Read the Docs build information Build id: 395800 Project: institute-for-disease-modeling-covasim Version: latest Commit: ec06c2f29be55733251938b06de4a47c017b62d5 Date: 2020-08-14T21:57:21.254139Z State: finished Success: True [rtd-command-info] start-time: 2020-08-14T21:57:22.812856Z, end-time: 2020-08-14T21:57:24.258218Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/JSchripsema-IDM/covasim.git . Cloning into '.'... [rtd-command-info] start-time: 2020-08-14T21:57:24.570100Z, end-time: 2020-08-14T21:57:24.643718Z, duration: 0, exit-code: 0 git checkout --force origin/rtd Note: checking out 'origin/rtd'. 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 ec06c2f removed covasim/requirements.txt from yaml file [rtd-command-info] start-time: 2020-08-14T21:57:24.790134Z, end-time: 2020-08-14T21:57:24.841967Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-08-14T21:57:25.990278Z, end-time: 2020-08-14T21:57:29.967905Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-08-14T21:57:30.129760Z, end-time: 2020-08-14T21:57:30.802868Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (20.2.2) [rtd-command-info] start-time: 2020-08-14T21:57:30.983451Z, end-time: 2020-08-14T21:57:39.184938Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 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pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) 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=23754 sha256=e08411bbf9ff6c25cc94c17b0c4cad004c6c08d9ea29287a0c63d02410fbf2c1 Stored in directory: /tmp/pip-ephem-wheel-cache-ku35ih_a/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b 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=491059 sha256=c44b9f6e0433cdf094ef017cbf5585f2c6053d6e7ca2764656ca8603eee52711 Stored in directory: /tmp/pip-ephem-wheel-cache-ku35ih_a/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, imagesize, MarkupSafe, Jinja2, urllib3, certifi, chardet, idna, requests, six, pyparsing, packaging, snowballstemmer, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 49.6.0 Uninstalling setuptools-49.6.0: Successfully uninstalled setuptools-49.6.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10 [rtd-command-info] start-time: 2020-08-14T21:57:39.289697Z, end-time: 2020-08-14T21:58:25.395107Z, duration: 46, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting numpy Downloading numpy-1.19.1-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB) Collecting pandas Downloading pandas-1.1.0-cp37-cp37m-manylinux1_x86_64.whl (10.5 MB) Collecting scipy Downloading scipy-1.5.2-cp37-cp37m-manylinux1_x86_64.whl (25.9 MB) Collecting matplotlib Downloading matplotlib-3.3.1-cp37-cp37m-manylinux1_x86_64.whl (11.6 MB) Collecting statsmodels Downloading statsmodels-0.11.1-cp37-cp37m-manylinux1_x86_64.whl (8.7 MB) Collecting numba==0.48 Downloading numba-0.48.0-1-cp37-cp37m-manylinux2014_x86_64.whl (3.5 MB) Collecting sciris>=0.17.0 Downloading sciris-0.17.4-py3-none-any.whl (99 kB) Collecting scirisweb>=0.17.0 Downloading scirisweb-0.17.0-py3-none-any.whl (37 kB) Collecting gunicorn Downloading 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collected packages: fire, memory-profiler, dill, psutil, mpld3, retrying, termcolor, et-xmlfile, tornado, pyrsistent, pandocfilters Building wheel for fire (setup.py): started Building wheel for fire (setup.py): finished with status 'done' Created wheel for fire: filename=fire-0.3.1-py2.py3-none-any.whl size=111005 sha256=8477256ff0f301422c153dfab5952f265aae4ee06c2ac2ff984470a64f4e883f Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/95/38/e1/8b62337a8ecf5728bdc1017e828f253f7a9cf25db999861bec Building wheel for memory-profiler (setup.py): started Building wheel for memory-profiler (setup.py): finished with status 'done' Created wheel for memory-profiler: filename=memory_profiler-0.57.0-py3-none-any.whl size=28993 sha256=17c5c477abe056847e172ac80e845d303f5221fe65d2e3d5e066ebc58e9ba152 Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/0c/84/4a/8afc0620ec149b2c0a4ed08b021e3a2dc7063fa08e1fcb40c8 Building wheel for dill (setup.py): started Building wheel for dill (setup.py): finished with status 'done' Created wheel for dill: filename=dill-0.3.2-py3-none-any.whl size=78912 sha256=15d254d6374103770e90615e884fcf6de868534159047693740062b57f9859e2 Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/72/6b/d5/5548aa1b73b8c3d176ea13f9f92066b02e82141549d90e2100 Building wheel for psutil (setup.py): started Building wheel for psutil (setup.py): finished with status 'done' Created wheel for psutil: filename=psutil-5.7.2-cp37-cp37m-linux_x86_64.whl size=283648 sha256=4ee757d53fa7369138a9e9be090320fbcac21afab3bae4dd23d78d44b8bd116d Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/2d/43/97/00701864a7bee6d9e1a52dd682537dcbf1d013d0e2e6f0c1f1 Building wheel for mpld3 (setup.py): started Building wheel for mpld3 (setup.py): finished with status 'done' Created wheel for mpld3: filename=mpld3-0.5.1-py3-none-any.whl size=364063 sha256=4da9874f4608d8e461deec29d6aa89d73415b6dcbbae98164ee7b0c9f401f59f Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/b9/36/27/d61b9f1327012961fa31f05a20b190f836dd3fcb1c0264177b Building wheel for retrying (setup.py): started Building wheel for retrying (setup.py): finished with status 'done' Created wheel for retrying: filename=retrying-1.3.3-py3-none-any.whl size=11429 sha256=5b5c9cfaa3a36383172cdcf36513addafd841384727e1587412dabcb70b58d4f Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/f9/8d/8d/f6af3f7f9eea3553bc2fe6d53e4b287dad18b06a861ac56ddf Building wheel for termcolor (setup.py): started Building wheel for termcolor (setup.py): finished with status 'done' Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4830 sha256=bbe78b5cc54a51554772ee022f94c9e63789abd2d1b267ebb87e4d99aa9e6420 Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2 Building wheel for et-xmlfile (setup.py): started Building wheel for et-xmlfile (setup.py): finished with status 'done' Created wheel for et-xmlfile: filename=et_xmlfile-1.0.1-py3-none-any.whl size=8917 sha256=5e5f4e2bbd1020e8176e06e901947c6ee0b79d3a468c463986521a57da9889f7 Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/e2/bd/55/048b4fd505716c4c298f42ee02dffd9496bb6d212b266c7f31 Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Created wheel for tornado: filename=tornado-6.0.4-cp37-cp37m-linux_x86_64.whl size=428560 sha256=9457c3374617327677363a01275490bb728fefb1a8f49fe1ce484197e933cc9b Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/7d/14/fa/d88fb5da77d813ea0ffca38a2ab2a052874e9e1142bad0b348 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp37-cp37m-linux_x86_64.whl size=116009 sha256=4903aaa21f2ac1359393970e843f5e181dd24b1c0695d2ff56e1f87dc9c70959 Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/22/52/11/f0920f95c23ed7d2d0b05f2b7b2f4509e87a20cfe8ea43d987 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7855 sha256=63cc7b4c2b47ba4de0b47d6f7d1ebd9db9beecfae6256532471fce09167d61e8 Stored in directory: /tmp/pip-ephem-wheel-cache-a015g_sk/wheels/63/99/01/9fe785b86d1e091a6b2a61e06ddb3d8eb1bc9acae5933d4740 Successfully built fire memory-profiler dill psutil mpld3 retrying termcolor et-xmlfile tornado pyrsistent pandocfilters Installing collected packages: numpy, python-dateutil, pandas, scipy, kiwisolver, cycler, pillow, matplotlib, patsy, statsmodels, llvmlite, numba, psutil, memory-profiler, dill, pickleshare, parso, jedi, decorator, ipython-genutils, traitlets, backcall, wcwidth, prompt-toolkit, ptyprocess, pexpect, ipython, line-profiler, xlsxwriter, smmap, gitdb, gitpython, zipp, importlib-metadata, jsonpickle, jellyfish, jdcal, et-xmlfile, openpyexcel, xlrd, sciris, sqlalchemy, pyasn1, itsdangerous, werkzeug, click, flask, flask-login, mpld3, attrs, Automat, constantly, incremental, PyHamcrest, zope.interface, hyperlink, twisted, pycparser, cffi, cryptography, pyasn1-modules, service-identity, redis, cachelib, flask-session, vine, amqp, kombu, billiard, celery, scirisweb, gunicorn, retrying, plotly, jupyter-core, pyzmq, tornado, jupyter-client, ipykernel, pyrsistent, jsonschema, nbformat, testpath, defusedxml, mistune, entrypoints, webencodings, bleach, pandocfilters, nbconvert, terminado, prometheus-client, argon2-cffi, Send2Trash, notebook, widgetsnbextension, ipywidgets, termcolor, fire Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed Automat-20.2.0 PyHamcrest-2.0.2 Send2Trash-1.5.0 amqp-2.6.1 argon2-cffi-20.1.0 attrs-19.3.0 backcall-0.2.0 billiard-3.6.3.0 bleach-3.1.5 cachelib-0.1.1 celery-4.4.7 cffi-1.14.1 click-7.1.2 constantly-15.1.0 cryptography-3.0 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 dill-0.3.2 entrypoints-0.3 et-xmlfile-1.0.1 fire-0.3.1 flask-1.1.2 flask-login-0.5.0 flask-session-0.3.2 gitdb-4.0.5 gitpython-3.1.7 gunicorn-20.0.4 hyperlink-20.0.1 importlib-metadata-1.7.0 incremental-17.5.0 ipykernel-5.3.4 ipython-7.17.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 itsdangerous-1.1.0 jdcal-1.4.1 jedi-0.17.2 jellyfish-0.8.2 jsonpickle-1.4.1 jsonschema-3.2.0 jupyter-client-6.1.6 jupyter-core-4.6.3 kiwisolver-1.2.0 kombu-4.6.11 line-profiler-3.0.2 llvmlite-0.31.0 matplotlib-3.3.1 memory-profiler-0.57.0 mistune-0.8.4 mpld3-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 notebook-6.1.3 numba-0.48.0 numpy-1.19.1 openpyexcel-2.5.14 pandas-1.1.0 pandocfilters-1.4.2 parso-0.7.1 patsy-0.5.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-7.2.0 plotly-4.9.0 prometheus-client-0.8.0 prompt-toolkit-3.0.6 psutil-5.7.2 ptyprocess-0.6.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pycparser-2.20 pyrsistent-0.16.0 python-dateutil-2.8.1 pyzmq-19.0.2 redis-2.10.6 retrying-1.3.3 scipy-1.5.2 sciris-0.17.4 scirisweb-0.17.0 service-identity-18.1.0 smmap-3.0.4 sqlalchemy-1.3.18 statsmodels-0.11.1 termcolor-1.1.0 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 traitlets-4.3.3 twisted-20.3.0 vine-1.3.0 wcwidth-0.2.5 webencodings-0.5.1 werkzeug-1.0.1 widgetsnbextension-3.5.1 xlrd-1.2.0 xlsxwriter-1.3.3 zipp-3.1.0 zope.interface-5.1.0 [rtd-command-info] start-time: 2020-08-14T21:58:25.508182Z, end-time: 2020-08-14T21:58:30.539687Z, duration: 5, 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-0.5.0-py2.py3-none-any.whl (10.8 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.0 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting pytest Downloading pytest-6.0.1-py3-none-any.whl (270 kB) Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/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: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.0.0) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-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-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (41.0.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.2.0) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.3.1) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.8.0) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.11.2) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (20.4) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.24.0) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.1.4) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (0.14) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: attrs>=17.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from pytest->-r docs/requirements.txt (line 5)) (19.3.0) Collecting toml Downloading toml-0.10.1-py2.py3-none-any.whl (19 kB) Collecting more-itertools>=4.0.0 Downloading more_itertools-8.4.0-py3-none-any.whl (43 kB) Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from pytest->-r docs/requirements.txt (line 5)) (1.7.0) Collecting pluggy<1.0,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting iniconfig Downloading iniconfig-1.0.1-py3-none-any.whl (4.2 kB) Collecting py>=1.8.2 Downloading py-1.9.0-py2.py3-none-any.whl (99 kB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2020.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.1.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.4.7) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.25.10) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.10) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2020.6.20) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->-r docs/requirements.txt (line 5)) (3.1.0) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-jsmath, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, toml, more-itertools, pluggy, iniconfig, py, pytest Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed iniconfig-1.0.1 more-itertools-8.4.0 plantweb-1.2.1 pluggy-0.13.1 pockets-0.9.1 py-1.9.0 pytest-6.0.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3 toml-0.10.1 [rtd-command-info] start-time: 2020-08-14T21:58:30.736264Z, end-time: 2020-08-14T21:58:32.176205Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating covasim.egg-info writing covasim.egg-info/PKG-INFO writing dependency_links to covasim.egg-info/dependency_links.txt writing requirements to covasim.egg-info/requires.txt writing top-level names to covasim.egg-info/top_level.txt writing manifest file 'covasim.egg-info/SOURCES.txt' reading manifest file 'covasim.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: manifest_maker: MANIFEST.in, line 3: 'recursive-include' expects ... warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution writing manifest file 'covasim.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/covasim copying covasim/run.py -> build/lib/covasim copying covasim/people.py -> build/lib/covasim copying covasim/analysis.py -> build/lib/covasim copying covasim/parameters.py -> build/lib/covasim copying covasim/misc.py -> build/lib/covasim copying covasim/defaults.py -> build/lib/covasim copying covasim/__init__.py -> build/lib/covasim copying covasim/base.py -> build/lib/covasim copying covasim/interventions.py -> build/lib/covasim copying covasim/version.py -> build/lib/covasim copying covasim/utils.py -> build/lib/covasim copying covasim/population.py -> build/lib/covasim copying covasim/requirements.py -> build/lib/covasim copying covasim/sim.py -> build/lib/covasim copying covasim/plotting.py -> build/lib/covasim creating build/lib/covasim/data copying covasim/data/loaders.py -> build/lib/covasim/data copying covasim/data/household_size_data.py -> build/lib/covasim/data copying covasim/data/__init__.py -> build/lib/covasim/data copying covasim/data/state_age_data.py -> build/lib/covasim/data copying covasim/data/country_age_data.py -> build/lib/covasim/data creating build/lib/covasim/webapp copying covasim/webapp/cova_app.py -> build/lib/covasim/webapp copying covasim/webapp/__init__.py -> build/lib/covasim/webapp creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/run.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/people.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/analysis.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/parameters.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/misc.py -> build/bdist.linux-x86_64/egg/covasim creating build/bdist.linux-x86_64/egg/covasim/data copying build/lib/covasim/data/loaders.py -> build/bdist.linux-x86_64/egg/covasim/data copying build/lib/covasim/data/household_size_data.py -> build/bdist.linux-x86_64/egg/covasim/data copying build/lib/covasim/data/__init__.py -> build/bdist.linux-x86_64/egg/covasim/data copying build/lib/covasim/data/state_age_data.py -> build/bdist.linux-x86_64/egg/covasim/data copying build/lib/covasim/data/country_age_data.py -> build/bdist.linux-x86_64/egg/covasim/data copying build/lib/covasim/defaults.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/__init__.py -> build/bdist.linux-x86_64/egg/covasim creating build/bdist.linux-x86_64/egg/covasim/webapp copying build/lib/covasim/webapp/cova_app.py -> build/bdist.linux-x86_64/egg/covasim/webapp copying build/lib/covasim/webapp/__init__.py -> build/bdist.linux-x86_64/egg/covasim/webapp copying build/lib/covasim/base.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/interventions.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/version.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/utils.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/population.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/requirements.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/sim.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/plotting.py -> build/bdist.linux-x86_64/egg/covasim byte-compiling build/bdist.linux-x86_64/egg/covasim/run.py to run.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/people.py to people.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/analysis.py to analysis.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/parameters.py to parameters.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/misc.py to misc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/loaders.py to loaders.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/household_size_data.py to household_size_data.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/state_age_data.py to state_age_data.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/country_age_data.py to country_age_data.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/defaults.py to defaults.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/webapp/cova_app.py to cova_app.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/webapp/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/base.py to base.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/interventions.py to interventions.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/version.py to version.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/utils.py to utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/population.py to population.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/requirements.py to requirements.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/sim.py to sim.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/plotting.py to plotting.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying covasim.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying covasim.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying covasim.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying covasim.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying covasim.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... covasim.__pycache__.interventions.cpython-37: module MAY be using inspect.getouterframes covasim.__pycache__.interventions.cpython-37: module MAY be using inspect.trace covasim.__pycache__.misc.cpython-37: module references __file__ covasim.__pycache__.misc.cpython-37: module MAY be using inspect.getouterframes covasim.webapp.__pycache__.cova_app.cpython-37: module references __file__ creating dist creating 'dist/covasim-1.4.7-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 covasim-1.4.7-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/covasim-1.4.7-py3.7.egg Extracting covasim-1.4.7-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding covasim 1.4.7 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/covasim-1.4.7-py3.7.egg Processing dependencies for covasim==1.4.7 Searching for fire==0.3.1 Best match: fire 0.3.1 Adding fire 0.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for ipywidgets==7.5.1 Best match: ipywidgets 7.5.1 Adding ipywidgets 7.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for plotly==4.9.0 Best match: plotly 4.9.0 Adding plotly 4.9.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for gunicorn==20.0.4 Best match: gunicorn 20.0.4 Adding gunicorn 20.0.4 to easy-install.pth file Installing gunicorn script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for scirisweb==0.17.0 Best match: scirisweb 0.17.0 Adding scirisweb 0.17.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for sciris==0.17.4 Best match: sciris 0.17.4 Adding sciris 0.17.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for numba==0.48.0 Best match: numba 0.48.0 Adding numba 0.48.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for statsmodels==0.11.1 Best match: statsmodels 0.11.1 Adding statsmodels 0.11.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for matplotlib==3.3.1 Best match: matplotlib 3.3.1 Adding matplotlib 3.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for scipy==1.5.2 Best match: scipy 1.5.2 Adding scipy 1.5.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pandas==1.1.0 Best match: pandas 1.1.0 Adding pandas 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for numpy==1.19.1 Best match: numpy 1.19.1 Adding numpy 1.19.1 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for termcolor==1.1.0 Best match: termcolor 1.1.0 Adding termcolor 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for widgetsnbextension==3.5.1 Best match: widgetsnbextension 3.5.1 Adding widgetsnbextension 3.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for nbformat==5.0.7 Best match: nbformat 5.0.7 Adding nbformat 5.0.7 to easy-install.pth file Installing jupyter-trust script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for traitlets==4.3.3 Best match: traitlets 4.3.3 Adding traitlets 4.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for ipython==7.17.0 Best match: ipython 7.17.0 Adding ipython 7.17.0 to easy-install.pth file Installing iptest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing iptest3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for ipykernel==5.3.4 Best match: ipykernel 5.3.4 Adding ipykernel 5.3.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for retrying==1.3.3 Best match: retrying 1.3.3 Adding retrying 1.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for setuptools==41.0.1 Best match: setuptools 41.0.1 Adding setuptools 41.0.1 to easy-install.pth file Installing easy_install script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing easy_install-3.6 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Werkzeug==1.0.1 Best match: Werkzeug 1.0.1 Adding Werkzeug 1.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Flask-Login==0.5.0 Best match: Flask-Login 0.5.0 Adding Flask-Login 0.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for SQLAlchemy==1.3.18 Best match: SQLAlchemy 1.3.18 Adding SQLAlchemy 1.3.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pyparsing==2.4.7 Best match: pyparsing 2.4.7 Adding pyparsing 2.4.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pyasn1==0.4.8 Best match: pyasn1 0.4.8 Adding pyasn1 0.4.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Flask-Session==0.3.2 Best match: Flask-Session 0.3.2 Adding Flask-Session 0.3.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Flask==1.1.2 Best match: Flask 1.1.2 Adding Flask 1.1.2 to easy-install.pth file Installing flask script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for redis==2.10.6 Best match: redis 2.10.6 Adding redis 2.10.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Twisted==20.3.0 Best match: Twisted 20.3.0 Adding Twisted 20.3.0 to easy-install.pth file Installing cftp script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing ckeygen script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing conch script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing mailmail script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing pyhtmlizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing tkconch script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing trial script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing twist script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing twistd script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for service-identity==18.1.0 Best match: service-identity 18.1.0 Adding service-identity 18.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for celery==4.4.7 Best match: celery 4.4.7 Adding celery 4.4.7 to easy-install.pth file Installing celery script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for decorator==4.4.2 Best match: decorator 4.4.2 Adding decorator 4.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for mpld3==0.5.1 Best match: mpld3 0.5.1 Adding mpld3 0.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for line-profiler==3.0.2 Best match: line-profiler 3.0.2 Adding line-profiler 3.0.2 to easy-install.pth file Installing kernprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for requests==2.24.0 Best match: requests 2.24.0 Adding requests 2.24.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for xlrd==1.2.0 Best match: xlrd 1.2.0 Adding xlrd 1.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jellyfish==0.8.2 Best match: jellyfish 0.8.2 Adding jellyfish 0.8.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for dill==0.3.2 Best match: dill 0.3.2 Adding dill 0.3.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for XlsxWriter==1.3.3 Best match: XlsxWriter 1.3.3 Adding XlsxWriter 1.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jsonpickle==1.4.1 Best match: jsonpickle 1.4.1 Adding jsonpickle 1.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for memory-profiler==0.57.0 Best match: memory-profiler 0.57.0 Adding memory-profiler 0.57.0 to easy-install.pth file Installing mprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for psutil==5.7.2 Best match: psutil 5.7.2 Adding psutil 5.7.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for openpyexcel==2.5.14 Best match: openpyexcel 2.5.14 Adding openpyexcel 2.5.14 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for GitPython==3.1.7 Best match: GitPython 3.1.7 Adding GitPython 3.1.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for llvmlite==0.31.0 Best match: llvmlite 0.31.0 Adding llvmlite 0.31.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for patsy==0.5.1 Best match: patsy 0.5.1 Adding patsy 0.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 Adding kiwisolver 1.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for certifi==2020.6.20 Best match: certifi 2020.6.20 Adding certifi 2020.6.20 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 Adding cycler 0.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Pillow==7.2.0 Best match: Pillow 7.2.0 Adding Pillow 7.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 Adding python-dateutil 2.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pytz==2020.1 Best match: pytz 2020.1 Adding pytz 2020.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for notebook==6.1.3 Best match: notebook 6.1.3 Adding notebook 6.1.3 to easy-install.pth file Installing jupyter-bundlerextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-nbextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-notebook script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-serverextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for ipython-genutils==0.2.0 Best match: ipython-genutils 0.2.0 Adding ipython-genutils 0.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jsonschema==3.2.0 Best match: jsonschema 3.2.0 Adding jsonschema 3.2.0 to easy-install.pth file Installing jsonschema script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jupyter-core==4.6.3 Best match: jupyter-core 4.6.3 Adding jupyter-core 4.6.3 to easy-install.pth file Installing jupyter script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-migrate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-troubleshoot script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for prompt-toolkit==3.0.6 Best match: prompt-toolkit 3.0.6 Adding prompt-toolkit 3.0.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for backcall==0.2.0 Best match: backcall 0.2.0 Adding backcall 0.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Pygments==2.3.1 Best match: Pygments 2.3.1 Adding Pygments 2.3.1 to easy-install.pth file Installing pygmentize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pexpect==4.8.0 Best match: pexpect 4.8.0 Adding pexpect 4.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jedi==0.17.2 Best match: jedi 0.17.2 Adding jedi 0.17.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pickleshare==0.7.5 Best match: pickleshare 0.7.5 Adding pickleshare 0.7.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for tornado==6.0.4 Best match: tornado 6.0.4 Adding tornado 6.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jupyter-client==6.1.6 Best match: jupyter-client 6.1.6 Adding jupyter-client 6.1.6 to easy-install.pth file Installing jupyter-kernel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-kernelspec script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing jupyter-run script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for cachelib==0.1.1 Best match: cachelib 0.1.1 Adding cachelib 0.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/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-covasim/envs/latest/lib/python3.7/site-packages Searching for itsdangerous==1.1.0 Best match: itsdangerous 1.1.0 Adding itsdangerous 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Jinja2==2.11.2 Best match: Jinja2 2.11.2 Adding Jinja2 2.11.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for hyperlink==20.0.1 Best match: hyperlink 20.0.1 Adding hyperlink 20.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for attrs==19.3.0 Best match: attrs 19.3.0 Adding attrs 19.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for PyHamcrest==2.0.2 Best match: PyHamcrest 2.0.2 Adding PyHamcrest 2.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for constantly==15.1.0 Best match: constantly 15.1.0 Adding constantly 15.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for incremental==17.5.0 Best match: incremental 17.5.0 Adding incremental 17.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Automat==20.2.0 Best match: Automat 20.2.0 Adding Automat 20.2.0 to easy-install.pth file Installing automat-visualize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for zope.interface==5.1.0 Best match: zope.interface 5.1.0 Adding zope.interface 5.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pyasn1-modules==0.2.8 Best match: pyasn1-modules 0.2.8 Adding pyasn1-modules 0.2.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for cryptography==3.0 Best match: cryptography 3.0 Adding cryptography 3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for vine==1.3.0 Best match: vine 1.3.0 Adding vine 1.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for billiard==3.6.3.0 Best match: billiard 3.6.3.0 Adding billiard 3.6.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for kombu==4.6.11 Best match: kombu 4.6.11 Adding kombu 4.6.11 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for urllib3==1.25.10 Best match: urllib3 1.25.10 Adding urllib3 1.25.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for chardet==3.0.4 Best match: chardet 3.0.4 Adding chardet 3.0.4 to easy-install.pth file Installing chardetect script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for idna==2.10 Best match: idna 2.10 Adding idna 2.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for importlib-metadata==1.7.0 Best match: importlib-metadata 1.7.0 Adding importlib-metadata 1.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for et-xmlfile==1.0.1 Best match: et-xmlfile 1.0.1 Adding et-xmlfile 1.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for jdcal==1.4.1 Best match: jdcal 1.4.1 Adding jdcal 1.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for gitdb==4.0.5 Best match: gitdb 4.0.5 Adding gitdb 4.0.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for nbconvert==5.6.1 Best match: nbconvert 5.6.1 Adding nbconvert 5.6.1 to easy-install.pth file Installing jupyter-nbconvert script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for prometheus-client==0.8.0 Best match: prometheus-client 0.8.0 Adding prometheus-client 0.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for argon2-cffi==20.1.0 Best match: argon2-cffi 20.1.0 Adding argon2-cffi 20.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for Send2Trash==1.5.0 Best match: Send2Trash 1.5.0 Adding Send2Trash 1.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pyzmq==19.0.2 Best match: pyzmq 19.0.2 Adding pyzmq 19.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for terminado==0.8.3 Best match: terminado 0.8.3 Adding terminado 0.8.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pyrsistent==0.16.0 Best match: pyrsistent 0.16.0 Adding pyrsistent 0.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for wcwidth==0.2.5 Best match: wcwidth 0.2.5 Adding wcwidth 0.2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for ptyprocess==0.6.0 Best match: ptyprocess 0.6.0 Adding ptyprocess 0.6.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for parso==0.7.1 Best match: parso 0.7.1 Adding parso 0.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for MarkupSafe==1.1.1 Best match: MarkupSafe 1.1.1 Adding MarkupSafe 1.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for cffi==1.14.1 Best match: cffi 1.14.1 Adding cffi 1.14.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for amqp==2.6.1 Best match: amqp 2.6.1 Adding amqp 2.6.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for zipp==3.1.0 Best match: zipp 3.1.0 Adding zipp 3.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for smmap==3.0.4 Best match: smmap 3.0.4 Adding smmap 3.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for defusedxml==0.6.0 Best match: defusedxml 0.6.0 Adding defusedxml 0.6.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for mistune==0.8.4 Best match: mistune 0.8.4 Adding mistune 0.8.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for testpath==0.4.4 Best match: testpath 0.4.4 Adding testpath 0.4.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for bleach==3.1.5 Best match: bleach 3.1.5 Adding bleach 3.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for entrypoints==0.3 Best match: entrypoints 0.3 Adding entrypoints 0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pandocfilters==1.4.2 Best match: pandocfilters 1.4.2 Adding pandocfilters 1.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for pycparser==2.20 Best match: pycparser 2.20 Adding pycparser 2.20 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for webencodings==0.5.1 Best match: webencodings 0.5.1 Adding webencodings 0.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Searching for packaging==20.4 Best match: packaging 20.4 Adding packaging 20.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Finished processing dependencies for covasim==1.4.7 [rtd-command-info] start-time: 2020-08-14T21:58:33.183315Z, end-time: 2020-08-14T21:58:33.234933Z, duration: 0, exit-code: 0 cat docs/conf.py # Sphinx Demo documentation 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 # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme 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__))) # -- General configuration ------------------------------------------------ # If your documentation 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.imgmath', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'plantweb.directive' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None } autodoc_mock_imports = [] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = 'Covasim' copyright = u'2020, Bill & Melinda Gates Foundation. All rights reserved.' author = '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. import covasim version = covasim.__version__ # The full version, including alpha/beta/rc tags. # release = '1.0' # The language for content autogenerated by Sphinx. Refer to documentation # 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'] # suppress warnings for multiple possible Python references in the namespace # suppress_warnings = ['ref.python'] # 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 documentation 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 # documentation. # # # 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 documentation" by default. # # html_title = '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' ] } # 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 documentation. # # 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 = 'Covasim' # -- 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': '%XeLaTeX packages' '\\usepackage{xltxtra}' '\\usepackage{fontspec} %%Font package' '\\usepackage{xunicode}' '%%Select fonts' '\\setmainfont[Mapping=tex-text]{nimbusserif}' '\\setsansfont[Mapping=tex-text]{nimbussans}' '\\setmonofont{nimbusmono}', # 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, 'covasim-docs.tex', 'Covasim', '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, 'covasim-docs', 'Covasim', [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, 'covasim-docs', 'Covasim', author, 'Institute for Disease Modeling', 'How to use IDM-Tools 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 # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': 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 # import importlib import sys import os.path from six import string_types 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': [ ("pdf", "//institute-for-disease-modeling-idm.readthedocs-hosted.com/_/downloads/covasim/en/latest/pdf/"), ("html", "//institute-for-disease-modeling-idm.readthedocs-hosted.com/_/downloads/covasim/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-covasim', 'name': u'covasim', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://institute-for-disease-modeling-idm.readthedocs-hosted.com/projects/covasim/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'JSchripsema-IDM', 'proxied_api_host': '/_', 'github_repo': 'covasim', 'github_version': 'rtd', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'rtd', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'rtd', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': 'ec06c2f2', } 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") 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: 2020-08-14T21:58:33.392796Z, end-time: 2020-08-14T21:58:47.370275Z, duration: 13, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.2.1 Covasim 1.4.7 (2020-06-02) — © 2020 by IDM loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] conduct reading sources... [ 18%] contributing reading sources... [ 27%] covasim.data reading sources... [ 36%] covasim.webapp reading sources... [ 45%] data reading sources... [ 54%] docker reading sources... [ 63%] index reading sources... [ 72%] modules reading sources... [ 81%] parameters reading sources... [ 90%] webapp reading sources... [100%] whatsnew looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 9%] conduct writing output... [ 18%] contributing writing output... [ 27%] covasim.data writing output... [ 36%] covasim.webapp writing output... [ 45%] data writing output... [ 54%] docker writing output... [ 63%] index writing output... [ 72%] modules writing output... [ 81%] parameters writing output... [ 90%] webapp writing output... [100%] whatsnew generating indices... genindex py-modindexdone writing additional pages... search opensearchdone copying static files... ... done copying readthedocs static files... done copying searchtools... 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. [rtd-command-info] start-time: 2020-08-14T21:58:47.507188Z, end-time: 2020-08-14T21:58:56.042225Z, duration: 8, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.2.1 Covasim 1.4.7 (2020-06-02) — © 2020 by IDM loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] conduct reading sources... [ 18%] contributing reading sources... [ 27%] covasim.data reading sources... [ 36%] covasim.webapp reading sources... [ 45%] data reading sources... [ 54%] docker reading sources... [ 63%] index reading sources... [ 72%] modules reading sources... [ 81%] parameters reading sources... [ 90%] webapp reading sources... [100%] whatsnew looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... parameters whatsnew contributing conduct webapp docker data modules covasim.data covasim.webapp done writing... done writing additional files... opensearchdone copying static files... ... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2020-08-14T21:58:56.198500Z, end-time: 2020-08-14T21:59:04.798391Z, duration: 8, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 Covasim 1.4.7 (2020-06-02) — © 2020 by IDM loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] conduct reading sources... [ 18%] contributing reading sources... [ 27%] covasim.data reading sources... [ 36%] covasim.webapp reading sources... [ 45%] data reading sources... [ 54%] docker reading sources... [ 63%] index reading sources... [ 72%] modules reading sources... [ 81%] parameters reading sources... [ 90%] webapp reading sources... [100%] whatsnew looking for now-outdated files... none found pickling environment... done checking consistency... done processing covasim-docs.tex... index parameters whatsnew contributing conduct webapp docker data modules covasim.data covasim.webapp 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). [rtd-command-info] start-time: 2020-08-14T21:59:05.012013Z, end-time: 2020-08-14T21:59:05.066635Z, 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: 2020-08-14T21:59:05.231198Z, end-time: 2020-08-14T21:59:08.086297Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-covasim -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-covasim" "covasim-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 (./covasim-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Warning: Hyper reference `index:licenses' on page 1 undefined on input li ne 157. LaTeX Warning: Hyper reference `index:tests' on page 1 undefined on input line 160. LaTeX Warning: Hyper reference `index:disclaimer' on page 1 undefined on input line 165. [1] [2] Chapter 1. [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [5] [6] Chapter 3. [7] [8] Chapter 4. [9] [10] Chapter 5. [11] [12] Chapter 6. [13] [14] Chapter 7. [15] [16] Chapter 8. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [17] [18] LaTeX Warning: Hyper reference `whatsnew:latest-versions-1-4-x' on page 19 unde fined on input line 591. LaTeX Warning: Hyper reference `whatsnew:versions-1-3-x-1-3-0-1-3-5' on page 19 undefined on input line 594. LaTeX Warning: Hyper reference `whatsnew:versions-1-2-x-1-2-0-1-2-3' on page 19 undefined on input line 597. LaTeX Warning: Hyper reference `whatsnew:versions-1-1-x-1-1-0-1-1-7' on page 19 undefined on input line 600. 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LaTeX Warning: Reference `modules:module-covasim.requirements' on page 93 undef ined on input line 8487. LaTeX Warning: Reference `modules:module-covasim.run' on page 93 undefined on i nput line 8488. LaTeX Warning: Reference `modules:module-covasim.sim' on page 93 undefined on i nput line 8489. LaTeX Warning: Reference `modules:module-covasim.utils' on page 93 undefined on input line 8490. LaTeX Warning: Reference `modules:module-covasim.version' on page 93 undefined on input line 8491. LaTeX Warning: Reference `covasim.webapp:module-covasim.webapp' on page 93 unde fined on input line 8492. LaTeX Warning: Reference `covasim.webapp:module-covasim.webapp.cova_app' on pag e 93 undefined on input line 8493. [93] No file institute-for-disease-modeling-covasim.ind. (./institute-for-disease-modeling-covasim.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-covasim.ou t' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on institute-for-disease-modeling-covasim.pdf (97 pages, 346650 bytes). Transcript written on institute-for-disease-modeling-covasim.log. Latexmk: Index file 'institute-for-disease-modeling-covasim.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-covasim.ind' from line 'No file institute-for-disease-modeling-covasim.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-covasim.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-covasim.pdf' Latexmk: List of undefined refs and citations: Reference `covasim.data:module-covasim.data' on page 93 undefined on input line 8475 Reference `covasim.data:module-covasim.data.country_age_data' on page 93 undefined on input line 8476 Reference `covasim.data:module-covasim.data.household_size_data' on page 93 undefined on input line 8477 Reference `covasim.data:module-covasim.data.loaders' on page 93 undefined on input line 8478 Reference `covasim.data:module-covasim.data.state_age_data' on page 93 undefined on input line 8479 Reference `covasim.webapp:module-covasim.webapp' on page 93 undefined on input line 8492 Reference `covasim.webapp:module-covasim.webapp.cova_app' on page 93 undefined on input line 8493 Reference `modules:module-covasim' on page 93 undefined on input line 8472 Reference `modules:module-covasim.analysis' on page 93 undefined on input line 8473 Reference `modules:module-covasim.base' on page 93 undefined on input line 8474 Reference `modules:module-covasim.defaults' on page 93 undefined on input line 8480 Reference `modules:module-covasim.interventions' on page 93 undefined on input line 8481 Reference `modules:module-covasim.misc' on page 93 undefined on input line 8482 Reference `modules:module-covasim.parameters' on page 93 undefined on input line 8483 Reference `modules:module-covasim.people' on page 93 undefined on input line 8484 Reference `modules:module-covasim.plotting' on page 93 undefined on input line 8485 Reference `modules:module-covasim.population' on page 93 undefined on input line 8486 Reference `modules:module-covasim.requirements' on page 93 undefined on input line 8487 Reference `modules:module-covasim.run' on page 93 undefined on input line 8488 Reference `modules:module-covasim.sim' on page 93 undefined on input line 8489 Reference `modules:module-covasim.utils' on page 93 undefined on input line 8490 Reference `modules:module-covasim.version' on page 93 undefined on input line 8491 Latexmk: Summary of warnings: Latex failed to resolve 22 reference(s) Rule 'makeindex institute-for-disease-modeling-covasim.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-covasim.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-covasim.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-covasim.ind" "institute-for-disease-modeling-covasim.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-covasim.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-covasim.idx....done (327 entries accepted, 0 rejected). Sorting entries.....done (2912 comparisons). Generating output file institute-for-disease-modeling-covasim.ind....done (424 lines written, 0 warnings). Output written in institute-for-disease-modeling-covasim.ind. Transcript written in institute-for-disease-modeling-covasim.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-covasim.aux' 'institute-for-disease-modeling-covasim.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-covasim" "covasim-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 (./covasim-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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sim_pars=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 epi_pars=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 int_pars=None\T1/ptm/m/n/10 , [45] [46] [47] [48] Underfull \hbox (badness 6775) in paragraph at lines 3803--3803 []\T1/ptm/m/it/10 start_day=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end_day=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 bins=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 width= 0.8\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fig_args=None\T1/ptm/m/n/10 , [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 5045--5045 []\T1/ptm/m/it/10 daily_tests\T1/ptm/m/n/10 , \T1/ptm/m/it/10 symp_test=100.0\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 quar_test=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5045--5045 \T1/ptm/m/it/10 sen-si-tiv-ity=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 loss_prob=0\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 test_delay=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5045--5045 \T1/ptm/m/it/10 start_day=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end_day=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 swab_delay=None\T1/ptm/m/n/10 , [59] Underfull \hbox (badness 10000) in paragraph at lines 5135--5135 []\T1/ptm/m/it/10 symp_prob\T1/ptm/m/n/10 , \T1/ptm/m/it/10 asymp_prob=0.0\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5135--5135 \T1/ptm/m/it/10 symp_quar_prob=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 asymp_quar_ prob=None\T1/ptm/m/n/10 , Underfull \hbox (badness 7133) in paragraph at lines 5135--5135 \T1/ptm/m/it/10 test_sensitivity=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 loss_prob= 0.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 test_delay=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5135--5135 \T1/ptm/m/it/10 start_day=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end_day=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 swab_delay=None\T1/ptm/m/n/10 , [60] Underfull \hbox (badness 10000) in paragraph at lines 5210--5210 []\T1/ptm/m/it/10 trace_probs=None\T1/ptm/m/n/10 , 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[67] [68] [69] Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 leg-end_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 show_args=Non e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 as_dates=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 date- Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 for-mat=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter-val=None\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 n_cols=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_ size=18\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 font_family=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 grid=False\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 com-mat-icks=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 setylim=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 log_scale=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-ors=None\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 la-bels=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 do_s how=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 []\T1/ptm/m/it/10 scens\T1/ptm/m/n/10 , \T1/ptm/m/it/10 to_plot=None\T1/ptm/m/n /10 , \T1/ptm/m/it/10 do_save=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fig_path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 fig_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_args=None\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 scat-ter_args=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 axis_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fill_args=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 leg-end_args=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 show_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 as_dates=True\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 date-for-mat=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter- Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 val=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 n_cols=None\T1/ptm/m/n /10 , \T1/ptm/m/it/10 font_size=18\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_family= None\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 grid=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 com-mat-icks=True\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 setylim=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 log_ scale=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 col-ors=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 la-bels=None\T1/pt m/m/n/10 , \T1/ptm/m/it/10 do_show=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sep_fig s=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6205--6205 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 log_scale=True\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 fig_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_args=No ne\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6205--6205 \T1/ptm/m/it/10 axis_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 scat-ter_args=No ne\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_size=18\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6213--6213 []\T1/ptm/m/it/10 people\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bins=None\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 width=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_size=18\T1/p tm/m/n/10 , \T1/ptm/m/it/10 al-pha=0.6\T1/ptm/m/n/10 , [70] Underfull \hbox (badness 10000) in paragraph at lines 6291--6291 []\T1/ptm/m/it/10 sim\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_age_data=True\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 use_household_data=True\T1/ptm/m/n/10 , [71] Underfull \hbox (badness 10000) in paragraph at lines 6344--6344 []\T1/ptm/m/it/10 pop_size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-tacts\T1/ptm/m/n /10 , \T1/ptm/m/it/10 over-shoot=1.2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-per- Underfull \hbox (badness 7613) in paragraph at lines 6384--6384 []\T1/ptm/m/it/10 pop_size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ages\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-tacts\T1/ptm/m/n/10 , \T1/ptm/m/it/10 school_ages=None\T1/ ptm/m/n/10 , [72] Underfull \hbox (badness 10000) in paragraph at lines 6472--6472 []\T1/ptm/m/it/10 sims=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 base_sim=None\T1/pt m/m/n/10 , \T1/ptm/m/it/10 quan-tiles=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ini- tial-ize=False\T1/ptm/m/n/10 , [73] [74] [75] [76] [77] [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 7221--7221 \T1/ptm/m/it/10 com-bine=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 keep_people=None \T1/ptm/m/n/10 , \T1/ptm/m/it/10 run_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sim_args=None\T1/ptm/m/n/10 , [80] [81] [82] [83] [84] [85] ! Package inputenc Error: Unicode char μ (U+3BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.7959 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} ! Package inputenc Error: Unicode char σ (U+3C3) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.7959 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} [86] [87] [88] [89] [90] [91] [92] [93] (./institute-for-disease-modeling-covasim.ind [94] Underfull \hbox (badness 10000) in paragraph at lines 18--19 []\T1/pcr/m/n/10 apply() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.intervention s.contact_tracing Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 apply() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.intervention s.dynamic_pars Underfull \hbox (badness 10000) in paragraph at lines 38--39 []\T1/pcr/m/n/10 check_diagnosed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.pe ople.People Underfull \hbox (badness 10000) in paragraph at lines 40--41 []\T1/pcr/m/n/10 check_infectious() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.p eople.People Underfull \hbox (badness 10000) in paragraph at lines 45--46 []\T1/pcr/m/n/10 check_scirisweb() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule c o-v- Underfull \hbox (badness 10000) in paragraph at lines 47--48 []\T1/pcr/m/n/10 check_symptomatic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim. people.People Underfull \hbox (badness 10000) in paragraph at lines 48--49 []\T1/pcr/m/n/10 check_synthpops() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule c o-v- Underfull \hbox (badness 10000) in paragraph at lines 64--65 []\T1/pcr/m/n/10 compute_mismatch() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.a nalysis.Fit Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/pcr/m/n/10 compute_windows() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v- [95] Underfull \hbox (badness 10000) in paragraph at lines 77--78 []\T1/pcr/m/n/10 count_targets() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.anal ysis.TransTree Underfull \hbox (badness 10000) in paragraph at lines 154--155 []\T1/pcr/m/n/10 from_sim() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.analysis. age_histogram Underfull \hbox (badness 10000) in paragraph at lines 164--166 []\T1/pcr/m/n/10 get_age_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule co-v- 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on institute-for-disease-modeling-covasim.pdf (103 pages, 378732 bytes). Transcript written on institute-for-disease-modeling-covasim.log. Latexmk: Index file 'institute-for-disease-modeling-covasim.idx' was written Latexmk: References changed. 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sim_pars=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 epi_pars=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 int_pars=None\T1/ptm/m/n/10 , [45] [46] [47] [48] Underfull \hbox (badness 6775) in paragraph at lines 3803--3803 []\T1/ptm/m/it/10 start_day=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end_day=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 bins=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 width= 0.8\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fig_args=None\T1/ptm/m/n/10 , [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 5045--5045 []\T1/ptm/m/it/10 daily_tests\T1/ptm/m/n/10 , \T1/ptm/m/it/10 symp_test=100.0\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 quar_test=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5045--5045 \T1/ptm/m/it/10 sen-si-tiv-ity=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 loss_prob=0\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 test_delay=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5045--5045 \T1/ptm/m/it/10 start_day=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end_day=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 swab_delay=None\T1/ptm/m/n/10 , [59] Underfull \hbox (badness 10000) in paragraph at lines 5135--5135 []\T1/ptm/m/it/10 symp_prob\T1/ptm/m/n/10 , \T1/ptm/m/it/10 asymp_prob=0.0\T1/p tm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5135--5135 \T1/ptm/m/it/10 symp_quar_prob=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 asymp_quar_ prob=None\T1/ptm/m/n/10 , Underfull \hbox (badness 7133) in paragraph at lines 5135--5135 \T1/ptm/m/it/10 test_sensitivity=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 loss_prob= 0.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 test_delay=0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5135--5135 \T1/ptm/m/it/10 start_day=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 end_day=None\T1/ptm /m/n/10 , \T1/ptm/m/it/10 swab_delay=None\T1/ptm/m/n/10 , [60] Underfull \hbox (badness 10000) in paragraph at lines 5210--5210 []\T1/ptm/m/it/10 trace_probs=None\T1/ptm/m/n/10 , 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[67] [68] [69] Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 leg-end_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 show_args=Non e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 as_dates=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 date- Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 for-mat=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter-val=None\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 n_cols=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_ size=18\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 font_family=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 grid=False\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 com-mat-icks=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 setylim=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6181--6181 \T1/ptm/m/it/10 log_scale=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 col-ors=None\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 la-bels=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 do_s how=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 []\T1/ptm/m/it/10 scens\T1/ptm/m/n/10 , \T1/ptm/m/it/10 to_plot=None\T1/ptm/m/n /10 , \T1/ptm/m/it/10 do_save=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fig_path=Non e\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 fig_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_args=None\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 scat-ter_args=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 axis_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fill_args=None\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 leg-end_args=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 show_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 as_dates=True\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 date-for-mat=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter- Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 val=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 n_cols=None\T1/ptm/m/n /10 , \T1/ptm/m/it/10 font_size=18\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_family= None\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 grid=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 com-mat-icks=True\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 setylim=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 log_ scale=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6189--6189 \T1/ptm/m/it/10 col-ors=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 la-bels=None\T1/pt m/m/n/10 , \T1/ptm/m/it/10 do_show=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sep_fig s=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6205--6205 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 log_scale=True\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 fig_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 plot_args=No ne\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6205--6205 \T1/ptm/m/it/10 axis_args=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 scat-ter_args=No ne\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_size=18\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6213--6213 []\T1/ptm/m/it/10 people\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bins=None\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 width=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 font_size=18\T1/p tm/m/n/10 , \T1/ptm/m/it/10 al-pha=0.6\T1/ptm/m/n/10 , [70] Underfull \hbox (badness 10000) in paragraph at lines 6291--6291 []\T1/ptm/m/it/10 sim\T1/ptm/m/n/10 , \T1/ptm/m/it/10 use_age_data=True\T1/ptm/ m/n/10 , \T1/ptm/m/it/10 use_household_data=True\T1/ptm/m/n/10 , [71] Underfull \hbox (badness 10000) in paragraph at lines 6344--6344 []\T1/ptm/m/it/10 pop_size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-tacts\T1/ptm/m/n /10 , \T1/ptm/m/it/10 over-shoot=1.2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-per- Underfull \hbox (badness 7613) in paragraph at lines 6384--6384 []\T1/ptm/m/it/10 pop_size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ages\T1/ptm/m/n/10 , \T1/ptm/m/it/10 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Package inputenc Error: Unicode char μ (U+3BC) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.7959 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} ! Package inputenc Error: Unicode char σ (U+3C3) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. 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written on institute-for-disease-modeling-covasim.pdf (103 pages, 378883 bytes). 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