Read the Docs build information Build id: 865867 Project: institute-for-disease-modeling-hiv-workflow Version: latest Commit: 11174ab3042080996baa72c0489a471ad77bc592 Date: 2022-02-25T22:06:24.854258Z State: finished Success: True [rtd-command-info] start-time: 2022-02-25T22:06:26.917014Z, end-time: 2022-02-25T22:06:33.700484Z, duration: 6, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/hiv_workflow.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-02-25T22:06:33.948309Z, end-time: 2022-02-25T22:06:35.070918Z, duration: 1, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 11174ab Merge pull request #64 from JSchripsema-IDM/workflow [rtd-command-info] start-time: 2022-02-25T22:06:35.240261Z, end-time: 2022-02-25T22:06:35.316636Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-02-25T22:06:36.728648Z, end-time: 2022-02-25T22:06:43.569915Z, duration: 6, exit-code: 0 python3.7 -mvirtualenv --system-site-packages 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-hiv-workflow/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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sha256=233a249d39eea355702bbe9346c34a8dd31a6073da2f07f464b29e3b3db21f7f Stored in directory: /tmp/pip-ephem-wheel-cache-wk40i3ab/wheels/59/f9/bf/01e56e422aee5062f2ae1890a7f6593443981ae37e18fecbfb Successfully built mock future Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark 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. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.3 MarkupSafe-2.1.0 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.11.1 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.27.1 setuptools-58.2.0 snowballstemmer-2.2.0 sphinx-4.4.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.1.1 urllib3-1.26.8 zipp-3.7.0 [rtd-command-info] start-time: 2022-02-25T22:06:59.971719Z, end-time: 2022-02-25T22:07:34.718210Z, duration: 34, 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 idmtools_calibra~=1.0.5 Downloading 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https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.6.4/idmtools_models-1.6.4-py3-none-any.whl (24 kB) 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 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 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 emod-api<2.0,>=1.20 Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-api/1.22.2/emod_api-1.22.2-py3-none-any.whl (130 kB) 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Collecting PyYaml<5.5,>=5.3.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7a/a5/393c087efdc78091afa2af9f1378762f9821c9c1d7a22c5753fb5ac5f97a/PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (636 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 636.6/636.6 KB 18.0 MB/s eta 0:00:00 Collecting backoff<1.11,>=1.10.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/32/c5dd4f4b0746e9ec05ace2a5045c1fc375ae67ee94355344ad6c7005fd87/backoff-1.10.0-py2.py3-none-any.whl (31 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 pandas<1.2,>=1.1.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fd/70/e8eee0cbddf926bf51958c7d6a86bc69167c300fa2ba8e592330a2377d1b/pandas-1.1.5-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) 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Building wheels for collected packages: sklearn, bs4, docopt, prodict Building wheel for sklearn (setup.py): started Building wheel for sklearn (setup.py): finished with status 'done' Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1310 sha256=02a3e0f2a4540fe3ff08056bb651069fc43247270a0e97620dca3ec8650a5e7b Stored in directory: /tmp/pip-ephem-wheel-cache-97_vfm1r/wheels/50/94/aa/ed6f0a3d3e190b800a88139f52ca17b8094f144fd402719641 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=1272 sha256=0a67eb7dfe659f27b007799028a4e8dac41cad130f89797e4fe22a0af6d999f4 Stored in directory: /tmp/pip-ephem-wheel-cache-97_vfm1r/wheels/f1/23/17/3fcd260137068c2aa94da5806487146928f092eae4c2405b28 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=580652fd521e2d5cdfaf447dbe62180fd1258b11582caf98e76d6146df5860d9 Stored in directory: /tmp/pip-ephem-wheel-cache-97_vfm1r/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c 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=c1691c876e3328cfba26b80da7156a7e30e50874a76a76c6b26b5e13c92fe011 Stored in directory: /tmp/pip-ephem-wheel-cache-97_vfm1r/wheels/a1/47/0e/cbfbed83f6077c4d538850a09e49b8d78284632fc1d48bf122 Successfully built sklearn bs4 docopt prodict Installing collected packages: tabulate, prodict, iniconfig, geographiclib, emod-hiv, docopt, cached-property, xdg, tqdm, tomli, threadpoolctl, soupsieve, shapely, scipy, PyYaml, pyproj, pycparser, py, pillow, patsy, packaging, more-itertools, lz4, joblib, jeepney, humanfriendly, geopy, fasteners, et-xmlfile, diskcache, click, backoff, attrs, astunparse, astor, yarg, scikit-learn, pyCOMPS, pluggy, pandas, openpyxl, coloredlogs, cffi, beautifulsoup4, statsmodels, sklearn, seaborn, pytest, pygit2, pipreqs, cryptography, bs4, SecretStorage, pytest-lazy-fixture, idmtools, emod-api, keyring, idmtools-platform-comps, idmtools-models, idmtools_calibra, emodpy, emodpy-hiv Attempting uninstall: scipy Found existing installation: scipy 1.5.3 Not uninstalling scipy at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest Can't uninstall 'scipy'. No files were found to uninstall. 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 21.3 Uninstalling packaging-21.3: Successfully uninstalled packaging-21.3 Attempting uninstall: pandas Found existing installation: pandas 1.1.3 Not uninstalling pandas at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest Can't uninstall 'pandas'. No files were found to uninstall. Successfully installed PyYaml-5.4.1 SecretStorage-3.3.1 astor-0.8.1 astunparse-1.6.3 attrs-21.4.0 backoff-1.10.0 beautifulsoup4-4.10.0 bs4-0.0.1 cached-property-1.5.2 cffi-1.15.0 click-7.1.2 coloredlogs-15.0.1 cryptography-36.0.1 diskcache-5.2.1 docopt-0.6.2 emod-api-1.22.2 emod-hiv-0.0.4 emodpy-1.17.1 emodpy-hiv-1.0.2 et-xmlfile-1.1.0 fasteners-0.17.3 geographiclib-1.52 geopy-2.0.0 humanfriendly-10.0 idmtools-1.6.4 idmtools-models-1.6.4 idmtools-platform-comps-1.6.4 idmtools_calibra-1.0.5 iniconfig-1.1.1 jeepney-0.7.1 joblib-1.1.0 keyring-23.5.0 lz4-4.0.0 more-itertools-8.8.0 openpyxl-3.0.9 packaging-20.9 pandas-1.1.5 patsy-0.5.2 pillow-9.0.1 pipreqs-0.4.11 pluggy-0.13.1 prodict-0.8.18 py-1.11.0 pyCOMPS-2.5.0 pycparser-2.21 pygit2-1.5.0 pyproj-3.2.1 pytest-7.0.1 pytest-lazy-fixture-0.6.3 scikit-learn-1.0.2 scipy-1.5.4 seaborn-0.11.2 shapely-1.8.1.post1 sklearn-0.0 soupsieve-2.3.1 statsmodels-0.12.2 tabulate-0.8.9 threadpoolctl-3.1.0 tomli-2.0.1 tqdm-4.62.3 xdg-5.1.1 yarg-0.1.9 [rtd-command-info] start-time: 2022-02-25T22:07:34.897385Z, end-time: 2022-02-25T22:07:36.146472Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating hiv_workflow.egg-info writing hiv_workflow.egg-info/PKG-INFO writing dependency_links to hiv_workflow.egg-info/dependency_links.txt writing requirements to hiv_workflow.egg-info/requires.txt writing top-level names to hiv_workflow.egg-info/top_level.txt writing manifest file 'hiv_workflow.egg-info/SOURCES.txt' reading manifest file 'hiv_workflow.egg-info/SOURCES.txt' writing manifest file 'hiv_workflow.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/hiv_workflow copying hiv_workflow/__init__.py -> build/lib/hiv_workflow creating build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/dtk_post_process.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/calibrate.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/run.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/download.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/resample.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/available_parameters.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/__init__.py -> build/lib/hiv_workflow/scripts creating build/lib/hiv_workflow/lib copying hiv_workflow/lib/__init__.py -> build/lib/hiv_workflow/lib creating build/lib/hiv_workflow/lib/calibration copying hiv_workflow/lib/calibration/__init__.py -> build/lib/hiv_workflow/lib/calibration creating build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/hiv_analyzer.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/channel.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/hiv_calib_site.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/condition.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/age_bin.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/data_frame_wrapper.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/base_distribution.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/population_obs.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/gaussian_distribution.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/beta_distribution.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/download_analyzer_by_experiment.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/__init__.py -> build/lib/hiv_workflow/lib/analysis creating build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/project_data.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/analysis.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/runtime.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/wrappers.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/__init__.py -> build/lib/hiv_workflow/lib/utils creating build/lib/hiv_workflow/lib/calibration/algorithms copying hiv_workflow/lib/calibration/algorithms/optim_tool.py -> build/lib/hiv_workflow/lib/calibration/algorithms copying hiv_workflow/lib/calibration/algorithms/__init__.py -> build/lib/hiv_workflow/lib/calibration/algorithms creating build/lib/hiv_workflow/lib/utils/builders copying hiv_workflow/lib/utils/builders/demographics.py -> build/lib/hiv_workflow/lib/utils/builders copying hiv_workflow/lib/utils/builders/general.py -> build/lib/hiv_workflow/lib/utils/builders copying hiv_workflow/lib/utils/builders/__init__.py -> build/lib/hiv_workflow/lib/utils/builders creating build/lib/hiv_workflow/lib/utils/io copying hiv_workflow/lib/utils/io/excel.py -> build/lib/hiv_workflow/lib/utils/io copying hiv_workflow/lib/utils/io/__init__.py -> build/lib/hiv_workflow/lib/utils/io creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/hiv_workflow creating build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/dtk_post_process.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/calibrate.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/run.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/download.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/resample.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/available_parameters.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts creating build/bdist.linux-x86_64/egg/hiv_workflow/lib creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms copying build/lib/hiv_workflow/lib/calibration/algorithms/optim_tool.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms copying build/lib/hiv_workflow/lib/calibration/algorithms/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms copying build/lib/hiv_workflow/lib/calibration/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/hiv_analyzer.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/channel.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/hiv_calib_site.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/condition.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/age_bin.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/data_frame_wrapper.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/base_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/population_obs.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/gaussian_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/beta_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/download_analyzer_by_experiment.