Read the Docs build information
Build id: 1298193
Project: institute-for-disease-modeling-emodpy-hiv
Version: latest
Commit: 8214912a410b0032fadf6b38bf24475b4fb58565
Date: 2023-02-13T22:20:44.202942Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-02-13T22:20:46.338499Z, end-time: 2023-02-13T22:20:47.983633Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emodpy-hiv.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2023-02-13T22:20:48.178036Z, end-time: 2023-02-13T22:20:48.298876Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

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

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

  git switch -c <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 8214912 Bump version: 1.0.7 → 1.0.8

[rtd-command-info] start-time: 2023-02-13T22:20:48.479798Z, end-time: 2023-02-13T22:20:48.546056Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-02-13T22:20:49.644632Z, end-time: 2023-02-13T22:20:55.279232Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-02-13T22:20:55.456382Z, end-time: 2023-02-13T22:20:57.965257Z, duration: 2, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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-hiv/envs/latest/lib/python3.7/site-packages (23.0)
Collecting setuptools<58.3.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/41/f4/a7ca4859317232b1efb64a826b8d2d7299bb77fb60bdb08e2bd1d61cf80d/setuptools-58.2.0-py3-none-any.whl (946 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 13.7 MB/s eta 0:00:00
Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.2.0
    Uninstalling setuptools-67.2.0:
      Successfully uninstalled setuptools-67.2.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2023-02-13T22:20:58.139822Z, end-time: 2023-02-13T22:21:11.004700Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow==5.4.1 mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.3
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting pillow==5.4.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ae/2a/0a0ab2833e5270664fb5fae590717f867ac6319b124160c09f1d3291de28/Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 12.8 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/15/45/30273ee91feb60dabb8fbb2da7868520525f02cf910279b3047182feed80/mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 14.3 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/64/88/c7083fc61120ab661c5d0b82cb77079fc1429d3f913a456c1c82cf4658f7/alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting commonmark==0.9.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b1/92/dfd892312d822f36c55366118b95d914e5f16de11044a27cf10a7d71bbbf/commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 164.4 MB/s eta 0:00:00
Collecting recommonmark==0.5.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/67/a7/01dd6fd9653c056258d65032aa09a615b5d7b07dd840845a9f41a8860fbc/sphinx-5.3.0-py3-none-any.whl (3.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 12.9 MB/s eta 0:00:00
Collecting sphinx-rtd-theme
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b3/46/c167351699e5dc126798385cf37c26ba9df7a26c6f8855661d9f966d6ced/sphinx_rtd_theme-1.2.0-py2.py3-none-any.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 13.1 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.3
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/91/63/1228bc6c9162b19c5553697fa29eb60d734ba5967378b44f07c2512ae91e/readthedocs_sphinx_ext-2.2.0-py2.py3-none-any.whl (11 kB)
Collecting docutils>=0.11
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/93/69/e391bd51bc08ed9141ecd899a0ddb61ab6465309f1eb470905c0c8868081/docutils-0.19-py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 14.3 MB/s eta 0:00:00
Collecting babel>=2.9
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/92/f7/86301a69926e11cd52f73396d169554d09b20b1723a040c2dcc1559ef588/Babel-2.11.0-py3-none-any.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 12.7 MB/s eta 0:00:00
Collecting Jinja2>=3.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/bc/c3/f068337a370801f372f2f8f6bad74a5c140f6fda3d9de154052708dd3c65/Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 15.7 MB/s eta 0:00:00
Collecting Pygments>=2.12
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0b/42/d9d95cc461f098f204cd20c85642ae40fbff81f74c300341b8d0e0df14e0/Pygments-2.14.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 13.7 MB/s eta 0:00:00
Collecting sphinxcontrib-serializinghtml>=1.1.5
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c6/77/5464ec50dd0f1c1037e3c93249b040c8fc8078fdda97530eeb02424b6eea/sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 196.2 MB/s eta 0:00:00
Collecting sphinxcontrib-devhelp
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c5/09/5de5ed43a521387f18bdf5f5af31d099605c992fd25372b2b9b825ce48ee/sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 195.1 MB/s eta 0:00:00
Collecting snowballstemmer>=2.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ed/dc/c02e01294f7265e63a7315fe086dd1df7dacb9f840a804da846b96d01b96/snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 192.9 MB/s eta 0:00:00
Collecting sphinxcontrib-jsmath
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c2/42/4c8646762ee83602e3fb3fbe774c2fac12f317deb0b5dbeeedd2d3ba4b77/sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting requests>=2.5.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/f4/274d1dbe96b41cf4e0efb70cbced278ffd61b5c7bb70338b62af94ccb25b/requests-2.28.2-py3-none-any.whl (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 156.4 MB/s eta 0:00:00
Collecting sphinxcontrib-applehelp
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/dc/47/86022665a9433d89a66f5911b558ddff69861766807ba685de2e324bd6ed/sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 kB 207.4 MB/s eta 0:00:00
Collecting importlib-metadata>=4.8
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/26/a7/9da7d5b23fc98ab3d424ac2c65613d63c1f401efb84ad50f2fa27b2caab4/importlib_metadata-6.0.0-py3-none-any.whl (21 kB)
Collecting imagesize>=1.3
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ff/62/85c4c919272577931d407be5ba5d71c20f0b616d31a0befe0ae45bb79abd/imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-qthelp
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/14/05f9206cf4e9cfca1afb5fd224c7cd434dcc3a433d6d9e4e0264d29c6cdb/sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 204.3 MB/s eta 0:00:00
Collecting packaging>=21.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ed/35/a31aed2993e398f6b09a790a181a7927eb14610ee8bbf02dc14d31677f1c/packaging-23.0-py3-none-any.whl (42 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 155.4 MB/s eta 0:00:00
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/63/40/c854ef09500e25f6432dcbad0f37df87fd7046d376272292d8654cc71c95/sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 kB 197.8 MB/s eta 0:00:00
Collecting docutils>=0.11
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8d/14/69b4bad34e3f250afe29a854da03acb6747711f3df06c359fa053fae4e76/docutils-0.18.1-py2.py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 14.3 MB/s eta 0:00:00
Collecting sphinxcontrib-jquery!=3.0.0,>=2.0.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/42/e0/c492f21bf39616ea34a83994c3add2132134f9803e3516d918ef0b6a2a45/sphinxcontrib_jquery-2.0.0-py3-none-any.whl (3.2 kB)
Collecting pytz>=2015.7
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2e/09/fbd3c46dce130958ee8e0090f910f1fe39e502cc5ba0aadca1e8a2b932e5/pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 499.4/499.4 kB 16.4 MB/s eta 0:00:00
Collecting typing-extensions>=3.6.4
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0b/8e/f1a0a5a76cfef77e1eb6004cb49e5f8d72634da638420b9ea492ce8305e8/typing_extensions-4.4.0-py3-none-any.whl (26 kB)
Collecting zipp>=0.5
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/95/7b/1608a7344743f54a8c072d64d2a279934fd204d6d015278b0a0ed4ce104b/zipp-3.13.0-py3-none-any.whl (6.7 kB)
Collecting MarkupSafe>=2.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/95/88/8c8cce021ac1b1eedde349c6a41f6c256da60babf95e572071361ff3f66b/MarkupSafe-2.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting certifi>=2017.4.17
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/71/4c/3db2b8021bd6f2f0ceb0e088d6b2d49147671f25832fb17970e9b583d742/certifi-2022.12.7-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 18.9 MB/s eta 0:00:00
Collecting idna<4,>=2.5
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fc/34/3030de6f1370931b9dbb4dad48f6ab1015ab1d32447850b9fc94e60097be/idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 180.2 MB/s eta 0:00:00
Collecting charset-normalizer<4,>=2
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c1/b2/d81606aebeb7e9a33dc877ff3a206c9946f5bb374c99d22d4a28825aa270/charset_normalizer-3.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (170 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.5/170.5 kB 20.3 MB/s eta 0:00:00
Collecting urllib3<1.27,>=1.21.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fe/ca/466766e20b767ddb9b951202542310cba37ea5f2d792dae7589f1741af58/urllib3-1.26.14-py2.py3-none-any.whl (140 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.6/140.6 kB 17.2 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-jquery!=3.0.0,>=2.0.0->sphinx-rtd-theme) (58.2.0)
Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=e36640fbd6270bd8d2a963d37693547cc20ab4ea337055effc3d44134bf3150a
  Stored in directory: /tmp/pip-ephem-wheel-cache-i1b2rrcm/wheels/39/db/d5/e22e622f3ac6beb40ab992464b2b5ae38526942ed4ffff7c05
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, charset-normalizer, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-jquery, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.0.0 mock-1.0.1 packaging-23.0 pillow-5.4.1 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.2.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jquery-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.4.0 urllib3-1.26.14 zipp-3.13.0

