Read the Docs build information Build id: 1669947 Project: institute-for-disease-modeling-emodpy-hiv Version: latest Commit: 0f49e48659b8f10df27a79a94d72415c0e9244f6 Date: 2023-08-18T20:51:56.034252Z State: finished Success: True [rtd-command-info] start-time: 2023-08-18T21:06:59.200879Z, end-time: 2023-08-18T21:07:01.850681Z, duration: 2, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/emodpy-hiv.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2023-08-18T21:07:02.309272Z, end-time: 2023-08-18T21:07:04.300069Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/emodpy-hiv * [new tag] v0.0.22 -> v0.0.22 * [new tag] v0.0.35 -> v0.0.35 * [new tag] v0.0.37 -> v0.0.37 * [new tag] v0.0.38 -> v0.0.38 * [new tag] v0.0.41 -> v0.0.41 * [new tag] v0.0.6 -> v0.0.6 * [new tag] v0.0.8 -> v0.0.8 * [new tag] v0.0.9 -> v0.0.9 * [new tag] v1.0.1 -> v1.0.1 * [new tag] v1.0.2 -> v1.0.2 [rtd-command-info] start-time: 2023-08-18T21:07:04.758059Z, end-time: 2023-08-18T21:07:04.835473Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip - pdf # Optionally set the version of Python and requirements required to build your docs python: version: 3.7 install: - requirements: requirements.txt - requirements: docs/requirements.txt - method: setuptools path: . # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank # search: # ranking: [rtd-command-info] start-time: 2023-08-18T21:07:08.590371Z, end-time: 2023-08-18T21:07:14.543156Z, 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. 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/tmp/pip-ephem-wheel-cache-wtjvlt4z/wheels/39/db/d5/e22e622f3ac6beb40ab992464b2b5ae38526942ed4ffff7c05 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinxcontrib-jquery, recommonmark, sphinx-rtd-theme Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.7.0 mock-1.0.1 packaging-23.1 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.2.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.7.1 urllib3-2.0.4 zipp-3.15.0 [rtd-command-info] start-time: 2023-08-18T21:07:33.171873Z, end-time: 2023-08-18T21:08:14.679814Z, 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 (from -r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.21.1/emodpy-1.21.1-py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.7/121.7 kB 11.6 MB/s eta 0:00:00 Collecting emod-hiv==1.0.1 (from -r requirements.txt (line 3)) 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) 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Collecting idmtools-models~=1.7 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.7.8/idmtools_models-1.7.8-py3-none-any.whl (24 kB) Collecting emod-api~=1.24 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-api/1.29.7/emod_api-1.29.7-py3-none-any.whl (166 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 166.5/166.5 kB 16.4 MB/s eta 0:00:00 Collecting matplotlib (from emodpy~=1.15->-r requirements.txt (line 2)) 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 14.2 MB/s eta 0:00:00 Collecting astor (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading 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wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13724 sha256=322271e3f1d68ed7c6ee8a3cb6dcf2090a73202d21ffee095578d2486807a536 Stored in directory: /tmp/pip-ephem-wheel-cache-vd7zruag/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c Successfully built bs4 future prodict docopt Installing collected packages: prodict, parse, 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, filelock, 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 23.1 Uninstalling packaging-23.1: Successfully uninstalled packaging-23.1 Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 beautifulsoup4-4.12.2 bs4-0.0.1 cached-property-1.5.2 cffi-1.15.1 click-7.1.2 coloredlogs-15.0.1 cryptography-41.0.3 cycler-0.11.0 diskcache-5.4.0 docopt-0.6.2 emod-api-1.29.7 emod-hiv-1.0.1 emodpy-1.21.1 filelock-3.12.2 fonttools-4.38.0 future-0.18.3 geographiclib-2.0 graphviz-0.20.1 humanfriendly-10.0 idmtools-1.7.8 idmtools-models-1.7.8 idmtools-platform-comps-1.7.8 importlib-resources-5.12.0 jaraco.classes-3.2.3 jeepney-0.8.0 joblib-1.3.2 keyring-24.1.1 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-1.19.1 pillow-9.5.0 pipreqs-0.4.13 pluggy-1.0.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.21 pygit2-1.10.1 pyparsing-3.1.1 pyproj-3.2.1 python-dateutil-2.8.2 pyyaml-6.0.1 scikit-learn-1.0.2 scipy-1.7.3 shapely-2.0.1 six-1.16.0 soupsieve-2.4.1 tabulate-0.9.0 threadpoolctl-3.1.0 tqdm-4.66.1 xdg-6.0.0 yarg-0.1.9 [rtd-command-info] start-time: 2023-08-18T21:08:15.242739Z, end-time: 2023-08-18T21:08:21.115069Z, 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 (from -r docs/requirements.txt (line 1)) 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 16.8 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon~=0.7 (from -r docs/requirements.txt (line 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125.7/125.7 kB 156.1 MB/s eta 0:00:00 Collecting MarkupSafe<=2.0.1 (from sphinxext.remoteliteralinclude->-r docs/requirements.txt (line 6)) 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)) (2023.3) 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)) (3.15.0) 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)) (4.7.1) 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)) (3.2.0) 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: urllib3<3,>=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)) (2.0.4) 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)) (2023.7.22) 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)) (3.1.1) 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 2.1.3 Uninstalling MarkupSafe-2.1.3: Successfully uninstalled MarkupSafe-2.1.3 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 1.2.2 Uninstalling sphinx-rtd-theme-1.2.2: Successfully uninstalled sphinx-rtd-theme-1.2.2 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 1.7.8 requires jinja2~=3.1.2, but you have jinja2 2.11.3 which is incompatible. idmtools-models 1.7.8 requires jinja2~=3.1.2, but you have jinja2 2.11.3 