Read the Docs build information Build id: 1669983 Project: institute-for-disease-modeling-pycomps Version: latest Commit: bceb8620fb33fc73d82dceffc142f51f2e1cf773 Date: 2023-08-18T20:59:57.785036Z State: finished Success: True [rtd-command-info] start-time: 2023-08-18T21:01:50.103155Z, end-time: 2023-08-18T21:01:51.760649Z, duration: 1, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/pyCOMPS.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2023-08-18T21:01:53.272817Z, end-time: 2023-08-18T21:02:00.129889Z, duration: 6, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/pyCOMPS * [new tag] v0.2 -> v0.2 * [new tag] v1.0 -> v1.0 * [new tag] v1.0.1 -> v1.0.1 * [new tag] v2.0 -> v2.0 * [new tag] v2.0.1 -> v2.0.1 * [new tag] v2.1 -> v2.1 * [new tag] v2.2 -> v2.2 * [new tag] v2.3 -> v2.3 * [new tag] v2.3.1 -> v2.3.1 * [new tag] v2.3.2 -> v2.3.2 * [new tag] v2.3.3 -> v2.3.3 * [new tag] v2.3.4 -> v2.3.4 * [new tag] v2.3.5 -> v2.3.5 * [new tag] v2.3.6 -> v2.3.6 * [new tag] v2.3.7 -> v2.3.7 * [new tag] v2.3.8 -> v2.3.8 * [new tag] v2.3.9 -> v2.3.9 * [new tag] v2.4.0 -> v2.4.0 * [new tag] v2.4.1 -> v2.4.1 * [new tag] v2.5.0 -> v2.5.0 * [new tag] v2.6.0 -> v2.6.0 * [new tag] v2.7.0 -> v2.7.0 * [new tag] v2.7.1 -> v2.7.1 * [new tag] v2.7.2 -> v2.7.2 * [new tag] v2.7.3 -> v2.7.3 * [new tag] v2.8.0 -> v2.8.0 * [new tag] v2.9.0 -> v2.9.0 * [new tag] v2.9.1 -> v2.9.1 [rtd-command-info] start-time: 2023-08-18T21:02:00.709304Z, end-time: 2023-08-18T21:02:00.789660Z, 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: 3.7 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: [rtd-command-info] start-time: 2023-08-18T21:02:04.503354Z, end-time: 2023-08-18T21:02:09.447880Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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(setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=14eea687f8f68ea2a2615e7ea648894e200626f6eda5ca6b15feef9c7d4fe6df Stored in directory: /tmp/pip-ephem-wheel-cache-34oqmp1w/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 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filename=docopt-0.6.2-py2.py3-none-any.whl size=13724 sha256=fe6e42d4d68012d195828f854c8831edfb1bc5ba665a75291625f9c072f20144 Stored in directory: /tmp/pip-ephem-wheel-cache-8ntyk9tf/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9 Successfully built docopt Installing collected packages: docopt, cached-property, wrapt, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pycparser, py-make, pockets, MarkupSafe, docutils, sphinxcontrib-napoleon, pyjwt, plantweb, Jinja2, deprecated, cffi, sphinxext.remoteliteralinclude, sphinx, pynacl, pygit2, cryptography, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, PyGithub Attempting uninstall: MarkupSafe Found existing installation: MarkupSafe 2.1.3 Uninstalling MarkupSafe-2.1.3: Successfully uninstalled MarkupSafe-2.1.3 Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed Jinja2-2.11.3 MarkupSafe-2.0.1 PyGithub-1.59.1 cached-property-1.5.2 cffi-1.15.1 cryptography-41.0.3 deprecated-1.2.14 docopt-0.6.2 docutils-0.16 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.21 pygit2-1.4.0 pyjwt-2.8.0 pynacl-1.5.0 sphinx-3.3.1 sphinx-copybutton-0.3.3 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxcontrib-qthelp-1.0.3 sphinxext.remoteliteralinclude-0.4.0 typing-extensions-4.7.1 wrapt-1.15.0 [rtd-command-info] start-time: 2023-08-18T21:02:28.643763Z, end-time: 2023-08-18T21:02:30.795670Z, duration: 2, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating pyCOMPS.egg-info writing pyCOMPS.egg-info/PKG-INFO writing dependency_links to pyCOMPS.egg-info/dependency_links.txt writing entry points to pyCOMPS.egg-info/entry_points.txt writing requirements to pyCOMPS.egg-info/requires.txt writing top-level names to pyCOMPS.egg-info/top_level.txt writing manifest file 'pyCOMPS.egg-info/SOURCES.txt' reading manifest file 'pyCOMPS.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'pyCOMPS.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/COMPS copying COMPS/Client.py -> build/lib/COMPS copying COMPS/__main__.py -> build/lib/COMPS copying COMPS/CredentialPrompt.py -> build/lib/COMPS copying COMPS/__init__.py -> build/lib/COMPS copying COMPS/AuthManager.py -> build/lib/COMPS creating build/lib/COMPS/utils copying COMPS/utils/main.py -> build/lib/COMPS/utils copying COMPS/utils/__example_utility_template__.py -> build/lib/COMPS/utils copying COMPS/utils/create_asset_collection.py -> build/lib/COMPS/utils copying COMPS/utils/get_output_files_for_experiment.py -> build/lib/COMPS/utils copying COMPS/utils/clone_simulation.py -> build/lib/COMPS/utils copying COMPS/utils/__init__.py -> build/lib/COMPS/utils copying COMPS/utils/get_status.py -> build/lib/COMPS/utils copying COMPS/utils/rerun_failed_simulations_for_experiment.py -> build/lib/COMPS/utils copying COMPS/utils/get_output_tail.py -> build/lib/COMPS/utils copying COMPS/utils/get_output_files_for_workitem.py -> build/lib/COMPS/utils creating build/lib/COMPS/Data copying COMPS/Data/TaggableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/SimulationFile.py -> build/lib/COMPS/Data copying COMPS/Data/Priority.py -> build/lib/COMPS/Data copying COMPS/Data/CommissionableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/Experiment.py -> build/lib/COMPS/Data copying COMPS/Data/AssetCollection.py -> build/lib/COMPS/Data copying COMPS/Data/SerializableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/WorkItem.py -> build/lib/COMPS/Data copying COMPS/Data/AssetFile.py -> build/lib/COMPS/Data copying COMPS/Data/WorkItemFile.py -> build/lib/COMPS/Data copying COMPS/Data/__init__.py -> build/lib/COMPS/Data copying COMPS/Data/Simulation.py -> build/lib/COMPS/Data copying COMPS/Data/QueryCriteria.py -> build/lib/COMPS/Data copying COMPS/Data/AssetType.py -> build/lib/COMPS/Data copying COMPS/Data/AssetManager.py -> build/lib/COMPS/Data copying COMPS/Data/Configuration.py -> build/lib/COMPS/Data copying COMPS/Data/BaseEntity.py -> build/lib/COMPS/Data copying COMPS/Data/HpcJob.py -> build/lib/COMPS/Data copying COMPS/Data/RelatableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/OutputFileMetadata.py -> build/lib/COMPS/Data copying COMPS/Data/AssetCollectionFile.py -> build/lib/COMPS/Data copying COMPS/Data/Suite.py -> build/lib/COMPS/Data creating build/lib/COMPS/Data/WorkItems copying COMPS/Data/WorkItems/BuilderWorkItem.py -> build/lib/COMPS/Data/WorkItems copying COMPS/Data/WorkItems/__init__.py -> build/lib/COMPS/Data/WorkItems copying COMPS/logging.ini -> build/lib/COMPS creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/Client.py -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/__main__.py -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/CredentialPrompt.py -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/__init__.py -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/AuthManager.py -> build/bdist.linux-x86_64/egg/COMPS creating build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/main.