[rtd-command-info] start-time: 2023-02-13T22:21:11.189481Z, end-time: 2023-02-13T22:21:52.571070Z, duration: 41, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting emodpy~=1.15
  Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.20.0/emodpy-1.20.0-py3-none-any.whl (127 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 127.7/127.7 kB 10.6 MB/s eta 0:00:00
Collecting emod-hiv==1.0.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-hiv/1.0.1/emod_hiv-1.0.1-py3-none-any.whl (2.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 12.8 MB/s eta 0:00:00
Collecting emod-malaria==0.0.17
  Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-malaria/0.0.17/emod_malaria-0.0.17-py3-none-any.whl (3.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 12.9 MB/s eta 0:00:00
Collecting numpy
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6d/ad/ff3b21ebfe79a4d25b4a4f8e5cf9fd44a204adb6b33c09010f566f51027a/numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 12.7 MB/s eta 0:00:00
Collecting astunparse
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/03/13dde6512ad7b4557eb792fbcf0c653af6076b81e5941d36ec61f7ce6028/astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting click~=7.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 82.8/82.8 kB 160.0 MB/s eta 0:00:00
Collecting idmtools~=1.6
  Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.7.5/idmtools-1.7.5-py3-none-any.whl (165 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 165.0/165.0 kB 14.5 MB/s eta 0:00:00
Collecting emod-api~=1.24
  Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-api/1.28.1/emod_api-1.28.1-py3-none-any.whl (160 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 160.5/160.5 kB 14.4 MB/s eta 0:00:00
Collecting idmtools-models~=1.6
  Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.7.5/idmtools_models-1.7.5-py3-none-any.whl (24 kB)
Collecting idmtools-platform-comps~=1.6
  Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-platform-comps/1.7.5/idmtools_platform_comps-1.7.5-py3-none-any.whl (185 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 185.1/185.1 kB 16.5 MB/s eta 0:00:00
Collecting astor
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting keyring
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/62/db/0e9a09b2b95986dcd73ac78be6ed2bd73ebe8bac65cba7add5b83eb9d899/keyring-23.13.1-py3-none-any.whl (37 kB)
Collecting matplotlib
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ad/62/7b662284352867a86acfb636761ba351723fc3a235efd8397578d903413d/matplotlib-3.5.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 12.5 MB/s eta 0:00:00
Collecting bs4
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/ed/7e8b97591f6f456174139ec089c769f89a94a1a4025fe967691de971f314/bs4-0.0.1.tar.gz (1.1 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pyCOMPS~=2.6
  Downloading https://packages.idmod.org/api/pypi/pypi-production/pyCOMPS/2.10.0/pyCOMPS-2.10.0-py2.py3-none-any.whl (74 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 74.5/74.5 kB 165.0 MB/s eta 0:00:00
Collecting lz4
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/15/f5/3ba9dbc251413c836f0be0d0c9070c7095528c93383314ac942bfe9b0ac1/lz4-4.3.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 13.0 MB/s eta 0:00:00
Collecting parse
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/89/a1/82ce536be577ba09d4dcee45db58423a180873ad38a2d014d26ab7b7cb8a/parse-1.19.0.tar.gz (30 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting prodict
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5a/0b/594c85ac539dda877198e7d5541982127d0929e3b0e8e6018004cfbd9ac9/prodict-0.8.18.tar.gz (4.2 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting scikit-learn
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/bd/05/e561bc99a615b5c099c7a9355409e5e57c525a108f1c2e156abb005b90a6/scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.8/24.8 MB 12.8 MB/s eta 0:00:00
Collecting graphviz
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/de/5e/fcbb22c68208d39edff467809d06c9d81d7d27426460ebc598e55130c1aa/graphviz-0.20.1-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 121.9 MB/s eta 0:00:00
Collecting pandas
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/0c/23764c4635dcb0a784a787498d56847b90ebf974e65f4ab4053a5d97b1a5/pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 12.8 MB/s eta 0:00:00
Collecting geographiclib
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9f/5a/a26132406f1f40cf51ea349a5f11b0a46cec02a2031ff82e391c2537247a/geographiclib-2.0-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.3/40.3 kB 128.5 MB/s eta 0:00:00
Collecting scipy
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/58/4f/11f34cfc57ead25752a7992b069c36f5d18421958ebd6466ecd849aeaf86/scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 12.8 MB/s eta 0:00:00
Collecting pyproj
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/57/4648d607dd92d09e9a685a8cc20adeafb0c49ed61397bd77c85392a5eb05/pyproj-3.2.1-cp37-cp37m-manylinux2010_x86_64.whl (6.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 12.8 MB/s eta 0:00:00
Collecting pyyaml
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/eb/5f/6e6fe6904e1a9c67bc2ca5629a69e7a5a0b17f079da838bab98a1e548b25/PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 596.3/596.3 kB 14.1 MB/s eta 0:00:00
Collecting shapely
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1d/a4/931d0780f31f3ea8c4f9ef6464a2825137c5241e6707a5fb03bef760a7eb/shapely-2.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 12.5 MB/s eta 0:00:00
Collecting pygit2<=1.10.1,>=1.4.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a2/36/53df6e5a49b84416a114147c97a7602c808ad72d5223b0e47cde89866091/pygit2-1.10.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 12.8 MB/s eta 0:00:00
Collecting coloredlogs~=15.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 115.3 MB/s eta 0:00:00
Collecting backoff<2.3,>=1.10.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/df/73/b6e24bd22e6720ca8ee9a85a0c4a2971af8497d8f3193fa05390cbd46e09/backoff-2.2.1-py3-none-any.whl (15 kB)
Collecting diskcache~=5.4.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a1/c4/80d38cf6852ba87f8b506a91f18b3a485c668f452700689add960d7e2ecc/diskcache-5.4.0-py3-none-any.whl (44 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.0/45.0 kB 138.6 MB/s eta 0:00:00
Collecting more-itertools~=9.0.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5d/87/1ec3fcc09d2c04b977eabf8a1083222f82eaa2f46d5a4f85f403bf8e7b30/more_itertools-9.0.0-py3-none-any.whl (52 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.8/52.8 kB 144.2 MB/s eta 0:00:00
Collecting packaging<22.0,>=20.4
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/8e/8de486cbd03baba4deef4142bd643a3e7bbe954a784dc1bb17142572d127/packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 132.6 MB/s eta 0:00:00
Collecting tqdm<5,>=4.52.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/47/bb/849011636c4da2e44f1253cd927cfb20ada4374d8b3a4e425416e84900cc/tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 172.1 MB/s eta 0:00:00
Collecting tabulate<0.10,>=0.8.9
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/40/44/4a5f08c96eb108af5cb50b41f76142f0afa346dfa99d5296fe7202a11854/tabulate-0.9.0-py3-none-any.whl (35 kB)
Collecting pipreqs<0.5,>=0.4.10
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1a/cd/74bbb901d65c375e2e8ab5601a4071d4ef38c745f6d4da74add61f964b9a/pipreqs-0.4.11-py2.py3-none-any.whl (32 kB)
Collecting pluggy~=1.0.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9e/01/f38e2ff29715251cf25532b9082a1589ab7e4f571ced434f98d0139336dc/pluggy-1.0.0-py2.py3-none-any.whl (13 kB)
Requirement already satisfied: jinja2~=3.1.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from idmtools-models~=1.6->emodpy~=1.15->-r requirements.txt (line 2)) (3.1.2)
Collecting natsort~=8.2.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/58/61c4b4fd9e597affdcd3347d5991fa5be404af26f19932d3116b67e133da/natsort-8.2.0-py3-none-any.whl (37 kB)
Requirement already satisfied: requests>=2.11.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) (2.28.2)
Collecting xdg>=4.0.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ea/09/4a0f30aada49e142b94bbb232c023abcbc6ced7e2a9776533fb14977e9db/xdg-5.1.1-py3-none-any.whl (5.0 kB)
Requirement already satisfied: pytz>=2016.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) (2022.7.1)
Collecting future>=0.16.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8f/2e/cf6accf7415237d6faeeebdc7832023c90e0282aa16fd3263db0eb4715ec/future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 13.4 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting six<2.0,>=1.6.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from astunparse->emodpy~=1.15->-r requirements.txt (line 2)) (0.38.4)
Collecting beautifulsoup4
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c6/ee/16d6f808f5668317d7c23f942091fbc694bcded6aa39678e5167f61b2ba0/beautifulsoup4-4.11.2-py3-none-any.whl (129 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 129.4/129.4 kB 199.8 MB/s eta 0:00:00
Requirement already satisfied: importlib-metadata>=4.11.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from keyring->emodpy~=1.15->-r requirements.txt (line 2)) (6.0.0)
Collecting jaraco.classes
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/60/28/220d3ae0829171c11e50dded4355d17824d60895285631d7eb9dee0ab5e5/jaraco.classes-3.2.3-py3-none-any.whl (6.0 kB)
Collecting SecretStorage>=3.2
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/54/24/b4293291fa1dd830f353d2cb163295742fa87f179fcc8a20a306a81978b7/SecretStorage-3.3.3-py3-none-any.whl (15 kB)
Collecting jeepney>=0.4.2
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ae/72/2a1e2290f1ab1e06f71f3d0f1646c9e4634e70e1d37491535e19266e8dc9/jeepney-0.8.0-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.4/48.4 kB 137.7 MB/s eta 0:00:00
Collecting importlib-resources
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/0f/bd3e7fa47cc43276051c557d3b2fe946664781d2ecf08b05d074e1a3ee59/importlib_resources-5.10.2-py3-none-any.whl (34 kB)
Collecting python-dateutil>=2.7
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 21.2 MB/s eta 0:00:00
Collecting fonttools>=4.22.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e3/d9/e9bae85e84737e76ebbcbea13607236da0c0699baed0ae4f1151b728a608/fonttools-4.38.0-py3-none-any.whl (965 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 13.3 MB/s eta 0:00:00
Collecting pillow>=6.2.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/dc/8a/ee6c0ecdf39a5674881a9ea82b488751be6feb7723b62c7df64229d60f85/Pillow-9.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 13.1 MB/s eta 0:00:00
Collecting pyparsing>=2.2.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6c/10/a7d0fa5baea8fe7b50f448ab742f26f52b80bfca85ac2be9d35cdd9a3246/pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 163.5 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ab/8f/8dbe2d4efc4c0b08ec67d6efb7cc31fbfd688c80afad85f65980633b0d37/kiwisolver-1.4.4-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 13.7 MB/s eta 0:00:00
Collecting cycler>=0.10
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5c/f9/695d6bedebd747e5eb0fe8fad57b72fdf25411273a39791cde838d5a8f51/cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting humanfriendly>=9.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 173.6 MB/s eta 0:00:00
Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.11.4->keyring->emodpy~=1.15->-r requirements.txt (line 2)) (4.4.0)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.11.4->keyring->emodpy~=1.15->-r requirements.txt (line 2)) (3.13.0)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from jinja2~=3.1.2->idmtools-models~=1.6->emodpy~=1.15->-r requirements.txt (line 2)) (2.1.2)
Collecting yarg
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8b/90/89a2ff242ccab6a24fbab18dbbabc67c51a6f0ed01f9a0f41689dc177419/yarg-0.1.9-py2.py3-none-any.whl (19 kB)
Collecting docopt
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting cffi>=1.9.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/93/d0/2e2b27ea2f69b0ec9e481647822f8f77f5fc23faca2dd00d1ff009940eb7/cffi-1.15.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (427 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 427.9/427.9 kB 13.4 MB/s eta 0:00:00
Collecting cached-property
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/48/19/f2090f7dad41e225c7f2326e4cfe6fff49e57dedb5b53636c9551f86b069/cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) (1.26.14)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) (3.0.1)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) (2022.12.7)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) (3.4)
Collecting cryptography>=2.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2f/c7/06087b04cd870f5acfdc10f8ba252f7985b32c82d4ff96cba05e5f034bf3/cryptography-39.0.1-cp36-abi3-manylinux_2_24_x86_64.whl (4.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 12.9 MB/s eta 0:00:00
Collecting soupsieve>1.2
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/16/e3/4ad79882b92617e3a4a0df1960d6bce08edfb637737ac5c3f3ba29022e25/soupsieve-2.3.2.post1-py3-none-any.whl (37 kB)
Collecting joblib>=0.11
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/91/d4/3b4c8e5a30604df4c7518c562d4bf0502f2fa29221459226e140cf846512/joblib-1.2.0-py3-none-any.whl (297 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 13.9 MB/s eta 0:00:00
Collecting threadpoolctl>=2.0.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/61/cf/6e354304bcb9c6413c4e02a747b600061c21d38ba51e7e544ac7bc66aecc/threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting pycparser
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 184.0 MB/s eta 0:00:00
Building wheels for collected packages: bs4, future, parse, prodict, docopt
  Building wheel for bs4 (setup.py): started
  Building wheel for bs4 (setup.py): finished with status 'done'
  Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1271 sha256=e2e2adc02628e237e9085c1f0da9f10e1e5ea051e6ccf9da5a07a2f0af48ee68
  Stored in directory: /tmp/pip-ephem-wheel-cache-7by1le5k/wheels/f1/23/17/3fcd260137068c2aa94da5806487146928f092eae4c2405b28
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492036 sha256=1c74386e983c0d22b7bc511120a6bcf390698815769dc3ad6d07fefc99acd9da
  Stored in directory: /tmp/pip-ephem-wheel-cache-7by1le5k/wheels/c4/f7/54/ce38ea620e2cd4e42cac68b1ca4904d1989313cd96c0b06673
  Building wheel for parse (setup.py): started
  Building wheel for parse (setup.py): finished with status 'done'
  Created wheel for parse: filename=parse-1.19.0-py3-none-any.whl size=24591 sha256=ed3f1a8ba24277ae1198a510c16179a6258033b10903249ba1ef9bcb008b8cc0
  Stored in directory: /tmp/pip-ephem-wheel-cache-7by1le5k/wheels/f8/66/d2/221f7d7edde4fbc7210b77a9e1ed2db3959a5ca85650d18e66
  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=4223 sha256=679ad004338911587b24f458aa9bf4f71bdcf757cb9625ec43be59463b39a86b
  Stored in directory: /tmp/pip-ephem-wheel-cache-7by1le5k/wheels/a1/47/0e/cbfbed83f6077c4d538850a09e49b8d78284632fc1d48bf122
  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=13723 sha256=b6e259f908a6c7c0e3df43fbe17c77541458d1e4ab248c4be854e1a00b1c7320
  Stored in directory: /tmp/pip-ephem-wheel-cache-7by1le5k/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c
Successfully built bs4 future parse prodict docopt
Installing collected packages: prodict, parse, emod-malaria, emod-hiv, docopt, cached-property, xdg, tqdm, threadpoolctl, tabulate, soupsieve, six, pyyaml, pyproj, pyparsing, pycparser, pillow, numpy, natsort, more-itertools, lz4, kiwisolver, joblib, jeepney, importlib-resources, humanfriendly, graphviz, geographiclib, future, fonttools, diskcache, cycler, click, backoff, astor, yarg, shapely, scipy, python-dateutil, pyCOMPS, pluggy, packaging, jaraco.classes, coloredlogs, cffi, beautifulsoup4, astunparse, scikit-learn, pygit2, pipreqs, pandas, matplotlib, cryptography, bs4, SecretStorage, idmtools, emod-api, keyring, idmtools-platform-comps, idmtools-models, emodpy
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
  Attempting uninstall: packaging
    Found existing installation: packaging 23.0
    Uninstalling packaging-23.0:
      Successfully uninstalled packaging-23.0
Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 beautifulsoup4-4.11.2 bs4-0.0.1 cached-property-1.5.2 cffi-1.15.1 click-7.1.2 coloredlogs-15.0.1 cryptography-39.0.1 cycler-0.11.0 diskcache-5.4.0 docopt-0.6.2 emod-api-1.28.1 emod-hiv-1.0.1 emod-malaria-0.0.17 emodpy-1.20.0 fonttools-4.38.0 future-0.18.3 geographiclib-2.0 graphviz-0.20.1 humanfriendly-10.0 idmtools-1.7.5 idmtools-models-1.7.5 idmtools-platform-comps-1.7.5 importlib-resources-5.10.2 jaraco.classes-3.2.3 jeepney-0.8.0 joblib-1.2.0 keyring-23.13.1 kiwisolver-1.4.4 lz4-4.3.2 matplotlib-3.5.3 more-itertools-9.0.0 natsort-8.2.0 numpy-1.21.6 packaging-21.3 pandas-1.3.5 parse-1.19.0 pillow-9.4.0 pipreqs-0.4.11 pluggy-1.0.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.21 pygit2-1.10.1 pyparsing-3.0.9 pyproj-3.2.1 python-dateutil-2.8.2 pyyaml-6.0 scikit-learn-1.0.2 scipy-1.7.3 shapely-2.0.1 six-1.16.0 soupsieve-2.3.2.post1 tabulate-0.9.0 threadpoolctl-3.1.0 tqdm-4.64.1 xdg-5.1.1 yarg-0.1.9

[rtd-command-info] start-time: 2023-02-13T22:21:52.752903Z, end-time: 2023-02-13T22:21:58.554695Z, duration: 5, 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
Collecting sphinx-rtd-theme~=0.5.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ac/24/2475e8f83519b54b2148d4a56eb1111f9cec630d088c3ffc214492c12107/sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 15.0 MB/s eta 0:00:00
Collecting sphinxcontrib-napoleon~=0.7
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/75/f2/6b7627dfe7b4e418e295e254bb15c3a6455f11f8c0ad0d43113f678049c3/sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB)
Collecting sphinx~=4.4.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c4/85/978c06c898331b72080242f18ab7a6021f1055285fb1db9e6554c79264cd/Sphinx-4.4.0-py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 15.4 MB/s eta 0:00:00
Collecting plantweb~=1.2.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d6/6f/9ab1a1c3e33aaa0c0931983578c09336b092c75dce777ea666d3032f756e/plantweb-1.2.1-py3-none-any.whl (20 kB)
Collecting sphinxcontrib-programoutput~=0.16
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/30/ee/b7be4b3f45f4e36bfa6c444cd234098e0d09880379c67a43e6bb9ab99a86/sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB)
Collecting sphinxext.remoteliteralinclude
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/13/0d/7e5009f48c33d5fd533dda80b42c4a79fce8dfdd1b617d0a9df9a9836145/sphinxext_remoteliteralinclude-0.4.0-py3-none-any.whl (6.4 kB)
Collecting sphinx-copybutton~=0.4.0
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/8b/7c9cf5956be80bfd826f2534e2b38ff2310f8c4274a77e4b3b2d846af552/sphinx_copybutton-0.4.0-py3-none-any.whl (12 kB)
Collecting docutils<0.17
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/44/8a15e45ffa96e6cf82956dd8d7af9e666357e16b0d93b253903475ee947f/docutils-0.16-py2.py3-none-any.whl (548 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 15.5 MB/s eta 0:00:00
Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 2)) (1.16.0)
Collecting pockets>=0.3
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e9/2f/a4583c70fbd8cd04910e2884bcc2bdd670e884061f7b4d70bc13e632a993/pockets-0.9.1-py2.py3-none-any.whl (26 kB)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2.2.0)
Requirement already satisfied: importlib-metadata>=4.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (6.0.0)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.0.3)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2.11.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.1.5)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (21.3)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.1.2)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2.14.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.4.1)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (0.7.13)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2.0.0)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2.28.2)
Collecting Jinja2>=2.3
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7e/c2/1eece8c95ddbc9b1aeb64f5783a9e07a286de42191b7204d67b7496ddf35/Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 125.7/125.7 kB 192.2 MB/s eta 0:00:00
Collecting MarkupSafe<=2.0.1
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/09/f1/5ca5da61ec071ce1e9c423f66a5bde508957601118be9cd37aeccfeab2f6/MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2022.7.1)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.4->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.13.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.4->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (4.4.0)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (2022.12.7)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (1.26.14)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.0.1)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=4.4.0->-r docs/requirements.txt (line 3)) (3.0.9)
Installing collected packages: pockets, MarkupSafe, docutils, sphinxcontrib-napoleon, plantweb, Jinja2, sphinxext.remoteliteralinclude, sphinx, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton
  Attempting uninstall: MarkupSafe
    Found existing installation: MarkupSafe 2.1.2
    Uninstalling MarkupSafe-2.1.2:
      Successfully uninstalled MarkupSafe-2.1.2
  Attempting uninstall: docutils
    Found existing installation: docutils 0.18.1
    Uninstalling docutils-0.18.1:
      Successfully uninstalled docutils-0.18.1
  Attempting uninstall: Jinja2
    Found existing installation: Jinja2 3.1.2
    Uninstalling Jinja2-3.1.2:
      Successfully uninstalled Jinja2-3.1.2
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 5.3.0
    Uninstalling Sphinx-5.3.0:
      Successfully uninstalled Sphinx-5.3.0
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 1.2.0
    Uninstalling sphinx-rtd-theme-1.2.0:
      Successfully uninstalled sphinx-rtd-theme-1.2.0
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.
idmtools-platform-comps 1.7.5 requires jinja2~=3.1.2, but you have jinja2 2.11.3 which is incompatible.
idmtools-models 1.7.5 requires jinja2~=3.1.2, but you have jinja2 2.11.3 which is incompatible.
Successfully installed Jinja2-2.11.3 MarkupSafe-2.0.1 docutils-0.16 plantweb-1.2.1 pockets-0.9.1 sphinx-4.4.0 sphinx-copybutton-0.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0

[rtd-command-info] start-time: 2023-02-13T22:21:58.756018Z, end-time: 2023-02-13T22:22:00.148892Z, duration: 1, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating emodpy_hiv.egg-info
writing emodpy_hiv.egg-info/PKG-INFO
writing dependency_links to emodpy_hiv.egg-info/dependency_links.txt
writing requirements to emodpy_hiv.egg-info/requires.txt
writing top-level names to emodpy_hiv.egg-info/top_level.txt
writing manifest file 'emodpy_hiv.egg-info/SOURCES.txt'
reading manifest file 'emodpy_hiv.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'emodpy_hiv.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_hiv
copying emodpy_hiv/__init__.py -> build/lib/emodpy_hiv
copying emodpy_hiv/utils.py -> build/lib/emodpy_hiv
copying emodpy_hiv/download.py -> build/lib/emodpy_hiv
creating build/lib/tests
copying tests/__init__.py -> build/lib/tests
creating build/lib/emodpy_hiv/demographics
copying emodpy_hiv/demographics/HIVDemographics.py -> build/lib/emodpy_hiv/demographics
copying emodpy_hiv/demographics/__init__.py -> build/lib/emodpy_hiv/demographics
copying emodpy_hiv/demographics/DemographicsTemplates.py -> build/lib/emodpy_hiv/demographics
creating build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/prep.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/art.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/random.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/drawblood.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/reftracker.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/outbreak.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/modcoinf.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/cascade_helpers.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/pmtct.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/delay.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/stipostdebut.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/malecirc.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/__init__.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/sigmoiddiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/utils.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artstagingbycd4diag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/artdropout.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/rapiddiag.py -> build/lib/emodpy_hiv/interventions
copying emodpy_hiv/interventions/yearandsexdiag.py -> build/lib/emodpy_hiv/interventions
creating build/lib/tests/unittests
copying tests/unittests/test_import.py -> build/lib/tests/unittests
copying tests/unittests/test_demographics.py -> build/lib/tests/unittests
copying tests/unittests/__init__.py -> build/lib/tests/unittests
copying tests/unittests/check_coverage.py -> build/lib/tests/unittests
copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests
copying tests/unittests/test_intervention.py -> build/lib/tests/unittests
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/emodpy_hiv
creating build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/demographics/HIVDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics
copying build/lib/emodpy_hiv/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
copying build/lib/emodpy_hiv/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
copying build/lib/emodpy_hiv/download.py -> build/bdist.linux-x86_64/egg/emodpy_hiv
creating build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/prep.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/art.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/random.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/drawblood.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/reftracker.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/modcoinf.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/cascade_helpers.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/pmtct.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/delay.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/stipostdebut.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/malecirc.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/sigmoiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/artstagingbycd4diag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/artdropout.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/rapiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
copying build/lib/emodpy_hiv/interventions/yearandsexdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions
creating build/bdist.linux-x86_64/egg/tests
copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests
creating build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_import.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_demographics.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/check_coverage.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/schema_path_file.py -> build/bdist.linux-x86_64/egg/tests/unittests
copying build/lib/tests/unittests/test_intervention.py -> build/bdist.linux-x86_64/egg/tests/unittests
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/HIVDemographics.py to HIVDemographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/download.py to download.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/prep.py to prep.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/art.py to art.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/random.py to random.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/drawblood.py to drawblood.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/reftracker.py to reftracker.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/outbreak.py to outbreak.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/modcoinf.py to modcoinf.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/cascade_helpers.py to cascade_helpers.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/pmtct.py to pmtct.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/delay.py to delay.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/stipostdebut.py to stipostdebut.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/malecirc.py to malecirc.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py to artstagingbycd4agnosticdiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/sigmoiddiag.py to sigmoiddiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4diag.py to artstagingbycd4diag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artdropout.py to artdropout.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/rapiddiag.py to rapiddiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/yearandsexdiag.py to yearandsexdiag.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_import.py to test_import.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demographics.py to test_demographics.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/check_coverage.py to check_coverage.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/schema_path_file.py to schema_path_file.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_intervention.py to test_intervention.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying emodpy_hiv.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
tests.unittests.__pycache__.schema_path_file.cpython-37: module references __file__
tests.unittests.__pycache__.test_demographics.cpython-37: module references __file__
tests.unittests.__pycache__.test_intervention.cpython-37: module references __file__
creating dist
creating 'dist/emodpy_hiv-1.0.8-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing emodpy_hiv-1.0.8-py3.7.egg
creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages/emodpy_hiv-1.0.8-py3.7.egg
Extracting emodpy_hiv-1.0.8-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Adding emodpy-hiv 1.0.8 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages/emodpy_hiv-1.0.8-py3.7.egg
Processing dependencies for emodpy-hiv==1.0.8
Searching for jinja2~=3.1.2
Reading https://pypi.org/simple/jinja2/
Downloading https://files.pythonhosted.org/packages/bc/c3/f068337a370801f372f2f8f6bad74a5c140f6fda3d9de154052708dd3c65/Jinja2-3.1.2-py3-none-any.whl#sha256=6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61
Best match: Jinja2 3.1.2
Processing Jinja2-3.1.2-py3-none-any.whl
Installing Jinja2-3.1.2-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Adding Jinja2 3.1.2 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages/Jinja2-3.1.2-py3.7.egg
Searching for numpy==1.21.6
Best match: numpy 1.21.6
Adding numpy 1.21.6 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emod-malaria==0.0.17
Best match: emod-malaria 0.0.17
Adding emod-malaria 0.0.17 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emod-hiv==1.0.1
Best match: emod-hiv 1.0.1
Adding emod-hiv 1.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emodpy==1.20.0
Best match: emodpy 1.20.0
Adding emodpy 1.20.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for bs4==0.0.1
Best match: bs4 0.0.1
Adding bs4 0.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for keyring==23.13.1
Best match: keyring 23.13.1
Adding keyring 23.13.1 to easy-install.pth file
Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for matplotlib==3.5.3
Best match: matplotlib 3.5.3
Adding matplotlib 3.5.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idmtools==1.7.5
Best match: idmtools 1.7.5
Adding idmtools 1.7.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idmtools-platform-comps==1.7.5
Best match: idmtools-platform-comps 1.7.5
Adding idmtools-platform-comps 1.7.5 to easy-install.pth file
Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idmtools-models==1.7.5
Best match: idmtools-models 1.7.5
Adding idmtools-models 1.7.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for emod-api==1.28.1
Best match: emod-api 1.28.1
Adding emod-api 1.28.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for beautifulsoup4==4.11.2
Best match: beautifulsoup4 4.11.2
Adding beautifulsoup4 4.11.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for future==0.18.3
Best match: future 0.18.3
Adding future 0.18.3 to easy-install.pth file
Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pytz==2022.7.1
Best match: pytz 2022.7.1
Adding pytz 2022.7.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for xdg==5.1.1
Best match: xdg 5.1.1
Adding xdg 5.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for requests==2.28.2
Best match: requests 2.28.2
Adding requests 2.28.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for importlib-resources==5.10.2
Best match: importlib-resources 5.10.2
Adding importlib-resources 5.10.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for importlib-metadata==6.0.0
Best match: importlib-metadata 6.0.0
Adding importlib-metadata 6.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for jaraco.classes==3.2.3
Best match: jaraco.classes 3.2.3
Adding jaraco.classes 3.2.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cycler==0.11.0
Best match: cycler 0.11.0
Adding cycler 0.11.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for fonttools==4.38.0
Best match: fonttools 4.38.0
Adding fonttools 4.38.0 to easy-install.pth file
Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin
Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for Pillow==9.4.0
Best match: Pillow 9.4.0
Adding Pillow 9.4.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for packaging==21.3
Best match: packaging 21.3
Adding packaging 21.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pyparsing==3.0.9
Best match: pyparsing 3.0.9
Adding pyparsing 3.0.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for python-dateutil==2.8.2
Best match: python-dateutil 2.8.2
Adding python-dateutil 2.8.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for kiwisolver==1.4.4
Best match: kiwisolver 1.4.4
Adding kiwisolver 1.4.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pipreqs==0.4.11
Best match: pipreqs 0.4.11
Adding pipreqs 0.4.11 to easy-install.pth file
Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pandas==1.3.5
Best match: pandas 1.3.5
Adding pandas 1.3.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pluggy==1.0.0
Best match: pluggy 1.0.0
Adding pluggy 1.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pygit2==1.10.1
Best match: pygit2 1.10.1
Adding pygit2 1.10.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for tqdm==4.64.1
Best match: tqdm 4.64.1
Adding tqdm 4.64.1 to easy-install.pth file
Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for PyYAML==6.0
Best match: PyYAML 6.0
Adding PyYAML 6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for more-itertools==9.0.0
Best match: more-itertools 9.0.0
Adding more-itertools 9.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for natsort==8.2.0
Best match: natsort 8.2.0
Adding natsort 8.2.0 to easy-install.pth file
Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for lz4==4.3.2
Best match: lz4 4.3.2
Adding lz4 4.3.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for shapely==2.0.1
Best match: shapely 2.0.1
Adding shapely 2.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pyproj==3.2.1
Best match: pyproj 3.2.1
Adding pyproj 3.2.1 to easy-install.pth file
Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.7.3
Best match: scipy 1.7.3
Adding scipy 1.7.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for parse==1.19.0
Best match: parse 1.19.0
Adding parse 1.19.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for scikit-learn==1.0.2
Best match: scikit-learn 1.0.2
Adding scikit-learn 1.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for graphviz==0.20.1
Best match: graphviz 0.20.1
Adding graphviz 0.20.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for wheel==0.38.4
Best match: wheel 0.38.4
Adding wheel 0.38.4 to easy-install.pth file
Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for soupsieve==2.3.2.post1
Best match: soupsieve 2.3.2.post1
Adding soupsieve 2.3.2.post1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for charset-normalizer==3.0.1
Best match: charset-normalizer 3.0.1
Adding charset-normalizer 3.0.1 to easy-install.pth file
Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for certifi==2022.12.7
Best match: certifi 2022.12.7
Adding certifi 2022.12.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for urllib3==1.26.14
Best match: urllib3 1.26.14
Adding urllib3 1.26.14 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for idna==3.4
Best match: idna 3.4
Adding idna 3.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for zipp==3.13.0
Best match: zipp 3.13.0
Adding zipp 3.13.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for typing-extensions==4.4.0
Best match: typing-extensions 4.4.0
Adding typing-extensions 4.4.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cryptography==39.0.1
Best match: cryptography 39.0.1
Adding cryptography 39.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for yarg==0.1.9
Best match: yarg 0.1.9
Adding yarg 0.1.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for docopt==0.6.2
Best match: docopt 0.6.2
Adding docopt 0.6.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/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-emodpy-hiv/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cached-property==1.5.2
Best match: cached-property 1.5.2
Adding cached-property 1.5.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for cffi==1.15.1
Best match: cffi 1.15.1
Adding cffi 1.15.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for MarkupSafe==2.0.1
Best match: MarkupSafe 2.0.1
Adding MarkupSafe 2.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for threadpoolctl==3.1.0
Best match: threadpoolctl 3.1.0
Adding threadpoolctl 3.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for joblib==1.2.0
Best match: joblib 1.2.0
Adding joblib 1.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Searching for pycparser==2.21
Best match: pycparser 2.21
Adding pycparser 2.21 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for emodpy-hiv==1.0.8

[rtd-command-info] start-time: 2023-02-13T22:22:02.228849Z, end-time: 2023-02-13T22:22:02.305113Z, 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 "emodpy-hiv" 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 ------------------------------------------------

tags.add('emodpyhiv')

# 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',
    'sphinxext.remoteliteralinclude',
    'sphinx_copybutton'
]

plantuml = 'plantweb'

autodoc_default_options = {
    'member-order': 'bysource',
    'members': None,
    'exclude-members': '__all__'
}

autodoc_mock_imports = []

napoleon_google_docstring = True
# napoleon_numpy_docstring = True

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

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

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

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'emodpy-hiv'
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 = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
# today = ''
#
# Else, today_fmt is used as the format for a strftime call.
#
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False

# RST epilog is added to the end of every topic. Useful for replace
# directives to use across the docset.

rst_epilog = "\n.. include:: /variables.txt"

# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the docs for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# docs.
# #
# html_theme_options = {
# }

# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# The name for this set of Sphinx documents.
# "<project> v<release> docs" by default.
#
# html_title = u'Sphinx Demo v1.0'

# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
html_logo = "images/IDM_white.png"

# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
html_favicon = "images/favicon.ico"

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']

html_context = {
    'css_files': [
        '_static/theme_overrides.css',
        '_static/copy_button.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/'

# 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 = 'emodpy-hiv'

# -- 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, 'emodpy-hiv-docs.tex', u'emodpy-hiv',
     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, 'emodpy-hiv-docs', u'emodpy-hiv',
     [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, 'emodpy-hiv-docs', u'emodpy-hiv',
     author, 'Institute for Disease Modeling', 'How to use emodpy for HIV simulations.',
     'Miscellaneous'),
]

# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []

# If false, no module index is generated.
#
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
                       'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None),
                       'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None),
                       'emodpy_generic': ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', None),
                       'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None),
                       'calibra': ('https://docs.idmod.org/projects/idmtools_calibra/en/latest/', None),
                       'emod-hiv': ('https://docs.idmod.org/projects/emod-hiv/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')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    '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/"),
    ("stable", "/en/stable/"),
    ("v1.0.2", "/en/v1.0.2/"),
    ("v1.0.1", "/en/v1.0.1/"),
    ("v0.0.41", "/en/v0.0.41/"),
    ("v0.0.38", "/en/v0.0.38/"),
    ("v0.0.37", "/en/v0.0.37/"),
    ("v0.0.35", "/en/v0.0.35/"),
    ("v0.0.22", "/en/v0.0.22/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/emodpy-hiv/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/emodpy-hiv/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-emodpy-hiv',
    'name': u'emodpy-hiv',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://docs.idmod.org/projects/emodpy-hiv/en/latest/',
    'analytics_code': 'UA-87656833-3',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'emodpy-hiv',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-87656833-3',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '8214912a',
}

# 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():
    
    html_context.update(context)
    
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-emodpy-hiv/builds/1298193/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2023-02-13T22:22:02.481834Z, end-time: 2023-02-13T22:22:07.673367Z, duration: 5, exit-code: 0
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . ../_readthedocs/html
Running Sphinx v4.4.0
rm: cannot remove 'modules.rst': No such file or directory
make: [generate-api] Error 1 (ignored)
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools_calibra/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 30 source files that are out of date
updating environment: [new config] 30 added, 0 changed, 0 removed
reading sources... [  3%] emodpy_hiv
reading sources... [  6%] emodpy_hiv.demographics
reading sources... [ 10%] emodpy_hiv.demographics.DemographicsTemplates
reading sources... [ 13%] emodpy_hiv.demographics.HIVDemographics
reading sources... [ 16%] emodpy_hiv.download
reading sources... [ 20%] emodpy_hiv.interventions
reading sources... [ 23%] emodpy_hiv.interventions.art
reading sources... [ 26%] emodpy_hiv.interventions.artdropout
reading sources... [ 30%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag
reading sources... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag
reading sources... [ 36%] emodpy_hiv.interventions.cascade_helpers
reading sources... [ 40%] emodpy_hiv.interventions.delay
reading sources... [ 43%] emodpy_hiv.interventions.drawblood
reading sources... [ 46%] emodpy_hiv.interventions.malecirc
reading sources... [ 50%] emodpy_hiv.interventions.modcoinf
reading sources... [ 53%] emodpy_hiv.interventions.outbreak
reading sources... [ 56%] emodpy_hiv.interventions.pmtct
reading sources... [ 60%] emodpy_hiv.interventions.prep
reading sources... [ 63%] emodpy_hiv.interventions.random
reading sources... [ 66%] emodpy_hiv.interventions.rapiddiag
reading sources... [ 70%] emodpy_hiv.interventions.reftracker
reading sources... [ 73%] emodpy_hiv.interventions.sigmoiddiag
reading sources... [ 76%] emodpy_hiv.interventions.stipostdebut
reading sources... [ 80%] emodpy_hiv.interventions.utils
reading sources... [ 83%] emodpy_hiv.interventions.yearandsexdiag
reading sources... [ 86%] emodpy_hiv.utils
reading sources... [ 90%] faq
reading sources... [ 93%] index
reading sources... [ 96%] installation
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  3%] emodpy_hiv
writing output... [  6%] emodpy_hiv.demographics
writing output... [ 10%] emodpy_hiv.demographics.DemographicsTemplates
writing output... [ 13%] emodpy_hiv.demographics.HIVDemographics
writing output... [ 16%] emodpy_hiv.download
writing output... [ 20%] emodpy_hiv.interventions
writing output... [ 23%] emodpy_hiv.interventions.art
writing output... [ 26%] emodpy_hiv.interventions.artdropout
writing output... [ 30%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag
writing output... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag
writing output... [ 36%] emodpy_hiv.interventions.cascade_helpers
writing output... [ 40%] emodpy_hiv.interventions.delay
writing output... [ 43%] emodpy_hiv.interventions.drawblood
writing output... [ 46%] emodpy_hiv.interventions.malecirc
writing output... [ 50%] emodpy_hiv.interventions.modcoinf
writing output... [ 53%] emodpy_hiv.interventions.outbreak
writing output... [ 56%] emodpy_hiv.interventions.pmtct
writing output... [ 60%] emodpy_hiv.interventions.prep
writing output... [ 63%] emodpy_hiv.interventions.random
writing output... [ 66%] emodpy_hiv.interventions.rapiddiag
writing output... [ 70%] emodpy_hiv.interventions.reftracker
writing output... [ 73%] emodpy_hiv.interventions.sigmoiddiag
writing output... [ 76%] emodpy_hiv.interventions.stipostdebut
writing output... [ 80%] emodpy_hiv.interventions.utils
writing output... [ 83%] emodpy_hiv.interventions.yearandsexdiag
writing output... [ 86%] emodpy_hiv.utils
writing output... [ 90%] faq
writing output... [ 93%] index
writing output... [ 96%] installation
writing output... [100%] modules

generating indices... genindex py-modindex done
writing additional pages... search opensearch done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in ../_readthedocs/html.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2023-02-13T22:22:07.869938Z, end-time: 2023-02-13T22:22:12.048070Z, duration: 4, exit-code: 0
python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . ../_readthedocs/htmlzip
Running Sphinx v4.4.0
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools_calibra/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: [new config] 30 added, 0 changed, 0 removed
reading sources... [  3%] emodpy_hiv
reading sources... [  6%] emodpy_hiv.demographics
reading sources... [ 10%] emodpy_hiv.demographics.DemographicsTemplates
reading sources... [ 13%] emodpy_hiv.demographics.HIVDemographics
reading sources... [ 16%] emodpy_hiv.download
reading sources... [ 20%] emodpy_hiv.interventions
reading sources... [ 23%] emodpy_hiv.interventions.art
reading sources... [ 26%] emodpy_hiv.interventions.artdropout
reading sources... [ 30%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag
reading sources... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag
reading sources... [ 36%] emodpy_hiv.interventions.cascade_helpers
reading sources... [ 40%] emodpy_hiv.interventions.delay
reading sources... [ 43%] emodpy_hiv.interventions.drawblood
reading sources... [ 46%] emodpy_hiv.interventions.malecirc
reading sources... [ 50%] emodpy_hiv.interventions.modcoinf
reading sources... [ 53%] emodpy_hiv.interventions.outbreak
reading sources... [ 56%] emodpy_hiv.interventions.pmtct
reading sources... [ 60%] emodpy_hiv.interventions.prep
reading sources... [ 63%] emodpy_hiv.interventions.random
reading sources... [ 66%] emodpy_hiv.interventions.rapiddiag
reading sources... [ 70%] emodpy_hiv.interventions.reftracker
reading sources... [ 73%] emodpy_hiv.interventions.sigmoiddiag
reading sources... [ 76%] emodpy_hiv.interventions.stipostdebut
reading sources... [ 80%] emodpy_hiv.interventions.utils
reading sources... [ 83%] emodpy_hiv.interventions.yearandsexdiag
reading sources... [ 86%] emodpy_hiv.utils
reading sources... [ 90%] faq
reading sources... [ 93%] index
reading sources... [ 96%] installation
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... installation faq modules emodpy_hiv emodpy_hiv.demographics emodpy_hiv.demographics.DemographicsTemplates emodpy_hiv.demographics.HIVDemographics emodpy_hiv.interventions emodpy_hiv.interventions.art emodpy_hiv.interventions.artdropout emodpy_hiv.interventions.artstagingbycd4agnosticdiag emodpy_hiv.interventions.artstagingbycd4diag emodpy_hiv.interventions.cascade_helpers emodpy_hiv.interventions.delay emodpy_hiv.interventions.drawblood emodpy_hiv.interventions.malecirc emodpy_hiv.interventions.modcoinf emodpy_hiv.interventions.outbreak emodpy_hiv.interventions.pmtct emodpy_hiv.interventions.prep emodpy_hiv.interventions.random emodpy_hiv.interventions.rapiddiag emodpy_hiv.interventions.reftracker emodpy_hiv.interventions.sigmoiddiag emodpy_hiv.interventions.stipostdebut emodpy_hiv.interventions.utils emodpy_hiv.interventions.yearandsexdiag emodpy_hiv.download emodpy_hiv.utils done
writing... done
writing additional files...  opensearchdone
copying static files... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in ../_readthedocs/htmlzip.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2023-02-13T22:22:13.157833Z, end-time: 2023-02-13T22:22:17.104665Z, duration: 3, exit-code: 0
python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . ../_readthedocs/pdf
Running Sphinx v4.4.0
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/idmtools_calibra/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: [new config] 30 added, 0 changed, 0 removed
reading sources... [  3%] emodpy_hiv
reading sources... [  6%] emodpy_hiv.demographics
reading sources... [ 10%] emodpy_hiv.demographics.DemographicsTemplates
reading sources... [ 13%] emodpy_hiv.demographics.HIVDemographics
reading sources... [ 16%] emodpy_hiv.download
reading sources... [ 20%] emodpy_hiv.interventions
reading sources... [ 23%] emodpy_hiv.interventions.art
reading sources... [ 26%] emodpy_hiv.interventions.artdropout
reading sources... [ 30%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag
reading sources... [ 33%] emodpy_hiv.interventions.artstagingbycd4diag
reading sources... [ 36%] emodpy_hiv.interventions.cascade_helpers
reading sources... [ 40%] emodpy_hiv.interventions.delay
reading sources... [ 43%] emodpy_hiv.interventions.drawblood
reading sources... [ 46%] emodpy_hiv.interventions.malecirc
reading sources... [ 50%] emodpy_hiv.interventions.modcoinf
reading sources... [ 53%] emodpy_hiv.interventions.outbreak
reading sources... [ 56%] emodpy_hiv.interventions.pmtct
reading sources... [ 60%] emodpy_hiv.interventions.prep
reading sources... [ 63%] emodpy_hiv.interventions.random
reading sources... [ 66%] emodpy_hiv.interventions.rapiddiag
reading sources... [ 70%] emodpy_hiv.interventions.reftracker
reading sources... [ 73%] emodpy_hiv.interventions.sigmoiddiag
reading sources... [ 76%] emodpy_hiv.interventions.stipostdebut
reading sources... [ 80%] emodpy_hiv.interventions.utils
reading sources... [ 83%] emodpy_hiv.interventions.yearandsexdiag
reading sources... [ 86%] emodpy_hiv.utils
reading sources... [ 90%] faq
reading sources... [ 93%] index
reading sources... [ 96%] installation
reading sources... [100%] modules

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
processing emodpy-hiv-docs.tex... index installation faq modules emodpy_hiv emodpy_hiv.demographics emodpy_hiv.demographics.DemographicsTemplates emodpy_hiv.demographics.HIVDemographics emodpy_hiv.interventions emodpy_hiv.interventions.art emodpy_hiv.interventions.artdropout emodpy_hiv.interventions.artstagingbycd4agnosticdiag emodpy_hiv.interventions.artstagingbycd4diag emodpy_hiv.interventions.cascade_helpers emodpy_hiv.interventions.delay emodpy_hiv.interventions.drawblood emodpy_hiv.interventions.malecirc emodpy_hiv.interventions.modcoinf emodpy_hiv.interventions.outbreak emodpy_hiv.interventions.pmtct emodpy_hiv.interventions.prep emodpy_hiv.interventions.random emodpy_hiv.interventions.rapiddiag emodpy_hiv.interventions.reftracker emodpy_hiv.interventions.sigmoiddiag emodpy_hiv.interventions.stipostdebut emodpy_hiv.interventions.utils emodpy_hiv.interventions.yearandsexdiag emodpy_hiv.download emodpy_hiv.utils 
resolving references...
done
writing... done
copying TeX support files... copying TeX support files...
done
build succeeded.

The LaTeX files are in ../_readthedocs/pdf.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).
WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/checkouts/latest/_readthedocs/pdf/_static/searchtools.js

[rtd-command-info] start-time: 2023-02-13T22:22:17.424252Z, end-time: 2023-02-13T22:22:17.512198Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2023-02-13T22:22:17.713079Z, end-time: 2023-02-13T22:22:19.555493Z, duration: 1, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emodpy-hiv -interaction=nonstopmode
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, <GEN1> chunk 1.
Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, <GEN2> chunk 1.
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-hiv"  "emodpy-hiv-docs.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./emodpy-hiv-docs.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(./sphinxlatexgraphics.sty) (./sphinxlatexadmonitions.sty
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty))
(./sphinxlatexliterals.sty
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty))
(./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty)
(./sphinxhighlight.sty) (./sphinxlatextables.sty
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty))
(./sphinxlatexnumfig.sty
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty))
(./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty)
(./sphinxlatexindbibtoc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty))
(./sphinxlatexstylepage.sty
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty))
(./sphinxlatexstyleheadings.sty
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty))
(./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
(./sphinxmessages.sty)
Writing index file institute-for-disease-modeling-emodpy-hiv.idx
(./institute-for-disease-modeling-emodpy-hiv.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<<ot1.cmap>><<oml.cmap>><<oms.cma
p>><<omx.cmap>> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2]

LaTeX Warning: Hyper reference `faq::doc' on page 1 undefined on input line 97.


[1] [2]
Chapter 1.
(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4]
Chapter 2.

LaTeX Warning: Hyper reference `faq:how-do-i-set-configuration-parameters' on p
age 5 undefined on input line 254.


LaTeX Warning: Hyper reference `faq:are-there-parameter-defaults' on page 5 und
efined on input line 258.


LaTeX Warning: Hyper reference `faq:how-do-i-create-a-minimal-campaign-that-jus
t-seeds-an-outbreak' on page 5 undefined on input line 262.


LaTeX Warning: Hyper reference `faq:how-do-i-give-a-therapeutic-intervention-li
ke-art-to-people' on page 5 undefined on input line 266.


LaTeX Warning: Hyper reference `faq:how-do-i-give-out-an-intervention-to-people
-based-on-a-trigger-instead-of-at-a-particular-time' on page 5 undefined on inp
ut line 270.


LaTeX Warning: Hyper reference `faq:are-there-are-any-helper-functions-to-make-
this-a-little-more-concise' on page 5 undefined on input line 274.


LaTeX Warning: Hyper reference `faq:what-if-i-want-to-broadcast-an-event-when-i
-distribute-the-intervention' on page 5 undefined on input line 278.


LaTeX Warning: Hyper reference `faq:what-if-i-want-to-have-a-delay-between-the-
trigger-signal-and-when-the-intervention-is-actually-distributed' on page 5 und
efined on input line 282.


LaTeX Warning: Hyper reference `faq:what-if-i-want-to-change-someone-s-individu
al-property' on page 5 undefined on input line 286.


LaTeX Warning: Hyper reference `faq:now-i-want-to-distribute-tests-and-distribu
te-interventions-to-only-those-who-test-positive' on page 5 undefined on input 
line 290.


LaTeX Warning: Hyper reference `faq:i-see-lots-of-hiv-sim-examples-are-there-an
y-sti-sim-examples' on page 5 undefined on input line 294.


LaTeX Warning: Hyper reference `faq:i-pip-installed-emodpy-hiv-but-i-want-to-ma
ke-changes-how-should-i-do-that' on page 5 undefined on input line 298.


LaTeX Warning: Hyper reference `faq:what-s-the-command-to-get-all-the-latest-st
able-python-packages' on page 5 undefined on input line 302.

(/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [5]
Underfull \hbox (badness 10000) in paragraph at lines 352--356
[]\T1/qtm/m/n/10 The HIV team has some de-mo-graphic pa-ram-e-ter de-faults set
 us-ing \T1/txtt/m/n/10 emodpy_hiv.demographics.

Underfull \hbox (badness 10000) in paragraph at lines 352--356
\T1/txtt/m/n/10 DemographicsTemplates.AddDefaultSociety()\T1/qtm/m/n/10 . They 
can be seen in de-mo-graph-
[6] [7] [8] [9] [10]
Chapter 3.
[11] [12]

LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module-
emodpy_hiv.demographics.HIVDemographics' on page 13 undefined on input line 820
.


LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module-
emodpy_hiv.demographics.HIVDemographics' on page 13 undefined on input line 860
.


LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module-
emodpy_hiv.demographics.HIVDemographics' on page 13 undefined on input line 891
.

[13]

LaTeX Warning: Hyper reference `emodpy_hiv.demographics.HIVDemographics:module-
emodpy_hiv.demographics.HIVDemographics' on page 14 undefined on input line 919
.

[14] [15]
Overfull \hbox (1.30391pt too wide) in paragraph at lines 1137--1137
\T1/qtm/m/it/10 put_signal=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 HIVPositiveTest\TS
1/qtm/m/it/10 '\T1/qtm/m/n/10 , 
[16] [17] [18]
Overfull \hbox (19.06401pt too wide) in paragraph at lines 1492--1492
\T1/qtm/m/it/10 Event_Name=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 Scheduled_Campaign
_Event\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , 
[19] [20] [21] [22]

LaTeX Warning: Reference `emodpy_hiv:module-emodpy_hiv' on page 23 undefined on
 input line 1765.


LaTeX Warning: Reference `emodpy_hiv.demographics:module-emodpy_hiv.demographic
s' on page 23 undefined on input line 1766.


LaTeX Warning: Reference `emodpy_hiv.demographics.DemographicsTemplates:module-
emodpy_hiv.demographics.DemographicsTemplates' on page 23 undefined on input li
ne 1767.


Overfull \hbox (8.87181pt too wide) in paragraph at lines 1767--1768
[]\T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ,


LaTeX Warning: Reference `emodpy_hiv.demographics.HIVDemographics:module-emodpy
_hiv.demographics.HIVDemographics' on page 23 undefined on input line 1768.


LaTeX Warning: Reference `emodpy_hiv.download:module-emodpy_hiv.download' on pa
ge 23 undefined on input line 1769.


LaTeX Warning: Reference `emodpy_hiv.interventions:module-emodpy_hiv.interventi
ons' on page 23 undefined on input line 1770.


LaTeX Warning: Reference `emodpy_hiv.interventions.art:module-emodpy_hiv.interv
entions.art' on page 23 undefined on input line 1771.


LaTeX Warning: Reference `emodpy_hiv.interventions.artdropout:module-emodpy_hiv
.interventions.artdropout' on page 23 undefined on input line 1772.


LaTeX Warning: Reference `emodpy_hiv.interventions.artstagingbycd4agnosticdiag:
module-emodpy_hiv.interventions.artstagingbycd4agnosticdiag' on page 23 undefin
ed on input line 1773.


Overfull \hbox (45.6217pt too wide) in paragraph at lines 1773--1774
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m
/n/10 ,

LaTeX Warning: Reference `emodpy_hiv.interventions.artstagingbycd4diag:module-e
modpy_hiv.interventions.artstagingbycd4diag' on page 23 undefined on input line
 1774.


Overfull \hbox (3.62183pt too wide) in paragraph at lines 1774--1775
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ,

LaTeX Warning: Reference `emodpy_hiv.interventions.cascade_helpers:module-emodp
y_hiv.interventions.cascade_helpers' on page 23 undefined on input line 1775.


LaTeX Warning: Reference `emodpy_hiv.interventions.delay:module-emodpy_hiv.inte
rventions.delay' on page 23 undefined on input line 1776.


LaTeX Warning: Reference `emodpy_hiv.interventions.drawblood:module-emodpy_hiv.
interventions.drawblood' on page 23 undefined on input line 1777.


LaTeX Warning: Reference `emodpy_hiv.interventions.malecirc:module-emodpy_hiv.i
nterventions.malecirc' on page 23 undefined on input line 1778.


LaTeX Warning: Reference `emodpy_hiv.interventions.modcoinf:module-emodpy_hiv.i
nterventions.modcoinf' on page 23 undefined on input line 1779.


LaTeX Warning: Reference `emodpy_hiv.interventions.outbreak:module-emodpy_hiv.i
nterventions.outbreak' on page 23 undefined on input line 1780.


LaTeX Warning: Reference `emodpy_hiv.interventions.pmtct:module-emodpy_hiv.inte
rventions.pmtct' on page 23 undefined on input line 1781.


LaTeX Warning: Reference `emodpy_hiv.interventions.prep:module-emodpy_hiv.inter
ventions.prep' on page 23 undefined on input line 1782.


LaTeX Warning: Reference `emodpy_hiv.interventions.random:module-emodpy_hiv.int
erventions.random' on page 23 undefined on input line 1783.


LaTeX Warning: Reference `emodpy_hiv.interventions.rapiddiag:module-emodpy_hiv.
interventions.rapiddiag' on page 23 undefined on input line 1784.


LaTeX Warning: Reference `emodpy_hiv.interventions.reftracker:module-emodpy_hiv
.interventions.reftracker' on page 23 undefined on input line 1785.


LaTeX Warning: Reference `emodpy_hiv.interventions.sigmoiddiag:module-emodpy_hi
v.interventions.sigmoiddiag' on page 23 undefined on input line 1786.


LaTeX Warning: Reference `emodpy_hiv.interventions.stipostdebut:module-emodpy_h
iv.interventions.stipostdebut' on page 23 undefined on input line 1787.


LaTeX Warning: Reference `emodpy_hiv.interventions.utils:module-emodpy_hiv.inte
rventions.utils' on page 23 undefined on input line 1788.


LaTeX Warning: Reference `emodpy_hiv.interventions.yearandsexdiag:module-emodpy
_hiv.interventions.yearandsexdiag' on page 23 undefined on input line 1789.


LaTeX Warning: Reference `emodpy_hiv.utils:module-emodpy_hiv.utils' on page 23 
undefined on input line 1790.

[23]
No file institute-for-disease-modeling-emodpy-hiv.ind.
(./institute-for-disease-modeling-emodpy-hiv.aux)

Package rerunfilecheck Warning: File `institute-for-disease-modeling-emodpy-hiv
.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{
/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/publi
c/tex-gyre/qhvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvr.pfb></us
r/share/texmf/fonts/type1/public/tex-gyre/qtmb.pfb></usr/share/texmf/fonts/type
1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmri.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/times/utmr8a.pfb>
Output written on institute-for-disease-modeling-emodpy-hiv.pdf (27 pages, 2120
06 bytes).
Transcript written on institute-for-disease-modeling-emodpy-hiv.log.
Latexmk: Index file 'institute-for-disease-modeling-emodpy-hiv.idx' was written
Latexmk: Missing input file: 'institute-for-disease-modeling-emodpy-hiv.ind' from line
  'No file institute-for-disease-modeling-emodpy-hiv.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf'
Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf'
Latexmk: List of undefined refs and citations:
  Reference `emodpy_hiv.demographics.DemographicsTemplates:module-emodpy_hiv.demographics.DemographicsTemplates' on page 23 undefined on input line 1767
  Reference `emodpy_hiv.demographics.HIVDemographics:module-emodpy_hiv.demographics.HIVDemographics' on page 23 undefined on input line 1768
  Reference `emodpy_hiv.demographics:module-emodpy_hiv.demographics' on page 23 undefined on input line 1766
  Reference `emodpy_hiv.download:module-emodpy_hiv.download' on page 23 undefined on input line 1769
  Reference `emodpy_hiv.interventions.art:module-emodpy_hiv.interventions.art' on page 23 undefined on input line 1771
  Reference `emodpy_hiv.interventions.artdropout:module-emodpy_hiv.interventions.artdropout' on page 23 undefined on input line 1772
  Reference `emodpy_hiv.interventions.artstagingbycd4agnosticdiag:module-emodpy_hiv.interventions.artstagingbycd4agnosticdiag' on page 23 undefined on input line 1773
  Reference `emodpy_hiv.interventions.artstagingbycd4diag:module-emodpy_hiv.interventions.artstagingbycd4diag' on page 23 undefined on input line 1774
  Reference `emodpy_hiv.interventions.cascade_helpers:module-emodpy_hiv.interventions.cascade_helpers' on page 23 undefined on input line 1775
  Reference `emodpy_hiv.interventions.delay:module-emodpy_hiv.interventions.delay' on page 23 undefined on input line 1776
  Reference `emodpy_hiv.interventions.drawblood:module-emodpy_hiv.interventions.drawblood' on page 23 undefined on input line 1777
  Reference `emodpy_hiv.interventions.malecirc:module-emodpy_hiv.interventions.malecirc' on page 23 undefined on input line 1778
  Reference `emodpy_hiv.interventions.modcoinf:module-emodpy_hiv.interventions.modcoinf' on page 23 undefined on input line 1779
  Reference `emodpy_hiv.interventions.outbreak:module-emodpy_hiv.interventions.outbreak' on page 23 undefined on input line 1780
  Reference `emodpy_hiv.interventions.pmtct:module-emodpy_hiv.interventions.pmtct' on page 23 undefined on input line 1781
  Reference `emodpy_hiv.interventions.prep:module-emodpy_hiv.interventions.prep' on page 23 undefined on input line 1782
  Reference `emodpy_hiv.interventions.random:module-emodpy_hiv.interventions.random' on page 23 undefined on input line 1783
  Reference `emodpy_hiv.interventions.rapiddiag:module-emodpy_hiv.interventions.rapiddiag' on page 23 undefined on input line 1784
  Reference `emodpy_hiv.interventions.reftracker:module-emodpy_hiv.interventions.reftracker' on page 23 undefined on input line 1785
  Reference `emodpy_hiv.interventions.sigmoiddiag:module-emodpy_hiv.interventions.sigmoiddiag' on page 23 undefined on input line 1786
  Reference `emodpy_hiv.interventions.stipostdebut:module-emodpy_hiv.interventions.stipostdebut' on page 23 undefined on input line 1787
  Reference `emodpy_hiv.interventions.utils:module-emodpy_hiv.interventions.utils' on page 23 undefined on input line 1788
  Reference `emodpy_hiv.interventions.yearandsexdiag:module-emodpy_hiv.interventions.yearandsexdiag' on page 23 undefined on input line 1789
  Reference `emodpy_hiv.interventions:module-emodpy_hiv.interventions' on page 23 undefined on input line 1770
  Reference `emodpy_hiv.utils:module-emodpy_hiv.utils' on page 23 undefined on input line 1790
  Reference `emodpy_hiv:module-emodpy_hiv' on page 23 undefined on input line 1765
Latexmk: Summary of warnings:
  Latex failed to resolve 26 reference(s)
Rule 'makeindex institute-for-disease-modeling-emodpy-hiv.idx': File changes, etc:
   Non-existent destination files:
      'institute-for-disease-modeling-emodpy-hiv.ind'
------------
Run number 1 of rule 'makeindex institute-for-disease-modeling-emodpy-hiv.idx'
------------
------------
Running 'makeindex -s python.ist  -o "institute-for-disease-modeling-emodpy-hiv.ind" "institute-for-disease-modeling-emodpy-hiv.idx"'
------------
Latexmk: applying rule 'makeindex institute-for-disease-modeling-emodpy-hiv.idx'...
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
Scanning input file institute-for-disease-modeling-emodpy-hiv.idx....done (131 entries accepted, 0 rejected).
Sorting entries....done (967 comparisons).
Generating output file institute-for-disease-modeling-emodpy-hiv.ind....done (272 lines written, 0 warnings).
Output written in institute-for-disease-modeling-emodpy-hiv.ind.
Transcript written in institute-for-disease-modeling-emodpy-hiv.ilg.
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'institute-for-disease-modeling-emodpy-hiv.aux'
      'institute-for-disease-modeling-emodpy-hiv.ind'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-hiv"  "emodpy-hiv-docs.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./emodpy-hiv-docs.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(./sphinxlatexgraphics.sty) (./sphinxlatexadmonitions.sty
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty))
(./sphinxlatexliterals.sty
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty))
(./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty)
(./sphinxhighlight.sty) (./sphinxlatextables.sty
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty))
(./sphinxlatexnumfig.sty
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty))
(./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty)
(./sphinxlatexindbibtoc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty))
(./sphinxlatexstylepage.sty
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty))
(./sphinxlatexstyleheadings.sty
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty))
(./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
(./sphinxmessages.sty)
Writing index file institute-for-disease-modeling-emodpy-hiv.idx
(./institute-for-disease-modeling-emodpy-hiv.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./institute-for-disease-modeling-emodpy-hiv.out)
(./institute-for-disease-modeling-emodpy-hiv.out)
(/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<<ot1.cmap>><<oml.cmap>><<oms.cma
p>><<omx.cmap>> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(./institute-for-disease-modeling-emodpy-hiv.toc) [1] [2] [1] [2]
Chapter 1.
(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4]
Chapter 2.
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [5]
Underfull \hbox (badness 10000) in paragraph at lines 352--356
[]\T1/qtm/m/n/10 The HIV team has some de-mo-graphic pa-ram-e-ter de-faults set
 us-ing \T1/txtt/m/n/10 emodpy_hiv.demographics.

Underfull \hbox (badness 10000) in paragraph at lines 352--356
\T1/txtt/m/n/10 DemographicsTemplates.AddDefaultSociety()\T1/qtm/m/n/10 . They 
can be seen in de-mo-graph-
[6] [7] [8] [9] [10]
Chapter 3.
[11] [12] [13] [14] [15]
Overfull \hbox (1.30391pt too wide) in paragraph at lines 1137--1137
\T1/qtm/m/it/10 put_signal=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 HIVPositiveTest\TS
1/qtm/m/it/10 '\T1/qtm/m/n/10 , 
[16] [17] [18]
Overfull \hbox (19.06401pt too wide) in paragraph at lines 1492--1492
\T1/qtm/m/it/10 Event_Name=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 Scheduled_Campaign
_Event\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , 
[19] [20] [21] [22]
Overfull \hbox (8.87181pt too wide) in paragraph at lines 1767--1768
[]\T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ,


Overfull \hbox (45.6217pt too wide) in paragraph at lines 1773--1774
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m
/n/10 ,

Overfull \hbox (3.62183pt too wide) in paragraph at lines 1774--1775
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ,
[23] (./institute-for-disease-modeling-emodpy-hiv.ind [24]
Underfull \hbox (badness 10000) in paragraph at lines 8--10
[]\T1/txtt/m/n/10 add_art_from_trigger() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod
-ule

Underfull \hbox (badness 10000) in paragraph at lines 10--12
[]\T1/txtt/m/n/10 add_choice() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/txtt/m/n/10 add_default_society() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule

Overfull \hbox (23.5275pt too wide) in paragraph at lines 12--14
\T1/qtm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 14--16
[]\T1/txtt/m/n/10 add_or_update_initial_risk_distribution()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 14--16
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/txtt/m/n/10 add_society_from_template() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i
n mod-ule

Overfull \hbox (23.5275pt too wide) in paragraph at lines 16--18
\T1/qtm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 18--20
[]\T1/txtt/m/n/10 add_test() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 20--22
[]\T1/txtt/m/n/10 add_triggered_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/txtt/m/n/10 apply_assortivity()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 22--24
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 27--29
[]\T1/txtt/m/n/10 broadcast_event_delayed() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in 
mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 29--31
[]\T1/txtt/m/n/10 broadcast_event_immediate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i
n mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 34--35
[]\T1/txtt/m/n/10 declutter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 35--37
[]\T1/txtt/m/n/10 DistributeIVByRefTrack() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Overfull \hbox (6.37181pt too wide) in paragraph at lines 45--46
[]\T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates 

Overfull \hbox (43.1217pt too wide) in paragraph at lines 57--58
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag 

Overfull \hbox (1.12183pt too wide) in paragraph at lines 59--60
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag 
[25]
Overfull \hbox (94.58235pt too wide) in paragraph at lines 96--98
[]\T1/txtt/m/n/10 fertility() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demogr
aphics.HIVDemographics.HIVDemographics

Underfull \hbox (badness 10000) in paragraph at lines 98--100
[]\T1/txtt/m/n/10 from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 100--102
[]\T1/txtt/m/n/10 from_pop_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 102--104
[]\T1/txtt/m/n/10 from_template_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u
le

Underfull \hbox (badness 10000) in paragraph at lines 107--109
[]\T1/txtt/m/n/10 HIVDemographics \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in

Overfull \hbox (28.87181pt too wide) in paragraph at lines 115--116
[]| \T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10
 ,

Underfull \hbox (badness 10000) in paragraph at lines 116--117
[]| \T1/txtt/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/qtm/m/n/10 ,

Overfull \hbox (65.6217pt too wide) in paragraph at lines 121--122
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm
/m/n/10 ,

Overfull \hbox (23.62183pt too wide) in paragraph at lines 122--123
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 
,

Overfull \hbox (2.62189pt too wide) in paragraph at lines 123--124
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/qtm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 137--138
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ,

Overfull \hbox (94.58235pt too wide) in paragraph at lines 139--141
[]\T1/txtt/m/n/10 mortality() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demogr
aphics.HIVDemographics.HIVDemographics

Underfull \hbox (badness 10000) in paragraph at lines 144--145
[]\T1/txtt/m/n/10 new_delay() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 145--147
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Overfull \hbox (37.26247pt too wide) in paragraph at lines 145--147
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m/n
/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 147--149
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Overfull \hbox (3.47247pt too wide) in paragraph at lines 147--149
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 149--151
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 151--153
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 153--155
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 155--157
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 157--159
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 159--161
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 159--161
\T1/qtm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 161--163
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 163--165
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 169--171
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 171--173
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 173--175
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 175--177
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 177--179
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 179--181
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Overfull \hbox (37.26247pt too wide) in paragraph at lines 179--181
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m/n
/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 181--183
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Overfull \hbox (3.47247pt too wide) in paragraph at lines 181--183
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 183--185
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 185--187
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule
[26]
Underfull \hbox (badness 10000) in paragraph at lines 187--189
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 189--191
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 191--193
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 193--195
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 195--197
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 197--199
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 199--201
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 201--203
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 203--205
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 205--207
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 205--207
\T1/qtm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 207--209
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 209--211
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 211--213
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Overfull \hbox (37.26247pt too wide) in paragraph at lines 211--213
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m/n
/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 213--215
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Overfull \hbox (3.47247pt too wide) in paragraph at lines 213--215
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 215--217
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 217--219
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 219--221
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 221--223
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 223--225
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 225--227
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 227--229
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 229--231
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 231--233
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 233--235
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 235--237
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 235--237
\T1/qtm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ),

Overfull \hbox (29.70737pt too wide) in paragraph at lines 241--243
[]\T1/txtt/m/n/10 reset() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emodpy_hiv
.interventions.cascade_helpers\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 246--248
[]\T1/txtt/m/n/10 seed_infection() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 248--250
[]\T1/txtt/m/n/10 seed_infections() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 250--252
[]\T1/txtt/m/n/10 set_coital_act_rate()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 250--252
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 252--254
[]\T1/txtt/m/n/10 set_concurrency_params_by_type_and_risk()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 252--254
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 254--256
[]\T1/txtt/m/n/10 set_condom_usage_probs()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 254--256
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 256--258
[]\T1/txtt/m/n/10 set_pair_form_params()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 256--258
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 258--260
[]\T1/txtt/m/n/10 set_relationship_duration()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 258--260
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 260--262
[]\T1/txtt/m/n/10 set_tvmap_lists_from_map() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 265--267
[]\T1/txtt/m/n/10 trigger_art() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 267--269
[]\T1/txtt/m/n/10 trigger_art_from_pos_test() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i
n mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 269--271
[]\T1/txtt/m/n/10 triggered_event_common() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule
[27]) (./institute-for-disease-modeling-emodpy-hiv.aux)

Package rerunfilecheck Warning: File `institute-for-disease-modeling-emodpy-hiv
.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{
/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/publi
c/tex-gyre/qhvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvr.pfb></us
r/share/texmf/fonts/type1/public/tex-gyre/qtmb.pfb></usr/share/texmf/fonts/type
1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmri.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/times/utmr8a.pfb>
Output written on institute-for-disease-modeling-emodpy-hiv.pdf (31 pages, 2383
78 bytes).
Transcript written on institute-for-disease-modeling-emodpy-hiv.log.
Latexmk: Index file 'institute-for-disease-modeling-emodpy-hiv.idx' was written
Latexmk: References changed.
Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf'
Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf'
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'institute-for-disease-modeling-emodpy-hiv.aux'
      'institute-for-disease-modeling-emodpy-hiv.out'
      'institute-for-disease-modeling-emodpy-hiv.toc'
------------
Run number 3 of rule 'pdflatex'
------------
Latexmk: applying rule 'pdflatex'...
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-hiv"  "emodpy-hiv-docs.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./emodpy-hiv-docs.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(./sphinxlatexgraphics.sty) (./sphinxlatexadmonitions.sty
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty))
(./sphinxlatexliterals.sty
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty))
(./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty)
(./sphinxhighlight.sty) (./sphinxlatextables.sty
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty))
(./sphinxlatexnumfig.sty
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty))
(./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty)
(./sphinxlatexindbibtoc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty))
(./sphinxlatexstylepage.sty
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty))
(./sphinxlatexstyleheadings.sty
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty))
(./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
(./sphinxmessages.sty)
Writing index file institute-for-disease-modeling-emodpy-hiv.idx
(./institute-for-disease-modeling-emodpy-hiv.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./institute-for-disease-modeling-emodpy-hiv.out)
(./institute-for-disease-modeling-emodpy-hiv.out)
(/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<<ot1.cmap>><<oml.cmap>><<oms.cma
p>><<omx.cmap>> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(./institute-for-disease-modeling-emodpy-hiv.toc) [1] [2] [1] [2]
Chapter 1.
(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4]
Chapter 2.
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [5]
Underfull \hbox (badness 10000) in paragraph at lines 352--356
[]\T1/qtm/m/n/10 The HIV team has some de-mo-graphic pa-ram-e-ter de-faults set
 us-ing \T1/txtt/m/n/10 emodpy_hiv.demographics.

Underfull \hbox (badness 10000) in paragraph at lines 352--356
\T1/txtt/m/n/10 DemographicsTemplates.AddDefaultSociety()\T1/qtm/m/n/10 . They 
can be seen in de-mo-graph-
[6] [7] [8] [9] [10]
Chapter 3.
[11] [12] [13] [14] [15]
Overfull \hbox (1.30391pt too wide) in paragraph at lines 1137--1137
\T1/qtm/m/it/10 put_signal=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 HIVPositiveTest\TS
1/qtm/m/it/10 '\T1/qtm/m/n/10 , 
[16] [17] [18]
Overfull \hbox (19.06401pt too wide) in paragraph at lines 1492--1492
\T1/qtm/m/it/10 Event_Name=\TS1/qtm/m/it/10 '\T1/qtm/m/it/10 Scheduled_Campaign
_Event\TS1/qtm/m/it/10 '\T1/qtm/m/n/10 , 
[19] [20] [21] [22]
Overfull \hbox (8.87181pt too wide) in paragraph at lines 1767--1768
[]\T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ,


Overfull \hbox (45.6217pt too wide) in paragraph at lines 1773--1774
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m
/n/10 ,

Overfull \hbox (3.62183pt too wide) in paragraph at lines 1774--1775
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ,
[23] (./institute-for-disease-modeling-emodpy-hiv.ind [24]
Underfull \hbox (badness 10000) in paragraph at lines 8--10
[]\T1/txtt/m/n/10 add_art_from_trigger() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod
-ule

Underfull \hbox (badness 10000) in paragraph at lines 10--12
[]\T1/txtt/m/n/10 add_choice() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/txtt/m/n/10 add_default_society() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule

Overfull \hbox (23.5275pt too wide) in paragraph at lines 12--14
\T1/qtm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 14--16
[]\T1/txtt/m/n/10 add_or_update_initial_risk_distribution()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 14--16
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/txtt/m/n/10 add_society_from_template() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i
n mod-ule

Overfull \hbox (23.5275pt too wide) in paragraph at lines 16--18
\T1/qtm/m/it/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 18--20
[]\T1/txtt/m/n/10 add_test() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 20--22
[]\T1/txtt/m/n/10 add_triggered_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/txtt/m/n/10 apply_assortivity()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 22--24
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 27--29
[]\T1/txtt/m/n/10 broadcast_event_delayed() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in 
mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 29--31
[]\T1/txtt/m/n/10 broadcast_event_immediate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i
n mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 34--35
[]\T1/txtt/m/n/10 declutter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 35--37
[]\T1/txtt/m/n/10 DistributeIVByRefTrack() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Overfull \hbox (6.37181pt too wide) in paragraph at lines 45--46
[]\T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates 

Overfull \hbox (43.1217pt too wide) in paragraph at lines 57--58
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag 

Overfull \hbox (1.12183pt too wide) in paragraph at lines 59--60
[]\T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag 
[25]
Overfull \hbox (94.58235pt too wide) in paragraph at lines 96--98
[]\T1/txtt/m/n/10 fertility() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demogr
aphics.HIVDemographics.HIVDemographics

Underfull \hbox (badness 10000) in paragraph at lines 98--100
[]\T1/txtt/m/n/10 from_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 100--102
[]\T1/txtt/m/n/10 from_pop_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 102--104
[]\T1/txtt/m/n/10 from_template_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u
le

Underfull \hbox (badness 10000) in paragraph at lines 107--109
[]\T1/txtt/m/n/10 HIVDemographics \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in

Overfull \hbox (28.87181pt too wide) in paragraph at lines 115--116
[]| \T1/txtt/m/n/10 emodpy_hiv.demographics.DemographicsTemplates\T1/qtm/m/n/10
 ,

Underfull \hbox (badness 10000) in paragraph at lines 116--117
[]| \T1/txtt/m/n/10 emodpy_hiv.demographics.HIVDemographics\T1/qtm/m/n/10 ,

Overfull \hbox (65.6217pt too wide) in paragraph at lines 121--122
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm
/m/n/10 ,

Overfull \hbox (23.62183pt too wide) in paragraph at lines 122--123
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 
,

Overfull \hbox (2.62189pt too wide) in paragraph at lines 123--124
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.cascade_helpers\T1/qtm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 137--138
[]| \T1/txtt/m/n/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ,

Overfull \hbox (94.58235pt too wide) in paragraph at lines 139--141
[]\T1/txtt/m/n/10 mortality() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demogr
aphics.HIVDemographics.HIVDemographics

Underfull \hbox (badness 10000) in paragraph at lines 144--145
[]\T1/txtt/m/n/10 new_delay() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 145--147
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Overfull \hbox (37.26247pt too wide) in paragraph at lines 145--147
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m/n
/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 147--149
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Overfull \hbox (3.47247pt too wide) in paragraph at lines 147--149
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 149--151
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 151--153
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 153--155
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 155--157
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 157--159
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 159--161
[]\T1/txtt/m/n/10 new_diagnostic() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 159--161
\T1/qtm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 161--163
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 163--165
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 169--171
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 171--173
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 173--175
[]\T1/txtt/m/n/10 new_intervention() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule


Underfull \hbox (badness 10000) in paragraph at lines 175--177
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 177--179
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 179--181
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Overfull \hbox (37.26247pt too wide) in paragraph at lines 179--181
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m/n
/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 181--183
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Overfull \hbox (3.47247pt too wide) in paragraph at lines 181--183
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 183--185
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 185--187
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule
[26]
Underfull \hbox (badness 10000) in paragraph at lines 187--189
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 189--191
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 191--193
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 193--195
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 195--197
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 197--199
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 199--201
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 201--203
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 203--205
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 205--207
[]\T1/txtt/m/n/10 new_intervention_as_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 205--207
\T1/qtm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 207--209
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 209--211
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 211--213
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Overfull \hbox (37.26247pt too wide) in paragraph at lines 211--213
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4agnosticdiag\T1/qtm/m/n
/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 213--215
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Overfull \hbox (3.47247pt too wide) in paragraph at lines 213--215
\T1/qtm/m/it/10 emodpy_hiv.interventions.artstagingbycd4diag\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 215--217
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 217--219
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 219--221
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 221--223
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 223--225
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 225--227
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 227--229
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 229--231
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 231--233
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 233--235
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 235--237
[]\T1/txtt/m/n/10 new_intervention_event() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule

Underfull \hbox (badness 10000) in paragraph at lines 235--237
\T1/qtm/m/it/10 emodpy_hiv.interventions.yearandsexdiag\T1/qtm/m/n/10 ),

Overfull \hbox (29.70737pt too wide) in paragraph at lines 241--243
[]\T1/txtt/m/n/10 reset() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule emodpy_hiv
.interventions.cascade_helpers\T1/qtm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 246--248
[]\T1/txtt/m/n/10 seed_infection() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 248--250
[]\T1/txtt/m/n/10 seed_infections() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 250--252
[]\T1/txtt/m/n/10 set_coital_act_rate()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 250--252
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 252--254
[]\T1/txtt/m/n/10 set_concurrency_params_by_type_and_risk()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 252--254
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 254--256
[]\T1/txtt/m/n/10 set_condom_usage_probs()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 254--256
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 256--258
[]\T1/txtt/m/n/10 set_pair_form_params()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 256--258
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 258--260
[]\T1/txtt/m/n/10 set_relationship_duration()

Overfull \hbox (75.16252pt too wide) in paragraph at lines 258--260
\T1/qtm/m/n/10 (\T1/qtm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemo
graphics

Underfull \hbox (badness 10000) in paragraph at lines 260--262
[]\T1/txtt/m/n/10 set_tvmap_lists_from_map() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
 mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 265--267
[]\T1/txtt/m/n/10 trigger_art() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 267--269
[]\T1/txtt/m/n/10 trigger_art_from_pos_test() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i
n mod-ule

Underfull \hbox (badness 10000) in paragraph at lines 269--271
[]\T1/txtt/m/n/10 triggered_event_common() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule
[27]) (./institute-for-disease-modeling-emodpy-hiv.aux) )
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{
/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/publi
c/tex-gyre/qhvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvr.pfb></us
r/share/texmf/fonts/type1/public/tex-gyre/qtmb.pfb></usr/share/texmf/fonts/type
1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmri.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/times/utmr8a.pfb>
Output written on institute-for-disease-modeling-emodpy-hiv.pdf (31 pages, 2385
61 bytes).
Transcript written on institute-for-disease-modeling-emodpy-hiv.log.
Latexmk: Index file 'institute-for-disease-modeling-emodpy-hiv.idx' was written
Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf'
Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-hiv.pdf'
Latexmk: All targets (institute-for-disease-modeling-emodpy-hiv.pdf) are up-to-date