Read the Docs build information Build id: 1651898 Project: institute-for-disease-modeling-hpvsim Version: latest Commit: 87c7d033e9b027bcee42f41b822c6a5912d2175f Date: 2023-08-09T22:04:16.375982Z State: finished Success: True [rtd-command-info] start-time: 2023-08-09T22:04:20.775840Z, end-time: 2023-08-09T22:04:22.046267Z, 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: 2023-08-09T22:04:22.321481Z, end-time: 2023-08-09T22:04:22.416667Z, duration: 0, exit-code: 0 git checkout --force origin/develop Note: switching to 'origin/develop'. 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. 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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 87c7d03 Merge pull request #576 from amath-idm/precin [rtd-command-info] start-time: 2023-08-09T22:04:22.782088Z, end-time: 2023-08-09T22:04:22.859675Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-09T22:04:23.135034Z, end-time: 2023-08-09T22:04:23.199988Z, 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: 2023-08-09T22:04:28.776524Z, end-time: 2023-08-09T22:04:28.870177Z, duration: 0, exit-code: 0 asdf global python 3.9.17 [rtd-command-info] start-time: 2023-08-09T22:04:29.393902Z, end-time: 2023-08-09T22:04:30.319762Z, duration: 0, exit-code: 0 python -mvirtualenv --system-site-packages $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.17.final.0-64 in 618ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/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 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size=33260 sha256=f3b22906ef94f75ecb05e4e65aef1e63e6f30b3fa6275b2a266e0e3155895ec8 Stored in directory: /tmp/pip-ephem-wheel-cache-lwgc8qfc/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/latest/lib/python3.9/site-packages (from Mako->alembic>=1.5.0->optuna->hpvsim==1.2.0) (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-1.2.0-py3-none-any.whl size=193257 sha256=bad21d5e6d2b40fdc441a429b8c8b5bca3a3daf4542afe22d8183502cbc8f040 Stored in directory: /tmp/pip-ephem-wheel-cache-7_um6ctv/wheels/51/35/6f/df976332f8d726e8d5b6219b83a0569f551e10d63ed39a50fb Successfully built hpvsim Installing collected packages: zstandard, xlsxwriter, smmap, scipy, memory-profiler, line-profiler, jsonpickle, jellyfish, et-xmlfile, dill, openpyxl, multiprocess, gitdb, gitpython, sciris, hpvsim Successfully installed dill-0.3.7 et-xmlfile-1.1.0 gitdb-4.0.10 gitpython-3.1.32 hpvsim-1.2.0 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: 2023-08-09T22:06:06.077084Z, end-time: 2023-08-09T22:06:06.166186Z, 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. 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': [ ], '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': 'develop', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'develop', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'develop', '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': '87c7d033', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-hpvsim/builds/1651898/' 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: 2023-08-09T22:06:06.441666Z, end-time: 2023-08-09T22:14:50.846979Z, duration: 524, exit-code: 0 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 1.2.0 (2023-05-31) — © 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/latest/lib/python3.9/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.1.zip.zip... 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[rtd-command-info] start-time: 2023-08-09T22:14:51.599517Z, end-time: 2023-08-09T22:22:29.064704Z, duration: 457, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v6.2.1 HPVsim 1.2.0 (2023-05-31) — © 2023 by IDM 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] 33 added, 0 changed, 0 removed reading sources... [ 3%] hpvsim.analysis reading sources... [ 6%] hpvsim.base reading sources... [ 9%] hpvsim.calibration reading sources... [ 12%] hpvsim.data reading sources... [ 15%] hpvsim.data.get_data reading sources... [ 18%] hpvsim.data.loaders reading sources... [ 21%] hpvsim.defaults reading sources... [ 24%] hpvsim.hiv reading sources... [ 27%] hpvsim.immunity reading sources... [ 30%] hpvsim.interventions reading sources... 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' %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: 2023-08-09T22:22:29.955363Z, end-time: 2023-08-09T22:22:48.902776Z, duration: 18, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-hpvsim -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. 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[151] No file institute-for-disease-modeling-hpvsim.ind. (./institute-for-disease-modeling-hpvsim.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-hpvsim.out ' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-hpvsim.pdf (155 pages, 810098 bytes). Transcript written on institute-for-disease-modeling-hpvsim.log. Latexmk: Index file 'institute-for-disease-modeling-hpvsim.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-hpvsim.ind' from line 'No file institute-for-disease-modeling-hpvsim.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-hpvsim.