Read the Docs build information Build id: 1961823 Project: institute-for-disease-modeling-pycomps Version: latest Commit: adfa211c16de96035c44e1138fc1a9fc44897c25 Date: 2024-01-19T21:16:08.520168Z State: finished Success: True [rtd-command-info] start-time: 2024-01-19T21:16:09.724545Z, end-time: 2024-01-19T21:16:11.175479Z, 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: 2024-01-19T21:16:11.239672Z, end-time: 2024-01-19T21:16:14.030527Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master 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] v2.5.0 -> 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: 2024-01-19T21:16:14.160170Z, end-time: 2024-01-19T21:16:14.279840Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to 'origin/master'. 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 adfa211 Fixes doc search bug and adds analytics tag (#53) [rtd-command-info] start-time: 2024-01-19T21:16:14.336569Z, end-time: 2024-01-19T21:16:14.395580Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-01-19T21:16:14.462248Z, end-time: 2024-01-19T21:16:14.523599Z, 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: 2024-01-19T21:16:20.768289Z, end-time: 2024-01-19T21:16:20.859326Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-01-19T21:16:21.259150Z, end-time: 2024-01-19T21:16:22.549046Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 916ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest, 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 BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-01-19T21:16:22.615893Z, end-time: 2024-01-19T21:16:33.427056Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (23.1) Collecting pip Downloading pip-23.3.2-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 40.0 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (67.6.1) Collecting setuptools Downloading setuptools-69.0.3-py3-none-any.whl (819 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.5/819.5 kB 147.9 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 Uninstalling pip-23.1: Successfully uninstalled pip-23.1 Successfully installed pip-23.3.2 setuptools-69.0.3 [rtd-command-info] start-time: 2024-01-19T21:16:33.497243Z, end-time: 2024-01-19T21:16:40.112020Z, duration: 6, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext Collecting sphinx Downloading sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB) Collecting readthedocs-sphinx-ext Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl.metadata (1.5 kB) Collecting sphinxcontrib-applehelp (from sphinx) Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-devhelp (from sphinx) Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-jsmath (from sphinx) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx) Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx) Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB) Collecting sphinxcontrib-qthelp (from sphinx) Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB) Collecting Jinja2>=3.0 (from sphinx) Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB) Collecting Pygments>=2.14 (from sphinx) Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB) Collecting docutils<0.21,>=0.18.1 (from sphinx) Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB) Collecting snowballstemmer>=2.0 (from sphinx) Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 11.5 MB/s eta 0:00:00 Collecting babel>=2.9 (from sphinx) Downloading Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB) Collecting alabaster<0.8,>=0.7 (from sphinx) Downloading alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB) Collecting imagesize>=1.3 (from sphinx) Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting requests>=2.25.0 (from sphinx) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting packaging>=21.0 (from sphinx) Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting importlib-metadata>=4.8 (from sphinx) Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB) Collecting zipp>=0.5 (from importlib-metadata>=4.8->sphinx) Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->sphinx) Downloading MarkupSafe-2.1.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB) Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx) Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx) Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx) Downloading urllib3-2.1.0-py3-none-any.whl.metadata (6.4 kB) Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx) Downloading certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB) Downloading sphinx-7.2.6-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 99.7 MB/s eta 0:00:00 Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl (11 kB) Downloading alabaster-0.7.16-py3-none-any.whl (13 kB) Downloading Babel-2.14.0-py3-none-any.whl (11.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 186.4 MB/s eta 0:00:00 Downloading docutils-0.20.1-py3-none-any.whl (572 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 572.7/572.7 kB 252.2 MB/s eta 0:00:00 Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB) Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 223.0 MB/s eta 0:00:00 Downloading packaging-23.2-py3-none-any.whl (53 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 181.8 MB/s eta 0:00:00 Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 248.0 MB/s eta 0:00:00 Downloading requests-2.31.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 161.5 MB/s eta 0:00:00 Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl (99 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 99.2/99.2 kB 218.2 MB/s eta 0:00:00 Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl (92 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.7/92.7 kB 206.9 MB/s eta 0:00:00 Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl (120 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.0/120.0 kB 220.2 MB/s eta 0:00:00 Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl (83 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.5/83.5 kB 194.4 MB/s eta 0:00:00 Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl (89 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.4/89.4 kB 212.9 MB/s eta 0:00:00 Downloading certifi-2023.11.17-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.5/162.5 kB 230.6 MB/s eta 0:00:00 Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 224.5 MB/s eta 0:00:00 Downloading idna-3.6-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 180.7 MB/s eta 0:00:00 Downloading MarkupSafe-2.1.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Downloading urllib3-2.1.0-py3-none-any.whl (104 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 104.6/104.6 kB 216.6 MB/s eta 0:00:00 Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB) Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.3 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.1.0 zipp-3.17.0 [rtd-command-info] start-time: 2024-01-19T21:16:40.189444Z, end-time: 2024-01-19T21:17:03.017224Z, duration: 22, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting py-make (from -r docs/requirements.txt (line 1)) Downloading py_make-0.1.1-py2.py3-none-any.whl (9.4 kB) Collecting pygit2~=1.4.0 (from -r docs/requirements.txt (line 2)) Downloading pygit2-1.4.0-cp39-cp39-manylinux2010_x86_64.whl (3.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 53.3 MB/s eta 0:00:00 Collecting sphinxext.remoteliteralinclude (from -r docs/requirements.txt (line 3)) Downloading sphinxext_remoteliteralinclude-0.4.0-py3-none-any.whl (6.4 kB) Collecting sphinx~=6.2.1 (from -r docs/requirements.txt (line 4)) Downloading sphinx-6.2.1-py3-none-any.whl (3.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 199.9 MB/s eta 0:00:00 Collecting sphinx-rtd-theme~=1.2.2 (from -r docs/requirements.txt (line 5)) Downloading sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl.metadata (4.5 kB) Collecting sphinxcontrib-napoleon~=0.7 (from -r docs/requirements.txt (line 6)) Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting plantweb~=1.2.1 (from -r docs/requirements.txt (line 7)) Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.17 (from -r docs/requirements.txt (line 8)) Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting nbsphinx~=0.9.2 (from -r docs/requirements.txt (line 9)) Downloading nbsphinx-0.9.3-py3-none-any.whl.metadata (2.1 kB) Collecting jupyterlab~=4.0.2 (from -r docs/requirements.txt (line 10)) Downloading jupyterlab-4.0.11-py3-none-any.whl.metadata (15 kB) Collecting myst-parser~=2.0.0 (from -r docs/requirements.txt (line 11)) Downloading myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB) Collecting readthedocs-sphinx-search~=0.3.1 (from -r docs/requirements.txt (line 12)) Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB) Collecting sphinx-copybutton~=0.5.2 (from -r docs/requirements.txt (line 13)) Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB) Collecting pygithub~=1.57 (from -r docs/requirements.txt (line 14)) Downloading PyGithub-1.59.1-py3-none-any.whl.metadata (2.0 kB) Collecting sphinxcontrib-jquery~=4.1 (from -r docs/requirements.txt (line 15)) Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.1/121.1 kB 217.1 MB/s eta 0:00:00 Collecting docopt>=0.6.0 (from py-make->-r docs/requirements.txt (line 1)) Downloading docopt-0.6.2.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting cffi>=1.4.0 (from pygit2~=1.4.0->-r docs/requirements.txt (line 2)) Downloading cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB) Collecting cached-property (from pygit2~=1.4.0->-r docs/requirements.txt (line 2)) Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Collecting six (from sphinxext.remoteliteralinclude->-r docs/requirements.txt (line 3)) Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (1.0.8) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (1.0.6) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.0.5) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (1.1.10) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (1.0.7) Requirement already satisfied: Jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (3.1.3) Requirement already satisfied: Pygments>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.17.2) Collecting docutils<0.20,>=0.18.1 (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) Downloading docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 243.0 MB/s eta 0:00:00 Requirement already satisfied: snowballstemmer>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.2.0) Requirement already satisfied: babel>=2.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.14.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (0.7.16) Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (1.4.1) Requirement already satisfied: requests>=2.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.31.0) Requirement already satisfied: packaging>=21.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (23.2) Requirement already satisfied: importlib-metadata>=4.8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (7.0.1) Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 231.7 MB/s eta 0:00:00 Collecting pockets>=0.3 (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 6)) Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Collecting nbconvert!=5.4 (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading nbconvert-7.14.2-py3-none-any.whl.metadata (7.7 kB) Collecting traitlets>=5 (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading traitlets-5.14.1-py3-none-any.whl.metadata (10 kB) Collecting nbformat (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading nbformat-5.9.2-py3-none-any.whl.metadata (3.4 kB) Collecting async-lru>=1.0.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB) Collecting ipykernel (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading ipykernel-6.29.0-py3-none-any.whl.metadata (6.0 kB) Collecting jupyter-core (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyter_core-5.7.1-py3-none-any.whl.metadata (3.4 kB) Collecting jupyter-lsp>=2.0.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyter_lsp-2.2.2-py3-none-any.whl.metadata (1.8 kB) Collecting jupyter-server<3,>=2.4.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyter_server-2.12.5-py3-none-any.whl.metadata (8.4 kB) Collecting jupyterlab-server<3,>=2.19.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyterlab_server-2.25.2-py3-none-any.whl.metadata (5.9 kB) Collecting notebook-shim>=0.2 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading notebook_shim-0.2.3-py3-none-any.whl (13 kB) Collecting tomli (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading tomli-2.0.1-py3-none-any.whl (12 kB) Collecting tornado>=6.2.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting markdown-it-py~=3.0 (from myst-parser~=2.0.0->-r docs/requirements.txt (line 11)) Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB) Collecting mdit-py-plugins~=0.4 (from myst-parser~=2.0.0->-r docs/requirements.txt (line 11)) Downloading mdit_py_plugins-0.4.0-py3-none-any.whl.metadata (2.7 kB) Collecting pyyaml (from myst-parser~=2.0.0->-r docs/requirements.txt (line 11)) Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting deprecated (from pygithub~=1.57->-r docs/requirements.txt (line 14)) Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->pygithub~=1.57->-r docs/requirements.txt (line 14)) Downloading PyJWT-2.8.0-py3-none-any.whl.metadata (4.2 kB) Collecting pynacl>=1.4.0 (from pygithub~=1.57->-r docs/requirements.txt (line 14)) Downloading PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 856.7/856.7 kB 239.9 MB/s eta 0:00:00 Collecting typing-extensions>=4.0.0 (from async-lru>=1.0.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB) Collecting pycparser (from cffi>=1.4.0->pygit2~=1.4.0->-r docs/requirements.txt (line 2)) Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 208.4 MB/s eta 0:00:00 Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from importlib-metadata>=4.8->sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (3.17.0) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from Jinja2>=3.0->sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.1.3) Collecting anyio>=3.1.0 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading anyio-4.2.0-py3-none-any.whl.metadata (4.6 kB) Collecting argon2-cffi (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading argon2_cffi-23.1.0-py3-none-any.whl.metadata (5.2 kB) Collecting jupyter-client>=7.4.4 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyter_client-8.6.0-py3-none-any.whl.metadata (8.3 kB) Collecting jupyter-events>=0.9.0 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyter_events-0.9.0-py3-none-any.whl.metadata (5.7 kB) Collecting jupyter-server-terminals (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jupyter_server_terminals-0.5.1-py3-none-any.whl.metadata (5.6 kB) Collecting overrides (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading overrides-7.4.0-py3-none-any.whl.metadata (5.7 kB) Collecting prometheus-client (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading prometheus_client-0.19.0-py3-none-any.whl.metadata (1.8 kB) Collecting pyzmq>=24 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading pyzmq-25.1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (4.9 kB) Collecting send2trash>=1.8.2 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading Send2Trash-1.8.2-py3-none-any.whl (18 kB) Collecting terminado>=0.8.3 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading terminado-0.18.0-py3-none-any.whl.metadata (5.8 kB) Collecting websocket-client (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading websocket_client-1.7.0-py3-none-any.whl.metadata (7.9 kB) Collecting platformdirs>=2.5 (from jupyter-core->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading platformdirs-4.1.0-py3-none-any.whl.metadata (11 kB) Collecting json5>=0.9.0 (from jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading json5-0.9.14-py2.py3-none-any.whl.metadata (10 kB) Collecting jsonschema>=4.18.0 (from jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jsonschema-4.21.1-py3-none-any.whl.metadata (7.8 kB) Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser~=2.0.0->-r docs/requirements.txt (line 11)) Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB) Collecting beautifulsoup4 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB) Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading bleach-6.1.0-py3-none-any.whl.metadata (30 kB) Collecting defusedxml (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB) Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB) Collecting nbclient>=0.5.0 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading nbclient-0.9.0-py3-none-any.whl.metadata (7.8 kB) Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB) Collecting tinycss2 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB) Collecting fastjsonschema (from nbformat->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading fastjsonschema-2.19.1-py3-none-any.whl.metadata (2.1 kB) Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->pygithub~=1.57->-r docs/requirements.txt (line 14)) Downloading cryptography-41.0.7-cp37-abi3-manylinux_2_28_x86_64.whl.metadata (5.2 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (3.6) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2.1.0) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 4)) (2023.11.17) Collecting wrapt<2,>=1.10 (from deprecated->pygithub~=1.57->-r docs/requirements.txt (line 14)) Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB) Collecting comm>=0.1.1 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading comm-0.2.1-py3-none-any.whl.metadata (3.7 kB) Collecting debugpy>=1.6.5 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading debugpy-1.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.0 kB) Collecting ipython>=7.23.1 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading ipython-8.18.1-py3-none-any.whl.metadata (6.0 kB) Collecting matplotlib-inline>=0.1 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB) Collecting nest-asyncio (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading nest_asyncio-1.5.9-py3-none-any.whl.metadata (2.8 kB) Collecting psutil (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB) Collecting sniffio>=1.1 (from anyio>=3.1.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading sniffio-1.3.0-py3-none-any.whl (10 kB) Collecting exceptiongroup>=1.0.2 (from anyio>=3.1.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB) Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting decorator (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB) Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB) Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading prompt_toolkit-3.0.43-py3-none-any.whl.metadata (6.5 kB) Collecting stack-data (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB) Collecting pexpect>4.3 (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB) Collecting attrs>=22.2.0 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB) Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB) Collecting referencing>=0.28.4 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading referencing-0.32.1-py3-none-any.whl.metadata (2.7 kB) Collecting rpds-py>=0.7.1 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading rpds_py-0.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB) Collecting python-dateutil>=2.8.2 (from jupyter-client>=7.4.4->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 231.3 MB/s eta 0:00:00 Collecting python-json-logger>=2.0.4 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading python_json_logger-2.0.7-py3-none-any.whl (8.1 kB) Collecting rfc3339-validator (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading rfc3339_validator-0.1.4-py2.py3-none-any.whl (3.5 kB) Collecting rfc3986-validator>=0.1.1 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading rfc3986_validator-0.1.1-py2.py3-none-any.whl (4.2 kB) Collecting ptyprocess (from terminado>=0.8.3->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting argon2-cffi-bindings (from argon2-cffi->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (86 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.2/86.2 kB 179.8 MB/s eta 0:00:00 Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 9)) Downloading soupsieve-2.5-py3-none-any.whl.metadata (4.7 kB) Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 210.3 MB/s eta 0:00:00 Collecting fqdn (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading fqdn-1.5.1-py3-none-any.whl (9.1 kB) Collecting isoduration (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading isoduration-20.11.0-py3-none-any.whl (11 kB) Collecting jsonpointer>1.13 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading jsonpointer-2.4-py2.py3-none-any.whl.metadata (2.5 kB) Collecting uri-template (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading uri_template-1.3.0-py3-none-any.whl.metadata (8.8 kB) Collecting webcolors>=1.11 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading webcolors-1.13-py3-none-any.whl (14 kB) Collecting wcwidth (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) Collecting executing>=1.2.0 (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading executing-2.0.1-py2.py3-none-any.whl.metadata (9.0 kB) Collecting asttokens>=2.1.0 (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB) Collecting pure-eval (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB) Collecting arrow>=0.15.0 (from isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading arrow-1.3.0-py3-none-any.whl.metadata (7.5 kB) Collecting types-python-dateutil>=2.8.10 (from arrow>=0.15.0->isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 10)) Downloading types_python_dateutil-2.8.19.20240106-py3-none-any.whl.metadata (1.8 kB) Downloading sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 213.4 MB/s eta 0:00:00 Downloading nbsphinx-0.9.3-py3-none-any.whl (31 kB) Downloading jupyterlab-4.0.11-py3-none-any.whl (9.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.2/9.2 MB 205.5 MB/s eta 0:00:00 Downloading myst_parser-2.0.0-py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.2/77.2 kB 200.5 MB/s eta 0:00:00 Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB) Downloading PyGithub-1.59.1-py3-none-any.whl (342 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 342.2/342.2 kB 240.4 MB/s eta 0:00:00 Downloading async_lru-2.0.4-py3-none-any.whl (6.1 kB) Downloading cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (443 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 443.4/443.4 kB 244.6 MB/s eta 0:00:00 Downloading jupyter_lsp-2.2.2-py3-none-any.whl (68 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.8/68.8 kB 195.3 MB/s eta 0:00:00 Downloading jupyter_server-2.12.5-py3-none-any.whl (380 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 380.3/380.3 kB 238.4 MB/s eta 0:00:00 Downloading jupyter_core-5.7.1-py3-none-any.whl (28 kB) Downloading jupyterlab_server-2.25.2-py3-none-any.whl (58 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.9/58.9 kB 193.4 MB/s eta 0:00:00 Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 207.9 MB/s eta 0:00:00 Downloading mdit_py_plugins-0.4.0-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 182.5 MB/s eta 0:00:00 Downloading nbconvert-7.14.2-py3-none-any.whl (256 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 256.4/256.4 kB 225.9 MB/s eta 0:00:00 Downloading nbformat-5.9.2-py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.6/77.6 kB 207.0 MB/s eta 0:00:00 Downloading PyJWT-2.8.0-py3-none-any.whl (22 kB) Downloading tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (435 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 435.4/435.4 kB 240.2 MB/s eta 0:00:00 Downloading traitlets-5.14.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.4/85.4 kB 213.7 MB/s eta 0:00:00 Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB) Downloading ipykernel-6.29.0-py3-none-any.whl (116 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 116.1/116.1 kB 220.5 MB/s eta 0:00:00 Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 244.5 MB/s eta 0:00:00 Downloading anyio-4.2.0-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.5/85.5 kB 203.6 MB/s eta 0:00:00 Downloading bleach-6.1.0-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.8/162.8 kB 220.3 MB/s eta 0:00:00 Downloading comm-0.2.1-py3-none-any.whl (7.2 kB) Downloading cryptography-41.0.7-cp37-abi3-manylinux_2_28_x86_64.whl (4.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 195.5 MB/s eta 0:00:00 Downloading debugpy-1.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 214.2 MB/s eta 0:00:00 Downloading ipython-8.18.1-py3-none-any.whl (808 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 808.2/808.2 kB 244.9 MB/s eta 0:00:00 Downloading json5-0.9.14-py2.py3-none-any.whl (19 kB) Downloading jsonschema-4.21.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.5/85.5 kB 193.9 MB/s eta 0:00:00 Downloading jupyter_client-8.6.0-py3-none-any.whl (105 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 105.9/105.9 kB 196.7 MB/s eta 0:00:00 Downloading jupyter_events-0.9.0-py3-none-any.whl (18 kB) Downloading mistune-3.0.2-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.0/48.0 kB 181.5 MB/s eta 0:00:00 Downloading nbclient-0.9.0-py3-none-any.whl (24 kB) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB) Downloading platformdirs-4.1.0-py3-none-any.whl (17 kB) Downloading pyzmq-25.1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 156.4 MB/s eta 0:00:00 Downloading terminado-0.18.0-py3-none-any.whl (14 kB) Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB) Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 181.4 MB/s eta 0:00:00 Downloading argon2_cffi-23.1.0-py3-none-any.whl (15 kB) Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.9/147.9 kB 222.3 MB/s eta 0:00:00 Downloading fastjsonschema-2.19.1-py3-none-any.whl (23 kB) Downloading jupyter_server_terminals-0.5.1-py3-none-any.whl (13 kB) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB) Downloading nest_asyncio-1.5.9-py3-none-any.whl (5.3 kB) Downloading overrides-7.4.0-py3-none-any.whl (17 kB) Downloading prometheus_client-0.19.0-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 178.6 MB/s eta 0:00:00 Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 231.6 MB/s eta 0:00:00 Downloading websocket_client-1.7.0-py3-none-any.whl (58 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.5/58.5 kB 186.3 MB/s eta 0:00:00 Downloading attrs-23.2.0-py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.8/60.8 kB 190.7 MB/s eta 0:00:00 Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB) Downloading jedi-0.19.1-py2.py3-none-any.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 242.1 MB/s eta 0:00:00 Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.8/63.8 kB 179.4 MB/s eta 0:00:00 Downloading prompt_toolkit-3.0.43-py3-none-any.whl (386 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 386.1/386.1 kB 239.6 MB/s eta 0:00:00 Downloading referencing-0.32.1-py3-none-any.whl (26 kB) Downloading rpds_py-0.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 245.3 MB/s eta 0:00:00 Downloading soupsieve-2.5-py3-none-any.whl (36 kB) Downloading stack_data-0.6.3-py3-none-any.whl (24 kB) Downloading asttokens-2.4.1-py2.py3-none-any.whl (27 kB) Downloading executing-2.0.1-py2.py3-none-any.whl (24 kB) Downloading jsonpointer-2.4-py2.py3-none-any.whl (7.8 kB) Downloading uri_template-1.3.0-py3-none-any.whl (11 kB) Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Downloading arrow-1.3.0-py3-none-any.whl (66 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.4/66.4 kB 181.6 MB/s eta 0:00:00 Downloading types_python_dateutil-2.8.19.20240106-py3-none-any.whl (9.7 kB) Building wheels for 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=13707 sha256=d9f5d77f7c821209dc3ca27acf98f7f3947d24e6b18e43c2b1ffa70d8dd7067c Stored in directory: /tmp/pip-ephem-wheel-cache-pdeoub2k/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b Successfully built docopt Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, json5, fastjsonschema, docopt, cached-property, wrapt, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tomli, 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, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, attrs, 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, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, cryptography, arrow, argon2-cffi-bindings, sphinx-rtd-theme, 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 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 Successfully installed anyio-4.2.0 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-0.2.1 cryptography-41.0.7 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docopt-0.6.2 docutils-0.18.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.1 fqdn-1.5.1 ipykernel-6.29.0 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyter-events-0.9.0 jupyter-lsp-2.2.2 jupyter-server-2.12.5 jupyter-server-terminals-0.5.1 jupyterlab-4.0.11 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.9.0 nbconvert-7.14.2 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.5.9 notebook-shim-0.2.3 overrides-7.4.0 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.1.0 pockets-0.9.1 prometheus-client-0.19.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 py-make-0.1.1 pycparser-2.21 pygit2-1.4.0 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-dateutil-2.8.2 python-json-logger-2.0.7 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.32.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.17.1 send2trash-1.8.2 six-1.16.0 sniffio-1.3.0 soupsieve-2.5 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinx-rtd-theme-1.2.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0 stack-data-0.6.3 terminado-0.18.0 tinycss2-1.2.1 tomli-2.0.1 tornado-6.4 traitlets-5.14.1 types-python-dateutil-2.8.19.20240106 typing-extensions-4.9.0 uri-template-1.3.0 wcwidth-0.2.13 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 wrapt-1.16.0 [rtd-command-info] start-time: 2024-01-19T21:17:03.095131Z, end-time: 2024-01-19T21:17:05.993409Z, duration: 2, exit-code: 0 python ./setup.py install --force running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/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/latest/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/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/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/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-2.10.0-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-2.10.0-py3.9.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages/pyCOMPS-2.10.0-py3.9.egg Extracting pyCOMPS-2.10.0-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages/pyCOMPS-2.10.0-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 2.10.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages/pyCOMPS-2.10.0-py3.9.egg Processing dependencies for pyCOMPS==2.10.0 Searching for xdg>=4.0.1 Reading https://pypi.org/simple/xdg/ Downloading https://files.pythonhosted.org/packages/dd/54/3516c1cf349060fc3578686d271eba242f10ec00b4530c2985af9faac49b/xdg-6.0.0-py3-none-any.whl#sha256=df3510755b4395157fc04fc3b02467c777f3b3ca383257397f09ab0d4c16f936 Best match: xdg 6.0.0 Processing xdg-6.0.0-py3-none-any.whl Installing xdg-6.0.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages Adding xdg 6.0.0 to easy-install.pth file detected new path './pyCOMPS-2.10.0-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/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/8f/2e/cf6accf7415237d6faeeebdc7832023c90e0282aa16fd3263db0eb4715ec/future-0.18.3.tar.gz#sha256=34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307 Best match: future 0.18.3 Processing future-0.18.3.tar.gz Writing /tmp/easy_install-c29x8geh/future-0.18.3/setup.cfg Running future-0.18.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-c29x8geh/future-0.18.3/egg-dist-tmp-c68wfepk 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' /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/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() zip_safe flag not set; analyzing archive contents... future.backports.test.__pycache__.ssl_servers.cpython-39: module references __file__ future.backports.test.__pycache__.support.cpython-39: module references __file__ future.standard_library.__pycache__.__init__.cpython-39: module references __file__ future.standard_library.