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/utils/project_data.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/builders/demographics.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/builders/general.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/builders/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/analysis.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/utils/runtime.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io copying build/lib/hiv_workflow/lib/utils/io/excel.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io copying build/lib/hiv_workflow/lib/utils/io/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io copying build/lib/hiv_workflow/lib/utils/wrappers.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/utils/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib copying build/lib/hiv_workflow/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/dtk_post_process.py to dtk_post_process.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/calibrate.py to calibrate.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/run.py to run.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/download.py to download.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/resample.py to resample.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/available_parameters.py to available_parameters.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms/optim_tool.py to optim_tool.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/hiv_analyzer.py to hiv_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/channel.py to channel.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/hiv_calib_site.py to hiv_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/condition.py to condition.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/age_bin.py to age_bin.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/data_frame_wrapper.py to data_frame_wrapper.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/base_distribution.py to base_distribution.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/population_obs.py to population_obs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/gaussian_distribution.py to gaussian_distribution.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py to download_analyzer_by_experiment_receipt.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/beta_distribution.py to beta_distribution.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/download_analyzer_by_experiment.py to download_analyzer_by_experiment.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/project_data.py to project_data.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/demographics.py to demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/general.py to general.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/analysis.py to analysis.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/runtime.py to runtime.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io/excel.py to excel.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/wrappers.py to wrappers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/__init__.py to __init__.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... hiv_workflow.lib.analysis.__pycache__.base_distribution.cpython-37: module references __file__ hiv_workflow.lib.calibration.algorithms.__pycache__.optim_tool.cpython-37: module references __file__ hiv_workflow.lib.utils.__pycache__.runtime.cpython-37: module references __path__ hiv_workflow.scripts.__pycache__.available_parameters.cpython-37: module references __file__ hiv_workflow.scripts.__pycache__.calibrate.cpython-37: module references __file__ hiv_workflow.scripts.__pycache__.run.cpython-37: module references __file__ creating dist creating 'dist/hiv_workflow-1.0.0-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 hiv_workflow-1.0.0-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages/hiv_workflow-1.0.0-py3.7.egg Extracting hiv_workflow-1.0.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Adding hiv-workflow 1.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages/hiv_workflow-1.0.0-py3.7.egg Processing dependencies for hiv-workflow==1.0.0 Searching for lz4==4.0.0 Best match: lz4 4.0.0 Adding lz4 4.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for openpyxl==3.0.9 Best match: openpyxl 3.0.9 Adding openpyxl 3.0.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for emodpy-hiv==1.0.2 Best match: emodpy-hiv 1.0.2 Adding emodpy-hiv 1.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for idmtools-calibra==1.0.5 Best match: idmtools-calibra 1.0.5 Adding idmtools-calibra 1.0.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for et-xmlfile==1.1.0 Best match: et-xmlfile 1.1.0 Adding et-xmlfile 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for numpy==1.19.2 Best match: numpy 1.19.2 Adding numpy 1.19.2 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for emodpy==1.17.1 Best match: emodpy 1.17.1 Adding emodpy 1.17.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for emod-hiv==0.0.4 Best match: emod-hiv 0.0.4 Adding emod-hiv 0.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for fasteners==0.17.3 Best match: fasteners 0.17.3 Adding fasteners 0.17.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for seaborn==0.11.2 Best match: seaborn 0.11.2 Adding seaborn 0.11.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for geopy==2.0.0 Best match: geopy 2.0.0 Adding geopy 2.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for sklearn==0.0 Best match: sklearn 0.0 Adding sklearn 0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for statsmodels==0.12.2 Best match: statsmodels 0.12.2 Adding statsmodels 0.12.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for scipy==1.5.4 Best match: scipy 1.5.4 Adding scipy 1.5.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for idmtools==1.6.4 Best match: idmtools 1.6.4 Adding idmtools 1.6.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for keyring==23.5.0 Best match: keyring 23.5.0 Adding keyring 23.5.0 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for emod-api==1.22.2 Best match: emod-api 1.22.2 Adding emod-api 1.22.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for idmtools-models==1.6.4 Best match: idmtools-models 1.6.4 Adding idmtools-models 1.6.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for matplotlib==3.3.2 Best match: matplotlib 3.3.2 matplotlib 3.3.2 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for idmtools-platform-comps==1.6.4 Best match: idmtools-platform-comps 1.6.4 Adding idmtools-platform-comps 1.6.4 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for pandas==1.1.5 Best match: pandas 1.1.5 Adding pandas 1.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for geographiclib==1.52 Best match: geographiclib 1.52 Adding geographiclib 1.52 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for patsy==0.5.2 Best match: patsy 0.5.2 Adding patsy 0.5.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for tabulate==0.8.9 Best match: tabulate 0.8.9 Adding tabulate 0.8.9 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for pluggy==0.13.1 Best match: pluggy 0.13.1 Adding pluggy 0.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for diskcache==5.2.1 Best match: diskcache 5.2.1 Adding diskcache 5.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/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-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for PyYAML==5.4.1 Best match: PyYAML 5.4.1 Adding PyYAML 5.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for packaging==20.9 Best match: packaging 20.9 Adding packaging 20.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for tqdm==4.62.3 Best match: tqdm 4.62.3 Adding tqdm 4.62.3 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for backoff==1.10.0 Best match: backoff 1.10.0 Adding backoff 1.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for more-itertools==8.8.0 Best match: more-itertools 8.8.0 Adding more-itertools 8.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/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-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for pygit2==1.5.0 Best match: pygit2 1.5.0 Adding pygit2 1.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for importlib-metadata==4.11.1 Best match: importlib-metadata 4.11.1 Adding importlib-metadata 4.11.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for jeepney==0.7.1 Best match: jeepney 0.7.1 Adding jeepney 0.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for SecretStorage==3.3.1 Best match: SecretStorage 3.3.1 Adding SecretStorage 3.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for Shapely==1.8.1.post1 Best match: Shapely 1.8.1.post1 Adding Shapely 1.8.1.post1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for beautifulsoup4==4.10.0 Best match: beautifulsoup4 4.10.0 Adding beautifulsoup4 4.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for Jinja2==3.0.3 Best match: Jinja2 3.0.3 Adding Jinja2 3.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 kiwisolver 1.2.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pyparsing==3.0.7 Best match: pyparsing 3.0.7 Adding pyparsing 3.0.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for certifi==2021.10.8 Best match: certifi 2021.10.8 Adding certifi 2021.10.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 cycler 0.10.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for Pillow==9.0.1 Best match: Pillow 9.0.1 Adding Pillow 9.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for wheel==0.37.1 Best match: wheel 0.37.1 Adding wheel 0.37.1 to easy-install.pth file Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 six 1.15.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pytest-lazy-fixture==0.6.3 Best match: pytest-lazy-fixture 0.6.3 Adding pytest-lazy-fixture 0.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for pyCOMPS==2.5.0 Best match: pyCOMPS 2.5.0 Adding pyCOMPS 2.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for pytz==2021.3 Best match: pytz 2021.3 Adding pytz 2021.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for joblib==1.1.0 Best match: joblib 1.1.0 Adding joblib 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/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-hiv-workflow/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-hiv-workflow/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-hiv-workflow/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-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for cffi==1.15.0 Best match: cffi 1.15.0 Adding cffi 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for zipp==3.7.0 Best match: zipp 3.7.0 Adding zipp 3.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for typing-extensions==4.1.1 Best match: typing-extensions 4.1.1 Adding typing-extensions 4.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for cryptography==36.0.1 Best match: cryptography 36.0.1 Adding cryptography 36.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for soupsieve==2.3.1 Best match: soupsieve 2.3.1 Adding soupsieve 2.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for MarkupSafe==2.1.0 Best match: MarkupSafe 2.1.0 Adding MarkupSafe 2.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for pytest==7.0.1 Best match: pytest 7.0.1 Adding pytest 7.0.1 to easy-install.pth file Installing py.test script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Installing pytest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for future==0.18.2 Best match: future 0.18.2 Adding future 0.18.2 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for requests==2.27.1 Best match: requests 2.27.1 Adding requests 2.27.