Read the Docs build information
Build id: 2295112
Project: institute-for-disease-modeling-hiv-workflow
Version: latest
Commit: d12e51cd0d56647db1628703089c2d1c434f06ba
Date: 2024-06-18T23:07:48.072465Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2024-06-18T23:07:49.328924Z, end-time: 2024-06-18T23:07:53.598033Z, duration: 4, exit-code: 0
git clone --depth 1 git@github.com:InstituteforDiseaseModeling/hiv_workflow.git .
Cloning into '.'...
Warning: Permanently added 'github.com' (ED25519) to the list of known hosts.

[rtd-command-info] start-time: 2024-06-18T23:07:53.668239Z, end-time: 2024-06-18T23:07:54.940859Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main
Warning: Permanently added 'github.com' (ED25519) to the list of known hosts.

[rtd-command-info] start-time: 2024-06-18T23:07:55.073706Z, end-time: 2024-06-18T23:07:56.135151Z, duration: 1, 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 d12e51c Merge pull request #76 from RCarter-IDM/pydata

[rtd-command-info] start-time: 2024-06-18T23:07:56.205777Z, end-time: 2024-06-18T23:07:56.268574Z, 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: requirements.txt
    - method: setuptools
      path: .
    - 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:
    index.html: 3
    modules.html: 2

[rtd-command-info] start-time: 2024-06-18T23:08:02.228523Z, end-time: 2024-06-18T23:08:02.315168Z, duration: 0, exit-code: 0
asdf global python 3.9.19


[rtd-command-info] start-time: 2024-06-18T23:08:02.728425Z, end-time: 2024-06-18T23:08:03.929977Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.19.final.0-64 in 874ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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: 2024-06-18T23:08:03.999589Z, end-time: 2024-06-18T23:08:14.448748Z, duration: 10, 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-hiv-workflow/envs/latest/lib/python3.9/site-packages (23.1)
Collecting pip
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages (67.6.1)
Collecting setuptools
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/de/88/70c5767a0e43eb4451c2200f07d042a4bcd7639276003a9c54a68cfcc1f8/setuptools-70.0.0-py3-none-any.whl (863 kB)
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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-24.0 setuptools-70.0.0

[rtd-command-info] start-time: 2024-06-18T23:08:14.512273Z, end-time: 2024-06-18T23:08:24.209230Z, duration: 9, 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 sphinxcontrib-devhelp (from sphinx)
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Collecting tomli>=2 (from sphinx)
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Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->sphinx)
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Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->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, 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, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-0.7.16 babel-2.15.0 certifi-2024.6.2 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.7 imagesize-1.4.1 importlib-metadata-7.1.0 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-7.3.7 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 tomli-2.0.1 urllib3-2.2.2 zipp-3.19.2

