Read the Docs build information Build id: 1654088 Project: institute-for-disease-modeling-hpvsim Version: v0.4.16 Commit: 2605feb851e33309650d9b7b0622ac8af2f55307 Date: 2023-08-10T17:48:37.974065Z State: finished Success: False [rtd-command-info] start-time: 2023-08-10T17:54:33.725860Z, end-time: 2023-08-10T17:54:35.177372Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/InstituteforDiseaseModeling/hpvsim.git . Cloning into '.'... [rtd-command-info] start-time: 2023-08-10T17:54:35.567565Z, end-time: 2023-08-10T17:54:35.711630Z, duration: 0, exit-code: 0 git checkout --force 2605feb851e33309650d9b7b0622ac8af2f55307 Note: switching to '2605feb851e33309650d9b7b0622ac8af2f55307'. 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 2605feb update version and changelog [rtd-command-info] start-time: 2023-08-10T17:54:36.033301Z, end-time: 2023-08-10T17:54:36.118967Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-10T17:54:36.341790Z, end-time: 2023-08-10T17:54:36.417975Z, 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: - pdf # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . system_packages: true [rtd-command-info] start-time: 2023-08-10T17:54:44.600035Z, end-time: 2023-08-10T17:54:44.716469Z, duration: 0, exit-code: 0 asdf global python 3.9.17 [rtd-command-info] start-time: 2023-08-10T17:54:45.497807Z, end-time: 2023-08-10T17:54:47.372755Z, duration: 1, exit-code: 0 python -mvirtualenv --system-site-packages $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.17.final.0-64 in 1327ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16, 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 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size=33260 sha256=814dddf815716654a2e2f401748381c557a937532390b2f52ce068567fd32efc Stored in directory: /tmp/pip-ephem-wheel-cache-uhoa0qme/wheels/17/20/73/b6171d60f96c3f21affca3e77ebcc2d8be3b55e198349b1b54 Successfully built pandoc Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, ply, pickleshare, fastjsonschema, executing, backcall, tzdata, typing-extensions, traitlets, tqdm, tornado, tomli, tinycss2, soupsieve, rpds-py, pyzmq, PyYAML, python-dateutil, pyparsing, pypandoc, psutil, prompt-toolkit, pockets, plumbum, pluggy, pillow, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-pygments, iniconfig, importlib-resources, greenlet, fonttools, exceptiongroup, docutils, defusedxml, decorator, debugpy, cycler, colorlog, bleach, attrs, asttokens, stack-data, sqlalchemy, sphinxcontrib-napoleon, referencing, pytest, pandoc, pandas, matplotlib-inline, jupyter-core, jedi, contourpy, comm, cmaes, beautifulsoup4, matplotlib, jupyter-client, jsonschema-specifications, ipython, alembic, seaborn, optuna, jsonschema, ipykernel, nbformat, nbclient, nbconvert, sphinx, sphinxcontrib-jquery, sphinx-rtd-theme, nbsphinx Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.1.2 Uninstalling Sphinx-7.1.2: Successfully uninstalled Sphinx-7.1.2 Successfully installed Mako-1.2.4 PyYAML-6.0.1 alembic-1.11.2 asttokens-2.2.1 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 cmaes-0.10.0 colorlog-6.7.0 comm-0.1.4 contourpy-1.1.0 cycler-0.11.0 debugpy-1.6.7.post1 decorator-5.1.1 defusedxml-0.7.1 docutils-0.18.1 exceptiongroup-1.1.2 executing-1.2.0 fastjsonschema-2.18.0 fonttools-4.42.0 greenlet-2.0.2 importlib-resources-6.0.1 iniconfig-2.0.0 ipykernel-6.25.1 ipython-8.14.0 jedi-0.19.0 jsonschema-4.19.0 jsonschema-specifications-2023.7.1 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages (from Mako->alembic>=1.5.0->optuna->hpvsim==0.4.16) (2.1.3) Building wheels for collected packages: hpvsim Building wheel for hpvsim (setup.py): started Building wheel for hpvsim (setup.py): finished with status 'done' Created wheel for hpvsim: filename=hpvsim-0.4.16-py3-none-any.whl size=183600 sha256=365eae6cb74d4a8e9a86308cb9a4a7201249e83f6c21c99ce14f89b2ed1c699b Stored in directory: /tmp/pip-ephem-wheel-cache-h1ntsu84/wheels/d5/91/a0/163d61a044dc7863f96ded66a0454324a4f8a774f6b3f9914a 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-4.0.10 gitpython-3.1.32 hpvsim-0.4.16 jellyfish-1.0.0 jsonpickle-3.0.1 line-profiler-4.0.3 memory-profiler-0.61.0 multiprocess-0.70.15 openpyxl-3.1.2 scipy-1.11.1 sciris-3.0.0 smmap-5.0.0 xlsxwriter-3.1.2 zstandard-0.21.0 [rtd-command-info] start-time: 2023-08-10T17:57:18.252583Z, end-time: 2023-08-10T17:57:18.336679Z, 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 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 = 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. 