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/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-hiv-workflow/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-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for iniconfig==1.1.1 Best match: iniconfig 1.1.1 Adding iniconfig 1.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for attrs==21.4.0 Best match: attrs 21.4.0 Adding attrs 21.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for tomli==2.0.1 Best match: tomli 2.0.1 Adding tomli 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for py==1.11.0 Best match: py 1.11.0 Adding py 1.11.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for idna==3.3 Best match: idna 3.3 Adding idna 3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for charset-normalizer==2.0.12 Best match: charset-normalizer 2.0.12 Adding charset-normalizer 2.0.12 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Searching for urllib3==1.26.8 Best match: urllib3 1.26.8 Adding urllib3 1.26.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Finished processing dependencies for hiv-workflow==1.0.0 [rtd-command-info] start-time: 2022-02-25T22:07:36.364149Z, end-time: 2022-02-25T22:07:42.428861Z, duration: 6, 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 14.8 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon~=0.7 Downloading 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plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 sphinx-3.2.1 sphinx-copybutton-0.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.3.0 [rtd-command-info] start-time: 2022-02-25T22:07:43.809766Z, end-time: 2022-02-25T22:07:43.881415Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser from datetime import datetime if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "hiv_workflow" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx.ext.intersphinx', 'sphinx_copybutton' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = ['hiv_workflow.scripts'] 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'hiv_workflow' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = 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-generic' # -- 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-generic-docs.tex', u'emodpy-generic', 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-generic-docs', u'emodpy-generic', [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-generic-docs', u'emodpy-generic', author, 'Institute for Disease Modeling', 'How to use emodpy for disease simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False intersphinx_mapping = {'python': ('https://docs.python.org/3', None), 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/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: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] 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", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/hiv_workflow/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/hiv_workflow/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-hiv-workflow', 'name': u'hiv_workflow', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/hiv_workflow/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': 'hiv_workflow', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '11174ab3', } # 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-hiv-workflow/builds/865867/' 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: 2022-02-25T22:07:44.052373Z, end-time: 2022-02-25T22:07:54.568739Z, duration: 10, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.2.1 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/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 38 source files that are out of date updating environment: [new config] 38 added, 0 changed, 0 removed reading sources... [ 2%] hiv_workflow reading sources... [ 5%] hiv_workflow.lib reading sources... [ 7%] hiv_workflow.lib.analysis reading sources... [ 10%] hiv_workflow.lib.analysis.age_bin reading sources... [ 13%] hiv_workflow.lib.analysis.base_distribution reading sources... [ 15%] hiv_workflow.lib.analysis.beta_distribution reading sources... [ 18%] hiv_workflow.lib.analysis.channel reading sources... [ 21%] hiv_workflow.lib.analysis.condition reading sources... [ 23%] hiv_workflow.lib.analysis.data_frame_wrapper reading sources... [ 26%] hiv_workflow.lib.analysis.download_analyzer_by_experiment /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.6.4/configuration.html for details on how to configure idmtools. reading sources... [ 28%] hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt reading sources... [ 31%] hiv_workflow.lib.analysis.gaussian_distribution reading sources... 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[100%] project_workflow generating indices... genindex py-modindexdone writing additional pages... search opensearchdone 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 _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-02-25T22:07:54.775702Z, end-time: 2022-02-25T22:07:59.880895Z, duration: 5, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.2.1 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/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 38 added, 0 changed, 0 removed reading sources... [ 2%] hiv_workflow reading sources... [ 5%] hiv_workflow.lib reading sources... [ 7%] hiv_workflow.lib.analysis reading sources... [ 10%] hiv_workflow.lib.analysis.age_bin reading sources... [ 13%] hiv_workflow.lib.analysis.base_distribution reading sources... [ 15%] hiv_workflow.lib.analysis.beta_distribution reading sources... [ 18%] hiv_workflow.lib.analysis.channel reading sources... [ 21%] hiv_workflow.lib.analysis.condition reading sources... [ 23%] hiv_workflow.lib.analysis.data_frame_wrapper reading sources... [ 26%] hiv_workflow.lib.analysis.download_analyzer_by_experiment /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.6.4/configuration.html for details on how to configure idmtools. reading sources... [ 28%] hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt reading sources... [ 31%] hiv_workflow.lib.analysis.gaussian_distribution reading sources... 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[ 76%] hiv_workflow.scripts reading sources... [ 78%] hiv_workflow.scripts.available_parameters reading sources... [ 81%] hiv_workflow.scripts.calibrate reading sources... [ 84%] hiv_workflow.scripts.download reading sources... [ 86%] hiv_workflow.scripts.dtk_post_process reading sources... [ 89%] hiv_workflow.scripts.resample reading sources... [ 92%] hiv_workflow.scripts.run reading sources... [ 94%] index reading sources... [ 97%] modules reading sources... [100%] project_workflow looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... project_workflow modules hiv_workflow hiv_workflow.lib hiv_workflow.lib.analysis hiv_workflow.lib.analysis.age_bin hiv_workflow.lib.analysis.base_distribution hiv_workflow.lib.analysis.beta_distribution hiv_workflow.lib.analysis.channel hiv_workflow.lib.analysis.condition hiv_workflow.lib.analysis.data_frame_wrapper hiv_workflow.lib.analysis.download_analyzer_by_experiment hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt hiv_workflow.lib.analysis.gaussian_distribution hiv_workflow.lib.analysis.hiv_analyzer hiv_workflow.lib.analysis.hiv_calib_site hiv_workflow.lib.analysis.population_obs hiv_workflow.lib.calibration hiv_workflow.lib.calibration.algorithms hiv_workflow.lib.calibration.algorithms.optim_tool hiv_workflow.lib.utils hiv_workflow.lib.utils.builders hiv_workflow.lib.utils.builders.demographics hiv_workflow.lib.utils.builders.general hiv_workflow.lib.utils.io hiv_workflow.lib.utils.io.excel hiv_workflow.lib.utils.analysis hiv_workflow.lib.utils.project_data hiv_workflow.lib.utils.runtime hiv_workflow.lib.utils.wrappers hiv_workflow.scripts hiv_workflow.scripts.available_parameters hiv_workflow.scripts.calibrate hiv_workflow.scripts.download hiv_workflow.scripts.dtk_post_process hiv_workflow.scripts.resample hiv_workflow.scripts.run 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 _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-02-25T22:08:00.083250Z, end-time: 2022-02-25T22:08:01.765874Z, duration: 1, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done processing emodpy-generic-docs.tex... index project_workflow modules hiv_workflow hiv_workflow.lib hiv_workflow.lib.analysis hiv_workflow.lib.analysis.age_bin hiv_workflow.lib.analysis.base_distribution hiv_workflow.lib.analysis.beta_distribution hiv_workflow.lib.analysis.channel hiv_workflow.lib.analysis.condition hiv_workflow.lib.analysis.data_frame_wrapper hiv_workflow.lib.analysis.download_analyzer_by_experiment hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt hiv_workflow.lib.analysis.gaussian_distribution hiv_workflow.lib.analysis.hiv_analyzer hiv_workflow.lib.analysis.hiv_calib_site hiv_workflow.lib.analysis.population_obs hiv_workflow.lib.calibration hiv_workflow.lib.calibration.algorithms hiv_workflow.lib.calibration.algorithms.optim_tool hiv_workflow.lib.utils hiv_workflow.lib.utils.builders hiv_workflow.lib.utils.builders.demographics hiv_workflow.lib.utils.builders.general hiv_workflow.lib.utils.io hiv_workflow.lib.utils.io.excel hiv_workflow.lib.utils.analysis hiv_workflow.lib.utils.project_data hiv_workflow.lib.utils.runtime hiv_workflow.lib.utils.wrappers hiv_workflow.scripts hiv_workflow.scripts.available_parameters hiv_workflow.scripts.calibrate hiv_workflow.scripts.download hiv_workflow.scripts.dtk_post_process hiv_workflow.scripts.resample hiv_workflow.scripts.run resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. 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-hiv-workflow/checkouts/latest/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-02-25T22:08:02.063886Z, end-time: 2022-02-25T22:08:02.148606Z, 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: 2022-02-25T22:08:02.314803Z, end-time: 2022-02-25T22:08:05.264562Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-hiv-workflow -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. 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-hiv-workflow" "emodpy-generic-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-generic-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)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/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-hiv-workflow.idx (./institute-for-disease-modeling-hiv-workflow.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.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/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/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] [1] [2] Chapter 1. [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [5] [6] Chapter 3. [7] [8] Chapter 4. LaTeX Warning: Hyper reference `project_workflow:scripts' on page 9 undefined o n input line 234. LaTeX Warning: Hyper reference `project_workflow:calibrate-py' on page 9 undefi ned on input line 237. LaTeX Warning: Hyper reference `project_workflow:resample-py' on page 9 undefin ed on input line 240. LaTeX Warning: Hyper reference `project_workflow:run-py' on page 9 undefined on input line 243. LaTeX Warning: Hyper reference `project_workflow:download-py' on page 9 undefin ed on input line 246. LaTeX Warning: Hyper reference `project_workflow:available-parameters-py' on pa ge 9 undefined on input line 249. LaTeX Warning: Hyper reference `project_workflow:components-that-have-are-apis- definition-requirements' on page 9 undefined on input line 254. 