[rtd-command-info] start-time: 2024-06-18T23:08:24.279207Z, end-time: 2024-06-18T23:09:19.747684Z, duration: 55, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Collecting idmtools_calibra~=1.0.5 (from -r requirements.txt (line 2))
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Building wheels for collected packages: xmlrunner, prodict
  Building wheel for xmlrunner (setup.py): started
  Building wheel for xmlrunner (setup.py): finished with status 'done'
  Created wheel for xmlrunner: filename=xmlrunner-1.7.7-py3-none-any.whl size=6222 sha256=a057aece9d4c1edf151d86538dcb98053b5fc23b7e3191b1fce6f0c9ebc4194d
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  Building wheel for prodict (setup.py): started
  Building wheel for prodict (setup.py): finished with status 'done'
  Created wheel for prodict: filename=prodict-0.8.18-py3-none-any.whl size=4203 sha256=4523f710ad5e6855e54b2f22b23578a5e23ca37fa49cf3bb3489b7ba49b469b7
  Stored in directory: /tmp/pip-ephem-wheel-cache-waczbfz6/wheels/b0/9c/b9/694dc9fa35b338adf315c91781d2150a3bccd224174d897720
Successfully built xmlrunner prodict
Installing collected packages: xmlrunner, pytz, prodict, parse, emod-hiv, xdg, urllib3, tzdata, tqdm, threadpoolctl, tabulate, soupsieve, six, PyYaml, pyproj, pyparsing, pycparser, pluggy, pillow, numpy, natsort, more-itertools, lz4, kiwisolver, joblib, jeepney, iniconfig, importlib-resources, humanfriendly, graphviz, geographiclib, future, fonttools, filelock, fasteners, exceptiongroup, et-xmlfile, diskcache, cycler, click, backports.tarfile, backoff, astor, shapely, scipy, requests, python-dateutil, patsy, packaging, openpyxl, jaraco.functools, jaraco.context, jaraco.classes, geopy, contourpy, coloredlogs, cffi, beautifulsoup4, astunparse, scikit-learn, pytest, pyCOMPS, pandas, matplotlib, cryptography, bs4, statsmodels, SecretStorage, seaborn, idmtools, emod-api, keyring, idmtools-platform-comps, idmtools-models, idmtools_calibra, emodpy, emodpy-hiv
  Attempting uninstall: urllib3
    Found existing installation: urllib3 2.2.2
    Uninstalling urllib3-2.2.2:
      Successfully uninstalled urllib3-2.2.2
  Attempting uninstall: requests
    Found existing installation: requests 2.32.3
    Uninstalling requests-2.32.3:
      Successfully uninstalled requests-2.32.3
  Attempting uninstall: packaging
    Found existing installation: packaging 24.1
    Uninstalling packaging-24.1:
      Successfully uninstalled packaging-24.1
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.
sphinx 7.3.7 requires packaging>=21.0, but you have packaging 20.9 which is incompatible.
Successfully installed PyYaml-6.0.1 SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 backports.tarfile-1.2.0 beautifulsoup4-4.12.3 bs4-0.0.2 cffi-1.16.0 click-7.1.2 coloredlogs-15.0.1 contourpy-1.2.1 cryptography-42.0.8 cycler-0.12.1 diskcache-5.4.0 emod-api-1.33.3 emod-hiv-0.0.4 emodpy-1.22.1 emodpy-hiv-1.0.2 et-xmlfile-1.1.0 exceptiongroup-1.2.1 fasteners-0.19 filelock-3.15.1 fonttools-4.53.0 future-1.0.0 geographiclib-2.0 geopy-2.4.1 graphviz-0.20.3 humanfriendly-10.0 idmtools-1.7.10 idmtools-models-1.7.10 idmtools-platform-comps-1.7.10 idmtools_calibra-1.0.12 importlib-resources-6.4.0 iniconfig-2.0.0 jaraco.classes-3.4.0 jaraco.context-5.3.0 jaraco.functools-4.0.1 jeepney-0.8.0 joblib-1.4.2 keyring-25.2.1 kiwisolver-1.4.5 lz4-4.3.3 matplotlib-3.9.0 more-itertools-9.1.0 natsort-8.4.0 numpy-2.0.0 openpyxl-3.1.4 packaging-20.9 pandas-2.2.2 parse-1.20.2 patsy-0.5.6 pillow-10.3.0 pluggy-1.5.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.22 pyparsing-3.1.2 pyproj-3.6.1 pytest-8.1.2 python-dateutil-2.9.0.post0 pytz-2024.1 requests-2.29.0 scikit-learn-1.5.0 scipy-1.13.1 seaborn-0.13.2 shapely-2.0.4 six-1.16.0 soupsieve-2.5 statsmodels-0.13.1 tabulate-0.9.0 threadpoolctl-3.5.0 tqdm-4.66.4 tzdata-2024.1 urllib3-1.26.19 xdg-6.0.0 xmlrunner-1.7.7

[rtd-command-info] start-time: 2024-06-18T23:09:19.844997Z, end-time: 2024-06-18T23:09:20.885093Z, duration: 1, exit-code: 0
python ./setup.py install --force
/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/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-hiv-workflow/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 hiv_workflow.egg-info
writing hiv_workflow.egg-info/PKG-INFO
writing dependency_links to hiv_workflow.egg-info/dependency_links.txt
writing requirements to hiv_workflow.egg-info/requires.txt
writing top-level names to hiv_workflow.egg-info/top_level.txt
writing manifest file 'hiv_workflow.egg-info/SOURCES.txt'
reading manifest file 'hiv_workflow.egg-info/SOURCES.txt'
writing manifest file 'hiv_workflow.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/hiv_workflow
copying hiv_workflow/__init__.py -> build/lib/hiv_workflow
creating build/lib/hiv_workflow/lib
copying hiv_workflow/lib/__init__.py -> build/lib/hiv_workflow/lib
creating build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/download.py -> build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/available_parameters.py -> build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/resample.py -> build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/dtk_post_process.py -> build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/run.py -> build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/__init__.py -> build/lib/hiv_workflow/scripts
copying hiv_workflow/scripts/calibrate.py -> build/lib/hiv_workflow/scripts
creating build/lib/hiv_workflow/lib/calibration
copying hiv_workflow/lib/calibration/__init__.py -> build/lib/hiv_workflow/lib/calibration
creating build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/data_frame_wrapper.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/base_distribution.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/condition.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/channel.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/population_obs.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/download_analyzer_by_experiment.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/hiv_analyzer.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/__init__.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/age_bin.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/beta_distribution.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/gaussian_distribution.py -> build/lib/hiv_workflow/lib/analysis
copying hiv_workflow/lib/analysis/hiv_calib_site.py -> build/lib/hiv_workflow/lib/analysis
creating build/lib/hiv_workflow/lib/utils
copying hiv_workflow/lib/utils/project_data.py -> build/lib/hiv_workflow/lib/utils
copying hiv_workflow/lib/utils/wrappers.py -> build/lib/hiv_workflow/lib/utils
copying hiv_workflow/lib/utils/analysis.py -> build/lib/hiv_workflow/lib/utils
copying hiv_workflow/lib/utils/__init__.py -> build/lib/hiv_workflow/lib/utils
copying hiv_workflow/lib/utils/runtime.py -> build/lib/hiv_workflow/lib/utils
creating build/lib/hiv_workflow/lib/calibration/algorithms
copying hiv_workflow/lib/calibration/algorithms/optim_tool.py -> build/lib/hiv_workflow/lib/calibration/algorithms
copying hiv_workflow/lib/calibration/algorithms/__init__.py -> build/lib/hiv_workflow/lib/calibration/algorithms
creating build/lib/hiv_workflow/lib/utils/builders
copying hiv_workflow/lib/utils/builders/general.py -> build/lib/hiv_workflow/lib/utils/builders
copying hiv_workflow/lib/utils/builders/__init__.py -> build/lib/hiv_workflow/lib/utils/builders
copying hiv_workflow/lib/utils/builders/demographics.py -> build/lib/hiv_workflow/lib/utils/builders
creating build/lib/hiv_workflow/lib/utils/io
copying hiv_workflow/lib/utils/io/excel.py -> build/lib/hiv_workflow/lib/utils/io
copying hiv_workflow/lib/utils/io/__init__.py -> build/lib/hiv_workflow/lib/utils/io
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/hiv_workflow
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms
copying build/lib/hiv_workflow/lib/calibration/algorithms/optim_tool.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms
copying build/lib/hiv_workflow/lib/calibration/algorithms/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms
copying build/lib/hiv_workflow/lib/calibration/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration
copying build/lib/hiv_workflow/lib/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/data_frame_wrapper.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/base_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/condition.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/channel.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/population_obs.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/download_analyzer_by_experiment.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/hiv_analyzer.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/age_bin.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/beta_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/gaussian_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
copying build/lib/hiv_workflow/lib/analysis/hiv_calib_site.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils
copying build/lib/hiv_workflow/lib/utils/project_data.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders
copying build/lib/hiv_workflow/lib/utils/builders/general.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders
copying build/lib/hiv_workflow/lib/utils/builders/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders
copying build/lib/hiv_workflow/lib/utils/builders/demographics.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders
copying build/lib/hiv_workflow/lib/utils/wrappers.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils
copying build/lib/hiv_workflow/lib/utils/analysis.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils
copying build/lib/hiv_workflow/lib/utils/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils
creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io
copying build/lib/hiv_workflow/lib/utils/io/excel.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io
copying build/lib/hiv_workflow/lib/utils/io/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io
copying build/lib/hiv_workflow/lib/utils/runtime.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils
creating build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/download.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/available_parameters.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/resample.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/dtk_post_process.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/run.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/scripts/calibrate.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts
copying build/lib/hiv_workflow/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms/optim_tool.py to optim_tool.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/data_frame_wrapper.py to data_frame_wrapper.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/base_distribution.py to base_distribution.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/condition.py to condition.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py to download_analyzer_by_experiment_receipt.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/channel.py to channel.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/population_obs.py to population_obs.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/download_analyzer_by_experiment.py to download_analyzer_by_experiment.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/hiv_analyzer.py to hiv_analyzer.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/age_bin.py to age_bin.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/beta_distribution.py to beta_distribution.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/gaussian_distribution.py to gaussian_distribution.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/hiv_calib_site.py to hiv_calib_site.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/project_data.py to project_data.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/general.py to general.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/demographics.py to demographics.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/wrappers.py to wrappers.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/analysis.py to analysis.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io/excel.py to excel.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/runtime.py to runtime.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/download.py to download.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/available_parameters.py to available_parameters.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/resample.py to resample.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/dtk_post_process.py to dtk_post_process.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/run.py to run.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/calibrate.py to calibrate.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/__init__.py to __init__.cpython-39.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying hiv_workflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying hiv_workflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying hiv_workflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying hiv_workflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying hiv_workflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
hiv_workflow.lib.analysis.__pycache__.base_distribution.cpython-39: module references __file__
hiv_workflow.lib.calibration.algorithms.__pycache__.optim_tool.cpython-39: module references __file__
hiv_workflow.lib.utils.__pycache__.runtime.cpython-39: module references __path__
hiv_workflow.scripts.__pycache__.available_parameters.cpython-39: module references __file__
hiv_workflow.scripts.__pycache__.calibrate.cpython-39: module references __file__
hiv_workflow.scripts.__pycache__.run.cpython-39: module references __file__
creating dist
creating 'dist/hiv_workflow-1.0.0-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 hiv_workflow-1.0.0-py3.9.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages/hiv_workflow-1.0.0-py3.9.egg
Extracting hiv_workflow-1.0.0-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Adding hiv-workflow 1.0.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages/hiv_workflow-1.0.0-py3.9.egg
Processing dependencies for hiv-workflow==1.0.0
Searching for packaging==20.9
Best match: packaging 20.9
Adding packaging 20.9 to easy-install.pth file
detected new path './hiv_workflow-1.0.0-py3.9.egg'

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for lz4==4.3.3
Best match: lz4 4.3.3
Adding lz4 4.3.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for openpyxl==3.1.4
Best match: openpyxl 3.1.4
Adding openpyxl 3.1.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for emodpy-hiv==1.0.2
Best match: emodpy-hiv 1.0.2
Adding emodpy-hiv 1.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for idmtools-calibra==1.0.12
Best match: idmtools-calibra 1.0.12
Adding idmtools-calibra 1.0.12 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pyparsing==3.1.2
Best match: pyparsing 3.1.2
Adding pyparsing 3.1.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for et-xmlfile==1.1.0
Best match: et-xmlfile 1.1.0
Adding et-xmlfile 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for numpy==2.0.0
Best match: numpy 2.0.0
Adding numpy 2.0.0 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin
Installing numpy-config script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for emod-hiv==0.0.4
Best match: emod-hiv 0.0.4
Adding emod-hiv 0.0.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for emodpy==1.22.1
Best match: emodpy 1.22.1
Adding emodpy 1.22.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for statsmodels==0.13.1
Best match: statsmodels 0.13.1
Adding statsmodels 0.13.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for scikit-learn==1.5.0
Best match: scikit-learn 1.5.0
Adding scikit-learn 1.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for seaborn==0.13.2
Best match: seaborn 0.13.2
Adding seaborn 0.13.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for scipy==1.13.1
Best match: scipy 1.13.1
Adding scipy 1.13.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for idmtools-models==1.7.10
Best match: idmtools-models 1.7.10
Adding idmtools-models 1.7.10 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for idmtools-platform-comps==1.7.10
Best match: idmtools-platform-comps 1.7.10
Adding idmtools-platform-comps 1.7.10 to easy-install.pth file
Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for idmtools==1.7.10
Best match: idmtools 1.7.10
Adding idmtools 1.7.10 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for geopy==2.4.1
Best match: geopy 2.4.1
Adding geopy 2.4.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for fasteners==0.19
Best match: fasteners 0.19
Adding fasteners 0.19 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pytest==8.1.2
Best match: pytest 8.1.2
Adding pytest 8.1.2 to easy-install.pth file
Installing py.test script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin
Installing pytest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for xmlrunner==1.7.7
Best match: xmlrunner 1.7.7
Adding xmlrunner 1.7.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for requests==2.29.0
Best match: requests 2.29.0
Adding requests 2.29.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pyCOMPS==2.10.0
Best match: pyCOMPS 2.10.0
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-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for keyring==25.2.1
Best match: keyring 25.2.1
Adding keyring 25.2.1 to easy-install.pth file
Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for bs4==0.0.2
Best match: bs4 0.0.2
Adding bs4 0.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for astunparse==1.6.3
Best match: astunparse 1.6.3
Adding astunparse 1.6.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for astor==0.8.1
Best match: astor 0.8.1
Adding astor 0.8.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for matplotlib==3.9.0
Best match: matplotlib 3.9.0
Adding matplotlib 3.9.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for emod-api==1.33.3
Best match: emod-api 1.33.3
Adding emod-api 1.33.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for click==7.1.2
Best match: click 7.1.2
Adding click 7.1.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for patsy==0.5.6
Best match: patsy 0.5.6
Adding patsy 0.5.6 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pandas==2.2.2
Best match: pandas 2.2.2
Adding pandas 2.2.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for threadpoolctl==3.5.0
Best match: threadpoolctl 3.5.0
Adding threadpoolctl 3.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for joblib==1.4.2
Best match: joblib 1.4.2
Adding joblib 1.4.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for jinja2==3.1.4
Best match: jinja2 3.1.4
Adding jinja2 3.1.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for natsort==8.4.0
Best match: natsort 8.4.0
Adding natsort 8.4.0 to easy-install.pth file
Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for tqdm==4.66.4
Best match: tqdm 4.66.4
Adding tqdm 4.66.4 to easy-install.pth file
Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for tabulate==0.9.0
Best match: tabulate 0.9.0
Adding tabulate 0.9.0 to easy-install.pth file
Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for PyYAML==6.0.1
Best match: PyYAML 6.0.1
Adding PyYAML 6.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pluggy==1.5.0
Best match: pluggy 1.5.0
Adding pluggy 1.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for more-itertools==9.1.0
Best match: more-itertools 9.1.0
Adding more-itertools 9.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for filelock==3.15.1
Best match: filelock 3.15.1
Adding filelock 3.15.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for diskcache==5.4.0
Best match: diskcache 5.4.0
Adding diskcache 5.4.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for coloredlogs==15.0.1
Best match: coloredlogs 15.0.1
Adding coloredlogs 15.0.1 to easy-install.pth file
Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for backoff==2.2.1
Best match: backoff 2.2.1
Adding backoff 2.2.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for geographiclib==2.0
Best match: geographiclib 2.0
Adding geographiclib 2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for tomli==2.0.1
Best match: tomli 2.0.1
Adding tomli 2.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for exceptiongroup==1.2.1
Best match: exceptiongroup 1.2.1
Adding exceptiongroup 1.2.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for iniconfig==2.0.0
Best match: iniconfig 2.0.0
Adding iniconfig 2.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for certifi==2024.6.2
Best match: certifi 2024.6.2
Adding certifi 2024.6.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for urllib3==1.26.19
Best match: urllib3 1.26.19
Adding urllib3 1.26.19 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for idna==3.7
Best match: idna 3.7
Adding idna 3.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for xdg==6.0.0
Best match: xdg 6.0.0
Adding xdg 6.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for future==1.0.0
Best match: future 1.0.0
Adding future 1.0.0 to easy-install.pth file
Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin
Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pytz==2024.1
Best match: pytz 2024.1
Adding pytz 2024.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for jeepney==0.8.0
Best match: jeepney 0.8.0
Adding jeepney 0.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for SecretStorage==3.3.3
Best match: SecretStorage 3.3.3
Adding SecretStorage 3.3.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for importlib-metadata==7.1.0
Best match: importlib-metadata 7.1.0
Adding importlib-metadata 7.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for jaraco.context==5.3.0
Best match: jaraco.context 5.3.0
Adding jaraco.context 5.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for jaraco.functools==4.0.1
Best match: jaraco.functools 4.0.1
Adding jaraco.functools 4.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for jaraco.classes==3.4.0
Best match: jaraco.classes 3.4.0
Adding jaraco.classes 3.4.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for beautifulsoup4==4.12.3
Best match: beautifulsoup4 4.12.3
Adding beautifulsoup4 4.12.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for six==1.16.0
Best match: six 1.16.0
Adding six 1.16.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for wheel==0.40.0
Best match: wheel 0.40.0
Adding wheel 0.40.0 to easy-install.pth file
Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for importlib-resources==6.4.0
Best match: importlib-resources 6.4.0
Adding importlib-resources 6.4.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for python-dateutil==2.9.0.post0
Best match: python-dateutil 2.9.0.post0
Adding python-dateutil 2.9.0.post0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pillow==10.3.0
Best match: pillow 10.3.0
Adding pillow 10.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for kiwisolver==1.4.5
Best match: kiwisolver 1.4.5
Adding kiwisolver 1.4.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for fonttools==4.53.0
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Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin
Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin
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Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for cycler==0.12.1
Best match: cycler 0.12.1
Adding cycler 0.12.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for contourpy==1.2.1
Best match: contourpy 1.2.1
Adding contourpy 1.2.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for parse==1.20.2
Best match: parse 1.20.2
Adding parse 1.20.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for graphviz==0.20.3
Best match: graphviz 0.20.3
Adding graphviz 0.20.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for prodict==0.8.18
Best match: prodict 0.8.18
Adding prodict 0.8.18 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pyproj==3.6.1
Best match: pyproj 3.6.1
Adding pyproj 3.6.1 to easy-install.pth file
Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for shapely==2.0.4
Best match: shapely 2.0.4
Adding shapely 2.0.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for tzdata==2024.1
Best match: tzdata 2024.1
Adding tzdata 2024.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for MarkupSafe==2.1.5
Best match: MarkupSafe 2.1.5
Adding MarkupSafe 2.1.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for humanfriendly==10.0
Best match: humanfriendly 10.0
Adding humanfriendly 10.0 to easy-install.pth file
Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for cryptography==42.0.8
Best match: cryptography 42.0.8
Adding cryptography 42.0.8 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for zipp==3.19.2
Best match: zipp 3.19.2
Adding zipp 3.19.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for backports.tarfile==1.2.0
Best match: backports.tarfile 1.2.0
Adding backports.tarfile 1.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for soupsieve==2.5
Best match: soupsieve 2.5
Adding soupsieve 2.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for cffi==1.16.0
Best match: cffi 1.16.0
Adding cffi 1.16.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Searching for pycparser==2.22
Best match: pycparser 2.22
Adding pycparser 2.22 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.9/site-packages
Finished processing dependencies for hiv-workflow==1.0.0

[rtd-command-info] start-time: 2024-06-18T23:09:20.997746Z, end-time: 2024-06-18T23:09:51.590356Z, duration: 30, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
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Collecting docopt>=0.6.0 (from py-make->-r docs/requirements.txt (line 1))
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Collecting docutils<0.20,>=0.18.1 (from sphinx~=6.2.1->-r docs/requirements.txt (line 2))
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Collecting packaging>=21.0 (from sphinx~=6.2.1->-r docs/requirements.txt (line 2))
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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 8))
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  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c7/1b/af4f4c4f3f7339a4b7eb3c0ab13416db98f8ac09de3399129ee5fdfa282b/types_python_dateutil-2.9.0.20240316-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=84164b04898f54a8b33ca4a99e508aade63287ba4701bb542c2ab24b4fd24adf
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Successfully built docopt
Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, docopt, wrapt, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tinycss2, sniffio, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, requests, readthedocs-sphinx-search, pyzmq, python-json-logger, pyjwt, py-make, psutil, prompt-toolkit, prometheus-client, pockets, platformdirs, pexpect, parso, pandocfilters, packaging, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, json5, fqdn, executing, docutils, defusedxml, decorator, debugpy, bleach, attrs, asttokens, accessible-pygments, terminado, stack-data, sphinxcontrib-napoleon, sphinx, referencing, pynacl, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, async-lru, arrow, argon2-cffi-bindings, anyio, sphinxcontrib-programoutput, sphinx-copybutton, pydata-sphinx-theme, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, isoduration, ipython, argon2-cffi, pygithub, myst-parser, jsonschema, ipykernel, nbformat, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab
  Attempting uninstall: requests
    Found existing installation: requests 2.29.0
    Uninstalling requests-2.29.0:
      Successfully uninstalled requests-2.29.0
  Attempting uninstall: packaging
    Found existing installation: packaging 20.9
    Uninstalling packaging-20.9:
      Successfully uninstalled packaging-20.9
  Attempting uninstall: docutils
    Found existing installation: docutils 0.21.2
    Uninstalling docutils-0.21.2:
      Successfully uninstalled docutils-0.21.2
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 7.3.7
    Uninstalling Sphinx-7.3.7:
      Successfully uninstalled Sphinx-7.3.7
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 1.22.1 requires requests==2.29.0, but you have requests 2.32.3 which is incompatible.
hiv-workflow 1.0.0 requires packaging~=20.4, but you have packaging 24.1 which is incompatible.
Successfully installed accessible-pygments-0.0.5 anyio-4.4.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 bleach-6.1.0 comm-0.2.2 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docopt-0.6.2 docutils-0.19 executing-2.0.1 fastjsonschema-2.20.0 fqdn-1.5.1 ipykernel-6.29.4 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.25 jsonpointer-3.0.0 jsonschema-4.22.0 jsonschema-specifications-2023.12.1 jupyter-client-8.6.2 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.1 jupyter-server-terminals-0.5.3 jupyterlab-4.0.13 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.1 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.4 nest-asyncio-1.6.0 notebook-shim-0.2.4 overrides-7.7.0 packaging-24.1 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.2.2 pockets-0.9.1 prometheus-client-0.20.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.2 py-make-0.1.2 pydata-sphinx-theme-0.15.3 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-json-logger-2.0.7 pyzmq-26.0.3 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.18.1 send2trash-1.8.3 sniffio-1.3.1 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.3.0 tornado-6.4.1 traitlets-5.14.3 types-python-dateutil-2.9.0.20240316 typing-extensions-4.12.2 uri-template-1.3.0 wcwidth-0.2.13 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 wrapt-1.16.0