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-hpvsim.pdf' Latexmk: List of undefined refs and citations: Reference `hpvsim.analysis:module-hpvsim.analysis' on page 151 undefined on input line 16240 Reference `hpvsim.base:module-hpvsim.base' on page 151 undefined on input line 16241 Reference `hpvsim.calibration:module-hpvsim.calibration' on page 151 undefined on input line 16242 Reference `hpvsim.data.get_data:module-hpvsim.data.get_data' on page 151 undefined on input line 16244 Reference `hpvsim.data.loaders:module-hpvsim.data.loaders' on page 151 undefined on input line 16245 Reference `hpvsim.data:module-hpvsim.data' on page 151 undefined on input line 16243 Reference `hpvsim.defaults:module-hpvsim.defaults' on page 151 undefined on input line 16246 Reference `hpvsim.hiv:module-hpvsim.hiv' on page 151 undefined on input line 16247 Reference `hpvsim.immunity:module-hpvsim.immunity' on page 151 undefined on input line 16248 Reference `hpvsim.interventions:module-hpvsim.interventions' on page 151 undefined on input line 16249 Reference `hpvsim.misc:module-hpvsim.misc' on page 151 undefined on input line 16250 Reference `hpvsim.parameters:module-hpvsim.parameters' on page 151 undefined on input line 16251 Reference `hpvsim.people:module-hpvsim.people' on page 151 undefined on input line 16252 Reference `hpvsim.plotting:module-hpvsim.plotting' on page 151 undefined on input line 16253 Reference `hpvsim.population:module-hpvsim.population' on page 151 undefined on input line 16254 Reference `hpvsim.run:module-hpvsim.run' on page 151 undefined on input line 16255 Reference `hpvsim.settings:module-hpvsim.settings' on page 151 undefined on input line 16256 Reference `hpvsim.sim:module-hpvsim.sim' on page 151 undefined on input line 16257 Reference `hpvsim.utils:module-hpvsim.utils' on page 151 undefined on input line 16258 Reference `hpvsim.version:module-hpvsim.version' on page 151 undefined on input line 16259 Reference `modules:module-hpvsim' on page 151 undefined on input line 16239 Rule 'makeindex institute-for-disease-modeling-hpvsim.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-hpvsim.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-hpvsim.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-hpvsim.ind" "institute-for-disease-modeling-hpvsim.idx"' ------------ === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-hpvsim.idx'... This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-hpvsim.idx....done (492 entries accepted, 0 rejected). Sorting entries.......done (4690 comparisons). Generating output file institute-for-disease-modeling-hpvsim.ind....done (585 lines written, 0 warnings). Output written in institute-for-disease-modeling-hpvsim.ind. Transcript written in institute-for-disease-modeling-hpvsim.ilg. 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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.15433 ...\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.15433 ...\PYGZsh{} returns Normal(μ=3, σ=0.5)} [143] [144] [145] [146] [147] [148] [149] [150] [151] (./institute-for-disease-modeling-hpvsim.ind [152] Underfull \hbox (badness 10000) in paragraph at lines 80--81 []\T1/txtt/m/n/10 check_downloaded() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [153] Underfull \hbox (badness 10000) in paragraph at lines 188--189 []\T1/txtt/m/n/10 get_age_distribution() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 189--191 []\T1/txtt/m/n/10 get_age_distribution_over_time() \T1/qtm/m/n/10 (\T1/qtm/m/it /10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 197--198 []\T1/txtt/m/n/10 get_country_aliases() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule [154] Underfull \hbox (badness 5475) in paragraph at lines 200--201 []\T1/txtt/m/n/10 get_default_plots() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e hpvsim.defaults\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 207--208 []\T1/txtt/m/n/10 get_life_expectancy() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule [155] [156] Underfull \hbox (badness 10000) in paragraph at lines 436--437 []\T1/txtt/m/n/10 plot_scen_age_results() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 497--499 []\T1/txtt/m/n/10 set_intervention_attributes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [157] Underfull \hbox (badness 10000) in paragraph at lines 546--547 []\T1/txtt/m/n/10 trial_pars_to_sim_pars() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 Cal- i-bra-tion method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 566--567 []\T1/txtt/m/n/10 update_peak_immunity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule [158]) (./institute-for-disease-modeling-hpvsim.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-hpvsim.pdf (164 pages, 868796 bytes). Transcript written on institute-for-disease-modeling-hpvsim.log. Latexmk: Index file 'institute-for-disease-modeling-hpvsim.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-hpvsim.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-hpvsim.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-hpvsim.log' for details === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets