Read the Docs build information Build id: 2300570 Project: institute-for-disease-modeling-pycomps Version: v2.11.0 Commit: f66569587ec6f2a9e3371cffc462287cdd954be8 Date: 2024-06-20T23:17:40.093448Z State: finished Success: True [rtd-command-info] start-time: 2024-06-20T23:20:50.405569Z, end-time: 2024-06-20T23:20:51.889624Z, duration: 1, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/pyCOMPS.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2024-06-20T23:20:51.969544Z, end-time: 2024-06-20T23:20:54.231201Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/tags/v2.11.0:refs/tags/v2.11.0 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/pyCOMPS * [new tag] v2.10.0 -> v2.10.0 * [new tag] v2.4.0 -> v2.4.0 * [new tag] v2.4.1 -> v2.4.1 * [new tag] v2.5.0 -> v2.5.0 * [new tag] v2.6.0 -> v2.6.0 * [new tag] v2.7.0 -> v2.7.0 * [new tag] v2.7.1 -> v2.7.1 * [new tag] v2.7.2 -> v2.7.2 * [new tag] v2.7.3 -> v2.7.3 * [new tag] v2.8.0 -> v2.8.0 * [new tag] v2.9.0 -> v2.9.0 * [new tag] v2.9.1 -> v2.9.1 [rtd-command-info] start-time: 2024-06-20T23:20:54.385773Z, end-time: 2024-06-20T23:20:54.517403Z, duration: 0, exit-code: 0 git checkout --force f66569587ec6f2a9e3371cffc462287cdd954be8 Note: switching to 'f66569587ec6f2a9e3371cffc462287cdd954be8'. 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 f665695 Merge branch 'master' of https://github.com/InstituteforDiseaseModeling/pyCOMPS [rtd-command-info] start-time: 2024-06-20T23:20:54.587649Z, end-time: 2024-06-20T23:20:54.647649Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip # Optionally set the version of Python and requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: setuptools path: . # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank # search: # ranking: [rtd-command-info] start-time: 2024-06-20T23:21:00.374473Z, end-time: 2024-06-20T23:21:00.474212Z, duration: 0, exit-code: 0 asdf global python 3.9.19 [rtd-command-info] start-time: 2024-06-20T23:21:00.901566Z, end-time: 2024-06-20T23:21:02.149281Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.19.final.0-64 in 907ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators 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websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, readthedocs-sphinx-search, pyzmq, pyyaml, python-json-logger, pyjwt, pycparser, py-make, psutil, prompt-toolkit, prometheus-client, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, json5, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, attrs, accessible-pygments, terminado, sphinxext.remoteliteralinclude, sphinx, rfc3339-validator, referencing, python-dateutil, pockets, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, cffi, bleach, beautifulsoup4, async-lru, asttokens, anyio, stack-data, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinxcontrib-jquery, sphinx-copybutton, pynacl, pygit2, pydata-sphinx-theme, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, cryptography, arrow, argon2-cffi-bindings, myst-parser, jsonschema, isoduration, ipython, argon2-cffi, pygithub, nbformat, ipykernel, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab Attempting uninstall: docutils Found existing installation: docutils 0.21.2 Uninstalling docutils-0.21.2: Successfully uninstalled docutils-0.21.2 Attempting uninstall: sphinx Found existing installation: Sphinx 7.3.7 Uninstalling Sphinx-7.3.7: Successfully uninstalled Sphinx-7.3.7 Successfully installed accessible-pygments-0.0.5 anyio-4.4.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cached-property-1.5.2 cffi-1.16.0 comm-0.2.2 cryptography-42.0.8 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docopt-0.6.2 docutils-0.19 exceptiongroup-1.2.1 executing-2.0.1 fastjsonschema-2.20.0 fqdn-1.5.1 ipykernel-6.29.4 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.25 jsonpointer-3.0.0 jsonschema-4.22.0 jsonschema-specifications-2023.12.1 jupyter-client-8.6.2 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.1 jupyter-server-terminals-0.5.3 jupyterlab-4.0.13 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.1 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.4 nest-asyncio-1.6.0 notebook-shim-0.2.4 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.2.2 pockets-0.9.1 prometheus-client-0.20.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.2 py-make-0.1.2 pycparser-2.22 pydata-sphinx-theme-0.15.3 pygit2-1.4.0 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pyyaml-6.0.1 pyzmq-26.0.3 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.18.1 send2trash-1.8.3 six-1.16.0 sniffio-1.3.1 soupsieve-2.5 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.3.0 tornado-6.4.1 traitlets-5.14.3 types-python-dateutil-2.9.0.20240316 typing-extensions-4.12.2 uri-template-1.3.0 wcwidth-0.2.13 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 wrapt-1.16.0 [rtd-command-info] start-time: 2024-06-20T23:21:39.930855Z, end-time: 2024-06-20T23:21:41.364639Z, duration: 1, exit-code: 0 python ./setup.py install --force running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() 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/__main__.py -> build/lib/COMPS copying COMPS/Client.py -> build/lib/COMPS copying COMPS/__init__.py -> build/lib/COMPS copying COMPS/CredentialPrompt.py -> build/lib/COMPS copying COMPS/AuthManager.py -> build/lib/COMPS creating build/lib/COMPS/Data copying COMPS/Data/AssetCollectionFile.py -> build/lib/COMPS/Data copying COMPS/Data/Simulation.py -> build/lib/COMPS/Data copying COMPS/Data/BaseEntity.py -> build/lib/COMPS/Data copying COMPS/Data/QueryCriteria.py -> build/lib/COMPS/Data copying COMPS/Data/AssetFile.py -> build/lib/COMPS/Data copying COMPS/Data/SerializableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/Experiment.py -> build/lib/COMPS/Data copying COMPS/Data/Suite.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/WorkItemFile.py -> build/lib/COMPS/Data copying COMPS/Data/Priority.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/AssetCollection.py -> build/lib/COMPS/Data copying COMPS/Data/WorkItem.py -> build/lib/COMPS/Data copying COMPS/Data/TaggableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/__init__.py -> build/lib/COMPS/Data copying COMPS/Data/CommissionableEntity.py -> build/lib/COMPS/Data copying COMPS/Data/AssetType.py -> build/lib/COMPS/Data copying COMPS/Data/OutputFileMetadata.py -> build/lib/COMPS/Data copying COMPS/Data/SimulationFile.py -> build/lib/COMPS/Data creating build/lib/COMPS/utils copying COMPS/utils/get_output_files_for_workitem.py -> build/lib/COMPS/utils copying COMPS/utils/get_output_tail.py -> build/lib/COMPS/utils copying COMPS/utils/rerun_failed_simulations_for_experiment.py -> build/lib/COMPS/utils copying COMPS/utils/__example_utility_template__.py -> build/lib/COMPS/utils copying COMPS/utils/main.py -> build/lib/COMPS/utils copying COMPS/utils/get_user_info.py -> build/lib/COMPS/utils copying COMPS/utils/create_asset_collection.py -> build/lib/COMPS/utils copying COMPS/utils/get_status.py -> build/lib/COMPS/utils copying COMPS/utils/__init__.py -> build/lib/COMPS/utils copying COMPS/utils/clone_simulation.py -> build/lib/COMPS/utils copying COMPS/utils/get_output_files_for_experiment.py -> build/lib/COMPS/utils 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/__main__.py -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/Client.py -> build/bdist.linux-x86_64/egg/COMPS creating 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/Simulation.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/QueryCriteria.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/SerializableEntity.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/Suite.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/WorkItemFile.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/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/AssetCollection.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/TaggableEntity.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/CommissionableEntity.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/OutputFileMetadata.py -> build/bdist.linux-x86_64/egg/COMPS/Data copying build/lib/COMPS/Data/SimulationFile.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/__init__.py -> build/bdist.linux-x86_64/egg/COMPS creating 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/utils/get_output_tail.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/__example_utility_template__.py -> 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/get_user_info.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_status.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/clone_simulation.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/logging.ini -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/CredentialPrompt.py -> build/bdist.linux-x86_64/egg/COMPS copying build/lib/COMPS/AuthManager.py -> build/bdist.linux-x86_64/egg/COMPS byte-compiling build/bdist.linux-x86_64/egg/COMPS/__main__.py to __main__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Client.py to Client.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollectionFile.py to AssetCollectionFile.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Simulation.py to Simulation.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/BaseEntity.py to BaseEntity.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/QueryCriteria.py to QueryCriteria.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetFile.py to AssetFile.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/SerializableEntity.py to SerializableEntity.cpython-39.pyc build/bdist.linux-x86_64/egg/COMPS/Data/SerializableEntity.py:111: SyntaxWarning: "is not" with a literal. Did you mean "!="? if name[0] is not '_' or include_hidden_props: byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Experiment.py to Experiment.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Suite.py to Suite.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetManager.py to AssetManager.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Configuration.py to Configuration.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItemFile.py to WorkItemFile.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/Priority.py to Priority.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/HpcJob.py to HpcJob.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/RelatableEntity.py to RelatableEntity.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetCollection.py to AssetCollection.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItem.py to WorkItem.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/TaggableEntity.py to TaggableEntity.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/CommissionableEntity.py to CommissionableEntity.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/AssetType.py to AssetType.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/OutputFileMetadata.py to OutputFileMetadata.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/SimulationFile.py to SimulationFile.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems/BuilderWorkItem.py to BuilderWorkItem.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/Data/WorkItems/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_files_for_workitem.py to get_output_files_for_workitem.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_tail.py to get_output_tail.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/rerun_failed_simulations_for_experiment.py to rerun_failed_simulations_for_experiment.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/__example_utility_template__.py to __example_utility_template__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/main.py to main.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_user_info.py to get_user_info.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/create_asset_collection.py to create_asset_collection.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_status.py to get_status.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/clone_simulation.py to clone_simulation.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/utils/get_output_files_for_experiment.py to get_output_files_for_experiment.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/CredentialPrompt.py to CredentialPrompt.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/COMPS/AuthManager.py to AuthManager.cpython-39.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-2.11.0-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing pyCOMPS-2.11.0-py3.9.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/pyCOMPS-2.11.0-py3.9.egg Extracting pyCOMPS-2.11.0-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/pyCOMPS-2.11.0-py3.9.egg/COMPS/Data/SerializableEntity.py:111: SyntaxWarning: "is not" with a literal. Did you mean "!="? if name[0] is not '_' or include_hidden_props: Adding pyCOMPS 2.11.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/pyCOMPS-2.11.0-py3.9.egg Processing dependencies for pyCOMPS==2.11.0 Searching for xdg>=4.0.1 Reading https://pypi.org/simple/xdg/ Downloading https://files.pythonhosted.org/packages/dd/54/3516c1cf349060fc3578686d271eba242f10ec00b4530c2985af9faac49b/xdg-6.0.0-py3-none-any.whl#sha256=df3510755b4395157fc04fc3b02467c777f3b3ca383257397f09ab0d4c16f936 Best match: xdg 6.0.0 Processing xdg-6.0.0-py3-none-any.whl Installing xdg-6.0.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Adding xdg 6.0.0 to easy-install.pth file detected new path './pyCOMPS-2.11.0-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/xdg-6.0.0-py3.9.egg Searching for future>=0.16.0 Reading https://pypi.org/simple/future/ Downloading https://files.pythonhosted.org/packages/da/71/ae30dadffc90b9006d77af76b393cb9dfbfc9629f339fc1574a1c52e6806/future-1.0.0-py3-none-any.whl#sha256=929292d34f5872e70396626ef385ec22355a1fae8ad29e1a734c3e43f9fbc216 Best match: future 1.0.0 Processing future-1.0.0-py3-none-any.whl Installing future-1.0.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Adding future 1.0.0 to easy-install.pth file detected new path './xdg-6.0.0-py3.9.egg' Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/future-1.0.0-py3.9.egg Searching for pytz>=2016.3 Reading https://pypi.org/simple/pytz/ Downloading https://files.pythonhosted.org/packages/9c/3d/a121f284241f08268b21359bd425f7d4825cffc5ac5cd0e1b3d82ffd2b10/pytz-2024.1-py2.py3-none-any.whl#sha256=328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319 Best match: pytz 2024.1 Processing pytz-2024.1-py2.py3-none-any.whl Installing pytz-2024.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Adding pytz 2024.1 to easy-install.pth file detected new path './future-1.0.0-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages/pytz-2024.1-py3.9.egg Searching for requests==2.32.3 Best match: requests 2.32.3 Adding requests 2.32.3 to easy-install.pth file detected new path './pytz-2024.1-py3.9.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Searching for certifi==2024.6.2 Best match: certifi 2024.6.2 Adding certifi 2024.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Searching for urllib3==2.2.2 Best match: urllib3 2.2.2 Adding urllib3 2.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Searching for idna==3.7 Best match: idna 3.7 Adding idna 3.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Searching for charset-normalizer==3.3.2 Best match: charset-normalizer 3.3.2 Adding charset-normalizer 3.3.2 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/v2.11.0/lib/python3.9/site-packages Finished processing dependencies for pyCOMPS==2.11.0 [rtd-command-info] start-time: 2024-06-20T23:21:41.967099Z, end-time: 2024-06-20T23:21:42.029164Z, 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 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', 'sphinx_search.extension', # search across multiple docsets in domain 'sphinx.ext.viewcode', # link to view source code 'myst_parser', # source files written in MD or RST ] myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "linkify", "replacements", "smartquotes", "strikethrough", "substitution", "tasklist", ] 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'] # 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 = 'en' # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'pydata_sphinx_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 = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "Web", "url": "https://docs.idmod.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/institutefordiseasemodeling/pyCOMPS", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/idm-logo-transparent.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/pyCOMPS/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/pyCOMPS/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # Add any paths that contain custom themes here, relative to this directory. # 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-logo-transparent.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_css_files = ['theme_overrides.css'] #html_js_files = ['show_block_by_os.js'] # 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' # -- RTD Sphinx search for searching across the entire domain, default parent ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } # -- 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') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "v2.11.0", 'version_slug': "v2.11.0", '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/"), ("v2.11.0", "/en/v2.11.0/"), ("v2.10.0", "/en/v2.10.0/"), ("v2.9.1", "/en/v2.9.1/"), ("v2.9.0", "/en/v2.9.0/"), ("v2.8.0", "/en/v2.8.0/"), ("v2.7.3", "/en/v2.7.3/"), ("v2.7.2", "/en/v2.7.2/"), ("v2.7.1", "/en/v2.7.1/"), ("v2.7.0", "/en/v2.7.0/"), ("v2.6.0", "/en/v2.6.0/"), ("v2.5.0", "/en/v2.5.0/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-pycomps', 'name': u'pyCOMPS', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'pyCOMPS', 'github_version': 'v2.11.0', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'v2.11.0', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'v2.11.0', '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': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'f6656958', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'tag' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-pycomps/builds/2300570/' 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: 2024-06-20T23:21:42.096931Z, end-time: 2024-06-20T23:21:57.815698Z, duration: 15, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 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... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'deflist', 'fieldlist', 'html_admonition', 'attrs_inline', 'html_image', 'smartquotes', 'tasklist', 'strikethrough', 'colon_fence', 'dollarmath', 'replacements', 'amsmath', 'substitution', 'linkify'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 55 source files that are out of date updating environment: [new config] 55 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... [ 10%] 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... [ 21%] COMPS.Data.Configuration reading sources... [ 23%] COMPS.Data.Experiment reading sources... [ 25%] COMPS.Data.HpcJob reading sources... [ 27%] COMPS.Data.OutputFileMetadata reading sources... [ 29%] COMPS.Data.Priority reading sources... [ 30%] COMPS.Data.QueryCriteria reading sources... [ 32%] COMPS.Data.RelatableEntity reading sources... [ 34%] COMPS.Data.SerializableEntity reading sources... [ 36%] COMPS.Data.Simulation reading sources... 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[100%] images/terminology.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2024-06-20T23:21:57.895006Z, end-time: 2024-06-20T23:22:00.773512Z, duration: 2, exit-code: 0 python -m sphinx -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v6.2.1 making output directory... done loading pickled environment... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'dollarmath', 'linkify', 'tasklist', 'amsmath', 'fieldlist', 'strikethrough', 'substitution', 'html_image', 'attrs_inline', 'deflist', 'html_admonition', 'replacements', 'colon_fence', 'smartquotes'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] modules 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.get_user_info 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... 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