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/__example_utility_template__.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/create_asset_collection.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/get_output_files_for_experiment.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/clone_simulation.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/__init__.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/get_status.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/rerun_failed_simulations_for_experiment.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/get_output_tail.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/utils/get_output_files_for_workitem.py -> build/bdist.linux-x86_64/egg/COMPS/utils copying build/lib/COMPS/logging.ini -> build/bdist.linux-x86_64/egg/COMPS creating build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/TaggableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/SimulationFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/Priority.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/CommissionableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/Experiment.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/AssetCollection.py -> build/bdist.linux-x86_64/egg/COMPS/Data creating build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems copying build/lib/COMPS/Data/WorkItems/BuilderWorkItem.py -> build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems copying build/lib/COMPS/Data/WorkItems/__init__.py -> build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems copying build/lib/COMPS/Data/SerializableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/WorkItem.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/AssetFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/WorkItemFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/__init__.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/Simulation.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/QueryCriteria.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/AssetType.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/AssetManager.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/Configuration.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/BaseEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/HpcJob.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/RelatableEntity.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/OutputFileMetadata.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/AssetCollectionFile.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/Suite.py -> build/bdist.linux-x86_64/egg/COMPS/Data byte-compiling build/bdist.linux-x86_64/egg/COMPS/Client.py to Client.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/CredentialPrompt.py to CredentialPrompt.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/AuthManager.py to AuthManager.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/main.py to main.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/__example_utility_template__.py to __example_utility_template__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/create_asset_collection.py to create_asset_collection.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_files_for_experiment.py to get_output_files_for_experiment.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/clone_simulation.py to clone_simulation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_status.py to get_status.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/rerun_failed_simulations_for_experiment.py to rerun_failed_simulations_for_experiment.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_tail.py to get_output_tail.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_files_for_workitem.py to get_output_files_for_workitem.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/TaggableEntity.py to TaggableEntity.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/SimulationFile.py to SimulationFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Priority.py to Priority.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/CommissionableEntity.py to CommissionableEntity.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Experiment.py to Experiment.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollection.py to AssetCollection.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems/BuilderWorkItem.py to BuilderWorkItem.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/SerializableEntity.py to SerializableEntity.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItem.py to WorkItem.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetFile.py to AssetFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItemFile.py to WorkItemFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Simulation.py to Simulation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/QueryCriteria.py to QueryCriteria.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetType.py to AssetType.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetManager.py to AssetManager.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Configuration.py to Configuration.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/BaseEntity.py to BaseEntity.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/HpcJob.py to HpcJob.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/RelatableEntity.py to RelatableEntity.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/OutputFileMetadata.py to OutputFileMetadata.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollectionFile.py to AssetCollectionFile.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Suite.py to Suite.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pyCOMPS.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating dist creating 'dist/pyCOMPS-2.10.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing pyCOMPS-2.10.0-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/pyCOMPS-2.10.0-py3.7.egg Extracting pyCOMPS-2.10.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Adding pyCOMPS 2.10.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/pyCOMPS-2.10.0-py3.7.egg Processing dependencies for pyCOMPS==2.10.0 Searching for xdg>=4.0.1 Reading https://pypi.org/simple/xdg/ Downloading https://files.pythonhosted.org/packages/dd/54/3516c1cf349060fc3578686d271eba242f10ec00b4530c2985af9faac49b/xdg-6.0.0-py3-none-any.whl#sha256=df3510755b4395157fc04fc3b02467c777f3b3ca383257397f09ab0d4c16f936 Best match: xdg 6.0.0 Processing xdg-6.0.0-py3-none-any.whl Installing xdg-6.0.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Adding xdg 6.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/xdg-6.0.0-py3.7.egg Searching for future>=0.16.0 Reading https://pypi.org/simple/future/ Downloading https://files.pythonhosted.org/packages/8f/2e/cf6accf7415237d6faeeebdc7832023c90e0282aa16fd3263db0eb4715ec/future-0.18.3.tar.gz#sha256=34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307 Best match: future 0.18.3 Processing future-0.18.3.tar.gz Writing /tmp/easy_install-bd_8ncun/future-0.18.3/setup.cfg Running future-0.18.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-bd_8ncun/future-0.18.3/egg-dist-tmp-9hs8vzd6 warning: no files found matching '*.au' under directory 'tests' warning: no files found matching '*.gif' under directory 'tests' warning: no files found matching '*.txt' under directory 'tests' zip_safe flag not set; analyzing archive contents... future.backports.test.__pycache__.ssl_servers.cpython-37: module references __file__ future.backports.test.__pycache__.support.cpython-37: module references __file__ future.standard_library.__pycache__.__init__.cpython-37: module references __file__ future.standard_library.__pycache__.__init__.cpython-37: module references __path__ future.utils.__pycache__.__init__.cpython-37: module MAY be using inspect.stack past.builtins.__pycache__.misc.cpython-37: module MAY be using inspect.stack past.translation.__pycache__.__init__.cpython-37: module references __file__ past.translation.__pycache__.__init__.cpython-37: module references __path__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/future-0.18.3-py3.7.egg Extracting future-0.18.3-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Adding future 0.18.3 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages/future-0.18.3-py3.7.egg Searching for pytz==2023.3 Best match: pytz 2023.3 Adding pytz 2023.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Searching for requests==2.31.0 Best match: requests 2.31.0 Adding requests 2.31.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Searching for certifi==2023.7.22 Best match: certifi 2023.7.22 Adding certifi 2023.7.22 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Searching for idna==3.4 Best match: idna 3.4 Adding idna 3.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Searching for urllib3==2.0.4 Best match: urllib3 2.0.4 Adding urllib3 2.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Searching for charset-normalizer==3.2.0 Best match: charset-normalizer 3.2.0 Adding charset-normalizer 3.2.0 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.7/site-packages Finished processing dependencies for pyCOMPS==2.10.0 [rtd-command-info] start-time: 2023-08-18T21:02:38.959560Z, end-time: 2023-08-18T21:02:39.017453Z, 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 import configparser 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', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx_copybutton', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } 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'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'pyCOMPS' 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'1.0' # 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 = None # 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. # html_use_opensearch = 'www.idmod.org/docs' # 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 = 'pyCOMPS' # -- 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, 'pycomps-docs.tex', u'pyCOMPS', 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, 'pycomps-docs', u'pyCOMPS', [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, 'pycomps-docs', u'pyCOMPS', author, 'Institute for Disease Modeling', 'How to use pyCOMPS for running simulations.', '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} # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'python': ('https://docs.python.org/3', None), 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None), 'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', 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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/pycomps/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/pycomps/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-pycomps', 'name': u'pyCOMPS', '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': 'pyCOMPS', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', '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': 'bceb8620', } # 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-pycomps/builds/1669983/' 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: 2023-08-18T21:02:39.528208Z, end-time: 2023-08-18T21:02:46.975042Z, duration: 7, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v3.3.1 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 54 source files that are out of date updating environment: [new config] 54 added, 0 changed, 0 removed reading sources... [ 1%] COMPS.AuthManager reading sources... [ 3%] COMPS.Client reading sources... [ 5%] COMPS.CredentialPrompt reading sources... [ 7%] COMPS.Data reading sources... [ 9%] COMPS.Data.AssetCollection reading sources... [ 11%] COMPS.Data.AssetCollectionFile reading sources... [ 12%] COMPS.Data.AssetFile reading sources... [ 14%] COMPS.Data.AssetManager reading sources... [ 16%] COMPS.Data.AssetType reading sources... [ 18%] COMPS.Data.BaseEntity reading sources... [ 20%] COMPS.Data.CommissionableEntity reading sources... [ 22%] COMPS.Data.Configuration reading sources... [ 24%] COMPS.Data.Experiment reading sources... [ 25%] COMPS.Data.HpcJob reading sources... [ 27%] COMPS.Data.OutputFileMetadata reading sources... [ 29%] COMPS.Data.Priority reading sources... [ 31%] COMPS.Data.QueryCriteria reading sources... [ 33%] COMPS.Data.RelatableEntity reading sources... [ 35%] COMPS.Data.SerializableEntity reading sources... [ 37%] COMPS.Data.Simulation reading sources... 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[ 9%] COMPS.Data.AssetCollection writing output... [ 11%] COMPS.Data.AssetCollectionFile writing output... [ 12%] COMPS.Data.AssetFile writing output... [ 14%] COMPS.Data.AssetManager writing output... [ 16%] COMPS.Data.AssetType writing output... [ 18%] COMPS.Data.BaseEntity writing output... [ 20%] COMPS.Data.CommissionableEntity writing output... [ 22%] COMPS.Data.Configuration writing output... [ 24%] COMPS.Data.Experiment writing output... [ 25%] COMPS.Data.HpcJob writing output... [ 27%] COMPS.Data.OutputFileMetadata writing output... [ 29%] COMPS.Data.Priority writing output... [ 31%] COMPS.Data.QueryCriteria writing output... [ 33%] COMPS.Data.RelatableEntity writing output... [ 35%] COMPS.Data.SerializableEntity writing output... [ 37%] COMPS.Data.Simulation writing output... [ 38%] COMPS.Data.SimulationFile writing output... [ 40%] COMPS.Data.Suite writing output... [ 42%] COMPS.Data.TaggableEntity writing output... [ 44%] COMPS.Data.WorkItem writing output... [ 46%] COMPS.Data.WorkItemFile writing