Read the Docs build information Build id: 857890 Project: institute-for-disease-modeling-hiv-workflow Version: latest Commit: 8dbc330c7f9678a6440baa1f870d31f072d68e83 Date: 2022-02-17T18:00:35.752307Z State: finished Success: True [rtd-command-info] start-time: 2022-02-17T18:00:38.392183Z, end-time: 2022-02-17T18:00:42.804713Z, duration: 4, 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: 2022-02-17T18:00:42.994591Z, end-time: 2022-02-17T18:00:44.161608Z, duration: 1, exit-code: 0 git checkout --force origin/main Note: checking out '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 performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 8dbc330 Merge pull request #56 from JSchripsema-IDM/rtd [rtd-command-info] start-time: 2022-02-17T18:00:44.333698Z, end-time: 2022-02-17T18:00:44.425298Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-02-17T18:00:46.045267Z, end-time: 2022-02-17T18:00:51.773014Z, duration: 5, 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. [rtd-command-info] start-time: 2022-02-17T18:00:51.944065Z, end-time: 2022-02-17T18:00:53.828388Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (22.0.3) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 KB 27.0 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 60.9.2 Uninstalling setuptools-60.9.2: Successfully uninstalled setuptools-60.9.2 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-02-17T18:00:54.018368Z, end-time: 2022-02-17T18:01:03.417765Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2 setuptools<58.3.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 KB 16.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 143.8 MB/s eta 0:00:00 Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 KB 178.8 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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eta 0:00:00 Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 KB 192.2 MB/s eta 0:00:00 Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.7-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.0/98.0 KB 204.3 MB/s eta 0:00:00 Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=29d8159e4ebd02931bd62896ac990d7ff1ffd5b94bf451d24c96f0ce53e22804 Stored in directory: /tmp/pip-ephem-wheel-cache-yjak1y4k/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=247ead2a67bf4805e15d7b60d7644d0067b1ec1e22a016afe1d488883458375d Stored in directory: /tmp/pip-ephem-wheel-cache-yjak1y4k/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 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-2.0.1 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: 2022-02-17T18:01:03.595817Z, end-time: 2022-02-17T18:01:41.949234Z, duration: 38, 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 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/idmtools-calibra/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting idmtools_calibra~=1.0.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-calibra/1.0.5/idmtools_calibra-1.0.5-py3-none-any.whl (134 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 134.2/134.2 KB 6.3 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/emodpy-hiv/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting emodpy-hiv~=1.0.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy-hiv/1.0.2/emodpy_hiv-1.0.2-py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.3/46.3 KB 142.2 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/openpyxl/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting openpyxl Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1c/a6/8ce4d2ef2c29be3235c08bb00e0b81e29d38ebc47d82b17af681bf662b74/openpyxl-3.0.9-py2.py3-none-any.whl (242 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 242.2/242.2 KB 18.5 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/lz4/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting lz4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/65/3f/6eea2d108b7ba550e91798855b8ef3b9b8dcd5fe377e70ab29e7d7196a4e/lz4-4.0.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 17.7 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/idmtools/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting idmtools~=1.6.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.6.4/idmtools-1.6.4-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.0/163.0 KB 20.4 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/seaborn/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting seaborn~=0.11.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/5b/0479d7d845b5ba410ca702ffcd7f2cd95a14a4dfff1fde2637802b258b9b/seaborn-0.11.2-py3-none-any.whl (292 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 292.8/292.8 KB 19.4 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/geopy/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting geopy~=2.0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/07/e1/9c72de674d5c2b8fcb0738a5ceeb5424941fefa080bfe4e240d0bacb5a38/geopy-2.0.0-py3-none-any.whl (111 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 111.9/111.9 KB 197.5 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/fasteners/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting fasteners~=0.15 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f6/01/274da83334c20dc1ae7a48b1ea4ae50d3571d4e6aea65bb0368f841701ad/fasteners-0.17.3-py3-none-any.whl (18 kB) Requirement already satisfied: numpy!=1.19.4 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (1.19.2) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/statsmodels/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting statsmodels~=0.12.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/da/69/8eef30a6237c54f3c0b524140e2975f4b1eea3489b45eb3339574fc8acee/statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 18.1 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/sklearn/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting sklearn~=0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1e/7a/dbb3be0ce9bd5c8b7e3d87328e79063f8b263b2b1bfa4774cb1147bfcd3f/sklearn-0.0.tar.gz (1.1 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/scipy/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting scipy~=1.5.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/dc/7e/8f6a79b102ca1ea928bae8998b05bf5dc24a90571db13cd119f275ba6252/scipy-1.5.4-cp37-cp37m-manylinux1_x86_64.whl (25.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.9/25.9 MB 18.0 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/emodpy/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting emodpy~=1.15 Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.17.1/emodpy-1.17.1-py3-none-any.whl (116 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 116.8/116.8 KB 188.0 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/emod-hiv/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting emod-hiv==0.0.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-hiv/0.0.4/emod_hiv-0.0.4-py3-none-any.whl (44.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.0/44.0 MB 17.7 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/et-xmlfile/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting et-xmlfile Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/96/c2/3dd434b0108730014f1b96fd286040dc3bcb70066346f7e01ec2ac95865f/et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/astor/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/emod-api/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting emod-api<2.0,>=1.20 Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-api/1.21.1/emod_api-1.21.1-py3-none-any.whl (128 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 128.5/128.5 KB 185.9 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/idmtools-platform-comps/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting idmtools-platform-comps~=1.6.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-platform-comps/1.6.4/idmtools_platform_comps-1.6.4-py3-none-any.whl (177 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 177.1/177.1 KB 21.3 MB/s eta 0:00:00 Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (3.3.2) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/keyring/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting keyring Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0d/bb/8e715dbb1886e6d7e4c6a7024c11a7e137559cd85366f25c67c2bdb311c3/keyring-23.5.0-py3-none-any.whl (33 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/click/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting click~=7.