.99) pars.update_method_e ff({`Injectables':0.99, `Con- [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] ! Package inputenc Error: Unicode character μ (U+03BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.7413 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} ! Package inputenc Error: Unicode character σ (U+03C3) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.7413 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} [60] [61] (./institute-for-disease-modeling-fpsim.ind [62] Underfull \hbox (badness 10000) in paragraph at lines 37--38 []\T1/txtt/m/n/10 birth_spacing_pref() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le fp- Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/txtt/m/n/10 birth_spacing_pref() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le fp- Underfull \hbox (badness 10000) in paragraph at lines 87--88 []\T1/txtt/m/n/10 exposure_parity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule fp- [63] Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/txtt/m/n/10 fecundity_ratio_nullip() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule fp- Underfull \hbox (badness 10000) in paragraph at lines 99--101 []\T1/txtt/m/n/10 fecundity_ratio_nullip() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule fp- Underfull \hbox (badness 10000) in paragraph at lines 101--103 []\T1/txtt/m/n/10 female_age_fecundity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule fp- Underfull \hbox (badness 10000) in paragraph at lines 103--105 []\T1/txtt/m/n/10 female_age_fecundity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule fp- Underfull \hbox (badness 10000) in paragraph at lines 163--164 []\T1/txtt/m/n/10 infant_mortality() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule fp- Underfull \hbox (badness 10000) in paragraph at lines 164--165 []\T1/txtt/m/n/10 infant_mortality() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule fp- Underfull \hbox (badness 10000) in paragraph at lines 187--189 []\T1/txtt/m/n/10 lactational_amenorrhea() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule fp- Underfull \hbox (badness 10000) in paragraph at lines 189--191 []\T1/txtt/m/n/10 lactational_amenorrhea() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule fp- [64] Underfull \hbox (badness 10000) in paragraph at lines 206--207 []\T1/txtt/m/n/10 maternal_mortality() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le fp- Underfull \hbox (badness 10000) in paragraph at lines 207--209 []\T1/txtt/m/n/10 maternal_mortality() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le fp- Underfull \hbox (badness 10000) in paragraph at lines 220--221 []\T1/txtt/m/n/10 model_infant_mortality_rate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 Ex-per-i-ment [65] Underfull \hbox (badness 10000) in paragraph at lines 310--311 []\T1/txtt/m/n/10 sexual_activity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule fp- Underfull \hbox (badness 10000) in paragraph at lines 311--312 []\T1/txtt/m/n/10 sexual_activity_pp() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le fp- Underfull \hbox (badness 10000) in paragraph at lines 312--314 []\T1/txtt/m/n/10 sexual_activity_pp() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le fp- [66]) (./institute-for-disease-modeling-fpsim.aux) ) (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 (70 pages, 478823 by tes). Transcript written on institute-for-disease-modeling-fpsim.log. Latexmk: Index file 'institute-for-disease-modeling-fpsim.idx' was written 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: Summary of warnings from last run of (pdf)latex: =====Latex reported missing or unavailable character(s). =====See log file for details. Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'institute-for-disease-modeling-fpsim.log' for details === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets