Read the Docs build information
Build id: 2640633
Project: institute-for-disease-modeling-emod-generic-scripts
Version: latest
Commit: d57c23ad2db4dd44c9f7c5a010d50a3ae85e6c1e
Date: 2024-11-25T19:42:48.119595Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-11-25T19:42:49.361393Z, end-time: 2024-11-25T19:42:50.809560Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/EMOD-Hub/EMOD-Generic-Scripts.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-11-25T19:42:50.876694Z, end-time: 2024-11-25T19:42:51.955048Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main


[rtd-command-info] start-time: 2024-11-25T19:42:52.093721Z, end-time: 2024-11-25T19:42:52.500290Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at d57c23a Update builds

[rtd-command-info] start-time: 2024-11-25T19:42:52.569657Z, end-time: 2024-11-25T19:42:52.632122Z, 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
        
# 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: 2024-11-25T19:42:58.996187Z, end-time: 2024-11-25T19:42:59.733782Z, duration: 0, exit-code: 0
asdf global python 3.9.20


[rtd-command-info] start-time: 2024-11-25T19:43:00.476079Z, end-time: 2024-11-25T19:43:02.691448Z, duration: 2, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.20.final.0-64 in 823ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/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: 2024-11-25T19:43:02.773159Z, end-time: 2024-11-25T19:43:17.183355Z, duration: 14, 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-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (23.1)
Collecting pip
  Downloading pip-24.3.1-py3-none-any.whl (1.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 29.4 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (67.6.1)
Collecting setuptools
  Downloading setuptools-75.6.0-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 129.5 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-24.3.1 setuptools-75.6.0

[rtd-command-info] start-time: 2024-11-25T19:43:17.250053Z, end-time: 2024-11-25T19:43:27.627505Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
Collecting sphinx
  Downloading sphinx-7.4.7-py3-none-any.whl.metadata (6.1 kB)
Collecting sphinxcontrib-applehelp (from sphinx)
  Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-devhelp (from sphinx)
  Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-jsmath (from sphinx)
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx)
  Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx)
  Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinxcontrib-qthelp (from sphinx)
  Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting Jinja2>=3.1 (from sphinx)
  Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting Pygments>=2.17 (from sphinx)
  Downloading pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB)
Collecting docutils<0.22,>=0.20 (from sphinx)
  Downloading docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB)
Collecting snowballstemmer>=2.2 (from sphinx)
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl.metadata (6.5 kB)
Collecting babel>=2.13 (from sphinx)
  Downloading babel-2.16.0-py3-none-any.whl.metadata (1.5 kB)
Collecting alabaster~=0.7.14 (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.metadata (1.5 kB)
Collecting requests>=2.30.0 (from sphinx)
  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting packaging>=23.0 (from sphinx)
  Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting importlib-metadata>=6.0 (from sphinx)
  Downloading importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting tomli>=2 (from sphinx)
  Downloading tomli-2.1.0-py3-none-any.whl.metadata (10.0 kB)
Collecting zipp>=3.20 (from importlib-metadata>=6.0->sphinx)
  Downloading zipp-3.21.0-py3-none-any.whl.metadata (3.7 kB)
Collecting MarkupSafe>=2.0 (from Jinja2>=3.1->sphinx)
  Downloading MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.30.0->sphinx)
  Downloading charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx)
  Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx)
  Downloading urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx)
  Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
Downloading sphinx-7.4.7-py3-none-any.whl (3.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 108.8 MB/s eta 0:00:00
Downloading alabaster-0.7.16-py3-none-any.whl (13 kB)
Downloading babel-2.16.0-py3-none-any.whl (9.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.6/9.6 MB 191.9 MB/s eta 0:00:00
Downloading docutils-0.21.2-py3-none-any.whl (587 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 293.1 MB/s eta 0:00:00
Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Downloading importlib_metadata-8.5.0-py3-none-any.whl (26 kB)
Downloading jinja2-3.1.4-py3-none-any.whl (133 kB)
Downloading packaging-24.2-py3-none-any.whl (65 kB)
Downloading pygments-2.18.0-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 343.1 MB/s eta 0:00:00
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB)
Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB)
Downloading tomli-2.1.0-py3-none-any.whl (13 kB)
Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB)
Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB)
Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB)
Downloading certifi-2024.8.30-py3-none-any.whl (167 kB)
Downloading charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (144 kB)
Downloading idna-3.10-py3-none-any.whl (70 kB)
Downloading MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB)
Downloading urllib3-2.2.3-py3-none-any.whl (126 kB)
Downloading zipp-3.21.0-py3-none-any.whl (9.6 kB)
Installing collected packages: snowballstemmer, zipp, urllib3, tomli, 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
Successfully installed Jinja2-3.1.4 MarkupSafe-3.0.2 Pygments-2.18.0 alabaster-0.7.16 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 importlib-metadata-8.5.0 packaging-24.2 requests-2.32.3 snowballstemmer-2.2.0 sphinx-7.4.7 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 tomli-2.1.0 urllib3-2.2.3 zipp-3.21.0