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 82.8/82.8 KB 179.8 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/idmtools-models/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting idmtools-models~=1.6.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.6.4/idmtools_models-1.6.4-py3-none-any.whl (24 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/bs4/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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' warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/astunparse/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/geographiclib/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting geographiclib<2,>=1.49 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/df/60/d1d4c4944f9726228faa80fbe2206c8ddfd9757791b2de2facb8818c5d74/geographiclib-1.52-py3-none-any.whl (38 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pipreqs/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pyyaml/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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 20.9 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pygit2/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pygit2<1.6.0,>=1.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/98/ed/41a09ca93374015958a18e37280d02c833238272ce3f2e28b10c6253477d/pygit2-1.5.0-cp37-cp37m-manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 17.9 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pandas/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 17.9 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/tqdm/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting tqdm<5,>=4.52.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/63/f3/b7a1b8e40fd1bd049a34566eb353527bb9b8e9b98f8b6cf803bb64d8ce95/tqdm-4.62.3-py2.py3-none-any.whl (76 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.2/76.2 KB 173.2 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/more-itertools/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting more-itertools~=8.8.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5f/3c/e3ee43177a86b448c3fea1d090238c365ea1a80f015836a8a18fbbaccd63/more_itertools-8.8.0-py3-none-any.whl (48 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.8/48.8 KB 142.9 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pluggy/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pluggy~=0.13.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl (18 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/diskcache/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting diskcache~=5.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6a/5e/3deb8f9c83bead2af6f2cda97c4400516488464fede2853875a81e502953/diskcache-5.2.1-py3-none-any.whl (44 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.6/44.6 KB 143.1 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/coloredlogs/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting coloredlogs~=15.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 KB 143.7 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/tabulate/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting tabulate<0.9,>=0.8.9 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ca/80/7c0cad11bd99985cfe7c09427ee0b4f9bd6b048bd13d4ffb32c6db237dfb/tabulate-0.8.9-py3-none-any.whl (25 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/backoff/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. 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) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/packaging/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting packaging<21.0,>=20.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/89/7ea760b4daa42653ece2380531c90f64788d979110a2ab51049d92f408af/packaging-20.9-py2.py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.9/40.9 KB 143.4 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/scikit-learn/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting scikit-learn Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/bd/05/e561bc99a615b5c099c7a9355409e5e57c525a108f1c2e156abb005b90a6/scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.8/24.8 MB 18.1 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/patsy/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting patsy>=0.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/87/7f/d37cd027c25145eeba92b1a756976931c831803d92547c8637a3400c339f/patsy-0.5.2-py2.py3-none-any.whl (233 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.7/233.7 KB 27.5 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/humanfriendly/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting humanfriendly>=9.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl (86 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 KB 177.8 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pyproj/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pyproj Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/57/4648d607dd92d09e9a685a8cc20adeafb0c49ed61397bd77c85392a5eb05/pyproj-3.2.1-cp37-cp37m-manylinux2010_x86_64.whl (6.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 18.1 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/prodict/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting prodict Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5a/0b/594c85ac539dda877198e7d5541982127d0929e3b0e8e6018004cfbd9ac9/prodict-0.8.18.tar.gz (4.2 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/shapely/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting shapely Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9b/c6/22f2ca71d1cc44e36ccba8b8f2ea98d888d5c27bdcfacbada1128b1b1cc1/Shapely-1.8.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 18.6 MB/s eta 0:00:00 Requirement already satisfied: jinja2~=3.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from idmtools-models~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (3.0.3) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pytest-lazy-fixture/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pytest-lazy-fixture~=0.6.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2d/a1/2f2c1c2353350d66c4d110d283e422e4943eb5ad10effa9357ba66f7b5b9/pytest_lazy_fixture-0.6.3-py3-none-any.whl (4.9 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pycomps/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pyCOMPS~=2.5.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/pyCOMPS/2.5.0/pyCOMPS-2.5.0-py2.py3-none-any.whl (56 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.1/56.1 KB 138.3 MB/s eta 0:00:00 Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from matplotlib->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (3.0.7) Requirement already satisfied: python-dateutil>=2.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (2.8.1) Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (0.10.0) Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from matplotlib->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (2021.10.8) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (1.2.0) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pillow/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pillow>=6.2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c3/56/bdf1b802e111050e3fe11150e09d2e220478cf5af4256e7fa628663fa08f/Pillow-9.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 18.1 MB/s eta 0:00:00 Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from pandas<1.2,>=1.1.4->idmtools~=1.6.0->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (2021.3) Requirement already satisfied: six in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from patsy>=0.5->statsmodels~=0.12.1->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (1.15.0) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/yarg/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting yarg Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8b/90/89a2ff242ccab6a24fbab18dbbabc67c51a6f0ed01f9a0f41689dc177419/yarg-0.1.9-py2.py3-none-any.whl (19 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/docopt/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting docopt Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: importlib-metadata>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from pluggy~=0.13.1->idmtools~=1.6.0->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (4.11.1) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/cached-property/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting cached-property Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/48/19/f2090f7dad41e225c7f2326e4cfe6fff49e57dedb5b53636c9551f86b069/cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/cffi/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting cffi>=1.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/44/6b/5edf93698ef1dc745774e47e26f5995040dd3604562dd63f5959fcd3a49e/cffi-1.15.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (427 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 427.1/427.1 KB 19.2 MB/s eta 0:00:00 Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from astunparse->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (0.37.1) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/beautifulsoup4/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting beautifulsoup4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/69/bf/f0f194d3379d3f3347478bd267f754fc68c11cbf2fe302a6ab69447b1417/beautifulsoup4-4.10.0-py3-none-any.whl (97 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.4/97.4 KB 186.6 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/jeepney/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting jeepney>=0.4.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/14/b8/bb3e34d71472140f9bfdf5d77cd063e2cc964b72b1bb0b70fe3c1e7db932/jeepney-0.7.1-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 KB 98.0 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/secretstorage/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting SecretStorage>=3.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/1e/29cd69fdac7391aa51510dfd42aa70b4e6a826c8cd019ee2a8ab9ec0777f/SecretStorage-3.3.1-py3-none-any.whl (15 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/threadpoolctl/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting threadpoolctl>=2.0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/61/cf/6e354304bcb9c6413c4e02a747b600061c21d38ba51e7e544ac7bc66aecc/threadpoolctl-3.1.0-py3-none-any.whl (14 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/joblib/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting joblib>=0.11 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3e/d5/0163eb0cfa0b673aa4fe1cd3ea9d8a81ea0f32e50807b0c295871e4aab2e/joblib-1.1.0-py2.py3-none-any.whl (306 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 307.0/307.0 KB 15.3 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pycparser/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pycparser Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 KB 205.9 MB/s eta 0:00:00 Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=0.12->pluggy~=0.13.1->idmtools~=1.6.0->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (4.1.1) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=0.12->pluggy~=0.13.1->idmtools~=1.6.0->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (3.7.0) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from jinja2~=3.0.1->idmtools-models~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (2.0.1) Requirement already satisfied: future>=0.16.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (0.18.2) Requirement already satisfied: requests>=2.11.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (2.27.1) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/xdg/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting xdg>=4.0.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ea/09/4a0f30aada49e142b94bbb232c023abcbc6ced7e2a9776533fb14977e9db/xdg-5.1.1-py3-none-any.whl (5.0 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/pytest/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting pytest>=3.2.5 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/38/93/c7c0bd1e932b287fb948eb9ce5a3d6307c9fc619db1e199f8c8bc5dad95f/pytest-7.0.1-py3-none-any.whl (296 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 297.0/297.0 KB 14.7 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/cryptography/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting cryptography>=2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d8/0c/c0f8790bdeff9813722811500fd735c40a6c50fe0b4f8f6f4444f7a49cc0/cryptography-36.0.1-cp36-abi3-manylinux_2_24_x86_64.whl (3.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 12.7 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/soupsieve/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting soupsieve>1.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/72/a6/fd01694427f1c3fcadfdc5f1de901b813b9ac756f0806ef470cfed1de281/soupsieve-2.3.1-py3-none-any.whl (37 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/tomli/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting tomli>=1.0.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/97/75/10a9ebee3fd790d20926a90a2547f0bf78f371b2f13aa822c759680ca7b9/tomli-2.0.1-py3-none-any.whl (12 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/iniconfig/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting iniconfig Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9b/dd/b3c12c6d707058fa947864b67f0c4e0c39ef8610988d7baea9578f3c48f3/iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/attrs/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting attrs>=19.2.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/be/7abce643bfdf8ca01c48afa2ddf8308c2308b0c3b239a44e57d020afa0ef/attrs-21.4.0-py2.py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 KB 180.0 MB/s eta 0:00:00 warning: missing-index-doctype × The package index page being used does not have a proper HTML doctype declaration. ╰─> Problematic URL: https://packages.idmod.org/api/pypi/pypi-production/simple/py/ note: This is an issue with the page at the URL mentioned above. hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context. Collecting py>=1.8.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f6/f0/10642828a8dfb741e5f3fbaac830550a518a775c7fff6f04a007259b0548/py-1.11.0-py2.py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.7/98.7 KB 202.7 MB/s eta 0:00:00 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (1.26.8) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (3.3) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.11.1->pyCOMPS~=2.5.0->idmtools-platform-comps~=1.6.0->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (2.0.12) 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=b24bcab0e161a9e8d8d3de43e6d469114bce9548c84b7580374aef8e20a81a20 Stored in directory: /tmp/pip-ephem-wheel-cache-c0j0y78q/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=127ec66931307b9cbb46bfe11f4c84650bd0bdc201a98395149c64230ea45b97 Stored in directory: /tmp/pip-ephem-wheel-cache-c0j0y78q/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=904ebc88322311a0fd667cf3a73af5be7a9bd043791c9304764cd602e9f639bb Stored in directory: /tmp/pip-ephem-wheel-cache-c0j0y78q/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=56268dfa744ce45c83bde6e8fe77b8877c9a088b755ef925b7a40a55578f26ed Stored in directory: /tmp/pip-ephem-wheel-cache-c0j0y78q/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-1.21.1 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 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: 2022-02-17T18:01:42.143632Z, end-time: 2022-02-17T18:01:43.319862Z, 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 emod-api==1.21.1 Best match: emod-api 1.21.1 Adding emod-api 1.21.1 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-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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Shapely==1.8.1 Best match: Shapely 1.8.1 Adding Shapely 1.8.1 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 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 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 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 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 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 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 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 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 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 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 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 MarkupSafe==2.0.1 Best match: MarkupSafe 2.0.1 Adding MarkupSafe 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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 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 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 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 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 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 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 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 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 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 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 Finished processing dependencies for hiv-workflow==1.0.0 [rtd-command-info] start-time: 2022-02-17T18:01:43.496605Z, end-time: 2022-02-17T18:01:47.524596Z, duration: 4, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 110.2 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.1 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.9/2.9 MB 200.6 MB/s eta 0:00:00 Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting py-make Downloading py_make-0.1.1-py2.py3-none-any.whl (9.4 kB) Collecting sphinxext.remoteliteralinclude Downloading sphinxext_remoteliteralinclude-0.3.0-py3-none-any.whl (6.3 kB) Collecting sphinx-copybutton~=0.4.0 Downloading sphinx_copybutton-0.4.0-py3-none-any.whl (12 kB) Collecting docutils<0.17 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 KB 221.4 MB/s eta 0:00:00 Requirement already satisfied: six>=1.5.2 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 2)) (1.15.0) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (58.2.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (20.9) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.1.5) Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.3.0) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.2) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.27.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.9.1) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.2) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.2.0) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.3) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (3.0.3) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.11.2) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.0.1) Requirement already satisfied: docopt>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from py-make->-r docs/requirements.txt (line 6)) (0.6.2) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2021.3) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.1) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (3.3) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2021.10.8) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (1.26.8) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.12) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (3.0.7) Installing collected packages: py-make, pockets, docutils, sphinxcontrib-napoleon, sphinx, plantweb, sphinxext.remoteliteralinclude, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 4.4.0 Uninstalling Sphinx-4.4.0: Successfully uninstalled Sphinx-4.4.0 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 1.0.0 Uninstalling sphinx-rtd-theme-1.0.0: Successfully uninstalled sphinx-rtd-theme-1.0.0 Successfully installed docutils-0.16 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: 2022-02-17T18:01:48.734689Z, end-time: 2022-02-17T18:01:48.803241Z, 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': [ ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-hiv-workflow', 'name': u'hiv_workflow', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://institute-for-disease-modeling-hiv-workflow.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'hiv_workflow', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '8dbc330c', } # 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/857890/' 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: 2022-02-17T18:01:48.971475Z, end-time: 2022-02-17T18:01:58.335573Z, duration: 9, 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 37 source files that are out of date updating environment: [new config] 37 added, 0 changed, 0 removed reading sources... [ 2%] hiv_workflow reading sources... [ 5%] hiv_workflow.lib reading sources... [ 8%] hiv_workflow.lib.analysis reading sources... [ 10%] hiv_workflow.lib.analysis.age_bin reading sources... [ 13%] hiv_workflow.lib.analysis.base_distribution reading sources... [ 16%] hiv_workflow.lib.analysis.beta_distribution reading sources... [ 18%] hiv_workflow.lib.analysis.channel reading sources... [ 21%] hiv_workflow.lib.analysis.condition reading sources... [ 24%] hiv_workflow.lib.analysis.data_frame_wrapper reading sources... [ 27%] 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... [ 29%] hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt reading sources... [ 32%] hiv_workflow.lib.analysis.gaussian_distribution reading sources... 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[100%] modules 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: 2022-02-17T18:01:58.527705Z, end-time: 2022-02-17T18:02:03.549702Z, 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] 37 added, 0 changed, 0 removed reading sources... [ 2%] hiv_workflow reading sources... [ 5%] hiv_workflow.lib reading sources... [ 8%] hiv_workflow.lib.analysis reading sources... [ 10%] hiv_workflow.lib.analysis.age_bin reading sources... [ 13%] hiv_workflow.lib.analysis.base_distribution reading sources... [ 16%] hiv_workflow.lib.analysis.beta_distribution reading sources... [ 18%] hiv_workflow.lib.analysis.channel reading sources... [ 21%] hiv_workflow.lib.analysis.condition reading sources... [ 24%] hiv_workflow.lib.analysis.data_frame_wrapper reading sources... [ 27%] 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... [ 29%] hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt reading sources... [ 32%] hiv_workflow.lib.analysis.gaussian_distribution reading sources... 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[ 78%] hiv_workflow.scripts reading sources... [ 81%] hiv_workflow.scripts.available_parameters reading sources... [ 83%] hiv_workflow.scripts.calibrate reading sources... [ 86%] hiv_workflow.scripts.download reading sources... [ 89%] hiv_workflow.scripts.dtk_post_process reading sources... [ 91%] hiv_workflow.scripts.resample reading sources... [ 94%] hiv_workflow.scripts.run reading sources... [ 97%] index reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... 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: 2022-02-17T18:02:03.762971Z, end-time: 2022-02-17T18:02:05.417501Z, 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 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: 2022-02-17T18:02:05.749823Z, end-time: 2022-02-17T18:02:05.820876Z, 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: 2022-02-17T18:02:05.989820Z, end-time: 2022-02-17T18:02:07.893380Z, duration: 1, 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. 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[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. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [9] LaTeX Warning: Hyper reference `hiv_workflow.lib.analysis.data_frame_wrapper:hi v_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper' on page 10 undefin ed on input line 367. LaTeX Warning: Hyper reference `hiv_workflow.lib.analysis.data_frame_wrapper:hi v_workflow.lib.analysis.data_frame_wrapper.DataFrameWrapper' on page 10 undefin ed on input line 367. 