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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': "v0.4.16", 'version_slug': "v0.4.16", '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/"), ("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': 'v0.4.16', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'v0.4.16', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'v0.4.16', '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': '2605feb8', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'tag' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-hpvsim/builds/1654088/' 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: 2023-08-10T17:57:18.602637Z, end-time: 2023-08-10T17:57:59.594754Z, duration: 40, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 Matplotlib is building the font cache; this may take a moment. HPVsim 0.4.16 (2023-01-30) — © 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_v1.1.zip?raw=true... Saving to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.1.zip.zip... Time to download https://github.com/amath-idm/hpvsim_data/blob/main/hpvsim_data_v1.1.zip?raw=true: 3.39 s Time to download 1 URLs: 3.39 s Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.1.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 31 source files that are out of date updating environment: [new config] 31 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... [ 16%] hpvsim.data.get_data reading sources... [ 19%] hpvsim.data.loaders reading sources... [ 22%] hpvsim.defaults reading sources... [ 25%] hpvsim.immunity reading sources... [ 29%] hpvsim.interventions reading sources... [ 32%] hpvsim.misc reading sources... [ 35%] hpvsim.parameters reading sources... [ 38%] hpvsim.people reading sources... [ 41%] hpvsim.plotting reading sources... [ 45%] hpvsim.population reading sources... [ 48%] hpvsim.run reading sources... [ 51%] hpvsim.settings reading sources... [ 54%] 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... [ 74%] tutorials reading sources... [ 77%] tutorials/README reading sources... [ 80%] tutorials/tut_analyzers /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:54: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/jupyter_client/localinterfaces.py:54: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbsphinx/__init__.py", line 618, in parse rststring, resources = exporter.from_notebook_node(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbsphinx/__init__.py", line 397, in from_notebook_node nb, resources = pp.preprocess(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 100, in preprocess self.preprocess_cell(cell, resources, index) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 121, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped return loop.run_until_complete(inner) File "/home/docs/.asdf/installs/python/3.9.17/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete return future.result() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import numpy as np import sciris as sc import hpvsim as hpv # Create some parameters, setting beta (per-contact transmission probability) higher # to create more cancers for illutration pars = dict(beta=0.5, n_agents=50e3, start=1970, n_years=50, dt=1., location='tanzania') # Also set initial HPV prevalence to be high, again to generate more cancers pars['init_hpv_prev'] = { 'age_brackets' : np.array([ 12, 17, 24, 34, 44, 64, 80, 150]), 'm' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), 'f' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), } # Create the age analyzers. az1 = hpv.age_results( result_keys=sc.objdict( hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results timepoints=['2019'], # List the years that you want to generate results for edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), hpv_incidence=sc.objdict( timepoints=['2019'], edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), cancer_incidence=sc.objdict( timepoints=['2019'], edges=np.array([0.,20.,25.,30.,40.,45.,50.,55.,65.,100.]), ), cancer_mortality=sc.objdict( timepoints=['2019'], edges=np.array([0., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ) ) ) sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1]) sim.run() a = sim.get_analyzer() a.plot(); ------------------ ----- stdout ----- HPVsim 0.4.16 (2023-01-30) — © 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_v1.1.zip?raw=true... ----- stdout ----- Saving to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/tmp_hpvsim_data_v1.1.zip.zip... Time to download https://github.com/amath-idm/hpvsim_data/blob/main/hpvsim_data_v1.1.zip?raw=true: 0.895 s Time to download 1 URLs: 0.896 s ----- stdout ----- Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/tmp_hpvsim_data_v1.1.zip.zip" Data downloaded. Loading location-specific demographic data for "nigeria" ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:256, in get_death_rates(location, by_sex, overall)  255 try: --> 256 df = load_file(files.death)  257 except Exception as E: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:50, in load_file(path)  49 if strpath not in cache: ---> 50 obj = sc.load(path)  51 cache[strpath] = obj File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:167, in load(filename, folder, verbose, die, remapping, method, auto_remap, **kwargs)  166 # Load the file --> 167 filestr = _load_filestr(filename, folder)  169 # Unpickle it File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:103, in _load_filestr(filename, folder)  102 if exc == FileNotFoundError: # This is simple, just raise directly --> 103 raise E  104 elif exc == gz.BadGzipFile: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:98, in _load_filestr(filename, folder)  97 try: ---> 98 with gz.GzipFile(**fileargs) as fileobj:  99 filestr = fileobj.read() # Convert it to a string File ~/.asdf/installs/python/3.9.17/lib/python3.9/gzip.py:173, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  172 if fileobj is None: --> 173 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  174 if filename is None: FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/mx.obj' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/parameters.py:239, in get_births_deaths(location, verbose, by_sex, overall, die)  238 try: --> 239 death_rates = hpdata.get_death_rates(location=location, by_sex=by_sex, overall=overall)  240 birth_rates = hpdata.get_birth_rates(location=location) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:259, in get_death_rates(location, by_sex, overall)  258 errormsg = 'Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first.' --> 259 raise ValueError(errormsg) from E  261 raw_df = map_entries(df, location)[location] ValueError: Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first. During handling of the above exception, another exception occurred: RuntimeWarning Traceback (most recent call last) Cell In[1], line 38  16 # Create the age analyzers.  17 az1 = hpv.age_results(  18 result_keys=sc.objdict(  19 hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results  (...)  35 )  36 ) ---> 38 sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1])  39 sim.run()  40 a = sim.get_analyzer() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/sim.py:49, in Sim.__init__(self, pars, datafile, label, popfile, people, version, hiv_datafile, art_datafile, **kwargs)  47 # Make default parameters (using values from parameters.py)  48 default_pars = hppar.make_pars(version=version) # Start with default pars ---> 49 super().__init__(default_pars) # Initialize and set the parameters as attributes  51 # Load data, including datafile that are used to create additional optional parameters  52 location = pars.get('location') if pars else None File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:239, in BaseSim.__init__(self, *args, **kwargs)  238 def __init__(self, *args, **kwargs): --> 239 super().__init__(*args, **kwargs) # Initialize and set the parameters as attributes  240 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:72, in ParsObj.__init__(self, pars)  71 def __init__(self, pars): ---> 72 self.update_pars(pars, create=True)  73 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:299, in BaseSim.update_pars(self, pars, create, **kwargs)  297 if pars.get('location'):  298 location = pars['location'] --> 299 pars['birth_rates'], pars['death_rates'] = hppar.get_births_deaths(location=location) # Set birth and death rates  301 # Call update_pars() for ParsObj  302 super().update_pars(pars=pars, create=create) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/parameters.py:244, in get_births_deaths(location, verbose, by_sex, overall, die)  242 except ValueError as E:  243 warnmsg = f'Could not load demographic data for requested location "{location}" ({str(E)})' --> 244 hpm.warn(warnmsg, die=die) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/misc.py:726, in warn(msg, category, verbose, die)  724 # Handle the different options  725 if warnopt in ['error', 'errors']: # Include alias since hard to remember --> 726 raise category(msg)  727 elif warnopt == 'warn':  728 msg = '\n' + msg RuntimeWarning: Could not load demographic data for requested location "nigeria" (Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first.) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/cmd/build.py", line 285, in build_main app.build(args.force_all, args.filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/application.py", line 353, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 311, in build_update self.build(to_build, File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 328, in build updated_docnames = set(self.read()) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 435, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 456, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 512, in read_doc publisher.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/docutils/core.py", line 217, in publish self.document = self.reader.read(self.source, self.parser, File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sphinx/io.py", line 108, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/docutils/readers/__init__.py", line 78, in parse self.parser.parse(self.input, document) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/nbsphinx/__init__.py", line 625, in parse raise NotebookError('\n'.join(lines)) nbsphinx.NotebookError: CellExecutionError in tutorials/tut_analyzers.ipynb: ------------------ import numpy as np import sciris as sc import hpvsim as hpv # Create some parameters, setting beta (per-contact transmission probability) higher # to create more cancers for illutration pars = dict(beta=0.5, n_agents=50e3, start=1970, n_years=50, dt=1., location='tanzania') # Also set initial HPV prevalence to be high, again to generate more cancers pars['init_hpv_prev'] = { 'age_brackets' : np.array([ 12, 17, 24, 34, 44, 64, 80, 150]), 'm' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), 'f' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), } # Create the age analyzers. az1 = hpv.age_results( result_keys=sc.objdict( hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results timepoints=['2019'], # List the years that you want to generate results for edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), hpv_incidence=sc.objdict( timepoints=['2019'], edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), cancer_incidence=sc.objdict( timepoints=['2019'], edges=np.array([0.,20.,25.,30.,40.,45.,50.,55.,65.,100.]), ), cancer_mortality=sc.objdict( timepoints=['2019'], edges=np.array([0., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ) ) ) sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1]) sim.run() a = sim.get_analyzer() a.plot(); ------------------ ----- stdout ----- HPVsim 0.4.16 (2023-01-30) — © 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_v1.1.zip?raw=true... ----- stdout ----- Saving to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/tmp_hpvsim_data_v1.1.zip.zip... Time to download https://github.com/amath-idm/hpvsim_data/blob/main/hpvsim_data_v1.1.zip?raw=true: 0.895 s Time to download 1 URLs: 0.896 s ----- stdout ----- Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/tmp_hpvsim_data_v1.1.zip.zip" Data downloaded. Loading location-specific demographic data for "nigeria" ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:256, in get_death_rates(location, by_sex, overall)  255 try: --> 256 df = load_file(files.death)  257 except Exception as E: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:50, in load_file(path)  49 if strpath not in cache: ---> 50 obj = sc.load(path)  51 cache[strpath] = obj File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:167, in load(filename, folder, verbose, die, remapping, method, auto_remap, **kwargs)  166 # Load the file --> 167 filestr = _load_filestr(filename, folder)  169 # Unpickle it File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:103, in _load_filestr(filename, folder)  102 if exc == FileNotFoundError: # This is simple, just raise directly --> 103 raise E  104 elif exc == gz.BadGzipFile: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:98, in _load_filestr(filename, folder)  97 try: ---> 98 with gz.GzipFile(**fileargs) as fileobj:  99 filestr = fileobj.read() # Convert it to a string File ~/.asdf/installs/python/3.9.17/lib/python3.9/gzip.py:173, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  172 if fileobj is None: --> 173 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  174 if filename is None: FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/mx.obj' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/parameters.py:239, in get_births_deaths(location, verbose, by_sex, overall, die)  238 try: --> 239 death_rates = hpdata.get_death_rates(location=location, by_sex=by_sex, overall=overall)  240 birth_rates = hpdata.get_birth_rates(location=location) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:259, in get_death_rates(location, by_sex, overall)  258 errormsg = 'Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first.' --> 259 raise ValueError(errormsg) from E  261 raw_df = map_entries(df, location)[location] ValueError: Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first. During handling of the above exception, another exception occurred: RuntimeWarning Traceback (most recent call last) Cell In[1], line 38  16 # Create the age analyzers.  