which is incompatible. idmtools-platform-comps 1.7.8 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: 2023-08-18T21:08:22.132947Z, end-time: 2023-08-18T21:08:23.434069Z, 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-1.0.11-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-1.0.11-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-1.0.11-py3.7.egg Extracting emodpy_hiv-1.0.11-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 1.0.11 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-1.0.11-py3.7.egg Processing dependencies for emodpy-hiv==1.0.11 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 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==1.21.1 Best match: emodpy 1.21.1 Adding emodpy 1.21.1 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 emod-api==1.29.7 Best match: emod-api 1.29.7 Adding emod-api 1.29.7 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 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-models==1.7.8 Best match: idmtools-models 1.7.8 Adding idmtools-models 1.7.8 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==1.7.8 Best match: idmtools 1.7.8 Adding idmtools 1.7.8 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 idmtools-platform-comps==1.7.8 Best match: idmtools-platform-comps 1.7.8 Adding idmtools-platform-comps 1.7.8 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 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 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 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 keyring==24.1.1 Best match: keyring 24.1.1 Adding keyring 24.1.1 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 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 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 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 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 PyYAML==6.0.1 Best match: PyYAML 6.0.1 Adding PyYAML 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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 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 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 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 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 parse==1.19.1 Best match: parse 1.19.1 Adding parse 1.19.1 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 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 Pillow==9.5.0 Best match: Pillow 9.5.0 Adding Pillow 9.5.0 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 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 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 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 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 pyparsing==3.1.1 Best match: pyparsing 3.1.1 Adding pyparsing 3.1.1 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 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 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 filelock==3.12.2 Best match: filelock 3.12.2 Adding filelock 3.12.2 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 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 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 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 tqdm==4.66.1 Best match: tqdm 4.66.1 Adding tqdm 4.66.1 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 pipreqs==0.4.13 Best match: pipreqs 0.4.13 Adding pipreqs 0.4.13 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 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 beautifulsoup4==4.12.2 Best match: beautifulsoup4 4.12.2 Adding beautifulsoup4 4.12.2 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 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 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 xdg==6.0.0 Best match: xdg 6.0.0 Adding xdg 6.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.7/site-packages Searching for pytz==2023.3 Best match: pytz 2023.3 Adding pytz 2023.3 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 requests==2.31.0 Best match: requests 2.31.0 Adding requests 2.31.0 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==0.41.1 Best match: wheel 0.41.1 Adding wheel 0.41.1 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 importlib-metadata==6.7.0 Best match: importlib-metadata 6.7.0 Adding importlib-metadata 6.7.0 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 importlib-resources==5.12.0 Best match: importlib-resources 5.12.0 Adding importlib-resources 5.12.0 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 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 joblib==1.3.2 Best match: joblib 1.3.2 Adding joblib 1.3.2 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 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 certifi==2023.7.22 Best match: certifi 2023.7.22 Adding certifi 2023.7.22 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==4.7.1 Best match: typing-extensions 4.7.1 Adding typing-extensions 4.7.1 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 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 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 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 soupsieve==2.4.1 Best match: soupsieve 2.4.1 Adding soupsieve 2.4.1 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 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 urllib3==2.0.4 Best match: urllib3 2.0.4 Adding urllib3 2.0.4 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 charset-normalizer==3.2.0 Best match: charset-normalizer 3.2.0 Adding charset-normalizer 3.2.0 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 zipp==3.15.0 Best match: zipp 3.15.0 Adding zipp 3.15.0 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==41.0.3 Best match: cryptography 41.0.3 Adding cryptography 41.0.3 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 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==1.0.11 [rtd-command-info] start-time: 2023-08-18T21:08:31.879796Z, end-time: 2023-08-18T21:08:31.939716Z, 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. # " v 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 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': '', 'analytics_code': 'G-SVDSQH04EM', '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': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': '0f49e486', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-emodpy-hiv/builds/1669947/' 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: 2023-08-18T21:08:32.718806Z, end-time: 2023-08-18T21:08:38.031818Z, duration: 5, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/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: 2023-08-18T21:08:38.530739Z, end-time: 2023-08-18T21:08:42.918451Z, duration: 4, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/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: 2023-08-18T21:08:44.407873Z, end-time: 2023-08-18T21:08:48.574363Z, duration: 4, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/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: 2023-08-18T21:08:49.139172Z, end-time: 2023-08-18T21:08:49.233105Z, 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: 2023-08-18T21:08:49.784600Z, end-time: 2023-08-18T21:08:52.365985Z, duration: 2, 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, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, 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. 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[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. 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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. LaTeX Warning: Hyper reference `faq:how-do-i-install-from-conda' on page 5 unde fined on input line 306. LaTeX Warning: Hyper reference `faq:what-is-the-difference-between-transitory-a nd-informal-relationships' on page 5 undefined on input line 310. LaTeX Warning: Hyper reference `faq:how-do-individual-properties-like-risk-chan ge-model-behaviour-if-they-are-just-tags' on page 5 undefined on input line 314 . LaTeX Warning: Hyper reference `faq:what-is-the-difference-between-individual-t argeted-interventions-and-node-targeted-interventions' on page 5 undefined on i nput line 318. [5] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 368--372 []\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. 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[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} Output written on institute-for-disease-modeling-emodpy-hiv.pdf (27 pages, 2192 13 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 1916 Reference `emodpy_hiv.demographics.HIVDemographics:module-emodpy_hiv.demographics.HIVDemographics' on page 23 undefined on input line 1917 Reference `emodpy_hiv.demographics:module-emodpy_hiv.demographics' on page 23 undefined on input line 1915 Reference `emodpy_hiv.download:module-emodpy_hiv.download' on page 23 undefined on input line 1918 Reference `emodpy_hiv.interventions.art:module-emodpy_hiv.interventions.art' on page 23 undefined on input line 1920 Reference `emodpy_hiv.interventions.artdropout:module-emodpy_hiv.interventions.artdropout' on page 23 undefined on input line 1921 Reference `emodpy_hiv.interventions.artstagingbycd4agnosticdiag:module-emodpy_hiv.interventions.artstagingbycd4agnosticdiag' on page 23 undefined on input line 1922 Reference `emodpy_hiv.interventions.artstagingbycd4diag:module-emodpy_hiv.interventions.artstagingbycd4diag' on page 23 undefined on input line 1923 Reference `emodpy_hiv.interventions.cascade_helpers:module-emodpy_hiv.interventions.cascade_helpers' on page 23 undefined on input line 1924 Reference `emodpy_hiv.interventions.delay:module-emodpy_hiv.interventions.delay' on page 23 undefined on input line 1925 Reference `emodpy_hiv.interventions.drawblood:module-emodpy_hiv.interventions.drawblood' on page 23 undefined on input line 1926 Reference `emodpy_hiv.interventions.malecirc:module-emodpy_hiv.interventions.malecirc' on page 23 undefined on input line 1927 Reference `emodpy_hiv.interventions.modcoinf:module-emodpy_hiv.interventions.modcoinf' on page 23 undefined on input line 1928 Reference `emodpy_hiv.interventions.outbreak:module-emodpy_hiv.interventions.outbreak' on page 23 undefined on input line 1929 Reference `emodpy_hiv.interventions.pmtct:module-emodpy_hiv.interventions.pmtct' on page 23 undefined on input line 1930 Reference `emodpy_hiv.interventions.prep:module-emodpy_hiv.interventions.prep' on page 23 undefined on input line 1931 Reference `emodpy_hiv.interventions.random:module-emodpy_hiv.interventions.random' on page 23 undefined on input line 1932 Reference `emodpy_hiv.interventions.rapiddiag:module-emodpy_hiv.interventions.rapiddiag' on page 23 undefined on input line 1933 Reference `emodpy_hiv.interventions.reftracker:module-emodpy_hiv.interventions.reftracker' on page 23 undefined on input line 1934 Reference `emodpy_hiv.interventions.sigmoiddiag:module-emodpy_hiv.interventions.sigmoiddiag' on page 23 undefined on input line 1935 Reference `emodpy_hiv.interventions.stipostdebut:module-emodpy_hiv.interventions.stipostdebut' on page 23 undefined on input line 1936 Reference `emodpy_hiv.interventions.utils:module-emodpy_hiv.interventions.utils' on page 23 undefined on input line 1937 Reference `emodpy_hiv.interventions.yearandsexdiag:module-emodpy_hiv.interventions.yearandsexdiag' on page 23 undefined on input line 1938 Reference `emodpy_hiv.interventions:module-emodpy_hiv.interventions' on page 23 undefined on input line 1919 Reference `emodpy_hiv.utils:module-emodpy_hiv.utils' on page 23 undefined on input line 1939 Reference `emodpy_hiv:module-emodpy_hiv' on page 23 undefined on input line 1914 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'... 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [3] [4] Chapter 2. [5] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 368--372 []\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 368--372 \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. 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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