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[][]\T1/ptm/m/n/10 None[][] Overfull \hbox (63.42361pt too wide) in paragraph at lines 1253--1253 []\T1/ptm/m/it/10 parameter_setting_functions: Overfull \hbox (4.98395pt too wide) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 ex- Overfull \hbox (38.09406pt too wide) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 pected_first_argument: Underfull \hbox (badness 10000) in paragraph at lines 1253--1253 [][]\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 1253--1253 \T1/ptm/m/n/10 Dict[Callable, Underfull \hbox (badness 5985) in paragraph at lines 1259--1260 []\T1/pcr/b/n/10 parameter_setting_functions \T1/ptm/m/n/10 ^^U a list of func- tion ref-er-ences that pro- [21] Underfull \hbox (badness 10000) in paragraph at lines 1279--1279 [][]\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 1388--1388 \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 23 undefined on input line 1483. 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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} Output written on institute-for-disease-modeling-hiv-workflow.pdf (35 pages, 17 0463 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 31 undefined on input line 1876 Reference `hiv_workflow.lib.analysis.base_distribution:module-hiv_workflow.lib.analysis.base_distribution' on page 31 undefined on input line 1877 Reference `hiv_workflow.lib.analysis.beta_distribution:module-hiv_workflow.lib.analysis.beta_distribution' on page 31 undefined on input line 1878 Reference `hiv_workflow.lib.analysis.channel:module-hiv_workflow.lib.analysis.channel' on page 31 undefined on input line 1879 Reference `hiv_workflow.lib.analysis.condition:module-hiv_workflow.lib.analysis.condition' on page 31 undefined on input line 1880 Reference `hiv_workflow.lib.analysis.data_frame_wrapper:module-hiv_workflow.lib.analysis.data_frame_wrapper' on page 31 undefined on input line 1881 Reference `hiv_workflow.lib.analysis.download_analyzer_by_experiment:module-hiv_workflow.lib.analysis.download_analyzer_by_experiment' on page 31 undefined on input line 1882 Reference `hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt:module-hiv_workflow.lib.analysis.download_analyzer_by_experiment_receipt' on page 31 undefined on input line 1883 Reference `hiv_workflow.lib.analysis.gaussian_distribution:module-hiv_workflow.lib.analysis.gaussian_distribution' on page 31 undefined on input line 1884 Reference `hiv_workflow.lib.analysis.hiv_analyzer:module-hiv_workflow.lib.analysis.hiv_analyzer' on page 31 undefined on input line 1885 Reference `hiv_workflow.lib.analysis.hiv_calib_site:module-hiv_workflow.lib.analysis.hiv_calib_site' on page 31 undefined on input line 1886 Reference `hiv_workflow.lib.analysis.population_obs:module-hiv_workflow.lib.analysis.population_obs' on page 31 undefined on input line 1887 Reference `hiv_workflow.lib.analysis:module-hiv_workflow.lib.analysis' on page 31 undefined on input line 1875 Reference `hiv_workflow.lib.calibration.algorithms.optim_tool:module-hiv_workflow.lib.calibration.algorithms.optim_tool' on page 31 undefined on input line 1890 Reference `hiv_workflow.lib.calibration.algorithms:module-hiv_workflow.lib.calibration.algorithms' on page 31 undefined on input line 1889 Reference `hiv_workflow.lib.calibration:module-hiv_workflow.lib.calibration' on page 31 undefined on input line 1888 Reference `hiv_workflow.lib.utils.analysis:module-hiv_workflow.lib.utils.analysis' on page 31 undefined on input line 1892 Reference `hiv_workflow.lib.utils.builders.demographics:module-hiv_workflow.lib.utils.builders.demographics' on page 31 undefined on input line 1894 Reference `hiv_workflow.lib.utils.builders.general:module-hiv_workflow.lib.utils.builders.general' on page 31 undefined on input line 1895 Reference `hiv_workflow.lib.utils.builders:module-hiv_workflow.lib.utils.builders' on page 31 undefined on input line 1893 Reference `hiv_workflow.lib.utils.io.excel:module-hiv_workflow.lib.utils.io.excel' on page 31 undefined on input line 1897 Reference `hiv_workflow.lib.utils.io:module-hiv_workflow.lib.utils.io' on page 31 undefined on input line 1896 Reference `hiv_workflow.lib.utils.project_data:module-hiv_workflow.lib.utils.project_data' on page 31 undefined on input line 1898 Reference `hiv_workflow.lib.utils.runtime:module-hiv_workflow.lib.utils.runtime' on page 31 undefined on input line 1899 Reference `hiv_workflow.lib.utils.wrappers:module-hiv_workflow.lib.utils.wrappers' on page 31 undefined on input line 1900 Reference `hiv_workflow.lib.utils:module-hiv_workflow.lib.utils' on page 31 undefined on input line 1891 Reference `hiv_workflow.lib:module-hiv_workflow.lib' on page 31 undefined on input line 1874 Reference `hiv_workflow.scripts.available_parameters:module-hiv_workflow.scripts.available_parameters' on page 31 undefined on input line 1902 Reference `hiv_workflow.scripts.calibrate:module-hiv_workflow.scripts.calibrate' on page 31 undefined on input line 1903 Reference `hiv_workflow.scripts.download:module-hiv_workflow.scripts.download' on page 31 undefined on input line 1904 Reference `hiv_workflow.scripts.dtk_post_process:module-hiv_workflow.scripts.dtk_post_process' on page 31 undefined on input line 1905 Reference `hiv_workflow.scripts.resample:module-hiv_workflow.scripts.resample' on page 31 undefined on input line 1906 Reference `hiv_workflow.scripts.run:module-hiv_workflow.scripts.run' on page 31 undefined on input line 1907 Reference `hiv_workflow.scripts:module-hiv_workflow.scripts' on page 31 undefined on input line 1901 Reference `hiv_workflow:module-hiv_workflow' on page 31 undefined on input line 1873 Latexmk: Summary of warnings: Latex failed to resolve 36 reference(s) Rule 'makeindex institute-for-disease-modeling-hiv-workflow.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-hiv-workflow.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-hiv-workflow.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-hiv-workflow.ind" "institute-for-disease-modeling-hiv-workflow.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-hiv-workflow.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-hiv-workflow.idx....done (214 entries accepted, 0 rejected). Sorting entries.....done (1688 comparisons). Generating output file institute-for-disease-modeling-hiv-workflow.ind....done (432 lines written, 0 warnings). Output written in institute-for-disease-modeling-hiv-workflow.ind. Transcript written in institute-for-disease-modeling-hiv-workflow.ilg. 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. 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\hbox (97.01385pt too wide) in paragraph at lines 1230--1230 \T1/ptm/m/it/10 tory_weibull_scale=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1230--1230 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.90492pt too wide) in paragraph at lines 1230--1230 [][]\T1/ptm/m/n/10 None[][] [20] Overfull \hbox (64.9846pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demographics: Overfull \hbox (269.81337pt too wide) in paragraph at lines 1236--1236 \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 1236--1236 \T1/ptm/m/it/10 ini- Overfull \hbox (112.84337pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 tial_risk_distribution_low: Overfull \hbox (23.0249pt too wide) in paragraph at lines 1236--1236 [][]\T1/ptm/m/it/10 float[][] Overfull \hbox (11.99501pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 = Overfull \hbox (32.35487pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 None\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1236--1236 \OMS/cmsy/m/n/10 !$ Overfull \hbox (26.90492pt too wide) in paragraph at lines 1236--1236 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (63.42361pt too wide) in paragraph at lines 1253--1253 []\T1/ptm/m/it/10 parameter_setting_functions: Overfull \hbox (4.98395pt too wide) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 ex- Overfull \hbox (38.09406pt too wide) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 pected_first_argument: Underfull \hbox (badness 10000) in paragraph at lines 1253--1253 [][]\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 1253--1253 \T1/ptm/m/n/10 Dict[Callable, Underfull \hbox (badness 5985) in paragraph at lines 1259--1260 []\T1/pcr/b/n/10 parameter_setting_functions \T1/ptm/m/n/10 ^^U a list of func- tion ref-er-ences that pro- [21] Underfull \hbox (badness 10000) in paragraph at lines 1279--1279 [][]\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 1279--1279 \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 1279--1279 \T1/ptm/m/it/10 tion_arguments: Underfull \hbox (badness 10000) in paragraph at lines 1279--1279 \T1/ptm/m/it/10 Dict[Callable, List]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [22] Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 []\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 1388--1388 \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 1388--1388 \T1/ptm/m/it/10 high_age=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/ptm/m/it/10 age_bin=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \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 1388--1388 \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 1483--1483 []\T1/ptm/m/it/10 ingest_filename: Underfull \hbox (badness 10000) in paragraph at lines 1483--1483 [][]\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 1483--1483 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite[][]\T 1/ptm/m/n/10 ] [23] Underfull \hbox (badness 10000) in paragraph at lines 1494--1494 []\T1/ptm/m/it/10 wb: open- Overfull \hbox (60.96397pt too wide) in paragraph at lines 1494--1494 \T1/ptm/m/it/10 pyxl.workbook.workbook.Workbook\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1494--1494 \T1/ptm/m/it/10 sheet_name: Underfull \hbox (badness 10000) in paragraph at lines 1494--1494 [][]\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 1494--1494 [][]\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 1494--1494 \T1/ptm/m/n/10 pyxl.worksheet.worksheet.Worksheet Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 []\T1/ptm/m/it/10 filename: Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 [][]\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 1507--1507 \T1/ptm/m/n/10 ple[List[[][]dict[][]], Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 [][]\T1/ptm/m/n/10 dict[][], Overfull \hbox (169.82304pt too wide) in paragraph at lines 1507--1507 [][]\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 1507--1507 \T1/ptm/m/n/10 List[[][]dict[][]], Overfull \hbox (136.29294pt too wide) in paragraph at lines 1507--1507 \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 1521--1521 []\T1/ptm/m/it/10 task: [][]idm- Overfull \hbox (37.77344pt too wide) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 chan-nels: Overfull \hbox (136.20297pt too wide) in paragraph at lines 1521--1521 \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 1521--1521 \T1/ptm/m/it/10 ref-er- Underfull \hbox (badness 10000) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 ence_data: Overfull \hbox (170.10309pt too wide) in paragraph at lines 1521--1521 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][], Underfull \hbox (badness 10000) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 site_info: [24] Underfull \hbox (badness 10000) in paragraph at lines 1568--1568 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 1568--1568 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1600--1600 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 1600--1600 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1600--1600 \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 1622--1622 []\T1/ptm/m/it/10 simulation: [][]idm- Overfull \hbox (41.153pt too wide) in paragraph at lines 1622--1622 \T1/ptm/m/it/10 tools.entities.simulation.Simulation[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1622--1622 \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 1622--1622 \T1/ptm/m/it/10 mo-graph-ics_builder: Underfull \hbox (badness 10000) in paragraph at lines 1632--1633 []\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- [25] Underfull \hbox (badness 10000) in paragraph at lines 1662--1662 []\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 1685--1685 []\T1/ptm/m/it/10 executable_path: [][]str[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \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 1685--1685 \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 1685--1685 \T1/ptm/m/it/10 ics_paths: List[[][]str[][]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 python_processing_setter: Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \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 1685--1685 \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 1685--1685 \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 1685--1685 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][] Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \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 1685--1685 [][]\T1/ptm/m/it/10 dict[][] = None\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [26] Underfull \hbox (badness 10000) in paragraph at lines 1769--1769 []\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 1769--1769 \T1/ptm/m/it/10 go-rithm_root: [][]str[][] = Overfull \hbox (0.70457pt too wide) in paragraph at lines 1810--1810 []\T1/ptm/m/it/10 config_builder: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 [][]\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 1810--1810 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (13.66457pt too wide) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 max_memory_mb: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 [][]\T1/ptm/m/it/10 int[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 ics_paths: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 List[[][]str[][]] Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 5681) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 = False\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [27] Overfull \hbox (27.70444pt too wide) in paragraph at lines 1816--1816 []\T1/ptm/m/it/10 campaign_builder: Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (7.1947pt too wide) in paragraph at lines 1816--1816 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 \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 1822--1822 []\T1/ptm/m/it/10 demographics_builder: Overfull \hbox (12.19455pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 man- Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 i-fest: Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 mod- Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 ule\T1/ptm/m/n/10 , Overfull \hbox (7.0946pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 kwargs: Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (10.7947pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 [][]\T1/ptm/m/it/10 bool[][] Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 = Overfull \hbox (2.71472pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.57443pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/n/10 Callable Overfull \hbox (66.70457pt too wide) in paragraph at lines 1828--1828 []\T1/ptm/m/it/10 config_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (25.23488pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 cam- Overfull \hbox (65.04453pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 paign_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (18.01491pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 de- Overfull \hbox (20.79494pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 mo- Overfull \hbox (32.31496pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 graph- Overfull \hbox (53.37436pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 ics_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (22.31496pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 ran- Overfull \hbox (80.23463pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 dom_run_number: Overfull \hbox (29.0249pt too wide) in paragraph at lines 1828--1828 [][]\T1/ptm/m/it/10 bool[][]\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1828--1828 \OMS/cmsy/m/n/10 !$ Overfull \hbox (24.13475pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/n/10 idm- Overfull \hbox (207.823pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/n/10 tools_calibra.calib_manager.SampleIndexWrapper [28] Overfull \hbox (13.1938pt too wide) in paragraph at lines 1834--1834 []\T1/ptm/m/it/10 custom_sample_constrainer: Underfull \hbox (badness 7759) in paragraph at lines 1840--1840 []\T1/ptm/m/it/10 pre: [][]str[][] Underfull \hbox (badness 10000) in paragraph at lines 1840--1840 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1840--1840 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , [29] [30] Overfull \hbox (30.6225pt too wide) in paragraph at lines 1877--1878 []\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 1878--1879 []\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 1881--1882 []\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 1882--1883 []\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 1883--1884 []\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 1884--1885 []\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 1885--1886 []\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 1886--1887 []\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 1887--1888 []\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 1889--1890 []\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 1890--1891 []\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 1894--1895 []\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 1895--1896 []\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 1902--1903 []\T1/pcr/m/n/10 hiv_workflow.scripts.available_parameters\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1905--1906 []\T1/pcr/m/n/10 hiv_workflow.scripts.dtk_post_process\T1/ptm/m/n/10 , [31] (./institute-for-disease-modeling-hiv-workflow.ind [32] 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 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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. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [9] Underfull \hbox (badness 10000) in paragraph at lines 367--367 []\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 367--367 \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 400--400 []\T1/ptm/m/it/10 dfw: [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.data_frame_ wrapper.DataFrameWrapper[][], [10] Overfull \hbox (74.911pt too wide) in paragraph at lines 414--414 []\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 426--426 []\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 426--426 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.base_distribution.BaseDistributio n[][] [11] Overfull \hbox (27.48462pt too wide) in paragraph at lines 609--609 []\T1/ptm/m/it/10 filename=None\T1/ptm/m/n/10 , Overfull \hbox (34.56456pt too wide) in paragraph at lines 609--609 \T1/ptm/m/it/10 dataframe=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 609--609 \T1/ptm/m/it/10 strat-i- Overfull \hbox (14.22461pt too wide) in paragraph at lines 609--609 \T1/ptm/m/it/10 fiers=None\T1/pcr/m/n/10 ) [12] [13] Overfull \hbox (153.51465pt too wide) in paragraph at lines 738--738 []\T1/ptm/m/it/10 filenames\T1/ptm/m/n/10 , Overfull \hbox (129.35486pt too wide) in paragraph at lines 738--738 \T1/ptm/m/it/10 out- Overfull \hbox (151.3048pt too wide) in paragraph at lines 738--738 \T1/ptm/m/it/10 put_path\T1/ptm/m/n/10 , Overfull \hbox (208.60439pt too wide) in paragraph at lines 738--738 \T1/ptm/m/it/10 use_run_number=True\T1/ptm/m/n/10 , Overfull \hbox (217.45421pt too wide) in paragraph at lines 738--738 \T1/ptm/m/it/10 use_sample_index=True\T1/pcr/m/n/10 ) Overfull \hbox (243.51465pt too wide) in paragraph at lines 822--822 []\T1/ptm/m/it/10 filenames\T1/ptm/m/n/10 , Overfull \hbox (214.53479pt too wide) in paragraph at lines 822--822 \T1/ptm/m/it/10 re- Overfull \hbox (242.40451pt too wide) in paragraph at lines 822--822 \T1/ptm/m/it/10 ceipt_file\T1/ptm/m/n/10 , Overfull \hbox (298.60439pt too wide) in paragraph at lines 822--822 \T1/ptm/m/it/10 use_run_number=True\T1/ptm/m/n/10 , Overfull \hbox (307.45421pt too wide) in paragraph at lines 822--822 \T1/ptm/m/it/10 use_sample_index=True\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 823--824 \T1/ptm/m/n/10 Bases: [][]\T1/pcr/m/sl/10 hiv_workflow.lib.analysis.download_an alyzer_by_experiment. 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\hbox (97.01385pt too wide) in paragraph at lines 1230--1230 \T1/ptm/m/it/10 tory_weibull_scale=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1230--1230 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.90492pt too wide) in paragraph at lines 1230--1230 [][]\T1/ptm/m/n/10 None[][] [20] Overfull \hbox (64.9846pt too wide) in paragraph at lines 1236--1236 []\T1/ptm/m/it/10 demographics: Overfull \hbox (269.81337pt too wide) in paragraph at lines 1236--1236 \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 1236--1236 \T1/ptm/m/it/10 ini- Overfull \hbox (112.84337pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 tial_risk_distribution_low: Overfull \hbox (23.0249pt too wide) in paragraph at lines 1236--1236 [][]\T1/ptm/m/it/10 float[][] Overfull \hbox (11.99501pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 = Overfull \hbox (32.35487pt too wide) in paragraph at lines 1236--1236 \T1/ptm/m/it/10 None\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1236--1236 \OMS/cmsy/m/n/10 !$ Overfull \hbox (26.90492pt too wide) in paragraph at lines 1236--1236 [][]\T1/ptm/m/n/10 None[][] Overfull \hbox (63.42361pt too wide) in paragraph at lines 1253--1253 []\T1/ptm/m/it/10 parameter_setting_functions: Overfull \hbox (4.98395pt too wide) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 List[Callable]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 ex- Overfull \hbox (38.09406pt too wide) in paragraph at lines 1253--1253 \T1/ptm/m/it/10 pected_first_argument: Underfull \hbox (badness 10000) in paragraph at lines 1253--1253 [][]\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 1253--1253 \T1/ptm/m/n/10 Dict[Callable, Underfull \hbox (badness 5985) in paragraph at lines 1259--1260 []\T1/pcr/b/n/10 parameter_setting_functions \T1/ptm/m/n/10 ^^U a list of func- tion ref-er-ences that pro- [21] Underfull \hbox (badness 10000) in paragraph at lines 1279--1279 [][]\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 1279--1279 \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 1279--1279 \T1/ptm/m/it/10 tion_arguments: Underfull \hbox (badness 10000) in paragraph at lines 1279--1279 \T1/ptm/m/it/10 Dict[Callable, List]\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [22] Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 []\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 1388--1388 \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 1388--1388 \T1/ptm/m/it/10 high_age=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/ptm/m/it/10 age_bin=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \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 1388--1388 \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 1483--1483 []\T1/ptm/m/it/10 ingest_filename: Underfull \hbox (badness 10000) in paragraph at lines 1483--1483 [][]\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 1483--1483 [][]\T1/ptm/m/it/10 hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite[][]\T 1/ptm/m/n/10 ] [23] Underfull \hbox (badness 10000) in paragraph at lines 1494--1494 []\T1/ptm/m/it/10 wb: open- Overfull \hbox (60.96397pt too wide) in paragraph at lines 1494--1494 \T1/ptm/m/it/10 pyxl.workbook.workbook.Workbook\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1494--1494 \T1/ptm/m/it/10 sheet_name: Underfull \hbox (badness 10000) in paragraph at lines 1494--1494 [][]\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 1494--1494 [][]\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 1494--1494 \T1/ptm/m/n/10 pyxl.worksheet.worksheet.Worksheet Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 []\T1/ptm/m/it/10 filename: Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 [][]\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 1507--1507 \T1/ptm/m/n/10 ple[List[[][]dict[][]], Underfull \hbox (badness 10000) in paragraph at lines 1507--1507 [][]\T1/ptm/m/n/10 dict[][], Overfull \hbox (169.82304pt too wide) in paragraph at lines 1507--1507 [][]\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 1507--1507 \T1/ptm/m/n/10 List[[][]dict[][]], Overfull \hbox (136.29294pt too wide) in paragraph at lines 1507--1507 \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 