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[9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 533--536 \T1/pcr/m/n/10 config_builder(schema_path, max_memory_mb=None, demographics_pat hs=None, Underfull \hbox (badness 10000) in paragraph at lines 549--551 \T1/pcr/m/n/10 def build_demographics(manifest, params_to_modify=None, dry_run= False, [13] Underfull \hbox (badness 10000) in paragraph at lines 564--566 \T1/pcr/m/n/10 def build_campaign(schema_path, params_to_modify=None, dry_run=F alse, (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] LaTeX Warning: Hyper reference `hiv_workflow.lib.analysis.data_frame_wrapper:hi v_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper' on page 16 undefin ed on input line 807. LaTeX Warning: Hyper reference `hiv_workflow.lib.analysis.data_frame_wrapper:hi v_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper' on page 16 undefin ed on input line 807. 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paragraph at lines 1670--1670 [][]\T1/ptm/m/n/10 None[][] [26] Overfull \hbox (64.9846pt too wide) in paragraph at lines 1676--1676 []\T1/ptm/m/it/10 demographics: Overfull \hbox (269.81337pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (19.13475pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 ini- Overfull \hbox (112.84337pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 tial_risk_distribution_low: Overfull \hbox (23.0249pt too wide) in paragraph at lines 1676--1676 [][]\T1/ptm/m/it/10 float[][] Overfull \hbox (11.99501pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 = Overfull \hbox (32.35487pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 None\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1676--1676 \OMS/cmsy/m/n/10 !$ Overfull \hbox (26.90492pt too wide) in paragraph at lines 1676--1676 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (63.42361pt too wide) in paragraph at lines 1693--1693 []\T1/ptm/m/it/10 parameter_setting_functions: Overfull \hbox (4.98395pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 ex- Overfull \hbox (38.09406pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 pected_first_argument: Underfull \hbox (badness 10000) in paragraph at lines 1693--1693 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (1.62408pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/n/10 Dict[Callable, Underfull \hbox (badness 5985) in paragraph at lines 1699--1700 []\T1/pcr/b/n/10 parameter_setting_functions \T1/ptm/m/n/10 ^^U a list of func- tion ref-er-ences that pro- [27] Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 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year_col=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Year\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u- Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 la-tion_col=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Population\TS1/pt m/m/it/10 '\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `hiv_workflow.lib.analysis.hiv_calib_site:hiv_wo rkflow.lib.analysis.hiv_calib_site.HIVCalibSite' on page 29 undefined on input line 1923. 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Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on institute-for-disease-modeling-hiv-workflow.pdf (41 pages, 20 3612 bytes). Transcript written on institute-for-disease-modeling-hiv-workflow.log. Latexmk: Index file 'institute-for-disease-modeling-hiv-workflow.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-hiv-workflow.ind' from line 'No file institute-for-disease-modeling-hiv-workflow.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-hiv-workflow.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-hiv-workflow.pdf' Latexmk: List of undefined refs and citations: Reference `hiv_workflow.lib.analysis.age_bin:module-hiv_workflow.lib.analysis.age_bin' on page 37 undefined on input line 2316 Reference `hiv_workflow.lib.analysis.base_distribution:module-hiv_workflow.lib.analysis.base_distribution' on page 37 undefined on input line 2317 Reference `hiv_workflow.lib.analysis.beta_distribution:module-hiv_workflow.lib.analysis.beta_distribution' on page 37 undefined on input line 2318 Reference `hiv_workflow.lib.analysis.channel:module-hiv_workflow.lib.analysis.channel' on page 37 undefined on input line 2319 Reference `hiv_workflow.lib.analysis.condition:module-hiv_workflow.lib.analysis.condition' on page 37 undefined on input line 2320 Reference `hiv_workflow.lib.analysis.data_frame_wrapper:module-hiv_workflow.lib.analysis.data_frame_wrapper' 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`hiv_workflow.lib.analysis:module-hiv_workflow.lib.analysis' on page 37 undefined on input line 2315 Reference `hiv_workflow.lib.calibration.algorithms.optim_tool:module-hiv_workflow.lib.calibration.algorithms.optim_tool' on page 37 undefined on input line 2330 Reference `hiv_workflow.lib.calibration.algorithms:module-hiv_workflow.lib.calibration.algorithms' on page 37 undefined on input line 2329 Reference `hiv_workflow.lib.calibration:module-hiv_workflow.lib.calibration' on page 37 undefined on input line 2328 Reference `hiv_workflow.lib.utils.analysis:module-hiv_workflow.lib.utils.analysis' on page 37 undefined on input line 2332 Reference `hiv_workflow.lib.utils.builders.demographics:module-hiv_workflow.lib.utils.builders.demographics' on page 37 undefined on input line 2334 Reference `hiv_workflow.lib.utils.builders.general:module-hiv_workflow.lib.utils.builders.general' on page 37 undefined on input line 2335 Reference 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`hiv_workflow.scripts.available_parameters:module-hiv_workflow.scripts.available_parameters' on page 37 undefined on input line 2342 Reference `hiv_workflow.scripts.calibrate:module-hiv_workflow.scripts.calibrate' on page 37 undefined on input line 2343 Reference `hiv_workflow.scripts.download:module-hiv_workflow.scripts.download' on page 37 undefined on input line 2344 Reference `hiv_workflow.scripts.dtk_post_process:module-hiv_workflow.scripts.dtk_post_process' on page 37 undefined on input line 2345 Reference `hiv_workflow.scripts.resample:module-hiv_workflow.scripts.resample' on page 37 undefined on input line 2346 Reference `hiv_workflow.scripts.run:module-hiv_workflow.scripts.run' on page 37 undefined on input line 2347 Reference `hiv_workflow.scripts:module-hiv_workflow.scripts' on page 37 undefined on input line 2341 Reference `hiv_workflow:module-hiv_workflow' on page 37 undefined on input line 2313 Latexmk: Summary of warnings: Latex failed to resolve 36 reference(s) Rule 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Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-hiv-workflow.aux' 'institute-for-disease-modeling-hiv-workflow.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-hiv-workflow" "emodpy-generic-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-generic-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-hiv-workflow.out) (./institute-for-disease-modeling-hiv-workflow.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/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-hiv-workflow.toc) [1] [2] [1] [2] Chapter 1. [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [5] [6] Chapter 3. [7] [8] Chapter 4. [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 533--536 \T1/pcr/m/n/10 config_builder(schema_path, max_memory_mb=None, demographics_pat hs=None, Underfull \hbox (badness 10000) in paragraph at lines 549--551 \T1/pcr/m/n/10 def build_demographics(manifest, params_to_modify=None, dry_run= False, [13] Underfull \hbox (badness 10000) in paragraph at lines 564--566 \T1/pcr/m/n/10 def build_campaign(schema_path, params_to_modify=None, dry_run=F alse, (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 807--807 []\T1/ptm/m/it/10 dfw: [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.data_frame_ wrapper.DataFrameWrapper[][], Underfull \hbox (badness 7256) in paragraph at lines 807--807 \T1/ptm/m/it/10 chan-nel: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 weight_ch annel: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ad-di-tional_keep: List[[][] str[][]]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (55.16237pt too wide) in paragraph at lines 840--840 []\T1/ptm/m/it/10 dfw: [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.data_frame_ wrapper.DataFrameWrapper[][], [16] Overfull \hbox (74.911pt too wide) in paragraph at lines 854--854 []\T1/ptm/m/it/10 distribution_name: [][]str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n /10 !$ [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.BaseDist ribution[][] Underfull \hbox (badness 10000) in paragraph at lines 866--866 []\T1/ptm/m/it/10 uncertainty_channel: [][]str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m /n/10 !$ Overfull \hbox (43.2821pt too wide) in paragraph at lines 866--866 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.BaseDistributio n[][] [17] Overfull \hbox (27.48462pt too wide) in paragraph at lines 1049--1049 []\T1/ptm/m/it/10 filename=None\T1/ptm/m/n/10 , Overfull \hbox (34.56456pt too wide) in paragraph at lines 1049--1049 \T1/ptm/m/it/10 dataframe=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1049--1049 \T1/ptm/m/it/10 strat-i- Overfull \hbox (14.22461pt too wide) in paragraph at lines 1049--1049 \T1/ptm/m/it/10 fiers=None\T1/pcr/m/n/10 ) [18] [19] Overfull \hbox (153.51465pt too wide) in paragraph at lines 1178--1178 []\T1/ptm/m/it/10 filenames\T1/ptm/m/n/10 , Overfull \hbox (129.35486pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 out- Overfull \hbox (151.3048pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 put_path\T1/ptm/m/n/10 , Overfull \hbox (208.60439pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 use_run_number=True\T1/ptm/m/n/10 , Overfull \hbox (217.45421pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 use_sample_index=True\T1/pcr/m/n/10 ) Overfull \hbox (243.51465pt too wide) in paragraph at lines 1262--1262 []\T1/ptm/m/it/10 filenames\T1/ptm/m/n/10 , Overfull \hbox (214.53479pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 re- Overfull \hbox (242.40451pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 ceipt_file\T1/ptm/m/n/10 , Overfull \hbox (298.60439pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 use_run_number=True\T1/ptm/m/n/10 , Overfull \hbox (307.45421pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 use_sample_index=True\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1263--1264 \T1/ptm/m/n/10 Bases: [][]\T1/pcr/m/sl/10 hiv_workflow.lib.analysis.download_an alyzer_by_experiment. [20] Underfull \hbox (badness 10000) in paragraph at lines 1353--1353 []\T1/ptm/m/it/10 site\T1/ptm/m/n/10 , \T1/ptm/m/it/10 weight\T1/ptm/m/n/10 , \ T1/ptm/m/it/10 chan- Underfull \hbox (badness 10000) in paragraph at lines 1353--1353 \T1/ptm/m/it/10 nel\T1/ptm/m/n/10 , \T1/ptm/m/it/10 scale_population\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 1353--1353 \T1/ptm/m/it/10 dis-tri-bu-tion\T1/ptm/m/n/10 , \T1/ptm/m/it/10 provin- Underfull \hbox (badness 10000) in paragraph at lines 1353--1353 \T1/ptm/m/it/10 cial-ity\T1/ptm/m/n/10 , \T1/ptm/m/it/10 age_bins=\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 all\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1353--1353 \T1/ptm/m/it/10 de-bug=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver- Underfull \hbox (badness 10000) in paragraph at lines 1353--1353 \T1/ptm/m/it/10 bose=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 out- Underfull \hbox (badness 10000) in paragraph at lines 1354--1356 \T1/ptm/m/n/10 Bases: \T1/pcr/m/n/10 idmtools_calibra.analyzers.base_calibratio n_analyzer. [21] Underfull \hbox (badness 10000) in paragraph at lines 1495--1495 []\T1/ptm/m/it/10 filename=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1495--1495 \T1/ptm/m/it/10 dataframe=None\T1/ptm/m/n/10 , [22] Underfull \hbox (badness 10000) in paragraph at lines 1613--1613 []\T1/ptm/m/it/10 subparsers\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1619--1619 []\T1/ptm/m/it/10 args\T1/ptm/m/n/10 , \T1/ptm/m/it/10 params\T1/ptm/m/n/10 , Overfull \hbox (22.9846pt too wide) in paragraph at lines 1640--1640 []\T1/ptm/m/it/10 demographics: Overfull \hbox (227.81337pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (107.11305pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_commercial=None\T1/ptm/m/n/10 , Overfull \hbox (94.72316pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_informal=None\T1/ptm/m/n/10 , Overfull \hbox (89.72316pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_marital=None\T1/ptm/m/n/10 , Overfull \hbox (103.07301pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_transitory=None\T1/pcr/m/n/10 ) [23] Overfull \hbox (46.9846pt too wide) in paragraph at lines 1646--1646 []\T1/ptm/m/it/10 demographics: Overfull \hbox (251.81337pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (210.18271pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 max_relationships_commercial_high_risk_male=None\T1/ptm/m/n/10 , Overfull \hbox (217.40254pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 max_relationships_commercial_high_risk_female=None\T1/ptm/m/n/1 0 , Overfull \hbox (9.0149pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 prob- Underfull \hbox 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(29.01491pt too wide) in paragraph at lines 1664--1664 \T1/ptm/m/it/10 con- Overfull \hbox (155.71391pt too wide) in paragraph at lines 1664--1664 \T1/ptm/m/it/10 dom_usage_rate_transitory=None\T1/pcr/m/n/10 ) Overfull \hbox (21.24503pt too wide) in paragraph at lines 1664--1664 \OMS/cmsy/m/n/10 !