__pycache__.__init__.cpython-39: module references __path__ future.utils.__pycache__.__init__.cpython-39: module MAY be using inspect.stack past.builtins.__pycache__.misc.cpython-39: module MAY be using inspect.stack past.translation.__pycache__.__init__.cpython-39: module references __file__ past.translation.__pycache__.__init__.cpython-39: module references __path__ Adding future 0.18.3 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/latest/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages/future-0.18.3-py3.9.egg Searching for pytz>=2016.3 Reading https://pypi.org/simple/pytz/ Downloading https://files.pythonhosted.org/packages/32/4d/aaf7eff5deb402fd9a24a1449a8119f00d74ae9c2efa79f8ef9994261fc2/pytz-2023.3.post1-py2.py3-none-any.whl#sha256=ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7 Best match: pytz 2023.3.post1 Processing pytz-2023.3.post1-py2.py3-none-any.whl Installing pytz-2023.3.post1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages Adding pytz 2023.3.post1 to easy-install.pth file detected new path './future-0.18.3-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages/pytz-2023.3.post1-py3.9.egg Searching for requests==2.31.0 Best match: requests 2.31.0 Adding requests 2.31.0 to easy-install.pth file detected new path './pytz-2023.3.post1-py3.9.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages Searching for certifi==2023.11.17 Best match: certifi 2023.11.17 Adding certifi 2023.11.17 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages Searching for urllib3==2.1.0 Best match: urllib3 2.1.0 Adding urllib3 2.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages Searching for idna==3.6 Best match: idna 3.6 Adding idna 3.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/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/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-pycomps/envs/latest/lib/python3.9/site-packages Finished processing dependencies for pyCOMPS==2.10.0 [rtd-command-info] start-time: 2024-01-19T21:17:06.702203Z, end-time: 2024-01-19T21:17:06.762814Z, 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', '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 = '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_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': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("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': [ ("html", "//docs.idmod.org/_/downloads/pycomps/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-pycomps', 'name': u'pyCOMPS', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'G-SVDSQH04EM', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'pyCOMPS', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': 'adfa211c', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-pycomps/builds/1961823/' 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: 2024-01-19T21:17:06.845788Z, end-time: 2024-01-19T21:17:15.519710Z, duration: 8, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 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={'html_image', 'colon_fence', 'amsmath', 'fieldlist', 'smartquotes', 'dollarmath', 'html_admonition', 'substitution', 'tasklist', 'attrs_inline', 'strikethrough', 'replacements', 'linkify', 'deflist'}, 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 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... [ 38%] COMPS.Data.SimulationFile reading sources... [ 40%] COMPS.Data.Suite reading sources... [ 42%] COMPS.Data.TaggableEntity reading sources... [ 44%] COMPS.Data.WorkItem reading sources... [ 46%] COMPS.Data.WorkItemFile reading sources... [ 48%] COMPS.Data.WorkItems reading sources... [ 50%] COMPS.Data.WorkItems.BuilderWorkItem reading sources... [ 51%] COMPS.utils reading sources... [ 53%] COMPS.utils.clone_simulation reading sources... [ 55%] COMPS.utils.create_asset_collection reading sources... [ 57%] COMPS.utils.get_output_files_for_experiment reading sources... [ 59%] COMPS.utils.get_output_files_for_workitem reading sources... [ 61%] COMPS.utils.get_output_tail reading sources... [ 62%] COMPS.utils.get_status reading sources... [ 64%] COMPS.utils.main reading sources... [ 66%] COMPS.utils.rerun_failed_simulations_for_experiment reading sources... [ 68%] architecture reading sources... [ 70%] create-climateinput reading sources... [ 72%] create-simulations reading sources... [ 74%] create-workitems-simulations reading sources... [ 75%] glossary reading sources... [ 77%] howto-cleanup reading sources... [ 79%] howto-create-climateinput reading sources... [ 81%] howto-create-simulations reading sources... [ 83%] howto-dashboard reading sources... [ 85%] howto-example-campaign reading sources... [ 87%] howto-example-config reading sources... [ 88%] howto-multichart-view reading sources... [ 90%] howto-weather-view reading sources... [ 92%] index reading sources... [ 94%] manage-workitems-simulations reading sources... [ 96%] modules reading sources... [ 98%] overview-comps reading sources... [100%] overview-terminology looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 1%] COMPS.AuthManager writing output... [ 3%] COMPS.Client writing output... [ 5%] COMPS.CredentialPrompt writing output... [ 7%] COMPS.Data writing output... [ 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 highlighting module code... [ 3%] COMPS.AuthManager highlighting module code... [ 6%] COMPS.Client highlighting