[rtd-command-info] start-time: 2024-06-18T23:09:52.214274Z, end-time: 2024-06-18T23:09:52.275900Z, 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

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__)))

# Rename "hiv_workflow" to "API reference"
filename = 'modules.rst' # This must match the Makefile
with open(filename) as f: # Read existing file
    lines = f.readlines()
lines[0] = "API reference\n" # Blast away the existing heading and replace with this
lines[1] = "=============\n" # Ensure the heading is the right length
with open(filename, "w") as f: # Write new file
    f.writelines(lines)

# -- 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.ext.intersphinx',
    'sphinx_copybutton',
    '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']

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

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'hiv_workflow'
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 = 'pydata_sphinx_theme'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# docs.
# #
html_theme_options = {
    "collapse_navigation": False,
    "navigation_depth": 3,
    "show_prev_next": True,
    "icon_links": [
        {"name": "IDM docs", "url": "https://docs.idmod.org", "icon": "fas fa-home"},
        {
            "name": "GitHub",
            "url": "https://github.com/institutefordiseasemodeling/hiv_workflow",
            "icon": "fab fa-github-square",
        },
    ],
    "navbar_end": ["theme-switcher", "navbar-icon-links"],
    "secondary_sidebar_items": ["navbar-side"],
    "header_links_before_dropdown": 5,
    "footer_start": ["copyright", "footer_start"],
    "footer_end": ["theme-version", "footer_end"],
}
html_sidebars = {
    "**": ["sidebar-nav-bs", "page-toc"],
}
html_logo = "images/idm-logo-transparent.png"
html_favicon = "images/favicon.ico"
html_static_path = ['_static']
html_baseurl = "https://docs.idmod.org/projects/hiv_workflow/en/latest"
html_context = {
    'rtd_url': 'https://docs.idmod.org/projects/hiv_workflow/en/latest',
    "versions_dropdown": {
        "latest": "devel (latest)",
        "stable": "current (stable)",
    },
    "default_mode": "light",
}

# Add customizations
def setup(app):
    app.add_css_file("theme_overrides.css")

# Add any paths that contain custom themes here, relative to this directory.
#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 = 'hiv_workflow'

# -- 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, 'hiv_workflow-docs.tex', u'hiv_workflow',
     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, 'hiv_workflow-docs', u'hiv_workflow',
     [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, 'hiv_workflow-docs', u'hiv_workflow',
     author, 'Institute for Disease Modeling', 'How to use emodpy for disease 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

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),
                       '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)
                       }




###########################################################################
#          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/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/hiv_workflow/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/hiv_workflow/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-hiv-workflow',
    'name': u'hiv_workflow',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'hiv_workflow',
    'github_version': 'main',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'main',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'main',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'd12e51cd',
}

# 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-hiv-workflow/builds/2295112/'

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'])