$ Overfull \hbox (32.90492pt too wide) in paragraph at lines 1664--1664 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (46.9846pt too wide) in paragraph at lines 1670--1670 []\T1/ptm/m/it/10 demographics: Overfull \hbox (251.81337pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (7.23488pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 com- Overfull \hbox (5.92482pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 mer- Overfull \hbox (125.63351pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 cial_weibull_heterogeneity=None\T1/ptm/m/n/10 , Overfull \hbox (7.23488pt 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\hbox (97.01385pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 tory_weibull_scale=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1670--1670 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.90492pt too wide) in paragraph at lines 1670--1670 [][]\T1/ptm/m/n/10 None[][] [26] Overfull \hbox (64.9846pt too wide) in paragraph at lines 1676--1676 []\T1/ptm/m/it/10 demographics: Overfull \hbox (269.81337pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (19.13475pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 ini- Overfull \hbox (112.84337pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 tial_risk_distribution_low: Overfull \hbox (23.0249pt too wide) in paragraph at lines 1676--1676 [][]\T1/ptm/m/it/10 float[][] Overfull \hbox (11.99501pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 = Overfull \hbox (32.35487pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 None\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1676--1676 \OMS/cmsy/m/n/10 !$ Overfull \hbox (26.90492pt too wide) in paragraph at lines 1676--1676 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (63.42361pt too wide) in paragraph at lines 1693--1693 []\T1/ptm/m/it/10 parameter_setting_functions: Overfull \hbox (4.98395pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 ex- Overfull \hbox (38.09406pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 pected_first_argument: Underfull \hbox (badness 10000) in paragraph at lines 1693--1693 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (1.62408pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/n/10 Dict[Callable, Underfull \hbox (badness 5985) in paragraph at lines 1699--1700 []\T1/pcr/b/n/10 parameter_setting_functions \T1/ptm/m/n/10 ^^U a list of func- tion ref-er-ences that pro- [27] Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 set-ting_functions : Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 func- Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 \T1/ptm/m/it/10 tion_arguments: Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 \T1/ptm/m/it/10 Dict[Callable, List]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [28] Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 []\T1/ptm/m/it/10 year\T1/ptm/m/n/10 , \T1/ptm/m/it/10 obs_population\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 low_age=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 high_age=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 age_bin=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 year_col=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Year\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u- Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 la-tion_col=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Population\TS1/pt m/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1923--1923 []\T1/ptm/m/it/10 ingest_filename: Underfull \hbox (badness 10000) in paragraph at lines 1923--1923 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ \T1/ptm/m/n/10 Tu-ple[[][]dict[][], Overfull \hbox (128.51247pt too wide) in paragraph at lines 1923--1923 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite[][]\T 1/ptm/m/n/10 ] [29] Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 []\T1/ptm/m/it/10 wb: open- Overfull \hbox (60.96397pt too wide) in paragraph at lines 1934--1934 \T1/ptm/m/it/10 pyxl.workbook.workbook.Workbook\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 \T1/ptm/m/it/10 sheet_name: Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 [][]\T1/ptm/m/it/10 str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 wb_path: Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ \T1/ptm/m/n/10 open- Overfull \hbox (64.94374pt too wide) in paragraph at lines 1934--1934 \T1/ptm/m/n/10 pyxl.worksheet.worksheet.Worksheet Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 []\T1/ptm/m/it/10 filename: Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ \T1/ptm/m/n/10 Tu- Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 \T1/ptm/m/n/10 ple[List[[][]dict[][]], Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 [][]\T1/ptm/m/n/10 dict[][], Overfull \hbox (169.82304pt too wide) in paragraph at lines 1947--1947 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][]\ T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 \T1/ptm/m/n/10 List[[][]dict[][]], Overfull \hbox (136.29294pt too wide) in paragraph at lines 1947--1947 \T1/ptm/m/n/10 List[[][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.channel.Chann el[][]\T1/ptm/m/n/10 ]] Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 []\T1/ptm/m/it/10 task: [][]idm- Overfull \hbox (37.77344pt too wide) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 chan-nels: Overfull \hbox (136.20297pt too wide) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 List[[][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.channel.Chann el[][]\T1/ptm/m/it/10 ]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 ref-er- Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 ence_data: Overfull \hbox (170.10309pt too wide) in paragraph at lines 1961--1961 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][], Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 site_info: [30] Underfull \hbox (badness 10000) in paragraph at lines 2008--2008 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 2008--2008 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 \T1/ptm/m/it/10 path: [][]str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [][]\T1/ ptm/m/n/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 2062--2062 []\T1/ptm/m/it/10 simulation: [][]idm- Overfull \hbox (41.153pt too wide) in paragraph at lines 2062--2062 \T1/ptm/m/it/10 tools.entities.simulation.Simulation[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2062--2062 \T1/ptm/m/it/10 sam-ple: [][]dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2062--2062 \T1/ptm/m/it/10 mo-graph-ics_builder: Underfull \hbox (badness 10000) in paragraph at lines 2072--2073 []\T1/pcr/b/n/10 sample \T1/ptm/m/n/10 ^^U dict of pa-ram-e-ter names/values ov er-rides to use dur-ing con- [31] Underfull \hbox (badness 10000) in paragraph at lines 2102--2102 []\T1/ptm/m/it/10 sample: [][]dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cus- Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 []\T1/ptm/m/it/10 executable_path: [][]str[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 schema_path: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph-ics_builder: Underfull \hbox (badness 7963) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 ics_paths: List[[][]str[][]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 python_processing_setter: Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 Callable = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 chan-nels: Overfull \hbox (55.70297pt too wide) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 List[[][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.channel.Chann el[][]\T1/ptm/m/it/10 ] Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ref-er-ence: Overfull \hbox (89.60309pt too wide) in paragraph at lines 2125--2125 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][] Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 site_info: Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 [][]\T1/ptm/m/it/10 dict[][] = None\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [32] Underfull \hbox (badness 10000) in paragraph at lines 2209--2209 []\T1/ptm/m/it/10 algorithm_name: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 a l- Underfull \hbox (badness 10000) in paragraph at lines 2209--2209 \T1/ptm/m/it/10 go-rithm_root: [][]str[][] = Overfull \hbox (0.70457pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/it/10 config_builder: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 [][]\T1/ptm/m/it/10 str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 kwargs: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (13.66457pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 max_memory_mb: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 [][]\T1/ptm/m/it/10 int[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 ics_paths: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 List[[][]str[][]] Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 5681) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 = False\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [33] Overfull \hbox (27.70444pt too wide) in paragraph at lines 2256--2256 []\T1/ptm/m/it/10 campaign_builder: Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (7.1947pt too wide) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 False\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (68.67427pt too wide) in paragraph at lines 2262--2262 []\T1/ptm/m/it/10 demographics_builder: Overfull \hbox (12.19455pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 man- Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 i-fest: Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 mod- Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 ule\T1/ptm/m/n/10 , Overfull \hbox (7.0946pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 kwargs: Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (10.7947pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 [][]\T1/ptm/m/it/10 bool[][] Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 = Overfull \hbox (2.71472pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.57443pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/n/10 Callable Overfull \hbox (66.70457pt too wide) in paragraph at lines 2268--2268 []\T1/ptm/m/it/10 config_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (25.23488pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 cam- Overfull \hbox (65.04453pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 paign_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (18.01491pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 de- Overfull \hbox (20.79494pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 mo- Overfull \hbox (32.31496pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 graph- Overfull \hbox (53.37436pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 ics_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (22.31496pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 ran- Overfull \hbox (80.23463pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 dom_run_number: Overfull \hbox (29.0249pt too wide) in paragraph at lines 2268--2268 [][]\T1/ptm/m/it/10 bool[][]\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 2268--2268 \OMS/cmsy/m/n/10 !$ Overfull \hbox (24.13475pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/n/10 idm- Overfull \hbox (207.823pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/n/10 tools_calibra.calib_manager.SampleIndexWrapper [34] Overfull \hbox (13.1938pt too wide) in paragraph at lines 2274--2274 []\T1/ptm/m/it/10 custom_sample_constrainer: Underfull \hbox (badness 7759) in paragraph at lines 2280--2280 []\T1/ptm/m/it/10 pre: [][]str[][] Underfull \hbox (badness 10000) in paragraph at lines 2280--2280 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2280--2280 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , [35] [36] Overfull \hbox (30.6225pt too wide) in paragraph at lines 2317--2318 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.base_distribution\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2318--2319 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.beta_distribution\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2321--2322 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.data_frame_wrapper\T1/ptm/m/n/10 , Overfull \hbox (114.6225pt too wide) in paragraph at lines 2322--2323 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.download_analyzer_by_experiment\T1/p tm/m/n/10 , Overfull \hbox (162.6225pt too wide) in paragraph at lines 2323--2324 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.download_analyzer_by_experiment_rece ipt\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 2324--2325 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.gaussian_distribution\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2325--2326 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.hiv_analyzer\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2326--2327 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.hiv_calib_site\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2327--2328 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.population_obs\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2329--2330 []\T1/pcr/m/n/10 hiv_workflow.lib.calibration.algorithms\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 2330--2331 []\T1/pcr/m/n/10 hiv_workflow.lib.calibration.algorithms.optim_tool\T1/ptm/m/n/ 10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2334--2335 []\T1/pcr/m/n/10 hiv_workflow.lib.utils.builders.demographics\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2335--2336 []\T1/pcr/m/n/10 hiv_workflow.lib.utils.builders.general\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 2342--2343 []\T1/pcr/m/n/10 hiv_workflow.scripts.available_parameters\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2345--2346 []\T1/pcr/m/n/10 hiv_workflow.scripts.dtk_post_process\T1/ptm/m/n/10 , [37] (./institute-for-disease-modeling-hiv-workflow.ind [38] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/pcr/m/n/10 add_beta_parameters() Overfull \hbox (55.26955pt too wide) in paragraph at lines 8--10 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution.Bet aDistribution Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/pcr/m/n/10 add_ingest_form_to_assets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (57.48955pt too wide) in paragraph at lines 12--14 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.Bas eDistribution Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (55.26955pt too wide) in paragraph at lines 14--16 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution.Bet aDistribution Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (93.05922pt too wide) in paragraph at lines 16--18 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.gaussian_distribution .GaussianDistribution Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (41.53049pt too wide) in paragraph at lines 18--20 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.population_obs.Popula tionObs Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 add_post_channel_config_as_asset() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Overfull \hbox (87.43051pt too wide) in paragraph at lines 22--24 []\T1/pcr/m/n/10 adjust_years() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.li b.analysis.population_obs.PopulationObs Overfull \hbox (93.42992pt too wide) in paragraph at lines 27--29 []\T1/pcr/m/n/10 AGGREGATED_NODE \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.l ib.analysis.population_obs.PopulationObs Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 AGGREGATED_NODE_MAP Overfull \hbox (21.7002pt too wide) in paragraph at lines 29--31 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_analyzer.HIVAnaly zer Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 AGGREGATED_PROVINCE Overfull \hbox (41.53049pt too wide) in paragraph at lines 31--33 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.population_obs.Popula tionObs Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 ALL \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis. age_bin.AgeBin at- Overfull \hbox (24.8404pt too wide) in paragraph at lines 35--37 []\T1/pcr/m/n/10 ALLOWED_TYPES \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib .analysis.channel.Channel Overfull \hbox (1.23058pt too wide) in paragraph at lines 38--40 []\T1/pcr/m/n/10 apply() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analy sis.condition.Condition Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 available_algorithms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 45--47 []\T1/pcr/m/n/10 BaseDistribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 45--47 \T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution\T1/ptm/m/n/10 ), Overfull \hbox (42.6225pt too wide) in paragraph at lines 47--48 []\T1/pcr/m/n/10 BaseDistribution.UnknownDistributionException\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 48--50 []\T1/pcr/m/n/10 BetaDistribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 48--50 \T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution\T1/ptm/m/n/10 ), Overfull \hbox (42.6225pt too wide) in paragraph at lines 50--51 []\T1/pcr/m/n/10 BetaDistribution.InvalidCountChannelException\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 51--52 []\T1/pcr/m/n/10 BetaDistribution.InvalidEffectiveCountException\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 55--57 []\T1/pcr/m/n/10 can_upsample_bins() Underfull \hbox (badness 10000) in paragraph at lines 55--57 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.age_bin.AgeBin Overfull \hbox (106.3904pt too wide) in paragraph at lines 59--61 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.an alysis.data_frame_wrapper.DataFrameWrapper Overfull \hbox (73.38957pt too wide) in paragraph at lines 61--63 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.base_distribution.BaseDistribution Overfull \hbox (71.16957pt too wide) in paragraph at lines 63--65 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.beta_distribution.BetaDistribution Overfull \hbox (108.95924pt too wide) in paragraph at lines 65--67 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.gaussian_distribution.GaussianDistribution Overfull \hbox (37.60022pt too wide) in paragraph at lines 67--69 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.hiv_analyzer.HIVAnalyzer Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/pcr/m/n/10 compute_num_cores() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at 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[9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 533--536 \T1/pcr/m/n/10 config_builder(schema_path, max_memory_mb=None, demographics_pat hs=None, Underfull \hbox (badness 10000) in paragraph at lines 549--551 \T1/pcr/m/n/10 def build_demographics(manifest, params_to_modify=None, dry_run= False, [13] Underfull \hbox (badness 10000) in paragraph at lines 564--566 \T1/pcr/m/n/10 def build_campaign(schema_path, params_to_modify=None, dry_run=F alse, (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 807--807 []\T1/ptm/m/it/10 dfw: [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.data_frame_ wrapper.DataFrameWrapper[][], Underfull \hbox (badness 7256) in paragraph at lines 807--807 \T1/ptm/m/it/10 chan-nel: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 weight_ch annel: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ad-di-tional_keep: List[[][] str[][]]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (55.16237pt too wide) in paragraph at lines 840--840 []\T1/ptm/m/it/10 dfw: [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.data_frame_ wrapper.DataFrameWrapper[][], [16] Overfull \hbox (74.911pt too wide) in paragraph at lines 854--854 []\T1/ptm/m/it/10 distribution_name: [][]str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n /10 !$ [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.BaseDist ribution[][] Underfull \hbox (badness 10000) in paragraph at lines 866--866 []\T1/ptm/m/it/10 uncertainty_channel: [][]str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m /n/10 !$ Overfull \hbox (43.2821pt too wide) in paragraph at lines 866--866 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.BaseDistributio n[][] [17] Overfull \hbox (27.48462pt too wide) in paragraph at lines 1049--1049 []\T1/ptm/m/it/10 filename=None\T1/ptm/m/n/10 , Overfull \hbox (34.56456pt too wide) in paragraph at lines 1049--1049 \T1/ptm/m/it/10 dataframe=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1049--1049 \T1/ptm/m/it/10 strat-i- Overfull \hbox (14.22461pt too wide) in paragraph at lines 1049--1049 \T1/ptm/m/it/10 fiers=None\T1/pcr/m/n/10 ) [18] [19] Overfull \hbox (153.51465pt too wide) in paragraph at lines 1178--1178 []\T1/ptm/m/it/10 filenames\T1/ptm/m/n/10 , Overfull \hbox (129.35486pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 out- Overfull \hbox (151.3048pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 put_path\T1/ptm/m/n/10 , Overfull \hbox (208.60439pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 use_run_number=True\T1/ptm/m/n/10 , Overfull \hbox (217.45421pt too wide) in paragraph at lines 1178--1178 \T1/ptm/m/it/10 use_sample_index=True\T1/pcr/m/n/10 ) Overfull \hbox (243.51465pt too wide) in paragraph at lines 1262--1262 []\T1/ptm/m/it/10 filenames\T1/ptm/m/n/10 , Overfull \hbox (214.53479pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 re- Overfull \hbox (242.40451pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 ceipt_file\T1/ptm/m/n/10 , Overfull \hbox (298.60439pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 use_run_number=True\T1/ptm/m/n/10 , Overfull \hbox (307.45421pt too wide) in paragraph at lines 1262--1262 \T1/ptm/m/it/10 use_sample_index=True\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1263--1264 \T1/ptm/m/n/10 Bases: [][]\T1/pcr/m/sl/10 hiv_workflow.lib.analysis.download_an alyzer_by_experiment. 