17 az1 = hpv.age_results(  18 result_keys=sc.objdict(  19 hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results  (...)  35 )  36 ) ---> 38 sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1])  39 sim.run()  40 a = sim.get_analyzer() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/sim.py:49, in Sim.__init__(self, pars, datafile, label, popfile, people, version, hiv_datafile, art_datafile, **kwargs)  47 # Make default parameters (using values from parameters.py)  48 default_pars = hppar.make_pars(version=version) # Start with default pars ---> 49 super().__init__(default_pars) # Initialize and set the parameters as attributes  51 # Load data, including datafile that are used to create additional optional parameters  52 location = pars.get('location') if pars else None File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:239, in BaseSim.__init__(self, *args, **kwargs)  238 def __init__(self, *args, **kwargs): --> 239 super().__init__(*args, **kwargs) # Initialize and set the parameters as attributes  240 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:72, in ParsObj.__init__(self, pars)  71 def __init__(self, pars): ---> 72 self.update_pars(pars, create=True)  73 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:299, in BaseSim.update_pars(self, pars, create, **kwargs)  297 if pars.get('location'):  298 location = pars['location'] --> 299 pars['birth_rates'], pars['death_rates'] = hppar.get_births_deaths(location=location) # Set birth and death rates  301 # Call update_pars() for ParsObj  302 super().update_pars(pars=pars, create=create) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/parameters.py:244, in get_births_deaths(location, verbose, by_sex, overall, die)  242 except ValueError as E:  243 warnmsg = f'Could not load demographic data for requested location "{location}" ({str(E)})' --> 244 hpm.warn(warnmsg, die=die) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/misc.py:726, in warn(msg, category, verbose, die)  724 # Handle the different options  725 if warnopt in ['error', 'errors']: # Include alias since hard to remember --> 726 raise category(msg)  727 elif warnopt == 'warn':  728 msg = '\n' + msg RuntimeWarning: Could not load demographic data for requested location "nigeria" (Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first.) You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True Notebook error: CellExecutionError in tutorials/tut_analyzers.ipynb: ------------------ import numpy as np import sciris as sc import hpvsim as hpv # Create some parameters, setting beta (per-contact transmission probability) higher # to create more cancers for illutration pars = dict(beta=0.5, n_agents=50e3, start=1970, n_years=50, dt=1., location='tanzania') # Also set initial HPV prevalence to be high, again to generate more cancers pars['init_hpv_prev'] = { 'age_brackets' : np.array([ 12, 17, 24, 34, 44, 64, 80, 150]), 'm' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), 'f' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), } # Create the age analyzers. az1 = hpv.age_results( result_keys=sc.objdict( hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results timepoints=['2019'], # List the years that you want to generate results for edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), hpv_incidence=sc.objdict( timepoints=['2019'], edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), cancer_incidence=sc.objdict( timepoints=['2019'], edges=np.array([0.,20.,25.,30.,40.,45.,50.,55.,65.,100.]), ), cancer_mortality=sc.objdict( timepoints=['2019'], edges=np.array([0., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ) ) ) sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1]) sim.run() a = sim.get_analyzer() a.plot(); ------------------ ----- stdout ----- HPVsim 0.4.16 (2023-01-30) — © 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_v1.1.zip?raw=true... ----- stdout ----- Saving to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/tmp_hpvsim_data_v1.1.zip.zip... Time to download https://github.com/amath-idm/hpvsim_data/blob/main/hpvsim_data_v1.1.zip?raw=true: 0.895 s Time to download 1 URLs: 0.896 s ----- stdout ----- Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/tmp_hpvsim_data_v1.1.zip.zip" Data downloaded. Loading location-specific demographic data for "nigeria" ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:256, in get_death_rates(location, by_sex, overall)  255 try: --> 256 df = load_file(files.death)  257 except Exception as E: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:50, in load_file(path)  49 if strpath not in cache: ---> 50 obj = sc.load(path)  51 cache[strpath] = obj File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:167, in load(filename, folder, verbose, die, remapping, method, auto_remap, **kwargs)  166 # Load the file --> 167 filestr = _load_filestr(filename, folder)  169 # Unpickle it File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:103, in _load_filestr(filename, folder)  102 if exc == FileNotFoundError: # This is simple, just raise directly --> 103 raise E  104 elif exc == gz.BadGzipFile: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/sciris/sc_fileio.py:98, in _load_filestr(filename, folder)  97 try: ---> 98 with gz.GzipFile(**fileargs) as fileobj:  99 filestr = fileobj.read() # Convert it to a string File ~/.asdf/installs/python/3.9.17/lib/python3.9/gzip.py:173, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  172 if fileobj is None: --> 173 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  174 if filename is None: FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/v0.4.16/docs/tutorials/files/mx.obj' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/parameters.py:239, in get_births_deaths(location, verbose, by_sex, overall, die)  238 try: --> 239 death_rates = hpdata.get_death_rates(location=location, by_sex=by_sex, overall=overall)  240 birth_rates = hpdata.get_birth_rates(location=location) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/data/loaders.py:259, in get_death_rates(location, by_sex, overall)  258 errormsg = 'Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first.' --> 259 raise ValueError(errormsg) from E  261 raw_df = map_entries(df, location)[location] ValueError: Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first. During handling of the above exception, another exception occurred: RuntimeWarning Traceback (most recent call last) Cell In[1], line 38  16 # Create the age analyzers.  17 az1 = hpv.age_results(  18 result_keys=sc.objdict(  19 hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results  (...)  35 )  36 ) ---> 38 sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1])  39 sim.run()  40 a = sim.get_analyzer() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/sim.py:49, in Sim.__init__(self, pars, datafile, label, popfile, people, version, hiv_datafile, art_datafile, **kwargs)  47 # Make default parameters (using values from parameters.py)  48 default_pars = hppar.make_pars(version=version) # Start with default pars ---> 49 super().__init__(default_pars) # Initialize and set the parameters as attributes  51 # Load data, including datafile that are used to create additional optional parameters  52 location = pars.get('location') if pars else None File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:239, in BaseSim.__init__(self, *args, **kwargs)  238 def __init__(self, *args, **kwargs): --> 239 super().__init__(*args, **kwargs) # Initialize and set the parameters as attributes  240 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:72, in ParsObj.__init__(self, pars)  71 def __init__(self, pars): ---> 72 self.update_pars(pars, create=True)  73 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/base.py:299, in BaseSim.update_pars(self, pars, create, **kwargs)  297 if pars.get('location'):  298 location = pars['location'] --> 299 pars['birth_rates'], pars['death_rates'] = hppar.get_births_deaths(location=location) # Set birth and death rates  301 # Call update_pars() for ParsObj  302 super().update_pars(pars=pars, create=create) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/parameters.py:244, in get_births_deaths(location, verbose, by_sex, overall, die)  242 except ValueError as E:  243 warnmsg = f'Could not load demographic data for requested location "{location}" ({str(E)})' --> 244 hpm.warn(warnmsg, die=die) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/v0.4.16/lib/python3.9/site-packages/hpvsim/misc.py:726, in warn(msg, category, verbose, die)  724 # Handle the different options  725 if warnopt in ['error', 'errors']: # Include alias since hard to remember --> 726 raise category(msg)  727 elif warnopt == 'warn':  728 msg = '\n' + msg RuntimeWarning: Could not load demographic data for requested location "nigeria" (Could not locate datafile with age-specific death rates by country. Please run data/get_data.py first.) You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True