output... [ 48%] COMPS.Data.WorkItems writing output... [ 50%] COMPS.Data.WorkItems.BuilderWorkItem writing output... [ 51%] COMPS.utils writing output... [ 53%] COMPS.utils.clone_simulation writing output... [ 55%] COMPS.utils.create_asset_collection writing output... [ 57%] COMPS.utils.get_output_files_for_experiment writing output... [ 59%] COMPS.utils.get_output_files_for_workitem writing output... [ 61%] COMPS.utils.get_output_tail writing output... [ 62%] COMPS.utils.get_status writing output... [ 64%] COMPS.utils.main writing output... [ 66%] COMPS.utils.rerun_failed_simulations_for_experiment writing output... [ 68%] architecture writing output... [ 70%] create-climateinput writing output... [ 72%] create-simulations writing output... [ 74%] create-workitems-simulations writing output... [ 75%] glossary writing output... [ 77%] howto-cleanup writing output... [ 79%] howto-create-climateinput writing output... [ 81%] howto-create-simulations writing output... [ 83%] howto-dashboard writing output... [ 85%] howto-example-campaign writing output... [ 87%] howto-example-config writing output... [ 88%] howto-multichart-view writing output... [ 90%] howto-weather-view writing output... [ 92%] index writing output... [ 94%] manage-workitems-simulations writing output... [ 96%] modules writing output... [ 98%] overview-comps writing output... [100%] overview-terminology generating indices... genindex py-modindex done writing additional pages... search opensearch done copying images... [ 6%] ../_readthedocs/html/_images/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg copying images... [ 12%] images/input-search-vietnam.png copying images... [ 18%] images/input-search-vietnam-select.png copying images... [ 25%] images/input-search-vietnam-selected.png copying images... [ 31%] images/climate-submit.png copying images... [ 37%] images/create-input-files-generate.png copying images... [ 43%] images/dashboard-simsperstate.png copying images... [ 50%] images/chart-select.png copying images... [ 56%] images/chart-create.png copying images... [ 62%] images/chart-multi.png copying images... [ 68%] images/chart-ychannel.png copying images... [ 75%] images/weather-animation-climateproject.png copying images... [ 81%] images/weather-animation-play.png copying images... [ 87%] images/weather-animation-temperature-time.png copying images... [ 93%] images/weather-animation-chart.png copying images... [100%] images/terminology.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in ../_readthedocs/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-08-18T21:02:47.425585Z, end-time: 2023-08-18T21:02:53.225679Z, duration: 5, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v3.3.1 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 54 added, 0 changed, 0 removed reading sources... 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[100%] overview-terminology looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... overview-comps overview-terminology create-workitems-simulations create-simulations howto-create-simulations howto-example-config howto-example-campaign create-climateinput howto-create-climateinput manage-workitems-simulations howto-dashboard howto-multichart-view howto-weather-view howto-cleanup architecture modules COMPS.Data COMPS.Data.WorkItems COMPS.Data.WorkItems.BuilderWorkItem COMPS.Data.AssetCollection COMPS.Data.AssetCollectionFile COMPS.Data.AssetFile COMPS.Data.AssetManager COMPS.Data.AssetType COMPS.Data.BaseEntity COMPS.Data.CommissionableEntity COMPS.Data.Configuration COMPS.Data.Experiment COMPS.Data.HpcJob COMPS.Data.OutputFileMetadata COMPS.Data.Priority COMPS.Data.QueryCriteria COMPS.Data.RelatableEntity COMPS.Data.SerializableEntity COMPS.Data.Simulation COMPS.Data.SimulationFile COMPS.Data.Suite COMPS.Data.TaggableEntity COMPS.Data.WorkItem COMPS.Data.WorkItemFile COMPS.utils COMPS.utils.clone_simulation COMPS.utils.create_asset_collection COMPS.utils.get_output_files_for_experiment COMPS.utils.get_output_files_for_workitem COMPS.utils.get_output_tail COMPS.utils.get_status COMPS.utils.main COMPS.utils.rerun_failed_simulations_for_experiment COMPS.AuthManager COMPS.Client COMPS.CredentialPrompt glossary done writing... done writing additional files... opensearchdone copying images... [ 6%] images/terminology.png copying images... [ 12%] images/input-search-vietnam.png copying images... [ 18%] images/input-search-vietnam-select.png copying images... [ 25%] images/input-search-vietnam-selected.png copying images... [ 31%] images/climate-submit.png copying images... [ 37%] images/create-input-files-generate.png copying images... [ 43%] images/dashboard-simsperstate.png copying images... [ 50%] images/chart-select.png copying images... [ 56%] images/chart-create.png copying images... [ 62%] images/chart-multi.png copying images... [ 68%] images/chart-ychannel.png copying images... [ 75%] images/weather-animation-climateproject.png copying images... [ 81%] images/weather-animation-play.png copying images... [ 87%] images/weather-animation-temperature-time.png copying images... [ 93%] images/weather-animation-chart.png copying images... 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[rtd-command-info] start-time: 2023-08-18T21:02:54.808773Z, end-time: 2023-08-18T21:03:00.542318Z, duration: 5, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v3.3.1 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 54 added, 0 changed, 0 removed reading sources... 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[100%] overview-terminology looking for now-outdated files... none found pickling environment... done checking consistency... done processing pycomps-docs.tex... index overview-comps overview-terminology create-workitems-simulations create-simulations howto-create-simulations howto-example-config howto-example-campaign create-climateinput howto-create-climateinput manage-workitems-simulations howto-dashboard howto-multichart-view howto-weather-view howto-cleanup architecture modules COMPS.Data COMPS.Data.WorkItems COMPS.Data.WorkItems.BuilderWorkItem COMPS.Data.AssetCollection COMPS.Data.AssetCollectionFile COMPS.Data.AssetFile COMPS.Data.AssetManager COMPS.Data.AssetType COMPS.Data.BaseEntity COMPS.Data.CommissionableEntity COMPS.Data.Configuration COMPS.Data.Experiment COMPS.Data.HpcJob COMPS.Data.OutputFileMetadata COMPS.Data.Priority COMPS.Data.QueryCriteria COMPS.Data.RelatableEntity COMPS.Data.SerializableEntity COMPS.Data.Simulation COMPS.Data.SimulationFile COMPS.Data.Suite COMPS.Data.TaggableEntity COMPS.Data.WorkItem COMPS.Data.WorkItemFile COMPS.utils COMPS.utils.clone_simulation COMPS.utils.create_asset_collection COMPS.utils.get_output_files_for_experiment COMPS.utils.get_output_files_for_workitem COMPS.utils.get_output_tail COMPS.utils.get_status COMPS.utils.main COMPS.utils.rerun_failed_simulations_for_experiment COMPS.AuthManager COMPS.Client COMPS.CredentialPrompt glossary resolving references... done writing... done copying images... 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[100%] ../_readthedocs/pdf/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/checkouts/latest/_readthedocs/pdf/_static/searchtools.js [rtd-command-info] start-time: 2023-08-18T21:03:02.943302Z, end-time: 2023-08-18T21:03:02.996925Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . 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Latexmk: Log file says output to 'institute-for-disease-modeling-pycomps.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-pycomps.pdf' Latexmk: List of undefined refs and citations: Reference `COMPS.AuthManager:module-COMPS.AuthManager' on page 51 undefined on input line 4155 Reference `COMPS.Client:module-COMPS.Client' on page 51 undefined on input line 4156 Reference `COMPS.CredentialPrompt:module-COMPS.CredentialPrompt' on page 51 undefined on input line 4157 Reference `COMPS.Data.AssetCollection:module-COMPS.Data.AssetCollection' on page 51 undefined on input line 4159 Reference `COMPS.Data.AssetCollectionFile:module-COMPS.Data.AssetCollectionFile' on page 51 undefined on input line 4160 Reference `COMPS.Data.AssetFile:module-COMPS.Data.AssetFile' on page 51 undefined on input line 4161 Reference `COMPS.Data.AssetManager:module-COMPS.Data.AssetManager' on page 51 undefined on input line 4162 Reference `COMPS.Data.AssetType:module-COMPS.Data.AssetType' on page 51 undefined on input line 4163 Reference `COMPS.Data.BaseEntity:module-COMPS.Data.BaseEntity' on page 51 undefined on input line 4164 Reference `COMPS.Data.CommissionableEntity:module-COMPS.Data.CommissionableEntity' on page 51 undefined on input line 4165 Reference `COMPS.Data.Configuration:module-COMPS.Data.Configuration' on page 51 undefined on input line 4166 Reference `COMPS.Data.Experiment:module-COMPS.Data.Experiment' on page 51 undefined on input line 4167 Reference `COMPS.Data.HpcJob:module-COMPS.Data.HpcJob' on page 51 undefined on input line 4168 Reference `COMPS.Data.OutputFileMetadata:module-COMPS.Data.OutputFileMetadata' on page 51 undefined on input line 4169 Reference `COMPS.Data.Priority:module-COMPS.Data.Priority' on page 51 undefined on input line 4170 Reference `COMPS.Data.QueryCriteria:module-COMPS.Data.QueryCriteria' on page 51 undefined on input line 4171 Reference `COMPS.Data.RelatableEntity:module-COMPS.Data.RelatableEntity' on page 51 undefined on input line 4172 Reference `COMPS.Data.SerializableEntity:module-COMPS.Data.SerializableEntity' on page 51 undefined on input line 4173 Reference `COMPS.Data.Simulation:module-COMPS.Data.Simulation' on page 51 undefined on input line 4174 Reference `COMPS.Data.SimulationFile:module-COMPS.Data.SimulationFile' on page 51 undefined on input line 4175 Reference `COMPS.Data.Suite:module-COMPS.Data.Suite' on page 51 undefined on input line 4176 Reference `COMPS.Data.TaggableEntity:module-COMPS.Data.TaggableEntity' on page 51 undefined on input line 4177 Reference `COMPS.Data.WorkItem:module-COMPS.Data.WorkItem' on page 51 undefined on input line 4178 Reference `COMPS.Data.WorkItemFile:module-COMPS.Data.WorkItemFile' on page 51 undefined on input line 4179 Reference `COMPS.Data.WorkItems.BuilderWorkItem:module-COMPS.Data.WorkItems.BuilderWorkItem' on page 51 undefined on input line 4181 Reference `COMPS.Data.WorkItems:module-COMPS.Data.WorkItems' on page 51 undefined on input line 4180 Reference `COMPS.Data:module-COMPS.Data' on page 51 undefined on input line 4158 Reference `COMPS.utils.clone_simulation:module-COMPS.utils.clone_simulation' on page 51 undefined on input line 4183 Reference `COMPS.utils.create_asset_collection:module-COMPS.utils.create_asset_collection' on page 51 undefined on input line 4184 Reference `COMPS.utils.get_output_files_for_experiment:module-COMPS.utils.get_output_files_for_experiment' on page 51 undefined on input line 4185 Reference `COMPS.utils.get_output_files_for_workitem:module-COMPS.utils.get_output_files_for_workitem' on page 51 undefined on input line 4186 Reference `COMPS.utils.get_output_tail:module-COMPS.utils.get_output_tail' on page 51 undefined on input line 4187 Reference `COMPS.utils.get_status:module-COMPS.utils.get_status' on page 51 undefined on input line 4188 Reference `COMPS.utils.main:module-COMPS.utils.main' on page 51 undefined on input line 4189 Reference `COMPS.utils.rerun_failed_simulations_for_experiment:module-COMPS.utils.rerun_failed_simulations_for_experiment' on page 51 undefined on input line 4190 Reference `COMPS.utils:module-COMPS.utils' on page 51 undefined on input line 4182 Reference `modules:module-COMPS' on page 51 undefined on input line 4154 Latexmk: Summary of warnings: Latex failed to resolve 38 reference(s) Rule 'makeindex institute-for-disease-modeling-pycomps.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-pycomps.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-pycomps.idx' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-pycomps.idx'... ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-pycomps.ind" "institute-for-disease-modeling-pycomps.idx"' ------------ This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] [4 <./terminology .png>] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] Overfull \vbox (2.02188pt too high) detected at line 358 [6] [7] [8] Chapter 3. [9 <./input-search-vietnam.png>] [10 <./input-search-vietnam-select.png> <./inp ut-search-vietnam-selected.png> <./climate-submit.png>] [11 <./create-input-fil es-generate.png>] [12] Chapter 4. [13] [14 <./dashboard-simsperstate.png> <./chart-select.png> <./chart-create.pn g>] [15 <./chart-multi.png> <./chart-ychannel.png>] [16 <./weather-animation-cl imateproject.png> <./weather-animation-play.png>] [17 <./weather-animation-temp erature-time.png> <./weather-animation-chart.png>] [18] Chapter 5. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.753 ...2278f2a62260ac90b49fad6d64aef777fdd}.svg} \hspace*{\fill}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.753 ...2278f2a62260ac90b49fad6d64aef777fdd}.svg} \hspace*{\fill}} [19] [20] Chapter 6. Underfull \hbox (badness 10000) in paragraph at lines 783--783 []\T1/ptm/m/it/10 name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 en-vi-ron- [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 978--978 []\T1/ptm/m/it/10 file_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 rel- Underfull \hbox (badness 10000) in paragraph at lines 978--978 \T1/ptm/m/it/10 a-tive_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 978--978 \T1/ptm/m/it/10 md5_checksum=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 979--980 \T1/ptm/m/n/10 Bases: [][]\T1/pcr/m/sl/10 COMPS.Data.AssetFile.AssetFile[][]\T1 /ptm/m/n/10 , [][]\T1/pcr/m/sl/10 COMPS.Data.TaggableEntity. [23] Underfull \hbox (badness 10000) in paragraph at lines 1089--1089 []\T1/ptm/m/it/10 entity_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 en-tity_id\T1/ptm /m/n/10 , \T1/ptm/m/it/10 paths\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1095--1095 []\T1/ptm/m/it/10 entity_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 en-tity_id\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1095--1095 \T1/ptm/m/it/10 meta-data\T1/ptm/m/n/10 , \T1/ptm/m/it/10 job=None\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 1101--1101 []\T1/ptm/m/it/10 metadata\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 start-byte\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end- Underfull \hbox (badness 10000) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 byte=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1101--1101 \T1/ptm/m/it/10 ac-tu-al- Underfull \hbox (badness 10000) in paragraph at lines 1129--1129 []\T1/ptm/m/it/10 checksum\T1/ptm/m/n/10 , \T1/ptm/m/it/10 datas-tream\T1/ptm/m /n/10 , \T1/ptm/m/it/10 sta- [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 []\T1/ptm/m/it/10 environment_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sim-u- Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 la-tion_input_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 work- Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 ing_directory_root=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 ex-e-cutable_path=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 node_group_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 max- Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 i-mum_number_of_retries=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 pri-or-ity=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 min_cores=None\ T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1327--1327 \T1/ptm/m/it/10 max_cores=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex-clu-sive=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 as- [26] Underfull \hbox (badness 10000) in paragraph at lines 1453--1454 \T1/ptm/m/n/10 Bases: [][]\T1/pcr/m/sl/10 COMPS.Data.TaggableEntity.TaggableEnt ity[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/sl/10 COMPS.Data. 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[27] [28] [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 1970--1972 []\T1/pcr/b/n/10 filters \T1/ptm/m/n/10 ^^U A list of ba-sic prop-erty filter-c riteria; e.g. Underfull \hbox (badness 10000) in paragraph at lines 1989--1991 []\T1/pcr/b/n/10 tag_filters \T1/ptm/m/n/10 ^^U A list of tag filter-criteria; e.g. [`Repli- [31] Underfull \hbox (badness 10000) in paragraph at lines 2128--2128 []\T1/ptm/m/it/10 fget=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2128--2128 \T1/ptm/m/it/10 fset=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2128--2128 \T1/ptm/m/it/10 fdel=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2165--2165 []\T1/ptm/m/it/10 obj\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_property_map=True\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 in-clude_nulls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/ 10 in- Underfull \hbox (badness 10000) in paragraph at lines 2178--2179 \T1/ptm/m/n/10 Bases: [][]\T1/pcr/m/sl/10 COMPS.Data.TaggableEntity.TaggableEnt ity[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/sl/10 COMPS.Data. 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[32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2364--2364 []\T1/ptm/m/it/10 save_batch_callback=>\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 re- Underfull \hbox (badness 10000) in paragraph at lines 2386--2386 []\T1/ptm/m/it/10 simulationfile\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_path=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 data=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 up-l oad_callback=>\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 re- [41] Underfull \hbox (badness 10000) in paragraph at lines 3314--3314 []\T1/ptm/m/it/10 workitemfile\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file_path=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 data=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 up-loa d_callback=\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 3816--3816 []\T1/ptm/m/it/10 hoststring\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-ify_certs=Fals e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cre-den- [46] Underfull \hbox (badness 8038) in paragraph at lines 3992--3992 []\T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude_comps_auth_toke n=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 http_err_handle_exceptions=None\T1/ptm/m /n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3998--3998 []\T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude_comps_auth_toke n=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 http_err_handle_exceptions=None\T1/ptm/m /n/10 , [47] Underfull \hbox (badness 10000) in paragraph at lines 4004--4004 []\T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-clude_comps_auth_toke n=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 http_err_handle_exceptions=None\T1/ptm/m /n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4016--4016 []\T1/ptm/m/it/10 method\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \ T1/ptm/m/it/10 in-clude_comps_auth_token=True\T1/ptm/m/n/10 , [48] Chapter 7. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-pycomps.pdf (64 pages, 3138919 bytes). Transcript written on institute-for-disease-modeling-pycomps.log. Latexmk: Index file 'institute-for-disease-modeling-pycomps.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-pycomps.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-pycomps.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-pycomps.aux' 'institute-for-disease-modeling-pycomps.out' 'institute-for-disease-modeling-pycomps.toc' ------------ Run number 3 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-pycomps" "pycomps-docs.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./pycomps-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[49] [50] Underfull \hbox (badness 10000) in paragraph at lines 4181--4182 []\T1/pcr/m/n/10 COMPS.Data.WorkItems.BuilderWorkItem\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 4185--4186 []\T1/pcr/m/n/10 COMPS.utils.get_output_files_for_experiment\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 4186--4187 []\T1/pcr/m/n/10 COMPS.utils.get_output_files_for_workitem\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 4190--4191 []\T1/pcr/m/n/10 COMPS.utils.rerun_failed_simulations_for_experiment\T1/ptm/m/n /10 , [51] (./institute-for-disease-modeling-pycomps.ind [52] Underfull \hbox (badness 10000) in paragraph at lines 8--9 []\T1/pcr/m/n/10 AboveNormal \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Priorit y.Priority at- Overfull \hbox (27.74013pt too wide) in paragraph at lines 9--11 []\T1/pcr/m/n/10 add_asset() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.AssetCo llection.AssetCollection Underfull \hbox (badness 10000) in paragraph at lines 11--13 []\T1/pcr/m/n/10 add_extra_params() Underfull \hbox (badness 10000) in paragraph at lines 11--13 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCriteria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 13--14 []\T1/pcr/m/n/10 add_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulati on.Simulation Underfull \hbox (badness 10000) in paragraph at lines 14--15 []\T1/pcr/m/n/10 add_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem .WorkItem Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/pcr/m/n/10 add_related_asset_collection() Underfull \hbox (badness 10000) in paragraph at lines 15--17 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem method\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 17--19 []\T1/pcr/m/n/10 add_related_experiment() Underfull \hbox (badness 10000) in paragraph at lines 17--19 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem method\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 19--21 []\T1/pcr/m/n/10 add_related_simulation() Underfull \hbox (badness 10000) in paragraph at lines 19--21 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem method\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 add_related_suite() Underfull \hbox (badness 10000) in paragraph at lines 21--23 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem method\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 add_related_work_item() Underfull \hbox (badness 10000) in paragraph at lines 23--25 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem method\T1/ptm/m/n/ 10 ), Overfull \hbox (9.2014pt too wide) in paragraph at lines 25--26 []\T1/pcr/m/n/10 add_work_order() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Wo rkItem.WorkItem Underfull \hbox (badness 10000) in paragraph at lines 28--30 []\T1/pcr/m/n/10 asset_collection_id() Underfull \hbox (badness 10000) in paragraph at lines 28--30 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Configuration.Configuration Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 asset_collection_id() Underfull \hbox (badness 7685) in paragraph at lines 30--32 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem prop-erty\T1/ptm/m /n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 32--33 []\T1/pcr/m/n/10 AssetCollection \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 AssetCollectionFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (9.74013pt too wide) in paragraph at lines 36--38 []\T1/pcr/m/n/10 assets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.AssetColle ction.AssetCollection Underfull \hbox (badness 10000) in paragraph at lines 39--40 []\T1/pcr/m/n/10 auth_manager() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Client.Cl ient class Underfull \hbox (badness 10000) in paragraph at lines 44--45 []\T1/pcr/m/n/10 BelowNormal \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Priorit y.Priority at- Underfull \hbox (badness 10000) in paragraph at lines 45--47 []\T1/pcr/m/n/10 BuilderWorkItem \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (64.74998pt too wide) in paragraph at lines 50--52 []\T1/pcr/m/n/10 cancel() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Commission ableEntity.CommissionableEntity Underfull \hbox (badness 10000) in paragraph at lines 53--55 []\T1/pcr/m/n/10 Canceled \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation .SimulationState Underfull \hbox (badness 10000) in paragraph at lines 57--58 []\T1/pcr/m/n/10 Canceling \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem. 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last_modified() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Wor kItem.WorkItem Overfull \hbox (47.72054pt too wide) in paragraph at lines 358--360 []\T1/pcr/m/n/10 length() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.OutputFile Metadata.OutputFileMetadata Overfull \hbox (7.82019pt too wide) in paragraph at lines 368--369 []\T1/pcr/m/n/10 main() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule COMPS.utils. create_asset_collection\T1/ptm/m/n/10 ), Overfull \hbox (43.6301pt too wide) in paragraph at lines 369--371 []\T1/pcr/m/n/10 main() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule COMPS.utils. get_output_files_for_experiment\T1/ptm/m/n/10 ), Overfull \hbox (36.44017pt too wide) in paragraph at lines 371--373 []\T1/pcr/m/n/10 main() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule COMPS.utils. get_output_files_for_workitem\T1/ptm/m/n/10 ), Overfull \hbox (80.5894pt too wide) in paragraph at lines 376--378 []\T1/pcr/m/n/10 main() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule COMPS.utils. 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in paragraph at lines 388--390 []\T1/pcr/m/n/10 mime_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.OutputF ileMetadata.OutputFileMetadata Overfull \hbox (14.12157pt too wide) in paragraph at lines 390--392 []\T1/pcr/m/n/10 min_cores() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Configu ration.Configuration Overfull \hbox (8.6225pt too wide) in paragraph at lines 420--421 []| \T1/pcr/m/n/10 COMPS.Data.WorkItems.BuilderWorkItem\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 423--424 []| \T1/pcr/m/n/10 COMPS.utils.create_asset_collection\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 424--425 []| \T1/pcr/m/n/10 COMPS.utils.get_output_files_for_experiment\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 425--426 []| \T1/pcr/m/n/10 COMPS.utils.get_output_files_for_workitem\T1/ptm/m/n/10 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 429--430 []| \T1/pcr/m/n/10 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\T1/ptm/m/it/10 COMPS.utils.get_output_files_for_workitem\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 470--472 []\T1/pcr/m/n/10 path_builder_single_dir() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Overfull \hbox (1.38037pt too wide) in paragraph at lines 470--472 \T1/ptm/m/it/10 COMPS.utils.get_output_files_for_experiment\T1/ptm/m/n/10 ), Overfull \hbox (95.72054pt too wide) in paragraph at lines 472--474 []\T1/pcr/m/n/10 path_from_root() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Ou tputFileMetadata.OutputFileMetadata Overfull \hbox (8.12157pt too wide) in paragraph at lines 477--479 []\T1/pcr/m/n/10 priority() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Configur ation.Configuration Overfull \hbox (38.38023pt too wide) in paragraph at lines 481--483 []\T1/pcr/m/n/10 prompt() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.CredentialPromp