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[21] Underfull \hbox (badness 10000) in paragraph at lines 1495--1495 []\T1/ptm/m/it/10 filename=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1495--1495 \T1/ptm/m/it/10 dataframe=None\T1/ptm/m/n/10 , [22] Underfull \hbox (badness 10000) in paragraph at lines 1613--1613 []\T1/ptm/m/it/10 subparsers\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1619--1619 []\T1/ptm/m/it/10 args\T1/ptm/m/n/10 , \T1/ptm/m/it/10 params\T1/ptm/m/n/10 , Overfull \hbox (22.9846pt too wide) in paragraph at lines 1640--1640 []\T1/ptm/m/it/10 demographics: Overfull \hbox (227.81337pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (107.11305pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_commercial=None\T1/ptm/m/n/10 , Overfull \hbox (94.72316pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_informal=None\T1/ptm/m/n/10 , Overfull \hbox (89.72316pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_marital=None\T1/ptm/m/n/10 , Overfull \hbox (103.07301pt too wide) in paragraph at lines 1640--1640 \T1/ptm/m/it/10 risk_assortivity_transitory=None\T1/pcr/m/n/10 ) [23] Overfull \hbox (46.9846pt too wide) in paragraph at lines 1646--1646 []\T1/ptm/m/it/10 demographics: Overfull \hbox (251.81337pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (210.18271pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 max_relationships_commercial_high_risk_male=None\T1/ptm/m/n/10 , Overfull \hbox (217.40254pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 max_relationships_commercial_high_risk_female=None\T1/ptm/m/n/1 0 , Overfull \hbox (9.0149pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 prob- Underfull \hbox 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max_relationships_commercial_medium_risk_female=None\T1/ptm/m/n /10 , Overfull \hbox (9.0149pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 prob- Underfull \hbox (badness 10000) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 a- Overfull \hbox (1.13475pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 bil- Overfull \hbox (238.71233pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 ity_extra_relationship_commercial_medium_risk_male=None\T1/ptm/ m/n/10 , Overfull \hbox (9.0149pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 prob- Underfull \hbox (badness 10000) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 a- Overfull \hbox (1.13475pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 bil- Overfull \hbox (245.93216pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 ity_extra_relationship_commercial_medium_risk_female=None\T1/pt m/m/n/10 , Overfull \hbox (206.85263pt too wide) in paragraph at lines 1646--1646 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paragraph at lines 1646--1646 \T1/ptm/m/it/10 prob- Underfull \hbox (badness 10000) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 a- Overfull \hbox (1.13475pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 bil- Overfull \hbox (233.54227pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 ity_extra_relationship_informal_medium_risk_female=None\T1/ptm/ m/n/10 , Overfull \hbox (194.46274pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 max_relationships_informal_low_risk_male=None\T1/ptm/m/n/10 , Overfull \hbox (201.68257pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 max_relationships_informal_low_risk_female=None\T1/ptm/m/n/10 , Overfull \hbox (9.0149pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 prob- Underfull \hbox (badness 10000) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 a- Overfull \hbox (1.13475pt too wide) in paragraph at lines 1646--1646 \T1/ptm/m/it/10 bil- Overfull \hbox (209.11247pt too wide) in paragraph 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(29.01491pt too wide) in paragraph at lines 1664--1664 \T1/ptm/m/it/10 con- Overfull \hbox (155.71391pt too wide) in paragraph at lines 1664--1664 \T1/ptm/m/it/10 dom_usage_rate_transitory=None\T1/pcr/m/n/10 ) Overfull \hbox (21.24503pt too wide) in paragraph at lines 1664--1664 \OMS/cmsy/m/n/10 !$ Overfull \hbox (32.90492pt too wide) in paragraph at lines 1664--1664 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (46.9846pt too wide) in paragraph at lines 1670--1670 []\T1/ptm/m/it/10 demographics: Overfull \hbox (251.81337pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (7.23488pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 com- Overfull \hbox (5.92482pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 mer- Overfull \hbox (125.63351pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 cial_weibull_heterogeneity=None\T1/ptm/m/n/10 , Overfull \hbox (7.23488pt 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\hbox (97.01385pt too wide) in paragraph at lines 1670--1670 \T1/ptm/m/it/10 tory_weibull_scale=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1670--1670 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.90492pt too wide) in paragraph at lines 1670--1670 [][]\T1/ptm/m/n/10 None[][] [26] Overfull \hbox (64.9846pt too wide) in paragraph at lines 1676--1676 []\T1/ptm/m/it/10 demographics: Overfull \hbox (269.81337pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 emodpy_hiv.demographics.HIVDemographics.HIVDemographics\T1/ptm/ m/n/10 , Overfull \hbox (19.13475pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 ini- Overfull \hbox (112.84337pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 tial_risk_distribution_low: Overfull \hbox (23.0249pt too wide) in paragraph at lines 1676--1676 [][]\T1/ptm/m/it/10 float[][] Overfull \hbox (11.99501pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 = Overfull \hbox (32.35487pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 None\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1676--1676 \OMS/cmsy/m/n/10 !$ Overfull \hbox (26.90492pt too wide) in paragraph at lines 1676--1676 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (63.42361pt too wide) in paragraph at lines 1693--1693 []\T1/ptm/m/it/10 parameter_setting_functions: Overfull \hbox (4.98395pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 ex- Overfull \hbox (38.09406pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/it/10 pected_first_argument: Underfull \hbox (badness 10000) in paragraph at lines 1693--1693 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (1.62408pt too wide) in paragraph at lines 1693--1693 \T1/ptm/m/n/10 Dict[Callable, Underfull \hbox (badness 5985) in paragraph at lines 1699--1700 []\T1/pcr/b/n/10 parameter_setting_functions \T1/ptm/m/n/10 ^^U a list of func- tion ref-er-ences that pro- [27] Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 set-ting_functions : Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 func- Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 \T1/ptm/m/it/10 tion_arguments: Underfull \hbox (badness 10000) in paragraph at lines 1719--1719 \T1/ptm/m/it/10 Dict[Callable, List]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [28] Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 []\T1/ptm/m/it/10 year\T1/ptm/m/n/10 , \T1/ptm/m/it/10 obs_population\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 low_age=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 high_age=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 age_bin=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 year_col=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Year\TS1/ptm/m/it/10 '\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u- Underfull \hbox (badness 10000) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 la-tion_col=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Population\TS1/pt m/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1923--1923 []\T1/ptm/m/it/10 ingest_filename: Underfull \hbox (badness 10000) in paragraph at lines 1923--1923 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ \T1/ptm/m/n/10 Tu-ple[[][]dict[][], Overfull \hbox (128.51247pt too wide) in paragraph at lines 1923--1923 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite[][]\T 1/ptm/m/n/10 ] [29] Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 []\T1/ptm/m/it/10 wb: open- Overfull \hbox (60.96397pt too wide) in paragraph at lines 1934--1934 \T1/ptm/m/it/10 pyxl.workbook.workbook.Workbook\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 \T1/ptm/m/it/10 sheet_name: Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 [][]\T1/ptm/m/it/10 str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 wb_path: Underfull \hbox (badness 10000) in paragraph at lines 1934--1934 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ \T1/ptm/m/n/10 open- Overfull \hbox (64.94374pt too wide) in paragraph at lines 1934--1934 \T1/ptm/m/n/10 pyxl.worksheet.worksheet.Worksheet Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 []\T1/ptm/m/it/10 filename: Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 [][]\T1/ptm/m/it/10 str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ \T1/ptm/m/n/10 Tu- Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 \T1/ptm/m/n/10 ple[List[[][]dict[][]], Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 [][]\T1/ptm/m/n/10 dict[][], Overfull \hbox (169.82304pt too wide) in paragraph at lines 1947--1947 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][]\ T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1947--1947 \T1/ptm/m/n/10 List[[][]dict[][]], Overfull \hbox (136.29294pt too wide) in paragraph at lines 1947--1947 \T1/ptm/m/n/10 List[[][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.channel.Chann el[][]\T1/ptm/m/n/10 ]] Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 []\T1/ptm/m/it/10 task: [][]idm- Overfull \hbox (37.77344pt too wide) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 chan-nels: Overfull \hbox (136.20297pt too wide) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 List[[][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.channel.Chann el[][]\T1/ptm/m/it/10 ]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 ref-er- Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 ence_data: Overfull \hbox (170.10309pt too wide) in paragraph at lines 1961--1961 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][], Underfull \hbox (badness 10000) in paragraph at lines 1961--1961 \T1/ptm/m/it/10 site_info: [30] Underfull \hbox (badness 10000) in paragraph at lines 2008--2008 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 2008--2008 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2040--2040 \T1/ptm/m/it/10 path: [][]str[][]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [][]\T1/ ptm/m/n/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 2062--2062 []\T1/ptm/m/it/10 simulation: [][]idm- Overfull \hbox (41.153pt too wide) in paragraph at lines 2062--2062 \T1/ptm/m/it/10 tools.entities.simulation.Simulation[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2062--2062 \T1/ptm/m/it/10 sam-ple: [][]dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2062--2062 \T1/ptm/m/it/10 mo-graph-ics_builder: Underfull \hbox (badness 10000) in paragraph at lines 2072--2073 []\T1/pcr/b/n/10 sample \T1/ptm/m/n/10 ^^U dict of pa-ram-e-ter names/values ov er-rides to use dur-ing con- [31] Underfull \hbox (badness 10000) in paragraph at lines 2102--2102 []\T1/ptm/m/it/10 sample: [][]dict[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cus- Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 []\T1/ptm/m/it/10 executable_path: [][]str[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 schema_path: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph-ics_builder: Underfull \hbox (badness 7963) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 ics_paths: List[[][]str[][]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 python_processing_setter: Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 Callable = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 chan-nels: Overfull \hbox (55.70297pt too wide) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 List[[][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.channel.Chann el[][]\T1/ptm/m/it/10 ] Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ref-er-ence: Overfull \hbox (89.60309pt too wide) in paragraph at lines 2125--2125 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][] Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 site_info: Underfull \hbox (badness 10000) in paragraph at lines 2125--2125 [][]\T1/ptm/m/it/10 dict[][] = None\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [32] Underfull \hbox (badness 10000) in paragraph at lines 2209--2209 []\T1/ptm/m/it/10 algorithm_name: [][]str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 a l- Underfull \hbox (badness 10000) in paragraph at lines 2209--2209 \T1/ptm/m/it/10 go-rithm_root: [][]str[][] = Overfull \hbox (0.70457pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/it/10 config_builder: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 [][]\T1/ptm/m/it/10 str[][]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 kwargs: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (13.66457pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 max_memory_mb: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 [][]\T1/ptm/m/it/10 int[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 ics_paths: Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 List[[][]str[][]] Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 5681) in paragraph at lines 2250--2250 \T1/ptm/m/it/10 = False\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [33] Overfull \hbox (27.70444pt too wide) in paragraph at lines 2256--2256 []\T1/ptm/m/it/10 campaign_builder: Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (7.1947pt too wide) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 2256--2256 \T1/ptm/m/it/10 False\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ Overfull \hbox (68.67427pt too wide) in paragraph at lines 2262--2262 []\T1/ptm/m/it/10 demographics_builder: Overfull \hbox (12.19455pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 man- Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 i-fest: Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 mod- Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 ule\T1/ptm/m/n/10 , Overfull \hbox (7.0946pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 kwargs: Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (10.7947pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 [][]\T1/ptm/m/it/10 bool[][] Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 = Overfull \hbox (2.71472pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/it/10 False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 2262--2262 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.57443pt too wide) in paragraph at lines 2262--2262 \T1/ptm/m/n/10 Callable Overfull \hbox (66.70457pt too wide) in paragraph at lines 2268--2268 []\T1/ptm/m/it/10 config_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (25.23488pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 cam- Overfull \hbox (65.04453pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 paign_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (18.01491pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 de- Overfull \hbox (20.79494pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 mo- Overfull \hbox (32.31496pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 graph- Overfull \hbox (53.37436pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 ics_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (22.31496pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 ran- Overfull \hbox (80.23463pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/it/10 dom_run_number: Overfull \hbox (29.0249pt too wide) in paragraph at lines 2268--2268 [][]\T1/ptm/m/it/10 bool[][]\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 2268--2268 \OMS/cmsy/m/n/10 !$ Overfull \hbox (24.13475pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/n/10 idm- Overfull \hbox (207.823pt too wide) in paragraph at lines 2268--2268 \T1/ptm/m/n/10 tools_calibra.calib_manager.SampleIndexWrapper [34] Overfull \hbox (13.1938pt too wide) in paragraph at lines 2274--2274 []\T1/ptm/m/it/10 custom_sample_constrainer: Underfull \hbox (badness 7759) in paragraph at lines 2280--2280 []\T1/ptm/m/it/10 pre: [][]str[][] Underfull \hbox (badness 10000) in paragraph at lines 2280--2280 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2280--2280 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , [35] [36] Overfull \hbox (30.6225pt too wide) in paragraph at lines 2317--2318 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.base_distribution\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2318--2319 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.beta_distribution\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2321--2322 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.data_frame_wrapper\T1/ptm/m/n/10 , Overfull \hbox (114.6225pt too wide) in paragraph at lines 2322--2323 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.download_analyzer_by_experiment\T1/p tm/m/n/10 , Overfull \hbox (162.6225pt too wide) in paragraph at lines 2323--2324 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.download_analyzer_by_experiment_rece ipt\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 2324--2325 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.gaussian_distribution\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2325--2326 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.hiv_analyzer\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2326--2327 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.hiv_calib_site\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 2327--2328 []\T1/pcr/m/n/10 hiv_workflow.lib.analysis.population_obs\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2329--2330 []\T1/pcr/m/n/10 hiv_workflow.lib.calibration.algorithms\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 2330--2331 []\T1/pcr/m/n/10 hiv_workflow.lib.calibration.algorithms.optim_tool\T1/ptm/m/n/ 10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2334--2335 []\T1/pcr/m/n/10 hiv_workflow.lib.utils.builders.demographics\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2335--2336 []\T1/pcr/m/n/10 hiv_workflow.lib.utils.builders.general\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 2342--2343 []\T1/pcr/m/n/10 hiv_workflow.scripts.available_parameters\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2345--2346 []\T1/pcr/m/n/10 hiv_workflow.scripts.dtk_post_process\T1/ptm/m/n/10 , [37] (./institute-for-disease-modeling-hiv-workflow.ind [38] Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/pcr/m/n/10 add_beta_parameters() Overfull \hbox (55.26955pt too wide) in paragraph at lines 8--10 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution.Bet aDistribution Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/pcr/m/n/10 add_ingest_form_to_assets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (57.48955pt too wide) in paragraph at lines 12--14 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.Bas eDistribution Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (55.26955pt too wide) in paragraph at lines 14--16 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution.Bet aDistribution Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (93.05922pt too wide) in paragraph at lines 16--18 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.gaussian_distribution .GaussianDistribution Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 add_percentile_values() Overfull \hbox (41.53049pt too wide) in paragraph at lines 18--20 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.population_obs.Popula tionObs Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 add_post_channel_config_as_asset() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Overfull \hbox (87.43051pt too wide) in paragraph at lines 22--24 []\T1/pcr/m/n/10 adjust_years() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.li b.analysis.population_obs.PopulationObs Overfull \hbox (93.42992pt too wide) in paragraph at lines 27--29 []\T1/pcr/m/n/10 AGGREGATED_NODE \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.l ib.analysis.population_obs.PopulationObs Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 AGGREGATED_NODE_MAP Overfull \hbox (21.7002pt too wide) in paragraph at lines 29--31 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_analyzer.HIVAnaly zer Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 AGGREGATED_PROVINCE Overfull \hbox (41.53049pt too wide) in paragraph at lines 31--33 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.population_obs.Popula tionObs Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/pcr/m/n/10 ALL \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis. age_bin.AgeBin at- Overfull \hbox (24.8404pt too wide) in paragraph at lines 35--37 []\T1/pcr/m/n/10 ALLOWED_TYPES \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib .analysis.channel.Channel Overfull \hbox (1.23058pt too wide) in paragraph at lines 38--40 []\T1/pcr/m/n/10 apply() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analy sis.condition.Condition Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 available_algorithms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 45--47 []\T1/pcr/m/n/10 BaseDistribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 45--47 \T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution\T1/ptm/m/n/10 ), Overfull \hbox (42.6225pt too wide) in paragraph at lines 47--48 []\T1/pcr/m/n/10 BaseDistribution.UnknownDistributionException\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 48--50 []\T1/pcr/m/n/10 BetaDistribution \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 48--50 \T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution\T1/ptm/m/n/10 ), Overfull \hbox (42.6225pt too wide) in paragraph at lines 50--51 []\T1/pcr/m/n/10 BetaDistribution.InvalidCountChannelException\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 51--52 []\T1/pcr/m/n/10 BetaDistribution.InvalidEffectiveCountException\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 55--57 []\T1/pcr/m/n/10 can_upsample_bins() Underfull \hbox (badness 10000) in paragraph at lines 55--57 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.age_bin.AgeBin Overfull \hbox (106.3904pt too wide) in paragraph at lines 59--61 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.an alysis.data_frame_wrapper.DataFrameWrapper Overfull \hbox (73.38957pt too wide) in paragraph at lines 61--63 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.base_distribution.BaseDistribution Overfull \hbox (71.16957pt too wide) in paragraph at lines 63--65 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.beta_distribution.BetaDistribution Overfull \hbox (108.95924pt too wide) in paragraph at lines 65--67 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.gaussian_distribution.GaussianDistribution Overfull \hbox (37.60022pt too wide) in paragraph at lines 67--69 []\T1/pcr/m/n/10 compare() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.ana lysis.hiv_analyzer.HIVAnalyzer Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/pcr/m/n/10 compute_num_cores() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 71--73 []\T1/pcr/m/n/10 compute_pop_scaling_factor() Overfull \hbox (21.7002pt too wide) in paragraph at lines 71--73 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_analyzer.HIVAnaly zer Underfull \hbox (badness 10000) in paragraph at lines 73--75 []\T1/pcr/m/n/10 Condition \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 75--77 []\T1/pcr/m/n/10 constrain_sample() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/pcr/m/n/10 constrain_sample_wrapper() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 79--81 []\T1/pcr/m/n/10 construct_beta_channel() Overfull \hbox (55.26955pt too wide) in paragraph at lines 79--81 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 hiv_workflow.lib.analysis.beta_distribution.Bet aDistribution [39] Underfull \hbox (badness 10000) in paragraph at lines 81--83 []\T1/pcr/m/n/10 construct_gaussian_channel() 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