[rtd-command-info] start-time: 2024-11-25T19:43:27.719498Z, end-time: 2024-11-25T19:43:47.563030Z, duration: 19, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting sphinx~=6.2 (from -r docs/requirements.txt (line 1))
  Downloading sphinx-6.2.1-py3-none-any.whl.metadata (6.2 kB)
Collecting sphinx-rtd-theme~=1.2 (from -r docs/requirements.txt (line 2))
  Downloading sphinx_rtd_theme-1.3.0-py2.py3-none-any.whl.metadata (4.5 kB)
Collecting sphinxcontrib-napoleon~=0.7 (from -r docs/requirements.txt (line 3))
  Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl.metadata (6.2 kB)
Collecting plantweb~=1.2 (from -r docs/requirements.txt (line 4))
  Downloading plantweb-1.3.0-py3-none-any.whl.metadata (4.1 kB)
Collecting sphinxcontrib-programoutput~=0.17 (from -r docs/requirements.txt (line 5))
  Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl.metadata (7.2 kB)
Collecting nbsphinx~=0.9 (from -r docs/requirements.txt (line 6))
  Downloading nbsphinx-0.9.5-py3-none-any.whl.metadata (2.1 kB)
Collecting jupyterlab~=4.0 (from -r docs/requirements.txt (line 7))
  Downloading jupyterlab-4.3.1-py3-none-any.whl.metadata (16 kB)
Collecting myst-parser~=2.0 (from -r docs/requirements.txt (line 8))
  Downloading myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB)
Collecting readthedocs-sphinx-search~=0.3 (from -r docs/requirements.txt (line 9))
  Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinx-copybutton~=0.5 (from -r docs/requirements.txt (line 10))
  Downloading sphinx_copybutton-0.5.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pygithub~=1.57 (from -r docs/requirements.txt (line 11))
  Downloading PyGithub-1.59.1-py3-none-any.whl.metadata (2.0 kB)
Collecting sphinxext.remoteliteralinclude~=0.4 (from -r docs/requirements.txt (line 12))
  Downloading sphinxext_remoteliteralinclude-0.5.0-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinxcontrib-jquery~=4.1 (from -r docs/requirements.txt (line 13))
  Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl.metadata (2.6 kB)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.1.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: Jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (3.1.4)
Requirement already satisfied: Pygments>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.18.0)
Collecting docutils<0.20,>=0.18.1 (from sphinx~=6.2->-r docs/requirements.txt (line 1))
  Downloading docutils-0.19-py3-none-any.whl.metadata (2.7 kB)
Requirement already satisfied: snowballstemmer>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.2.0)
Requirement already satisfied: babel>=2.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.16.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (0.7.16)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (1.4.1)
Requirement already satisfied: requests>=2.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.32.3)
Requirement already satisfied: packaging>=21.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (24.2)
Requirement already satisfied: importlib-metadata>=4.8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2->-r docs/requirements.txt (line 1)) (8.5.0)
  Downloading docutils-0.18.1-py2.py3-none-any.whl.metadata (2.9 kB)
Collecting six>=1.5.2 (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 3))
  Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting pockets>=0.3 (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 3))
  Downloading pockets-0.9.1-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting nbconvert!=5.4,>=5.3 (from nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)
Collecting traitlets>=5 (from nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting nbformat (from nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting async-lru>=1.0.0 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB)
Collecting httpx>=0.25.0 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading httpx-0.27.2-py3-none-any.whl.metadata (7.1 kB)
Collecting ipykernel>=6.5.0 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading ipykernel-6.29.5-py3-none-any.whl.metadata (6.3 kB)
Collecting jupyter-core (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting jupyter-lsp>=2.0.0 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyter_lsp-2.2.5-py3-none-any.whl.metadata (1.8 kB)
Collecting jupyter-server<3,>=2.4.0 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyter_server-2.14.2-py3-none-any.whl.metadata (8.4 kB)
Collecting jupyterlab-server<3,>=2.27.1 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyterlab_server-2.27.3-py3-none-any.whl.metadata (5.9 kB)
Collecting notebook-shim>=0.2 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading notebook_shim-0.2.4-py3-none-any.whl.metadata (4.0 kB)
Requirement already satisfied: setuptools>=40.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from jupyterlab~=4.0->-r docs/requirements.txt (line 7)) (75.6.0)
Requirement already satisfied: tomli>=1.2.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from jupyterlab~=4.0->-r docs/requirements.txt (line 7)) (2.1.0)
Collecting tornado>=6.2.0 (from jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading tornado-6.4.2-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->-r docs/requirements.txt (line 8))
  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->-r docs/requirements.txt (line 8))
  Downloading mdit_py_plugins-0.4.2-py3-none-any.whl.metadata (2.8 kB)
Collecting pyyaml (from myst-parser~=2.0->-r docs/requirements.txt (line 8))
  Downloading PyYAML-6.0.2-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 11))
  Downloading Deprecated-1.2.15-py2.py3-none-any.whl.metadata (5.5 kB)
Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->pygithub~=1.57->-r docs/requirements.txt (line 11))
  Downloading PyJWT-2.10.0-py3-none-any.whl.metadata (4.0 kB)
Collecting pynacl>=1.4.0 (from pygithub~=1.57->-r docs/requirements.txt (line 11))
  Downloading PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (8.6 kB)
Collecting typing-extensions>=4.0.0 (from async-lru>=1.0.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting anyio (from httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading anyio-4.6.2.post1-py3-none-any.whl.metadata (4.7 kB)
Requirement already satisfied: certifi in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7)) (2024.8.30)
Collecting httpcore==1.* (from httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading httpcore-1.0.7-py3-none-any.whl.metadata (21 kB)
Requirement already satisfied: idna in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7)) (3.10)
Collecting sniffio (from httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB)
Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading h11-0.14.0-py3-none-any.whl.metadata (8.2 kB)
Requirement already satisfied: zipp>=3.20 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from importlib-metadata>=4.8->sphinx~=6.2->-r docs/requirements.txt (line 1)) (3.21.0)
Collecting comm>=0.1.1 (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading comm-0.2.2-py3-none-any.whl.metadata (3.7 kB)
Collecting debugpy>=1.6.5 (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading debugpy-1.8.9-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB)
Collecting ipython>=7.23.1 (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading ipython-8.18.1-py3-none-any.whl.metadata (6.0 kB)
Collecting jupyter-client>=6.1.12 (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyter_client-8.6.3-py3-none-any.whl.metadata (8.3 kB)
Collecting matplotlib-inline>=0.1 (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting nest-asyncio (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB)
Collecting psutil (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading psutil-6.1.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB)
Collecting pyzmq>=24 (from ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading pyzmq-26.2.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.2 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from Jinja2>=3.0->sphinx~=6.2->-r docs/requirements.txt (line 1)) (3.0.2)
Collecting platformdirs>=2.5 (from jupyter-core->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
Collecting argon2-cffi>=21.1 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading argon2_cffi-23.1.0-py3-none-any.whl.metadata (5.2 kB)
Collecting jupyter-events>=0.9.0 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyter_events-0.10.0-py3-none-any.whl.metadata (5.9 kB)
Collecting jupyter-server-terminals>=0.4.4 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jupyter_server_terminals-0.5.3-py3-none-any.whl.metadata (5.6 kB)
Collecting overrides>=5.0 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading overrides-7.7.0-py3-none-any.whl.metadata (5.8 kB)
Collecting prometheus-client>=0.9 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading prometheus_client-0.21.0-py3-none-any.whl.metadata (1.8 kB)
Collecting send2trash>=1.8.2 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading Send2Trash-1.8.3-py3-none-any.whl.metadata (4.0 kB)
Collecting terminado>=0.8.3 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading terminado-0.18.1-py3-none-any.whl.metadata (5.8 kB)
Collecting websocket-client>=1.7 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading websocket_client-1.8.0-py3-none-any.whl.metadata (8.0 kB)
Collecting json5>=0.9.0 (from jupyterlab-server<3,>=2.27.1->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading json5-0.9.28-py3-none-any.whl.metadata (32 kB)
Collecting jsonschema>=4.18.0 (from jupyterlab-server<3,>=2.27.1->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser~=2.0->-r docs/requirements.txt (line 8))
  Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting beautifulsoup4 (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
Collecting bleach!=5.0.0 (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading bleach-6.2.0-py3-none-any.whl.metadata (30 kB)
Collecting defusedxml (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB)
Collecting jupyterlab-pygments (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB)
Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB)
Collecting nbclient>=0.5.0 (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading nbclient-0.10.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting tinycss2 (from nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading tinycss2-1.4.0-py3-none-any.whl.metadata (3.0 kB)
Collecting fastjsonschema>=2.15 (from nbformat->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading fastjsonschema-2.20.0-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 11))
  Downloading cryptography-43.0.3-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (5.4 kB)
Collecting cffi>=1.4.1 (from pynacl>=1.4.0->pygithub~=1.57->-r docs/requirements.txt (line 11))
  Downloading cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2->-r docs/requirements.txt (line 1)) (3.4.0)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic-scripts/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2->-r docs/requirements.txt (line 1)) (2.2.3)
Collecting wrapt<2,>=1.10 (from deprecated->pygithub~=1.57->-r docs/requirements.txt (line 11))
  Downloading wrapt-1.17.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)
Collecting exceptiongroup>=1.0.2 (from anyio->httpx>=0.25.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB)
Collecting argon2-cffi-bindings (from argon2-cffi>=21.1->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)
Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB)
Collecting pycparser (from cffi>=1.4.1->pynacl>=1.4.0->pygithub~=1.57->-r docs/requirements.txt (line 11))
  Downloading pycparser-2.22-py3-none-any.whl.metadata (943 bytes)
Collecting decorator (from ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jedi-0.19.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading prompt_toolkit-3.0.48-py3-none-any.whl.metadata (6.4 kB)
Collecting stack-data (from ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting pexpect>4.3 (from ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  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,>=2.27.1->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading attrs-24.2.0-py3-none-any.whl.metadata (11 kB)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.27.1->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl.metadata (3.0 kB)
Collecting referencing>=0.28.4 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.27.1->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB)
Collecting rpds-py>=0.7.1 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.27.1->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading rpds_py-0.21.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB)
Collecting python-dateutil>=2.8.2 (from jupyter-client>=6.1.12->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting python-json-logger>=2.0.4 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading python_json_logger-2.0.7-py3-none-any.whl.metadata (6.5 kB)
Collecting rfc3339-validator (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading rfc3339_validator-0.1.4-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting rfc3986-validator>=0.1.1 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading rfc3986_validator-0.1.1-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting ptyprocess (from terminado>=0.8.3->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert!=5.4,>=5.3->nbsphinx~=0.9->-r docs/requirements.txt (line 6))
  Downloading soupsieve-2.6-py3-none-any.whl.metadata (4.6 kB)
Collecting parso<0.9.0,>=0.8.4 (from jedi>=0.16->ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading parso-0.8.4-py2.py3-none-any.whl.metadata (7.7 kB)
Collecting fqdn (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading fqdn-1.5.1-py3-none-any.whl.metadata (1.4 kB)
Collecting isoduration (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading isoduration-20.11.0-py3-none-any.whl.metadata (5.7 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->-r docs/requirements.txt (line 7))
  Downloading jsonpointer-3.0.0-py2.py3-none-any.whl.metadata (2.3 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->-r docs/requirements.txt (line 7))
  Downloading uri_template-1.3.0-py3-none-any.whl.metadata (8.8 kB)
