Read the Docs build information Build id: 1192385 Project: institute-for-disease-modeling-pycomps Version: v2.9.1 Commit: 59e0f7de6d413c5b45c59b44786b7a36fe4c2b87 Date: 2022-11-22T19:20:02.622304Z State: finished Success: True [rtd-command-info] start-time: 2022-11-22T19:21:41.525485Z, end-time: 2022-11-22T19:21:47.443151Z, duration: 5, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/pyCOMPS.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-11-22T19:21:47.635947Z, end-time: 2022-11-22T19:21:47.766453Z, duration: 0, exit-code: 0 git checkout --force 59e0f7de6d413c5b45c59b44786b7a36fe4c2b87 Note: switching to '59e0f7de6d413c5b45c59b44786b7a36fe4c2b87'. 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 59e0f7d Upgrade version to 2.9.0 [rtd-command-info] start-time: 2022-11-22T19:21:47.995681Z, end-time: 2022-11-22T19:21:48.055566Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-11-22T19:21:49.033952Z, end-time: 2022-11-22T19:21:53.635443Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv 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/v2.9.1/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/bin/python Installing setuptools, pip, wheel... done. 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collected packages: docopt Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13723 sha256=378bb3340650f41db53d57ff908e17bc68b15b9c942c7571d3c6aa5d14d04f76 Stored in directory: /tmp/pip-ephem-wheel-cache-aezdshzp/wheels/1f/e0/34/704e15d0b49f199ac74a2757d018d428ad4cf119c078c80f16 Successfully built docopt Installing collected packages: docopt, cached-property, wrapt, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyjwt, pycparser, py-make, pockets, MarkupSafe, docutils, sphinxcontrib-napoleon, plantweb, Jinja2, deprecated, cffi, sphinxext.remoteliteralinclude, sphinx, pynacl, pygit2, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, PyGithub Attempting uninstall: MarkupSafe Found existing installation: MarkupSafe 2.1.1 Uninstalling MarkupSafe-2.1.1: Successfully uninstalled MarkupSafe-2.1.1 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-1.57 cached-property-1.5.2 cffi-1.15.1 deprecated-1.2.13 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-2.6.0 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 wrapt-1.14.1 [rtd-command-info] start-time: 2022-11-22T19:22:08.965155Z, end-time: 2022-11-22T19:22:10.971977Z, 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-2.9.0-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-2.9.0-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages/pyCOMPS-2.9.0-py3.7.egg Extracting pyCOMPS-2.9.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Adding pyCOMPS 2.9.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages/pyCOMPS-2.9.0-py3.7.egg Processing dependencies for pyCOMPS==2.9.0 Searching for xdg>=4.0.1 Reading https://pypi.org/simple/xdg/ Downloading https://files.pythonhosted.org/packages/ea/09/4a0f30aada49e142b94bbb232c023abcbc6ced7e2a9776533fb14977e9db/xdg-5.1.1-py3-none-any.whl#sha256=865a7b56ed1d4cd2fce2ead1eddf97360843619757f473cd90b75f1817ca541d Best match: xdg 5.1.1 Processing xdg-5.1.1-py3-none-any.whl Installing xdg-5.1.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Adding xdg 5.1.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages/xdg-5.1.1-py3.7.egg Searching for future>=0.16.0 Reading https://pypi.org/simple/future/ Downloading https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz#sha256=b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d Best match: future 0.18.2 Processing future-0.18.2.tar.gz Writing /tmp/easy_install-dj9tbu7v/future-0.18.2/setup.cfg Running future-0.18.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-dj9tbu7v/future-0.18.2/egg-dist-tmp-dxdy19bl 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/v2.9.1/lib/python3.7/site-packages/future-0.18.2-py3.7.egg Extracting future-0.18.2-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Adding future 0.18.2 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages/future-0.18.2-py3.7.egg Searching for pytz==2022.6 Best match: pytz 2022.6 Adding pytz 2022.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Searching for requests==2.28.1 Best match: requests 2.28.1 Adding requests 2.28.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Searching for charset-normalizer==2.1.1 Best match: charset-normalizer 2.1.1 Adding charset-normalizer 2.1.1 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Searching for urllib3==1.26.12 Best match: urllib3 1.26.12 Adding urllib3 1.26.12 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/lib/python3.7/site-packages Searching for certifi==2022.9.24 Best match: certifi 2022.9.24 Adding certifi 2022.9.24 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.9.1/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/v2.9.1/lib/python3.7/site-packages Finished processing dependencies for pyCOMPS==2.9.0 [rtd-command-info] start-time: 2022-11-22T19:22:12.929597Z, end-time: 2022-11-22T19:22:12.996682Z, 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: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] 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': "v2.9.1", 'version_slug': "v2.9.1", '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/v2.9.1/pdf/"), ("html", "//docs.idmod.org/_/downloads/pycomps/en/v2.9.1/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-pycomps', 'name': u'pyCOMPS', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/pycomps/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'pyCOMPS', 'github_version': 'v2.9.1', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'v2.9.1', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'v2.9.1', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '59e0f7de', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'tag' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-pycomps/builds/1192385/' 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: 2022-11-22T19:22:13.194097Z, end-time: 2022-11-22T19:22:19.863770Z, duration: 6, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/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%] _build/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... 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[rtd-command-info] start-time: 2022-11-22T19:22:20.089049Z, end-time: 2022-11-22T19:22:25.249079Z, duration: 5, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia 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... [ 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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[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... [100%] _build/localmedia/_images/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg copying static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-11-22T19:22:25.633199Z, end-time: 2022-11-22T19:22:27.473459Z, duration: 1, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.3.1 loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] modules 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... [ 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... [100%] _build/localmedia/_images/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. 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/v2.9.1/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-11-22T19:22:29.557250Z, end-time: 2022-11-22T19:22:29.623530Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2022-11-22T19:22:29.803400Z, end-time: 2022-11-22T19:22:35.087431Z, duration: 5, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-pycomps -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-pycomps" "pycomps-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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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(/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) LaTeX Warning: Hyper reference `howto-example-config::doc' on page 5 undefined on input line 239. LaTeX Warning: Hyper reference `howto-example-campaign::doc' on page 5 undefine d on input line 239. [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. LaTeX Warning: Hyper reference `glossary:term-dashboard' on page 13 undefined o n input line 505. [13] LaTeX Warning: Hyper reference `glossary:term-multi-chart' on page 14 undefined on input line 565. 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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 4137 Reference `COMPS.Client:module-COMPS.Client' on page 51 undefined on input line 4138 Reference `COMPS.CredentialPrompt:module-COMPS.CredentialPrompt' on page 51 undefined on input line 4139 Reference `COMPS.Data.AssetCollection:module-COMPS.Data.AssetCollection' on page 51 undefined on input line 4141 Reference `COMPS.Data.AssetCollectionFile:module-COMPS.Data.AssetCollectionFile' on page 51 undefined on input line 4142 Reference `COMPS.Data.AssetFile:module-COMPS.Data.AssetFile' on page 51 undefined on input line 4143 Reference `COMPS.Data.AssetManager:module-COMPS.Data.AssetManager' on page 51 undefined on input line 4144 Reference `COMPS.Data.AssetType:module-COMPS.Data.AssetType' on page 51 undefined on input line 4145 Reference `COMPS.Data.BaseEntity:module-COMPS.Data.BaseEntity' on page 51 undefined on input line 4146 Reference `COMPS.Data.CommissionableEntity:module-COMPS.Data.CommissionableEntity' on page 51 undefined on input line 4147 Reference `COMPS.Data.Configuration:module-COMPS.Data.Configuration' on page 51 undefined on input line 4148 Reference `COMPS.Data.Experiment:module-COMPS.Data.Experiment' on page 51 undefined on input line 4149 Reference `COMPS.Data.HpcJob:module-COMPS.Data.HpcJob' on page 51 undefined on input line 4150 Reference `COMPS.Data.OutputFileMetadata:module-COMPS.Data.OutputFileMetadata' on page 51 undefined on input line 4151 Reference `COMPS.Data.Priority:module-COMPS.Data.Priority' on page 51 undefined on input line 4152 Reference `COMPS.Data.QueryCriteria:module-COMPS.Data.QueryCriteria' on page 51 undefined on input line 4153 Reference `COMPS.Data.RelatableEntity:module-COMPS.Data.RelatableEntity' on page 51 undefined on input line 4154 Reference `COMPS.Data.SerializableEntity:module-COMPS.Data.SerializableEntity' on page 51 undefined on input line 4155 Reference `COMPS.Data.Simulation:module-COMPS.Data.Simulation' on page 51 undefined on input line 4156 Reference `COMPS.Data.SimulationFile:module-COMPS.Data.SimulationFile' on page 51 undefined on input line 4157 Reference `COMPS.Data.Suite:module-COMPS.Data.Suite' on page 51 undefined on input line 4158 Reference `COMPS.Data.TaggableEntity:module-COMPS.Data.TaggableEntity' on page 51 undefined on input line 4159 Reference `COMPS.Data.WorkItem:module-COMPS.Data.WorkItem' on page 51 undefined on input line 4160 Reference `COMPS.Data.WorkItemFile:module-COMPS.Data.WorkItemFile' on page 51 undefined on input line 4161 Reference `COMPS.Data.WorkItems.BuilderWorkItem:module-COMPS.Data.WorkItems.BuilderWorkItem' on page 51 undefined on input line 4163 Reference `COMPS.Data.WorkItems:module-COMPS.Data.WorkItems' on page 51 undefined on input line 4162 Reference `COMPS.Data:module-COMPS.Data' on page 51 undefined on input line 4140 Reference `COMPS.utils.clone_simulation:module-COMPS.utils.clone_simulation' on page 51 undefined on input line 4165 Reference `COMPS.utils.create_asset_collection:module-COMPS.utils.create_asset_collection' on page 51 undefined on input line 4166 Reference `COMPS.utils.get_output_files_for_experiment:module-COMPS.utils.get_output_files_for_experiment' on page 51 undefined on input line 4167 Reference `COMPS.utils.get_output_files_for_workitem:module-COMPS.utils.get_output_files_for_workitem' on page 51 undefined on input line 4168 Reference `COMPS.utils.get_output_tail:module-COMPS.utils.get_output_tail' on page 51 undefined on input line 4169 Reference `COMPS.utils.get_status:module-COMPS.utils.get_status' on page 51 undefined on input line 4170 Reference `COMPS.utils.main:module-COMPS.utils.main' on page 51 undefined on input line 4171 Reference `COMPS.utils.rerun_failed_simulations_for_experiment:module-COMPS.utils.rerun_failed_simulations_for_experiment' on page 51 undefined on input line 4172 Reference `COMPS.utils:module-COMPS.utils' on page 51 undefined on input line 4164 Reference `modules:module-COMPS' on page 51 undefined on input line 4136 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' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-pycomps.ind" "institute-for-disease-modeling-pycomps.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-pycomps.idx'... 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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 3798--3798 []\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 3974--3974 []\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 3980--3980 []\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 3986--3986 []\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 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 , [47] [48] Chapter 7. [49] [50] Underfull \hbox (badness 10000) in paragraph at lines 4163--4164 []\T1/pcr/m/n/10 COMPS.Data.WorkItems.BuilderWorkItem\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 4167--4168 []\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 4168--4169 []\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 4172--4173 []\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. WorkItemState Overfull \hbox (32.86098pt too wide) in paragraph at lines 58--60 []\T1/pcr/m/n/10 CancelRequested \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Sim ulation.SimulationState Overfull \hbox (23.20113pt too wide) in paragraph at lines 60--62 []\T1/pcr/m/n/10 CancelRequested \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Wor kItem.WorkItemState Overfull \hbox (10.62032pt too wide) in paragraph at lines 62--64 []\T1/pcr/m/n/10 children() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCri teria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 64--66 []\T1/pcr/m/n/10 clear_auth_token() Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/pcr/m/n/10 clone_simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (88.74998pt too wide) in paragraph at lines 69--71 []\T1/pcr/m/n/10 commission() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Commis sionableEntity.CommissionableEntity Underfull \hbox (badness 10000) in paragraph at lines 71--73 []\T1/pcr/m/n/10 CommissionableEntity \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [53] Overfull \hbox (14.86098pt too wide) in paragraph at lines 73--75 []\T1/pcr/m/n/10 Commissioned \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simula tion.SimulationState Overfull \hbox (5.20113pt too wide) in paragraph at lines 75--77 []\T1/pcr/m/n/10 Commissioned \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkIt em.WorkItemState Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/pcr/m/n/10 CommissionRequested Underfull \hbox (badness 10000) in paragraph at lines 77--79 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation.SimulationState Underfull \hbox (badness 10000) in paragraph at lines 79--81 []\T1/pcr/m/n/10 CommissionRequested Underfull \hbox (badness 10000) in paragraph at lines 79--81 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItemState Overfull \hbox (28.1225pt too wide) in paragraph at lines 143--144 []\T1/pcr/m/n/10 COMPS.utils.get_output_files_for_experiment Overfull \hbox (16.1225pt too wide) in paragraph at lines 145--146 []\T1/pcr/m/n/10 COMPS.utils.get_output_files_for_workitem Overfull \hbox (76.1225pt too wide) in paragraph at lines 153--154 []\T1/pcr/m/n/10 COMPS.utils.rerun_failed_simulations_for_experiment Underfull \hbox (badness 10000) in paragraph at lines 155--156 []\T1/pcr/m/n/10 Configuration \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (18.38109pt too wide) in paragraph at lines 156--158 []\T1/pcr/m/n/10 configuration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Exp eriment.Experiment Underfull \hbox (badness 10000) in paragraph at lines 158--159 []\T1/pcr/m/n/10 configuration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Hpc Job.HpcJob Overfull \hbox (12.86125pt too wide) in paragraph at lines 159--161 []\T1/pcr/m/n/10 configuration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Sim ulation.Simulation Underfull \hbox (badness 10000) in paragraph at lines 162--163 []\T1/pcr/m/n/10 Configuring \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.HpcJob. HpcState at- Underfull \hbox (badness 10000) in paragraph at lines 163--165 []\T1/pcr/m/n/10 ConsoleCredentialPrompt \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 165--167 []\T1/pcr/m/n/10 convert_if_string() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (68.96992pt too wide) in paragraph at lines 167--169 []\T1/pcr/m/n/10 convertToDict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Ser ializableEntity.SerializableEntity Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCriter ia.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 create_asset_collection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule [54] Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 Created \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.Re lationType at- Underfull \hbox (badness 10000) in paragraph at lines 176--177 []\T1/pcr/m/n/10 CredentialPrompt \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 177--178 []\T1/pcr/m/n/10 CustomCommandFormatter \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class i n Overfull \hbox (45.74013pt too wide) in paragraph at lines 183--185 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Asse tCollection.AssetCollection Overfull \hbox (12.38109pt too wide) in paragraph at lines 185--187 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Expe riment.Experiment Overfull \hbox (6.86125pt too wide) in paragraph at lines 187--189 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simu lation.Simulation Underfull \hbox (badness 10000) in paragraph at lines 189--190 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Suit e.Suite prop- Overfull \hbox (10.4513pt too wide) in paragraph at lines 191--193 []\T1/pcr/m/n/10 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10000) in paragraph at lines 232--234 []\T1/pcr/m/n/10 ExternalValidation Underfull \hbox (badness 10000) in paragraph at lines 232--234 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.HpcJob.HpcState at-tribute\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 239--240 []\T1/pcr/m/n/10 Failed \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.Wor kItemState at- Overfull \hbox (20.03084pt too wide) in paragraph at lines 243--245 []\T1/pcr/m/n/10 file_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulat ionFile.SimulationFile Overfull \hbox (10.37099pt too wide) in paragraph at lines 245--247 []\T1/pcr/m/n/10 file_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkIte mFile.WorkItemFile Underfull \hbox (badness 10000) in paragraph at lines 249--250 []\T1/pcr/m/n/10 fill_parser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 250--252 []\T1/pcr/m/n/10 fill_parser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule 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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. 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[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 3798--3798 []\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 3974--3974 []\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 3980--3980 []\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 3986--3986 []\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 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 , [47] [48] Chapter 7. [49] [50] Underfull \hbox (badness 10000) in paragraph at lines 4163--4164 []\T1/pcr/m/n/10 COMPS.Data.WorkItems.BuilderWorkItem\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 4167--4168 []\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 4168--4169 []\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 4172--4173 []\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. WorkItemState Overfull \hbox (32.86098pt too wide) in paragraph at lines 58--60 []\T1/pcr/m/n/10 CancelRequested \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Sim ulation.SimulationState Overfull \hbox (23.20113pt too wide) in paragraph at lines 60--62 []\T1/pcr/m/n/10 CancelRequested \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Wor kItem.WorkItemState Overfull \hbox (10.62032pt too wide) in paragraph at lines 62--64 []\T1/pcr/m/n/10 children() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCri teria.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 64--66 []\T1/pcr/m/n/10 clear_auth_token() Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/pcr/m/n/10 clone_simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (88.74998pt too wide) in paragraph at lines 69--71 []\T1/pcr/m/n/10 commission() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Commis sionableEntity.CommissionableEntity Underfull \hbox (badness 10000) in paragraph at lines 71--73 []\T1/pcr/m/n/10 CommissionableEntity \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in [53] Overfull \hbox (14.86098pt too wide) in paragraph at lines 73--75 []\T1/pcr/m/n/10 Commissioned \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simula tion.SimulationState Overfull \hbox (5.20113pt too wide) in paragraph at lines 75--77 []\T1/pcr/m/n/10 Commissioned \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkIt em.WorkItemState Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/pcr/m/n/10 CommissionRequested Underfull \hbox (badness 10000) in paragraph at lines 77--79 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation.SimulationState Underfull \hbox (badness 10000) in paragraph at lines 79--81 []\T1/pcr/m/n/10 CommissionRequested Underfull \hbox (badness 10000) in paragraph at lines 79--81 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.WorkItemState Overfull \hbox (28.1225pt too wide) in paragraph at lines 143--144 []\T1/pcr/m/n/10 COMPS.utils.get_output_files_for_experiment Overfull \hbox (16.1225pt too wide) in paragraph at lines 145--146 []\T1/pcr/m/n/10 COMPS.utils.get_output_files_for_workitem Overfull \hbox (76.1225pt too wide) in paragraph at lines 153--154 []\T1/pcr/m/n/10 COMPS.utils.rerun_failed_simulations_for_experiment Underfull \hbox (badness 10000) in paragraph at lines 155--156 []\T1/pcr/m/n/10 Configuration \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (18.38109pt too wide) in paragraph at lines 156--158 []\T1/pcr/m/n/10 configuration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Exp eriment.Experiment Underfull \hbox (badness 10000) in paragraph at lines 158--159 []\T1/pcr/m/n/10 configuration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Hpc Job.HpcJob Overfull \hbox (12.86125pt too wide) in paragraph at lines 159--161 []\T1/pcr/m/n/10 configuration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Sim ulation.Simulation Underfull \hbox (badness 10000) in paragraph at lines 162--163 []\T1/pcr/m/n/10 Configuring \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.HpcJob. HpcState at- Underfull \hbox (badness 10000) in paragraph at lines 163--165 []\T1/pcr/m/n/10 ConsoleCredentialPrompt \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 165--167 []\T1/pcr/m/n/10 convert_if_string() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (68.96992pt too wide) in paragraph at lines 167--169 []\T1/pcr/m/n/10 convertToDict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Ser ializableEntity.SerializableEntity Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.QueryCriter ia.QueryCriteria Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 create_asset_collection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule [54] Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 Created \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.WorkItem.Re lationType at- Underfull \hbox (badness 10000) in paragraph at lines 176--177 []\T1/pcr/m/n/10 CredentialPrompt \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 177--178 []\T1/pcr/m/n/10 CustomCommandFormatter \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class i n Overfull \hbox (45.74013pt too wide) in paragraph at lines 183--185 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Asse tCollection.AssetCollection Overfull \hbox (12.38109pt too wide) in paragraph at lines 185--187 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Expe riment.Experiment Overfull \hbox (6.86125pt too wide) in paragraph at lines 187--189 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simu lation.Simulation Underfull \hbox (badness 10000) in paragraph at lines 189--190 []\T1/pcr/m/n/10 date_created() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Suit e.Suite prop- Overfull \hbox (10.4513pt too wide) in paragraph at lines 191--193 []\T1/pcr/m/n/10 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WorkItemState Underfull \hbox (badness 10000) in paragraph at lines 585--586 []\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 590--592 []\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 592--593 []\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 593--594 []\T1/pcr/m/n/10 TagOperationMode \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (28.90971pt too wide) in paragraph at lines 596--598 []\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 599--600 []\T1/pcr/m/n/10 tags() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Simulation.S imulation prop- [59] Underfull \hbox (badness 10000) in paragraph at lines 602--603 []\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 603--605 []\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 608--610 []\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 611--613 []\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 613--614 []\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 617--618 []\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 618--619 []\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 619--621 []\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 625--626 []\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 626--628 []\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 630--631 []\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 631--633 []\T1/pcr/m/n/10 worker_instance_id() Underfull \hbox (badness 7685) in paragraph at lines 631--633 \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 633--634 []\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 634--635 []\T1/pcr/m/n/10 working_directory() Underfull \hbox (badness 10000) in paragraph at lines 634--635 \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 635--637 []\T1/pcr/m/n/10 working_directory() Underfull \hbox (badness 7685) in paragraph at lines 635--637 \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 637--639 []\T1/pcr/m/n/10 working_directory_root() Underfull \hbox (badness 10000) in paragraph at lines 637--639 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 COMPS.Data.Configuration.Configuration Underfull \hbox (badness 10000) in paragraph at lines 639--641 []\T1/pcr/m/n/10 working_directory_size() Underfull \hbox (badness 7685) in paragraph at lines 639--641 \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--644 []\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 648--650 []\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, 3138500 bytes). 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