t.ConsoleCredentialPrompt Overfull \hbox (5.60059pt too wide) in paragraph at lines 483--485 []\T1/pcr/m/n/10 prompt() 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541--543 []\T1/pcr/m/n/10 retrieve_output_files_from_info() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (10.1225pt too wide) in paragraph at lines 543--545 []\T1/pcr/m/n/10 retrieve_partial_output_file_from_info() Underfull \hbox (badness 8000) in paragraph at lines 545--546 []\T1/pcr/m/n/10 Retry \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation.Si mulationState at- Underfull \hbox (badness 10000) in paragraph at lines 555--556 []\T1/pcr/m/n/10 save() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Experiment.E xperiment Underfull \hbox (badness 10000) in paragraph at lines 559--561 []\T1/pcr/m/n/10 save_all() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulati on.Simulation Underfull \hbox (badness 10000) in paragraph at lines 563--565 []\T1/pcr/m/n/10 select_children() Underfull \hbox (badness 10000) in paragraph at lines 563--565 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCriteria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 565--567 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static_retrieve_as_zip() Underfull \hbox (badness 10000) in paragraph at lines 579--581 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.AssetCollection.AssetCollection Underfull \hbox (badness 10000) in paragraph at lines 581--583 []\T1/pcr/m/n/10 static_retrieve_output_files() Underfull \hbox (badness 10000) in paragraph at lines 581--583 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation.Simulation static Underfull \hbox (badness 10000) in paragraph at lines 583--585 []\T1/pcr/m/n/10 static_retrieve_output_files() Underfull \hbox (badness 10000) in paragraph at lines 583--585 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem static Underfull \hbox (badness 10000) in paragraph at lines 589--590 []\T1/pcr/m/n/10 Succeeded \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem. WorkItemState Underfull \hbox (badness 10000) in paragraph at lines 591--592 []\T1/pcr/m/n/10 suite_id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Experime nt.Experiment Overfull \hbox (28.62032pt too wide) in paragraph at lines 596--598 []\T1/pcr/m/n/10 tag_filters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Query Criteria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 598--599 []\T1/pcr/m/n/10 TaggableEntity \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 599--600 []\T1/pcr/m/n/10 TagOperationMode \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [59] Overfull \hbox (28.90971pt too wide) in paragraph at lines 602--604 []\T1/pcr/m/n/10 tags() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.AssetCollect ionFile.AssetCollectionFile Underfull \hbox (badness 10000) in paragraph at lines 605--606 []\T1/pcr/m/n/10 tags() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation.S imulation prop- Underfull \hbox (badness 10000) in paragraph at lines 608--609 []\T1/pcr/m/n/10 TKCredentialPrompt \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (40.62032pt too wide) in paragraph at lines 609--611 []\T1/pcr/m/n/10 to_param_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Que ryCriteria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 614--616 []\T1/pcr/m/n/10 upload_large_asset() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (29.72054pt too wide) in paragraph at lines 617--619 []\T1/pcr/m/n/10 url() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.OutputFileMet adata.OutputFileMetadata Underfull \hbox (badness 10000) in paragraph at lines 619--620 []\T1/pcr/m/n/10 username() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.AuthManager.A uthManager Underfull \hbox (badness 10000) in paragraph at lines 623--624 []\T1/pcr/m/n/10 Validating \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.HpcJob.H pcState at- Underfull \hbox (badness 7047) in paragraph at lines 624--625 []\T1/pcr/m/n/10 Validating \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem .WorkItemState Overfull \hbox (10.34099pt too wide) in paragraph at lines 625--627 []\T1/pcr/m/n/10 version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem. WorkerOrPluginKey Underfull \hbox (badness 10000) in paragraph at lines 631--632 []\T1/pcr/m/n/10 where() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCriter ia.QueryCriteria Overfull \hbox (16.62032pt too wide) in paragraph at lines 632--634 []\T1/pcr/m/n/10 where_tag() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCr iteria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 636--637 []\T1/pcr/m/n/10 worker() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.W orkItem prop- Underfull \hbox (badness 10000) in paragraph at lines 637--639 []\T1/pcr/m/n/10 worker_instance_id() Underfull \hbox (badness 7685) in paragraph at lines 637--639 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem prop-erty\T1/ptm/m /n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 639--640 []\T1/pcr/m/n/10 WorkerOrPluginKey \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 640--641 []\T1/pcr/m/n/10 working_directory() Underfull \hbox (badness 10000) in paragraph at lines 640--641 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.HpcJob.HpcJob prop-erty\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 641--643 []\T1/pcr/m/n/10 working_directory() Underfull \hbox (badness 7685) in paragraph at lines 641--643 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem prop-erty\T1/ptm/m /n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 643--645 []\T1/pcr/m/n/10 working_directory_root() Underfull \hbox (badness 10000) in paragraph at lines 643--645 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Configuration.Configuration Underfull \hbox (badness 10000) in paragraph at lines 645--647 []\T1/pcr/m/n/10 working_directory_size() Underfull \hbox (badness 7685) in paragraph at lines 645--647 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItem prop-erty\T1/ptm/m /n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 649--650 []\T1/pcr/m/n/10 WorkItems \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.AssetMana ger.EntityType Overfull \hbox (4.62032pt too wide) in paragraph at lines 654--656 []\T1/pcr/m/n/10 xparams() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCrit eria.QueryCriteria [60]) (./institute-for-disease-modeling-pycomps.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-pycomps.pdf (64 pages, 3139021 bytes). Transcript written on institute-for-disease-modeling-pycomps.log. Latexmk: Index file 'institute-for-disease-modeling-pycomps.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-pycomps.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-pycomps.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256