1521--1521 []\T1/ptm/m/it/10 task: [][]idm- Overfull \hbox (37.77344pt too wide) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 chan-nels: Overfull \hbox (136.20297pt too wide) in paragraph at lines 1521--1521 \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 1521--1521 \T1/ptm/m/it/10 ref-er- Underfull \hbox (badness 10000) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 ence_data: Overfull \hbox (170.10309pt too wide) in paragraph at lines 1521--1521 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][], Underfull \hbox (badness 10000) in paragraph at lines 1521--1521 \T1/ptm/m/it/10 site_info: [24] Underfull \hbox (badness 10000) in paragraph at lines 1568--1568 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 1568--1568 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1600--1600 []\T1/ptm/m/it/10 task: [][]idm- Underfull \hbox (badness 10000) in paragraph at lines 1600--1600 \T1/ptm/m/it/10 tools.entities.itask.ITask[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1600--1600 \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 1622--1622 []\T1/ptm/m/it/10 simulation: [][]idm- Overfull \hbox (41.153pt too wide) in paragraph at lines 1622--1622 \T1/ptm/m/it/10 tools.entities.simulation.Simulation[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1622--1622 \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 1622--1622 \T1/ptm/m/it/10 mo-graph-ics_builder: Underfull \hbox (badness 10000) in paragraph at lines 1632--1633 []\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- [25] Underfull \hbox (badness 10000) in paragraph at lines 1662--1662 []\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 1685--1685 []\T1/ptm/m/it/10 executable_path: [][]str[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \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 1685--1685 \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 1685--1685 \T1/ptm/m/it/10 ics_paths: List[[][]str[][]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \T1/ptm/m/it/10 python_processing_setter: Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \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 1685--1685 \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 1685--1685 \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 1685--1685 [][]\T1/ptm/m/n/10 hiv_workflow.lib.analysis.population_obs.PopulationObs[][] Underfull \hbox (badness 10000) in paragraph at lines 1685--1685 \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 1685--1685 [][]\T1/ptm/m/it/10 dict[][] = None\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [26] Underfull \hbox (badness 10000) in paragraph at lines 1769--1769 []\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 1769--1769 \T1/ptm/m/it/10 go-rithm_root: [][]str[][] = Overfull \hbox (0.70457pt too wide) in paragraph at lines 1810--1810 []\T1/ptm/m/it/10 config_builder: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 [][]\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 1810--1810 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (13.66457pt too wide) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 max_memory_mb: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 [][]\T1/ptm/m/it/10 int[][] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 ics_paths: Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 List[[][]str[][]] Underfull \hbox (badness 10000) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 5681) in paragraph at lines 1810--1810 \T1/ptm/m/it/10 = False\T1/pcr/m/n/10 ) $\OMS/cmsy/m/n/10 !$ [27] Overfull \hbox (27.70444pt too wide) in paragraph at lines 1816--1816 []\T1/ptm/m/it/10 campaign_builder: Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (7.1947pt too wide) in paragraph at lines 1816--1816 \T1/ptm/m/it/10 schema_path: Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 [][]\T1/ptm/m/it/10 bool[][] = Underfull \hbox (badness 10000) in paragraph at lines 1816--1816 \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 1822--1822 []\T1/ptm/m/it/10 demographics_builder: Overfull \hbox (12.19455pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 man- Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 i-fest: Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 mod- Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 ule\T1/ptm/m/n/10 , Overfull \hbox (7.0946pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 kwargs: Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 [][]\T1/ptm/m/it/10 dict[][]\T1/ptm/m/n/10 , Overfull \hbox (10.7947pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 dry_run: Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 [][]\T1/ptm/m/it/10 bool[][] Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 = Overfull \hbox (2.71472pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/it/10 False\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1822--1822 \OMS/cmsy/m/n/10 !$ Overfull \hbox (8.57443pt too wide) in paragraph at lines 1822--1822 \T1/ptm/m/n/10 Callable Overfull \hbox (66.70457pt too wide) in paragraph at lines 1828--1828 []\T1/ptm/m/it/10 config_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (25.23488pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 cam- Overfull \hbox (65.04453pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 paign_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (18.01491pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 de- Overfull \hbox (20.79494pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 mo- Overfull \hbox (32.31496pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 graph- Overfull \hbox (53.37436pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 ics_builder: Overfull \hbox (42.19455pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 Callable\T1/ptm/m/n/10 , Overfull \hbox (22.31496pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 ran- Overfull \hbox (80.23463pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/it/10 dom_run_number: Overfull \hbox (29.0249pt too wide) in paragraph at lines 1828--1828 [][]\T1/ptm/m/it/10 bool[][]\T1/pcr/m/n/10 ) Overfull \hbox (15.24503pt too wide) in paragraph at lines 1828--1828 \OMS/cmsy/m/n/10 !$ Overfull \hbox (24.13475pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/n/10 idm- Overfull \hbox (207.823pt too wide) in paragraph at lines 1828--1828 \T1/ptm/m/n/10 tools_calibra.calib_manager.SampleIndexWrapper [28] Overfull \hbox (13.1938pt too wide) in paragraph at lines 1834--1834 []\T1/ptm/m/it/10 custom_sample_constrainer: Underfull \hbox (badness 7759) in paragraph at lines 1840--1840 []\T1/ptm/m/it/10 pre: [][]str[][] Underfull \hbox (badness 10000) in paragraph at lines 1840--1840 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1840--1840 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , [29] [30] Overfull \hbox (30.6225pt too wide) in paragraph at lines 1877--1878 []\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 1878--1879 []\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 1881--1882 []\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 1882--1883 []\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 1883--1884 []\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 1884--1885 []\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 1885--1886 []\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 1886--1887 []\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 1887--1888 []\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 1889--1890 []\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 1890--1891 []\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 1894--1895 []\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 1895--1896 []\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 1902--1903 []\T1/pcr/m/n/10 hiv_workflow.scripts.available_parameters\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1905--1906 []\T1/pcr/m/n/10 hiv_workflow.scripts.dtk_post_process\T1/ptm/m/n/10 , [31] (./institute-for-disease-modeling-hiv-workflow.ind [32] 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 [33] Underfull \hbox (badness 10000) in paragraph at lines 81--83 []\T1/pcr/m/n/10 construct_gaussian_channel() 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