Read the Docs build information
Build id: 1888082
Project: institute-for-disease-modeling-emodpy-typhoid
Version: latest
Commit: 9105bb74dca70ad33497ee6dbe05f8d3743107c6
Date: 2023-12-07T21:26:42.723608Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-12-07T21:27:02.491089Z, end-time: 2023-12-07T21:27:03.168612Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/InstituteforDiseaseModeling/emodpy-typhoid.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-12-07T21:27:03.241330Z, end-time: 2023-12-07T21:27:04.425103Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main
From https://github.com/InstituteforDiseaseModeling/emodpy-typhoid
 * [new tag]         v0.0.5     -> v0.0.5
 * [new tag]         v0.0.6     -> v0.0.6

[rtd-command-info] start-time: 2023-12-07T21:27:04.555319Z, end-time: 2023-12-07T21:27:04.643593Z, 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 9105bb7 Bump minor version 0.0.6 via Jenkins

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git clean -d -f -f


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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: requirements.txt
      - requirements: docs/requirements.txt
      - method: setuptools
        path: .
        
# Optionally rank topics in search results, between -10 (lower) and 10 (higher).
# 0 is normal rank, not no rank

# search:
#   ranking:

[rtd-command-info] start-time: 2023-12-07T21:27:10.272114Z, end-time: 2023-12-07T21:27:10.345857Z, duration: 0, exit-code: 0
asdf global python 3.9.18


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.18.final.0-64 in 878ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/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: 2023-12-07T21:27:12.036834Z, end-time: 2023-12-07T21:27:24.815032Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages (23.1)
Collecting pip
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/47/6a/453160888fab7c6a432a6e25f8afe6256d0d9f2cbd25971021da6491d899/pip-23.3.1-py3-none-any.whl (2.1 MB)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages (67.6.1)
Collecting setuptools
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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-23.3.1 setuptools-69.0.2

[rtd-command-info] start-time: 2023-12-07T21:27:24.901712Z, end-time: 2023-12-07T21:27:35.668004Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting sphinx
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Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx)
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Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-jsmath, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.17.2 alabaster-0.7.13 babel-2.13.1 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.0 packaging-23.2 readthedocs-sphinx-ext-2.2.3 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.1.0 zipp-3.17.0

[rtd-command-info] start-time: 2023-12-07T21:27:35.758274Z, end-time: 2023-12-07T21:28:20.008384Z, duration: 44, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Collecting emodpy~=1.16 (from -r requirements.txt (line 1))
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[rtd-command-info] start-time: 2023-12-07T21:28:20.094399Z, end-time: 2023-12-07T21:28:47.337251Z, duration: 27, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Installing collected packages: webencodings, wcwidth, types-python-dateutil, pure-eval, ptyprocess, json5, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, typing-extensions, traitlets, tornado, tomli, tinycss2, sphinxext.remoteliteralinclude, sniffio, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, requests, readthedocs-sphinx-search, pyzmq, python-json-logger, pyjwt, psutil, prompt-toolkit, prometheus-client, pockets, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, bleach, attrs, asttokens, terminado, stack-data, sphinxcontrib-napoleon, referencing, pynacl, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, async-lru, arrow, argon2-cffi-bindings, anyio, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, isoduration, ipython, argon2-cffi, pygithub, jsonschema, ipykernel, nbformat, nbclient, jupyter-events, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, sphinx, sphinxcontrib-jquery, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, nbsphinx, myst-parser
  Attempting uninstall: requests
    Found existing installation: requests 2.29.0
    Uninstalling requests-2.29.0:
      Successfully uninstalled requests-2.29.0
  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
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
emodpy 1.22.0 requires requests==2.29.0, but you have requests 2.31.0 which is incompatible.
Successfully installed anyio-4.1.0 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-23.1.0 bleach-6.1.0 comm-0.2.0 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docutils-0.18.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.0 fqdn-1.5.1 ipykernel-6.27.1 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.20.0 jsonschema-specifications-2023.11.2 jupyter-client-8.6.0 jupyter-core-5.5.0 jupyter-events-0.9.0 jupyter-lsp-2.2.1 jupyter-server-2.12.1 jupyter-server-terminals-0.4.4 jupyterlab-4.0.9 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-7.12.0 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.5.8 notebook-shim-0.2.3 overrides-7.4.0 pandocfilters-1.5.0 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-3.0.41 psutil-5.9.6 ptyprocess-0.7.0 pure-eval-0.2.2 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-json-logger-2.0.7 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.1 referencing-0.32.0 requests-2.31.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.13.2 send2trash-1.8.2 sniffio-1.3.0 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-5.14.0 types-python-dateutil-2.8.19.14 typing-extensions-4.8.0 uri-template-1.3.0 wcwidth-0.2.12 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 wrapt-1.16.0

[rtd-command-info] start-time: 2023-12-07T21:28:47.494685Z, end-time: 2023-12-07T21:29:17.485338Z, duration: 29, exit-code: 1
python ./setup.py install --force
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  dist.fetch_build_eggs(dist.setup_requires)
running install
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/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-emodpy-typhoid/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 emodpy_typhoid.egg-info
writing emodpy_typhoid.egg-info/PKG-INFO
writing dependency_links to emodpy_typhoid.egg-info/dependency_links.txt
writing requirements to emodpy_typhoid.egg-info/requires.txt
writing top-level names to emodpy_typhoid.egg-info/top_level.txt
writing manifest file 'emodpy_typhoid.egg-info/SOURCES.txt'
reading manifest file 'emodpy_typhoid.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'emodpy_typhoid.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/emodpy_typhoid
copying emodpy_typhoid/config.py -> build/lib/emodpy_typhoid
copying emodpy_typhoid/__init__.py -> build/lib/emodpy_typhoid
creating build/lib/emodpy_typhoid/demographics
copying emodpy_typhoid/demographics/TyphoidDemographics.py -> build/lib/emodpy_typhoid/demographics
copying emodpy_typhoid/demographics/__init__.py -> build/lib/emodpy_typhoid/demographics
creating build/lib/emodpy_typhoid/interventions
copying emodpy_typhoid/interventions/tcc.py -> build/lib/emodpy_typhoid/interventions
copying emodpy_typhoid/interventions/outbreak.py -> build/lib/emodpy_typhoid/interventions
copying emodpy_typhoid/interventions/tcd.py -> build/lib/emodpy_typhoid/interventions
copying emodpy_typhoid/interventions/__init__.py -> build/lib/emodpy_typhoid/interventions
copying emodpy_typhoid/interventions/typhoid_wash.py -> build/lib/emodpy_typhoid/interventions
copying emodpy_typhoid/interventions/typhoid_vaccine.py -> build/lib/emodpy_typhoid/interventions
creating build/lib/emodpy_typhoid/utility
copying emodpy_typhoid/utility/sweeping.py -> build/lib/emodpy_typhoid/utility
copying emodpy_typhoid/utility/__init__.py -> build/lib/emodpy_typhoid/utility
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/emodpy_typhoid
creating build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics
copying build/lib/emodpy_typhoid/demographics/TyphoidDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics
copying build/lib/emodpy_typhoid/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics
creating build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/interventions/tcc.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/interventions/tcd.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/interventions/typhoid_wash.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/interventions/typhoid_vaccine.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions
copying build/lib/emodpy_typhoid/config.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid
copying build/lib/emodpy_typhoid/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid
creating build/bdist.linux-x86_64/egg/emodpy_typhoid/utility
copying build/lib/emodpy_typhoid/utility/sweeping.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/utility
copying build/lib/emodpy_typhoid/utility/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/utility
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics/TyphoidDemographics.py to TyphoidDemographics.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/tcc.py to tcc.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/outbreak.py to outbreak.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/tcd.py to tcd.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/typhoid_wash.py to typhoid_wash.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/typhoid_vaccine.py to typhoid_vaccine.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/config.py to config.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/utility/sweeping.py to sweeping.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/utility/__init__.py to __init__.cpython-39.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_typhoid.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_typhoid.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_typhoid.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_typhoid.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_typhoid.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/emodpy_typhoid-0.1.0-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 emodpy_typhoid-0.1.0-py3.9.egg
Copying emodpy_typhoid-0.1.0-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages
Adding emodpy-typhoid 0.1.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/emodpy_typhoid-0.1.0-py3.9.egg
Processing dependencies for emodpy-typhoid==0.1.0
Searching for emod-typhoid==0.0.5
Reading https://pypi.org/simple/emod-typhoid/
Couldn't retrieve index page for 'emod-typhoid'
Scanning index of all packages (this may take a while)
Reading https://pypi.org/simple/
No local packages or working download links found for emod-typhoid==0.0.5
error: Could not find suitable distribution for Requirement.parse('emod-typhoid==0.0.5')