Collecting webcolors>=24.6.0 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading webcolors-24.11.1-py3-none-any.whl.metadata (2.2 kB)
Collecting wcwidth (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  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>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading executing-2.1.0-py2.py3-none-any.whl.metadata (8.9 kB)
Collecting asttokens>=2.1.0 (from stack-data->ipython>=7.23.1->ipykernel>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  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>=6.5.0->jupyterlab~=4.0->-r docs/requirements.txt (line 7))
  Downloading pure_eval-0.2.3-py3-none-any.whl.metadata (6.3 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->-r docs/requirements.txt (line 7))
  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->-r docs/requirements.txt (line 7))
  Downloading types_python_dateutil-2.9.0.20241003-py3-none-any.whl.metadata (1.9 kB)
Downloading sphinx-6.2.1-py3-none-any.whl (3.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 110.1 MB/s eta 0:00:00
Downloading sphinx_rtd_theme-1.3.0-py2.py3-none-any.whl (2.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 241.5 MB/s eta 0:00:00
Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB)
Downloading plantweb-1.3.0-py3-none-any.whl (20 kB)
Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB)
Downloading nbsphinx-0.9.5-py3-none-any.whl (31 kB)
Downloading jupyterlab-4.3.1-py3-none-any.whl (11.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 244.2 MB/s eta 0:00:00
Downloading myst_parser-2.0.0-py3-none-any.whl (77 kB)
Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB)
Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB)
Downloading PyGithub-1.59.1-py3-none-any.whl (342 kB)
Downloading sphinxext_remoteliteralinclude-0.5.0-py3-none-any.whl (6.4 kB)
Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB)
Downloading async_lru-2.0.4-py3-none-any.whl (6.1 kB)
Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 426.9 MB/s eta 0:00:00
Downloading httpx-0.27.2-py3-none-any.whl (76 kB)
Downloading httpcore-1.0.7-py3-none-any.whl (78 kB)
Downloading ipykernel-6.29.5-py3-none-any.whl (117 kB)
Downloading jupyter_core-5.7.2-py3-none-any.whl (28 kB)
Downloading jupyter_lsp-2.2.5-py3-none-any.whl (69 kB)
Downloading jupyter_server-2.14.2-py3-none-any.whl (383 kB)
Downloading jupyterlab_server-2.27.3-py3-none-any.whl (59 kB)
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
Downloading mdit_py_plugins-0.4.2-py3-none-any.whl (55 kB)
Downloading nbconvert-7.16.4-py3-none-any.whl (257 kB)
Downloading nbformat-5.10.4-py3-none-any.whl (78 kB)
Downloading notebook_shim-0.2.4-py3-none-any.whl (13 kB)
Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB)
Downloading PyJWT-2.10.0-py3-none-any.whl (23 kB)
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 460.6 MB/s eta 0:00:00
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Downloading tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (437 kB)
Downloading traitlets-5.14.3-py3-none-any.whl (85 kB)
Downloading Deprecated-1.2.15-py2.py3-none-any.whl (9.9 kB)
Downloading PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 737.4/737.4 kB 476.1 MB/s eta 0:00:00
Downloading anyio-4.6.2.post1-py3-none-any.whl (90 kB)
Downloading argon2_cffi-23.1.0-py3-none-any.whl (15 kB)
Downloading bleach-6.2.0-py3-none-any.whl (163 kB)
Downloading cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (445 kB)
Downloading comm-0.2.2-py3-none-any.whl (7.2 kB)
Downloading cryptography-43.0.3-cp39-abi3-manylinux_2_28_x86_64.whl (4.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.0/4.0 MB 302.8 MB/s eta 0:00:00
Downloading debugpy-1.8.9-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 275.7 MB/s eta 0:00:00
Downloading fastjsonschema-2.20.0-py3-none-any.whl (23 kB)
Downloading ipython-8.18.1-py3-none-any.whl (808 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 808.2/808.2 kB 476.3 MB/s eta 0:00:00
Downloading json5-0.9.28-py3-none-any.whl (30 kB)
Downloading jsonschema-4.23.0-py3-none-any.whl (88 kB)
Downloading jupyter_client-8.6.3-py3-none-any.whl (106 kB)
Downloading jupyter_events-0.10.0-py3-none-any.whl (18 kB)
Downloading jupyter_server_terminals-0.5.3-py3-none-any.whl (13 kB)
Downloading matplotlib_inline-0.1.7-py3-none-any.whl (9.9 kB)
Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading mistune-3.0.2-py3-none-any.whl (47 kB)
Downloading nbclient-0.10.0-py3-none-any.whl (25 kB)
Downloading overrides-7.7.0-py3-none-any.whl (17 kB)
Downloading pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB)
Downloading platformdirs-4.3.6-py3-none-any.whl (18 kB)
Downloading prometheus_client-0.21.0-py3-none-any.whl (54 kB)
Downloading pyzmq-26.2.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (862 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 862.1/862.1 kB 498.3 MB/s eta 0:00:00
Downloading Send2Trash-1.8.3-py3-none-any.whl (18 kB)
Downloading sniffio-1.3.1-py3-none-any.whl (10 kB)
Downloading terminado-0.18.1-py3-none-any.whl (14 kB)
Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Downloading websocket_client-1.8.0-py3-none-any.whl (58 kB)
Downloading wrapt-1.17.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (82 kB)
Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB)
Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB)
Downloading psutil-6.1.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (287 kB)
Downloading tinycss2-1.4.0-py3-none-any.whl (26 kB)
Downloading attrs-24.2.0-py3-none-any.whl (63 kB)
Downloading exceptiongroup-1.2.2-py3-none-any.whl (16 kB)
Downloading h11-0.14.0-py3-none-any.whl (58 kB)
Downloading jedi-0.19.2-py2.py3-none-any.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 525.2 MB/s eta 0:00:00
Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl (18 kB)
Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB)
Downloading prompt_toolkit-3.0.48-py3-none-any.whl (386 kB)
Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading python_json_logger-2.0.7-py3-none-any.whl (8.1 kB)
Downloading referencing-0.35.1-py3-none-any.whl (26 kB)
Downloading rfc3986_validator-0.1.1-py2.py3-none-any.whl (4.2 kB)
Downloading rpds_py-0.21.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (361 kB)
Downloading soupsieve-2.6-py3-none-any.whl (36 kB)
Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Downloading argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (86 kB)
Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Downloading pycparser-2.22-py3-none-any.whl (117 kB)
Downloading rfc3339_validator-0.1.4-py2.py3-none-any.whl (3.5 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-2.1.0-py2.py3-none-any.whl (25 kB)
Downloading jsonpointer-3.0.0-py2.py3-none-any.whl (7.6 kB)
Downloading parso-0.8.4-py2.py3-none-any.whl (103 kB)
Downloading webcolors-24.11.1-py3-none-any.whl (14 kB)
Downloading fqdn-1.5.1-py3-none-any.whl (9.1 kB)
Downloading isoduration-20.11.0-py3-none-any.whl (11 kB)
Downloading pure_eval-0.2.3-py3-none-any.whl (11 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)
Downloading types_python_dateutil-2.9.0.20241003-py3-none-any.whl (9.7 kB)
Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, readthedocs-sphinx-search, pyzmq, pyyaml, python-json-logger, pyjwt, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, json5, h11, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, bleach, attrs, terminado, sphinxext.remoteliteralinclude, sphinx, rfc3339-validator, referencing, python-dateutil, pockets, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, httpcore, deprecated, comm, cffi, beautifulsoup4, async-lru, asttokens, anyio, stack-data, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinxcontrib-jquery, sphinx-copybutton, pynacl, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, httpx, 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 0.21.2
    Uninstalling docutils-0.21.2:
      Successfully uninstalled docutils-0.21.2
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 7.4.7
    Uninstalling Sphinx-7.4.7:
      Successfully uninstalled Sphinx-7.4.7
Successfully installed anyio-4.6.2.post1 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-24.2.0 beautifulsoup4-4.12.3 bleach-6.2.0 cffi-1.17.1 comm-0.2.2 cryptography-43.0.3 debugpy-1.8.9 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.15 docutils-0.18.1 exceptiongroup-1.2.2 executing-2.1.0 fastjsonschema-2.20.0 fqdn-1.5.1 h11-0.14.0 httpcore-1.0.7 httpx-0.27.2 ipykernel-6.29.5 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.2 json5-0.9.28 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.2 jupyter-server-terminals-0.5.3 jupyterlab-4.3.1 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.3 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 nest-asyncio-1.6.0 notebook-shim-0.2.4 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 plantweb-1.3.0 platformdirs-4.3.6 pockets-0.9.1 prometheus-client-0.21.0 prompt-toolkit-3.0.48 psutil-6.1.0 ptyprocess-0.7.0 pure-eval-0.2.3 pycparser-2.22 pygithub-1.59.1 pyjwt-2.10.0 pynacl-1.5.0 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.21.0 send2trash-1.8.3 six-1.16.0 sniffio-1.3.1 soupsieve-2.6 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinx-rtd-theme-1.3.0 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.5.0 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.4.0 tornado-6.4.2 traitlets-5.14.3 types-python-dateutil-2.9.0.20241003 typing-extensions-4.12.2 uri-template-1.3.0 wcwidth-0.2.13 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.8.0 wrapt-1.17.0

[rtd-command-info] start-time: 2024-11-25T19:43:47.755755Z, end-time: 2024-11-25T19:43:47.816997Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Sphinx Demo docs 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
# docs 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

# -- General configuration ------------------------------------------------


# If your docs 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__'
}

autodoc_mock_imports = []

napoleon_google_docstring = True
# napoleon_numpy_docstring = True

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The encoding of source files.
#
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'EMOD-Generic-Scripts'
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.
#current_path = os.path.dirname(__file__)
#version_path = os.path.join(current_path, '..', '.bumpversion.cfg')
#config = configparser.ConfigParser()
#config.read(version_path)

#version = config['bumpversion']['current_version']
# The full version, including alpha/beta/rc tags.
# release = u'1.0'

# The language for content autogenerated by Sphinx. Refer to docs
# 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 docs 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
# docs.
# #
# 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.
# "<project> v<release> docs" 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 docs.
#
# 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 <link> 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/'

# -- 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}",
    }


# 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 = 'EMOD-Generic-Scripts'

# -- 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, 'EMOD-Generic-Scripts-docs.tex', u'EMOD-Generic-Scripts',
     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, 'EMOD-Generic-Scripts-docs', u'EMOD-Generic-Scripts',
     [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, 'EMOD-Generic-Scripts-docs', u'EMOD-Generic-Scripts',
     author, 'Institute for Disease Modeling', 'Scripts for running Generic EMOD simulations with emodpy.',
     '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 = {'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),
                       'emodpy-generic': ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', None),
                       'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None),
                       'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None),
                       'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None)
                       }

[rtd-command-info] start-time: 2024-11-25T19:43:47.918861Z, end-time: 2024-11-25T19:43:50.005197Z, duration: 2, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v6.2.1
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'strikethrough', 'colon_fence', 'html_admonition', 'deflist', 'amsmath', 'smartquotes', 'attrs_inline', 'dollarmath', 'fieldlist', 'linkify', 'html_image', 'replacements', 'substitution', 'tasklist'}, 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 18 source files that are out of date
updating environment: [new config] 18 added, 0 changed, 0 removed
reading sources... [  5%] cookiecutter
reading sources... [ 11%] examples
reading sources... [ 16%] examples/model_covariance01
reading sources... [ 22%] examples/model_covid01
reading sources... [ 27%] examples/model_demographics01
reading sources... [ 33%] examples/model_demographics02
reading sources... [ 38%] examples/model_measles01
reading sources... [ 44%] examples/model_measles_cod01
reading sources... [ 50%] examples/model_measles_gha01
reading sources... [ 55%] examples/model_measles_nga01
reading sources... [ 61%] examples/model_measles_nga02
reading sources... [ 66%] examples/model_network01
reading sources... [ 72%] examples/model_polio_nga01
reading sources... [ 77%] examples/model_rubella01
reading sources... [ 83%] examples/model_transtree01
reading sources... [ 88%] get-started
reading sources... [ 94%] index
reading sources... [100%] workflow