module code... [ 9%] COMPS.CredentialPrompt highlighting module code... [ 12%] COMPS.Data.AssetCollection highlighting module code... [ 15%] COMPS.Data.AssetCollectionFile highlighting module code... [ 18%] COMPS.Data.AssetFile highlighting module code... [ 21%] COMPS.Data.AssetManager highlighting module code... [ 24%] COMPS.Data.AssetType highlighting module code... [ 27%] COMPS.Data.BaseEntity highlighting module code... [ 30%] COMPS.Data.CommissionableEntity highlighting module code... [ 33%] COMPS.Data.Configuration highlighting module code... [ 36%] COMPS.Data.Experiment highlighting module code... [ 39%] COMPS.Data.HpcJob highlighting module code... [ 42%] COMPS.Data.OutputFileMetadata highlighting module code... [ 45%] COMPS.Data.Priority highlighting module code... [ 48%] COMPS.Data.QueryCriteria highlighting module code... [ 51%] COMPS.Data.RelatableEntity highlighting module code... [ 54%] COMPS.Data.SerializableEntity highlighting module code... [ 57%] COMPS.Data.Simulation highlighting module code... [ 60%] COMPS.Data.SimulationFile highlighting module code... [ 63%] COMPS.Data.Suite highlighting module code... [ 66%] COMPS.Data.TaggableEntity highlighting module code... [ 69%] COMPS.Data.WorkItem highlighting module code... [ 72%] COMPS.Data.WorkItemFile highlighting module code... [ 75%] COMPS.Data.WorkItems.BuilderWorkItem highlighting module code... [ 78%] COMPS.utils.clone_simulation highlighting module code... [ 81%] COMPS.utils.create_asset_collection highlighting module code... [ 84%] COMPS.utils.get_output_files_for_experiment highlighting module code... [ 87%] COMPS.utils.get_output_files_for_workitem highlighting module code... [ 90%] COMPS.utils.get_output_tail highlighting module code... [ 93%] COMPS.utils.get_status highlighting module code... [ 96%] COMPS.utils.main highlighting module code... [100%] COMPS.utils.rerun_failed_simulations_for_experiment writing additional pages... search opensearch done copying images... [ 6%] ../_readthedocs/html/_images/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg copying images... [ 12%] images/input-search-vietnam.png copying images... [ 18%] images/input-search-vietnam-select.png copying images... [ 25%] images/input-search-vietnam-selected.png copying images... [ 31%] images/climate-submit.png copying images... [ 37%] images/create-input-files-generate.png copying images... [ 43%] images/dashboard-simsperstate.png copying images... [ 50%] images/chart-select.png copying images... [ 56%] images/chart-create.png copying images... [ 62%] images/chart-multi.png copying images... [ 68%] images/chart-ychannel.png copying images... [ 75%] images/weather-animation-climateproject.png copying images... [ 81%] images/weather-animation-play.png copying images... [ 87%] images/weather-animation-temperature-time.png copying images... [ 93%] images/weather-animation-chart.png copying images... [100%] images/terminology.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2024-01-19T21:17:15.602651Z, end-time: 2024-01-19T21:17:22.314980Z, duration: 6, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v6.2.1 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={'dollarmath', 'smartquotes', 'amsmath', 'colon_fence', 'html_admonition', 'substitution', 'tasklist', 'attrs_inline', 'deflist', 'html_image', 'strikethrough', 'fieldlist', 'replacements', '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 [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... [ 38%] COMPS.Data.SimulationFile reading sources... [ 40%] COMPS.Data.Suite reading sources... [ 42%] COMPS.Data.TaggableEntity reading sources... [ 44%] COMPS.Data.WorkItem reading sources... [ 46%] COMPS.Data.WorkItemFile reading sources... [ 48%] COMPS.Data.WorkItems reading sources... [ 50%] COMPS.Data.WorkItems.BuilderWorkItem reading sources... [ 51%] COMPS.utils reading sources... [ 53%] COMPS.utils.clone_simulation reading sources... [ 55%] COMPS.utils.create_asset_collection reading sources... [ 57%] COMPS.utils.get_output_files_for_experiment reading sources... [ 59%] COMPS.utils.get_output_files_for_workitem reading sources... [ 61%] COMPS.utils.get_output_tail reading sources... [ 62%] COMPS.utils.get_status reading sources... [ 64%] COMPS.utils.main reading sources... [ 66%] COMPS.utils.rerun_failed_simulations_for_experiment reading sources... [ 68%] architecture reading sources... [ 70%] create-climateinput reading sources... [ 72%] create-simulations reading sources... [ 74%] create-workitems-simulations reading sources... [ 75%] glossary reading sources... [ 77%] howto-cleanup reading sources... [ 79%] howto-create-climateinput reading sources... [ 81%] howto-create-simulations reading sources... [ 83%] howto-dashboard reading sources... [ 85%] howto-example-campaign reading sources... [ 87%] howto-example-config reading sources... [ 88%] howto-multichart-view reading sources... [ 90%] howto-weather-view reading sources... [ 92%] index reading sources... [ 94%] manage-workitems-simulations reading sources... [ 96%] modules reading sources... [ 98%] overview-comps reading sources... [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%] ../_readthedocs/htmlzip/_images/plantweb/6dc61f6eaba29e2739ffacc32cbe82278f2a62260ac90b49fad6d64aef777fdd.svg copying static files... done copying extra files... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML page is in ../_readthedocs/htmlzip.