Read the Docs build information Build id: 1780750 Project: institute-for-disease-modeling-vis-tools Version: latest Commit: c37bca3b96077496600dd50d7765cc05a6fe77bd Date: 2023-10-13T16:43:24.661937Z State: finished Success: True [rtd-command-info] start-time: 2023-10-13T16:43:33.482715Z, end-time: 2023-10-13T16:43:42.982472Z, duration: 9, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/vis-tools.git . Cloning into '.'... [rtd-command-info] start-time: 2023-10-13T16:43:43.484302Z, end-time: 2023-10-13T16:43:48.999719Z, duration: 5, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main [rtd-command-info] start-time: 2023-10-13T16:43:49.692540Z, end-time: 2023-10-13T16:43:52.420863Z, duration: 2, 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 c37bca3 Merge pull request #22 from InstituteforDiseaseModeling/buildfix [rtd-command-info] start-time: 2023-10-13T16:43:52.922042Z, end-time: 2023-10-13T16:43:52.980165Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-10-13T16:43:53.789731Z, end-time: 2023-10-13T16:43:53.847517Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip - pdf # Optionally set the version of Python and requirements required to build your docs python: version: 3.8 install: - requirements: docs/requirements.txt - method: setuptools path: . # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank search: ranking: intro.html: 3 install.html: 3 vis_tools.*: 2 [rtd-command-info] start-time: 2023-10-13T16:43:57.691412Z, end-time: 2023-10-13T16:44:03.790297Z, duration: 6, exit-code: 0 python3.8 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 3)) (2023.7.22) Installing collected packages: six, readthedocs-sphinx-search, pyyaml, mdurl, jinja2, docutils, sphinx, pockets, plantweb, markdown-it-py, sphinxcontrib-napoleon, sphinxcontrib-jquery, numpydoc, mdit-py-plugins, sphinx-rtd-theme, myst-parser Attempting uninstall: jinja2 Found existing installation: Jinja2 3.1.2 Uninstalling Jinja2-3.1.2: Successfully uninstalled Jinja2-3.1.2 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 docutils-0.18.1 jinja2-3.0.3 markdown-it-py-3.0.0 mdit-py-plugins-0.4.0 mdurl-0.1.2 myst-parser-2.0.0 numpydoc-1.5.0 plantweb-1.2.1 pockets-0.9.1 pyyaml-6.0.1 readthedocs-sphinx-search-0.3.1 six-1.16.0 sphinx-6.2.1 sphinx-rtd-theme-1.2.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 [rtd-command-info] start-time: 2023-10-13T16:44:25.448964Z, end-time: 2023-10-13T16:44:26.889979Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating vis_tools.egg-info writing vis_tools.egg-info/PKG-INFO writing dependency_links to vis_tools.egg-info/dependency_links.txt writing entry points to vis_tools.egg-info/entry_points.txt writing requirements to vis_tools.egg-info/requires.txt writing top-level names to vis_tools.egg-info/top_level.txt writing manifest file 'vis_tools.egg-info/SOURCES.txt' reading manifest file 'vis_tools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'vis_tools.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/vis_tools copying vis_tools/Survey.py -> build/lib/vis_tools copying vis_tools/CZMLWriter.py -> build/lib/vis_tools copying vis_tools/MigrationHelpers.py -> build/lib/vis_tools copying vis_tools/Demographics.py -> build/lib/vis_tools copying vis_tools/Config.py -> build/lib/vis_tools copying vis_tools/Color.py -> build/lib/vis_tools copying vis_tools/SpatialReports.py -> build/lib/vis_tools copying vis_tools/__init__.py -> build/lib/vis_tools copying vis_tools/NamedColors.py -> build/lib/vis_tools copying vis_tools/VisSet.py -> build/lib/vis_tools copying vis_tools/CSVReport.py -> build/lib/vis_tools copying vis_tools/SpatialBinaryHeader.py -> build/lib/vis_tools copying vis_tools/Gradient.py -> build/lib/vis_tools copying vis_tools/SpatialBinary.py -> build/lib/vis_tools copying vis_tools/defaultvisset.json -> build/lib/vis_tools creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/Survey.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/CZMLWriter.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/MigrationHelpers.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/Demographics.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/Config.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/Color.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/SpatialReports.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/__init__.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/NamedColors.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/VisSet.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/CSVReport.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/SpatialBinaryHeader.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/Gradient.py -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/defaultvisset.json -> build/bdist.linux-x86_64/egg/vis_tools copying build/lib/vis_tools/SpatialBinary.py -> build/bdist.linux-x86_64/egg/vis_tools byte-compiling build/bdist.linux-x86_64/egg/vis_tools/Survey.py to Survey.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/CZMLWriter.py to CZMLWriter.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/MigrationHelpers.py to MigrationHelpers.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/Demographics.py to Demographics.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/Config.py to Config.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/Color.py to Color.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/SpatialReports.py to SpatialReports.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/NamedColors.py to NamedColors.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/VisSet.py to VisSet.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/CSVReport.py to CSVReport.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/SpatialBinaryHeader.py to SpatialBinaryHeader.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/Gradient.py to Gradient.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/vis_tools/SpatialBinary.py to SpatialBinary.cpython-38.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vis_tools.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating dist creating 'dist/vis_tools-1.4-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing vis_tools-1.4-py3.8.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg Extracting vis_tools-1.4-py3.8.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages Adding vis-tools 1.4 to easy-install.pth file Installing survey script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg Processing dependencies for vis-tools==1.4 Searching for czml==0.3.3 Reading https://pypi.org/simple/czml/ Downloading https://files.pythonhosted.org/packages/d9/86/910f69a4b9dd4421c4ce0b9ee1f95380b88517202b63ba201af74f227515/czml-0.3.3.tar.gz#sha256=ed14e24852082c71a19ec8e8ebe35cf838ab54df4886d4f68294f609b126347a Best match: czml 0.3.3 Processing czml-0.3.3.tar.gz Writing /tmp/easy_install-3zoqg22b/czml-0.3.3/setup.cfg Running czml-0.3.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-3zoqg22b/czml-0.3.3/egg-dist-tmp-qvlowt0v /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() build/bdist.linux-x86_64/egg/vis_tools/Survey.py:364: SyntaxWarning: "is not" with a literal. Did you mean "!="? if key not in known_fields and type(node_attrs[key]) is not "dict": build/bdist.linux-x86_64/egg/vis_tools/CZMLWriter.py:711: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Top": return "BOTTOM" build/bdist.linux-x86_64/egg/vis_tools/CZMLWriter.py:712: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Bottom": return "TOP" build/bdist.linux-x86_64/egg/vis_tools/CZMLWriter.py:718: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Left": return "RIGHT" build/bdist.linux-x86_64/egg/vis_tools/CZMLWriter.py:719: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Right": return "LEFT" build/bdist.linux-x86_64/egg/vis_tools/VisSet.py:774: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: build/bdist.linux-x86_64/egg/vis_tools/VisSet.py:861: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: build/bdist.linux-x86_64/egg/vis_tools/VisSet.py:965: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: build/bdist.linux-x86_64/egg/vis_tools/VisSet.py:1048: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/CZMLWriter.py:711: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Top": return "BOTTOM" /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/CZMLWriter.py:712: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Bottom": return "TOP" /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/CZMLWriter.py:718: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Left": return "RIGHT" /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/CZMLWriter.py:719: SyntaxWarning: "is" with a literal. Did you mean "=="? if placement is "Right": return "LEFT" /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/Survey.py:364: SyntaxWarning: "is not" with a literal. Did you mean "!="? if key not in known_fields and type(node_attrs[key]) is not "dict": /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/VisSet.py:774: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/VisSet.py:861: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/VisSet.py:965: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/vis_tools-1.4-py3.8.egg/vis_tools/VisSet.py:1048: SyntaxWarning: "is" with a literal. Did you mean "=="? if self.timestepCount is 0: warning: no previously-included files matching '*.pyo' found under directory '*.pyc' warning: no previously-included files found matching 'czml/.*' Adding czml 0.3.3 to easy-install.pth file detected new path './vis_tools-1.4-py3.8.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/czml-0.3.3-py3.8.egg Searching for python-dateutil Reading https://pypi.org/simple/python-dateutil/ Downloading https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl#sha256=961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9 Best match: python-dateutil 2.8.2 Processing python_dateutil-2.8.2-py2.py3-none-any.whl Installing python_dateutil-2.8.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages Adding python-dateutil 2.8.2 to easy-install.pth file detected new path './czml-0.3.3-py3.8.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/python_dateutil-2.8.2-py3.8.egg Searching for pygeoif Reading https://pypi.org/simple/pygeoif/ Downloading https://files.pythonhosted.org/packages/ff/7c/751cd7c9eb7e4b5aca8539ed91b0630ce0a83b382180a03d91735e391fa3/pygeoif-1.1.0-py3-none-any.whl#sha256=15defccd79e9179a655e8f7c4639563fd848306c6ce9df9bb362c5e76c1e7d7b Best match: pygeoif 1.1.0 Processing pygeoif-1.1.0-py3-none-any.whl Installing pygeoif-1.1.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages Adding pygeoif 1.1.0 to easy-install.pth file detected new path './python_dateutil-2.8.2-py3.8.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/pygeoif-1.1.0-py3.8.egg Searching for typing-extensions Reading https://pypi.org/simple/typing-extensions/ Downloading https://files.pythonhosted.org/packages/24/21/7d397a4b7934ff4028987914ac1044d3b7d52712f30e2ac7a2ae5bc86dd0/typing_extensions-4.8.0-py3-none-any.whl#sha256=8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0 Best match: typing-extensions 4.8.0 Processing typing_extensions-4.8.0-py3-none-any.whl Installing typing_extensions-4.8.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages Adding typing-extensions 4.8.0 to easy-install.pth file detected new path './pygeoif-1.1.0-py3.8.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/typing_extensions-4.8.0-py3.8.egg Searching for pytz==2023.3.post1 Best match: pytz 2023.3.post1 Adding pytz 2023.3.post1 to easy-install.pth file detected new path './typing_extensions-4.8.0-py3.8.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages Finished processing dependencies for vis-tools==1.4 /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-vis-tools/envs/latest/lib/python3.8/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() [rtd-command-info] start-time: 2023-10-13T16:44:33.585674Z, end-time: 2023-10-13T16:44:33.635995Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo documentation build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # 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 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__))) # -- 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', 'plantweb.directive', 'myst_parser', # source files can be written in Markdown or RST 'sphinx_search.extension' # search across all IDM docs ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None } autodoc_mock_imports = ['pygeoif.geometry'] napoleon_google_docstring = True # 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', '.md'] # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'Vis-Tools' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'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 short X.Y version. version = u'1.4' # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = 'en' # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # 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'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # 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' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v documentation" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # 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 = { 'css_files': [ '_static/theme_overrides.css' ] } # 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. # # html_extra_path = [] # 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 = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # 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. # -- RTD Sphinx search for searching across the entire domain ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project_parent}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } #html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'Vis-Tools' # -- 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': '', # 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, 'vis-tools-docs.tex', u'Vis-Tools', u'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 # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- 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, 'vis-tools-docs', u'Vis-Tools', [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, 'vis-tools-docs', u'Vis-Tools', author, 'Institute for Disease Modeling', 'How to use the IDM Vis-Tools toolkit.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/vis-tools/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/vis-tools/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-vis-tools', 'name': u'vis-tools', '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': 'vis-tools', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': 'c37bca3b', } # 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-vis-tools/builds/1780750/' 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: 2023-10-13T16:44:34.085612Z, end-time: 2023-10-13T16:44:40.978504Z, duration: 6, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 rm: cannot remove 'modules.rst': No such file or directory rm: cannot remove 'vis_tools_index.rst': No such file or directory make: [generate-api] Error 1 (ignored) making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 32 source files that are out of date updating environment: [new config] 32 added, 0 changed, 0 removed reading sources... [ 3%] example reading sources... [ 6%] geospat reading sources... [ 9%] geospat-controls reading sources... [ 12%] geospat-functions reading sources... [ 15%] geospat-overview reading sources... [ 18%] glossary reading sources... [ 21%] index reading sources... [ 25%] install reading sources... [ 28%] intro reading sources... [ 31%] overview reading sources... [ 34%] preproc reading sources... [ 37%] preproc-classes reading sources... [ 40%] preproc-components reading sources... [ 43%] preproc-cycle reading sources... [ 46%] prereqs reading sources... [ 50%] quickstartcomps reading sources... [ 53%] troubleshoot reading sources... [ 56%] vis_tools reading sources... [ 59%] vis_tools.CSVReport reading sources... [ 62%] vis_tools.CZMLWriter reading sources... [ 65%] vis_tools.Color reading sources... [ 68%] vis_tools.Config reading sources... [ 71%] vis_tools.Demographics reading sources... [ 75%] vis_tools.Gradient reading sources... [ 78%] vis_tools.MigrationHelpers reading sources... 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[rtd-command-info] start-time: 2023-10-13T16:44:41.810706Z, end-time: 2023-10-13T16:44:47.896484Z, duration: 6, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v6.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 32 added, 0 changed, 0 removed reading sources... [ 3%] example reading sources... [ 6%] geospat reading sources... [ 9%] geospat-controls reading sources... [ 12%] geospat-functions reading sources... [ 15%] geospat-overview reading sources... [ 18%] glossary reading sources... [ 21%] index reading sources... [ 25%] install reading sources... [ 28%] intro reading sources... [ 31%] overview reading sources... [ 34%] preproc reading sources... [ 37%] preproc-classes reading sources... [ 40%] preproc-components reading sources... [ 43%] preproc-cycle reading sources... [ 46%] prereqs reading sources... [ 50%] quickstartcomps reading sources... [ 53%] troubleshoot reading sources... [ 56%] vis_tools reading sources... [ 59%] vis_tools.CSVReport reading sources... [ 62%] vis_tools.CZMLWriter reading sources... [ 65%] vis_tools.Color reading sources... [ 68%] vis_tools.Config reading sources... [ 71%] vis_tools.Demographics reading sources... [ 75%] vis_tools.Gradient reading sources... [ 78%] vis_tools.MigrationHelpers reading sources... 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[100%] vis_tools_index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... overview prereqs intro quickstartcomps install example troubleshoot preproc preproc-cycle preproc-components preproc-classes vis_tools_index vis_tools vis_tools.CSVReport vis_tools.CZMLWriter vis_tools.Color vis_tools.Config vis_tools.Demographics vis_tools.Gradient vis_tools.MigrationHelpers vis_tools.NamedColors vis_tools.SpatialBinary vis_tools.SpatialBinaryHeader vis_tools.SpatialReports vis_tools.Survey vis_tools.VisSet geospat geospat-overview geospat-controls geospat-functions glossary done writing... done writing additional files... done copying images... [ 1%] images/vt-structure.png copying images... [ 3%] images/vt-comps.png copying images... [ 4%] images/vt-chrome-gpu.png copying images... [ 6%] images/vt-comps-navigate-explore.png copying images... 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[rtd-command-info] start-time: 2023-10-13T16:44:49.455492Z, end-time: 2023-10-13T16:44:55.226347Z, duration: 5, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v6.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: [new config] 32 added, 0 changed, 0 removed reading sources... 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[100%] vis_tools_index looking for now-outdated files... none found pickling environment... done checking consistency... done processing vis-tools-docs.tex... index overview prereqs intro quickstartcomps install example troubleshoot preproc preproc-cycle preproc-components preproc-classes vis_tools_index vis_tools vis_tools.CSVReport vis_tools.CZMLWriter vis_tools.Color vis_tools.Config vis_tools.Demographics vis_tools.Gradient vis_tools.MigrationHelpers vis_tools.NamedColors vis_tools.SpatialBinary vis_tools.SpatialBinaryHeader vis_tools.SpatialReports vis_tools.Survey vis_tools.VisSet geospat geospat-overview geospat-controls geospat-functions glossary resolving references... done writing... done copying images... [ 1%] images/vt-structure.png copying images... [ 3%] images/vt-comps.png copying images... [ 4%] images/vt-chrome-gpu.png copying images... [ 6%] images/vt-comps-navigate-explore.png copying images... [ 7%] images/vt-spatial-tab-needs-preprocessing.png copying images... 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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-vis-tools.pdf (121 pages, 1233 4087 bytes). Transcript written on institute-for-disease-modeling-vis-tools.log. Latexmk: Index file 'institute-for-disease-modeling-vis-tools.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-vis-tools.ind' from line 'No file institute-for-disease-modeling-vis-tools.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-vis-tools.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-vis-tools.pdf' Latexmk: List of undefined refs and citations: Reference `vis_tools.CSVReport:module-vis_tools.CSVReport' on page 117 undefined on input line 10824 Reference `vis_tools.CZMLWriter:module-vis_tools.CZMLWriter' on page 117 undefined on input line 10825 Reference `vis_tools.Color:module-vis_tools.Color' on page 117 undefined on input line 10822 Reference `vis_tools.Config:module-vis_tools.Config' on page 117 undefined on input line 10823 Reference `vis_tools.Demographics:module-vis_tools.Demographics' on page 117 undefined on input line 10826 Reference `vis_tools.Gradient:module-vis_tools.Gradient' on page 117 undefined on input line 10827 Reference `vis_tools.MigrationHelpers:module-vis_tools.MigrationHelpers' on page 117 undefined on input line 10828 Reference `vis_tools.NamedColors:module-vis_tools.NamedColors' on page 117 undefined on input line 10829 Reference `vis_tools.SpatialBinary:module-vis_tools.SpatialBinary' on page 117 undefined on input line 10830 Reference `vis_tools.SpatialBinaryHeader:module-vis_tools.SpatialBinaryHeader' on page 117 undefined on input line 10831 Reference `vis_tools.SpatialReports:module-vis_tools.SpatialReports' on page 117 undefined on input line 10832 Reference `vis_tools.Survey:module-vis_tools.Survey' on page 117 undefined on input line 10833 Reference `vis_tools.VisSet:module-vis_tools.VisSet' on page 117 undefined on input line 10834 Reference `vis_tools:module-vis_tools' on page 117 undefined on input line 10821 Latexmk: Summary of warnings: Latex failed to resolve 14 reference(s) Rule 'makeindex institute-for-disease-modeling-vis-tools.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-vis-tools.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-vis-tools.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-vis-tools.ind" "institute-for-disease-modeling-vis-tools.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-vis-tools.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-vis-tools.idx....done (317 entries accepted, 0 rejected). Sorting entries.....done (2719 comparisons). Generating output file institute-for-disease-modeling-vis-tools.ind....done (535 lines written, 0 warnings). Output written in institute-for-disease-modeling-vis-tools.ind. Transcript written in institute-for-disease-modeling-vis-tools.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-vis-tools.aux' 'institute-for-disease-modeling-vis-tools.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-vis-tools" "vis-tools-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[115] [116] [117] (./institute-for-disease-modeling-vis-tools.ind [118] Overfull \hbox (0.55228pt too wide) in paragraph at lines 10--12 []\T1/txtt/m/n/10 add_combiner() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 vis_tools.Spat ialBinary.SpatialBinary Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/txtt/m/n/10 add_event_markers() Underfull \hbox (badness 10000) in paragraph at lines 12--14 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 vis_tools.CZMLWriter.CZMLWriter method\T1/qtm/m /n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/txtt/m/n/10 add_infected_human_migrations() Overfull \hbox (1.24223pt too wide) in paragraph at lines 17--19 []\T1/txtt/m/n/10 add_migrations() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 vis_tools.CZ MLWriter.CZMLWriter Underfull \hbox (badness 10000) in paragraph at lines 20--21 []\T1/txtt/m/n/10 add_nodes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 vis_tools.CZMLWri ter.CZMLWriter Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/txtt/m/n/10 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Transcript written on institute-for-disease-modeling-vis-tools.log. Latexmk: Index file 'institute-for-disease-modeling-vis-tools.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-vis-tools.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-vis-tools.pdf' Latexmk: All targets (institute-for-disease-modeling-vis-tools.pdf) are up-to-date