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  5%] cookiecutter
writing output... [ 11%] examples
writing output... [ 16%] examples/model_covariance01
writing output... [ 22%] examples/model_covid01
writing output... [ 27%] examples/model_demographics01
writing output... [ 33%] examples/model_demographics02
writing output... [ 38%] examples/model_measles01
writing output... [ 44%] examples/model_measles_cod01
writing output... [ 50%] examples/model_measles_gha01
writing output... [ 55%] examples/model_measles_nga01
writing output... [ 61%] examples/model_measles_nga02
writing output... [ 66%] examples/model_network01
writing output... [ 72%] examples/model_polio_nga01
writing output... [ 77%] examples/model_rubella01
writing output... [ 83%] examples/model_transtree01
writing output... [ 88%] get-started
writing output... [ 94%] index
writing output... [100%] workflow

generating indices... genindex done
highlighting module code... 
writing additional pages... search opensearch done
copying images... [  7%] examples/figures/ref_het_distributions.png
copying images... [ 15%] examples/figures/ref_het_attackrate.png
copying images... [ 23%] examples/figures/ref_heatmap_measles01.png
copying images... [ 30%] examples/figures/ref_pyr_measles01.png
copying images... [ 38%] examples/figures/ref_trends_MCV2_measles01.png
copying images... [ 46%] examples/figures/ref_trends_SIAs_measles01.png
copying images... [ 53%] examples/figures/ref_rcv_baseline.png
copying images... [ 61%] examples/figures/ref_rcv_infectivity.png
copying images... [ 69%] examples/figures/ref_rcv_dist_ss.png
copying images... [ 76%] examples/figures/ref_rcv_demog_ss.png
copying images... [ 84%] examples/figures/ref_rcv_demog_med.png
copying images... [ 92%] examples/figures/ref_rcv_dist_med.png
copying images... [100%] examples/figures/ref_track_transtree.png

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in ../_readthedocs/html.

[rtd-command-info] start-time: 2024-11-25T19:43:50.090056Z, end-time: 2024-11-25T19:43:51.356765Z, duration: 1, exit-code: 0
python -m sphinx -T -W --keep-going -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip
Running Sphinx v6.2.1
making output directory... done
loading pickled environment... done
myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'tasklist', 'deflist', 'fieldlist', 'colon_fence', 'html_image', 'smartquotes', 'linkify', 'amsmath', 'replacements', 'substitution', 'attrs_inline', 'dollarmath', 'strikethrough', 'html_admonition'}, 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 [singlehtml]: all documents
updating environment: 0 added, 0 changed, 0 removed
reading sources... 
looking for now-outdated files... none found
preparing documents... done
assembling single document... get-started workflow cookiecutter examples examples/model_covariance01 examples/model_covid01 examples/model_demographics01 examples/model_demographics02 examples/model_measles_cod01 examples/model_measles_gha01 examples/model_measles_nga01 examples/model_measles_nga02 examples/model_measles01 examples/model_network01 examples/model_polio_nga01 examples/model_rubella01 examples/model_transtree01 done
writing... done
writing additional files...  opensearchdone
copying images... [  7%] examples/figures/ref_het_distributions.png
copying images... [ 15%] examples/figures/ref_het_attackrate.png
copying images... [ 23%] examples/figures/ref_heatmap_measles01.png
copying images... [ 30%] examples/figures/ref_pyr_measles01.png
copying images... [ 38%] examples/figures/ref_trends_MCV2_measles01.png
copying images... [ 46%] examples/figures/ref_trends_SIAs_measles01.png
copying images... [ 53%] examples/figures/ref_rcv_baseline.png
copying images... [ 61%] examples/figures/ref_rcv_infectivity.png
copying images... [ 69%] examples/figures/ref_rcv_dist_ss.png
copying images... [ 76%] examples/figures/ref_rcv_demog_ss.png
copying images... [ 84%] examples/figures/ref_rcv_demog_med.png
copying images... [ 92%] examples/figures/ref_rcv_dist_med.png
copying images... [100%] examples/figures/ref_track_transtree.png

copying static files... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in ../_readthedocs/htmlzip.