Read the Docs build information Build id: 460718 Project: institute-for-disease-modeling-covasim Version: latest Commit: a55a849b2a1666e866c552356020a85fe7bd521f Date: 2020-10-23T23:16:35.398330Z State: finished Success: True [rtd-command-info] start-time: 2020-10-23T23:16:36.807252Z, end-time: 2020-10-23T23:16:38.386967Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/covasim.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2020-10-23T23:16:38.895093Z, end-time: 2020-10-23T23:16:38.970468Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by 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 a55a849 Merge pull request #713 from amath-idm/schools-merge [rtd-command-info] start-time: 2020-10-23T23:16:39.282768Z, end-time: 2020-10-23T23:16:39.340247Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-10-23T23:16:40.996073Z, end-time: 2020-10-23T23:16:46.097445Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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: 2020-10-23T23:16:46.293934Z, end-time: 2020-10-23T23:16:47.039084Z, 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 (20.2.4) [rtd-command-info] start-time: 2020-10-23T23:16:47.453481Z, end-time: 2020-10-23T23:16:55.572687Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I 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 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 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.1-py3-none-any.whl (944 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pyparsing>=2.0.2 Downloading 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) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 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=8b46c7835f26fb5fb3346e1111b143d1388aaef704cbb58c4bb0bedffdd4882a Stored in directory: /tmp/pip-ephem-wheel-cache-97o_6vdv/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=5a05f89b92db508dee95a371b23c9054cfac13fe25df1b245106ea4507478a7f Stored in directory: /tmp/pip-ephem-wheel-cache-97o_6vdv/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, certifi, idna, chardet, urllib3, requests, snowballstemmer, imagesize, MarkupSafe, Jinja2, six, pyparsing, packaging, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, Pygments, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts. We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default. matplotlib 3.3.2 requires pillow>=6.2.0, but you'll have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 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-50.3.2 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 urllib3-1.25.11 [rtd-command-info] start-time: 2020-10-23T23:16:56.168290Z, end-time: 2020-10-23T23:17:03.470191Z, duration: 7, 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-6.1.1-py3-none-any.whl (272 kB) Collecting numba==0.48.0 Downloading numba-0.48.0-1-cp37-cp37m-manylinux2014_x86_64.whl (3.5 MB) 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) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) 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: 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) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 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)) (2.7.1) 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) 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: 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)) (50.3.2) 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) 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) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) 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-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) 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-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting attrs>=17.4.0 Downloading attrs-20.2.0-py2.py3-none-any.whl (48 kB) Collecting pluggy<1.0,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting toml Downloading toml-0.10.1-py2.py3-none-any.whl (19 kB) Collecting importlib-metadata>=0.12; python_version < "3.8" Downloading importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB) Collecting py>=1.8.2 Downloading py-1.9.0-py2.py3-none-any.whl (99 kB) Requirement already satisfied: numpy>=1.15 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from numba==0.48.0->-r docs/requirements.txt (line 6)) (1.19.2) Collecting llvmlite<0.32.0,>=0.31.0dev0 Downloading llvmlite-0.31.0-cp37-cp37m-manylinux1_x86_64.whl (20.2 MB) 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: 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)) (1.25.11) 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: 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: 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: 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: 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) Collecting zipp>=0.5 Downloading zipp-3.3.1-py3-none-any.whl (5.3 kB) Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-qthelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, iniconfig, attrs, zipp, importlib-metadata, pluggy, toml, py, pytest, llvmlite, numba 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 attrs-20.2.0 importlib-metadata-2.0.0 iniconfig-1.1.1 llvmlite-0.31.0 numba-0.48.0 plantweb-1.2.1 pluggy-0.13.1 pockets-0.9.1 py-1.9.0 pytest-6.1.1 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 zipp-3.3.1 [rtd-command-info] start-time: 2020-10-23T23:17:03.716575Z, end-time: 2020-10-23T23:17:38.235795Z, duration: 34, 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__.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-1.7.6-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-1.7.6-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/covasim-1.7.6-py3.7.egg Extracting covasim-1.7.6-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 1.7.6 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-1.7.6-py3.7.egg Processing dependencies for covasim==1.7.6 Searching for fire Reading https://pypi.org/simple/fire/ Downloading https://files.pythonhosted.org/packages/34/a7/0e22e70778aca01a52b9c899d9c145c6396d7b613719cd63db97ffa13f2f/fire-0.3.1.tar.gz#sha256=9736a16227c3d469e5d2d296bce5b4d8fa8d7851e953bda327a455fc2994307f Best match: fire 0.3.1 Processing fire-0.3.1.tar.gz Writing /tmp/easy_install-eisej30x/fire-0.3.1/setup.cfg Running fire-0.3.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-eisej30x/fire-0.3.1/egg-dist-tmp-x9zxzq3r zip_safe flag not set; analyzing archive contents... fire.__pycache__.core.cpython-37: module MAY be using inspect.stack fire.__pycache__.core.cpython-37: module MAY be using inspect.trace fire.__pycache__.inspectutils.cpython-37: module MAY be using inspect.getsourcefile fire.__pycache__.inspectutils.cpython-37: module MAY be using inspect.findsource creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/fire-0.3.1-py3.7.egg Extracting fire-0.3.1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding fire 0.3.1 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/fire-0.3.1-py3.7.egg Searching for ipywidgets Reading https://pypi.org/simple/ipywidgets/ Downloading https://files.pythonhosted.org/packages/75/cb/a6d9f104b2be9e0f373ae6deb205cca2186cce9ad96a833eefd4865f2d54/ipywidgets-8.0.0a0-py3-none-any.whl#sha256=9cb5590e583b8ea309a2d8e88fb02e44d054df2a77891f7d3356b0b883b99d3d Best match: ipywidgets 8.0.0a0 Processing ipywidgets-8.0.0a0-py3-none-any.whl Installing ipywidgets-8.0.0a0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/ipywidgets-8.0.0a0-py3.7.egg/EGG-INFO/requires.txt Adding ipywidgets 8.0.0a0 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/ipywidgets-8.0.0a0-py3.7.egg Searching for plotly Reading https://pypi.org/simple/plotly/ Downloading https://files.pythonhosted.org/packages/a6/66/af86e9d9bf1a3e4f2dabebeabd02a32e8ddf671a5d072b3af2b011efea99/plotly-4.12.0-py2.py3-none-any.whl#sha256=c50babbb4f8ad12e2a4f004df5d80c1dbf10c38e9325b5ffb1146b383687ef52 Best match: plotly 4.12.0 Processing plotly-4.12.0-py2.py3-none-any.whl Installing plotly-4.12.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/plotly-4.12.0-py3.7.egg/EGG-INFO/requires.txt Adding plotly 4.12.0 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/plotly-4.12.0-py3.7.egg Searching for gunicorn Reading https://pypi.org/simple/gunicorn/ Downloading https://files.pythonhosted.org/packages/69/ca/926f7cd3a2014b16870086b2d0fdc84a9e49473c68a8dff8b57f7c156f43/gunicorn-20.0.4-py2.py3-none-any.whl#sha256=cd4a810dd51bf497552cf3f863b575dabd73d6ad6a91075b65936b151cbf4f9c Best match: gunicorn 20.0.4 Processing gunicorn-20.0.4-py2.py3-none-any.whl Installing gunicorn-20.0.4-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/gunicorn-20.0.4-py3.7.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/gunicorn-20.0.4-py3.7.egg Searching for scirisweb>=0.17.0 Reading https://pypi.org/simple/scirisweb/ Downloading https://files.pythonhosted.org/packages/fd/95/1bdea6908657149c52a7a8172774e9340581aa76cb58b5cecfa31baebb51/scirisweb-0.17.0-py3-none-any.whl#sha256=d03c894fc6482cce3d4b0c24c3d57f2fe2ec33e01c205434c6ed8ce40a7d5dc5 Best match: scirisweb 0.17.0 Processing scirisweb-0.17.0-py3-none-any.whl Installing scirisweb-0.17.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/scirisweb-0.17.0-py3.7.egg/EGG-INFO/requires.txt Adding scirisweb 0.17.0 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/scirisweb-0.17.0-py3.7.egg Searching for sciris>=0.17.0 Reading https://pypi.org/simple/sciris/ Downloading https://files.pythonhosted.org/packages/00/41/b9d322d413080daff10aef2309a14f37342f7e1e50f3adf1db0573fee7dc/sciris-0.17.4-py3-none-any.whl#sha256=6baaa7d7cf0def872f624bdcf0525c02ab1a5a48a2a9adca4f4f91d47f61e626 Best match: sciris 0.17.4 Processing sciris-0.17.4-py3-none-any.whl Installing sciris-0.17.4-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/sciris-0.17.4-py3.7.egg/EGG-INFO/requires.txt Adding sciris 0.17.4 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/sciris-0.17.4-py3.7.egg Searching for statsmodels Reading https://pypi.org/simple/statsmodels/ Downloading https://files.pythonhosted.org/packages/ff/68/ca52fc6a114141f13dfaee340fc355e2825753f1cbe3702a13a5046e16de/statsmodels-0.12.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=9ada3ddf13e60a5728304e6ca176e6ad8ca83b80c85db593087d853c5c6d4a98 Best match: statsmodels 0.12.0 Processing statsmodels-0.12.0-cp37-cp37m-manylinux1_x86_64.whl Installing statsmodels-0.12.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/statsmodels-0.12.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding statsmodels 0.12.0 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/statsmodels-0.12.0-py3.7-linux-x86_64.egg Searching for termcolor Reading https://pypi.org/simple/termcolor/ Downloading https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz#sha256=1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b Best match: termcolor 1.1.0 Processing termcolor-1.1.0.tar.gz Writing /tmp/easy_install-uknf_fu9/termcolor-1.1.0/setup.cfg Running termcolor-1.1.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-uknf_fu9/termcolor-1.1.0/egg-dist-tmp-gw4hm4dd zip_safe flag not set; analyzing archive contents... Moving termcolor-1.1.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding termcolor 1.1.0 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/termcolor-1.1.0-py3.7.egg Searching for widgetsnbextension~=4.0a0 Reading https://pypi.org/simple/widgetsnbextension/ Downloading https://files.pythonhosted.org/packages/28/eb/093a3772a77e1c21cf60ce5880c09017fb33191b6c796e5b480ef8607690/widgetsnbextension-4.0.0a0-py3-none-any.whl#sha256=cb6181b4037da02deeabab39d5cb1113a7390aee7468b1f8237c2abbd6df6107 Best match: widgetsnbextension 4.0.0a0 Processing widgetsnbextension-4.0.0a0-py3-none-any.whl Installing widgetsnbextension-4.0.0a0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding widgetsnbextension 4.0.0a0 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/widgetsnbextension-4.0.0a0-py3.7.egg Searching for traitlets>=4.3.1 Reading https://pypi.org/simple/traitlets/ Downloading https://files.pythonhosted.org/packages/f6/7d/3ecb0ebd0ce8dcdfa7bd47ab85c1d4a521e6770ef283d0824f5804994dfe/traitlets-5.0.5-py3-none-any.whl#sha256=69ff3f9d5351f31a7ad80443c2674b7099df13cc41fc5fa6e2f6d3b0330b0426 Best match: traitlets 5.0.5 Processing traitlets-5.0.5-py3-none-any.whl Installing traitlets-5.0.5-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/traitlets-5.0.5-py3.7.egg/EGG-INFO/requires.txt Adding traitlets 5.0.5 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/traitlets-5.0.5-py3.7.egg Searching for nbformat>=4.2.0 Reading https://pypi.org/simple/nbformat/ Downloading https://files.pythonhosted.org/packages/40/f7/b9a7c82aff85b706f2824c97727b8e2106bb992bd553e93082b9c6dd45fe/nbformat-5.0.8-py3-none-any.whl#sha256=aa9450c16d29286dc69b92ea4913c1bffe86488f90184445996ccc03a2f60382 Best match: nbformat 5.0.8 Processing nbformat-5.0.8-py3-none-any.whl Installing nbformat-5.0.8-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbformat-5.0.8-py3.7.egg/EGG-INFO/requires.txt Adding nbformat 5.0.8 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/nbformat-5.0.8-py3.7.egg Searching for ipython>=6.1.0 Reading https://pypi.org/simple/ipython/ Downloading https://files.pythonhosted.org/packages/72/36/89e1bb437f4f2275c33acc6eb333ab2d1c64e732ad23d6f34825b512e1a3/ipython-7.18.1-py3-none-any.whl#sha256=2e22c1f74477b5106a6fb301c342ab8c64bb75d702e350f05a649e8cb40a0fb8 Best match: ipython 7.18.1 Processing ipython-7.18.1-py3-none-any.whl Installing ipython-7.18.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/ipython-7.18.1-py3.7.egg/EGG-INFO/requires.txt Adding ipython 7.18.1 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/ipython-7.18.1-py3.7.egg Searching for ipykernel>=4.5.1 Reading https://pypi.org/simple/ipykernel/ Downloading https://files.pythonhosted.org/packages/52/19/c2812690d8b340987eecd2cbc18549b1d130b94c5d97fcbe49f5f8710edf/ipykernel-5.3.4-py3-none-any.whl#sha256=d6fbba26dba3cebd411382bc484f7bc2caa98427ae0ddb4ab37fe8bfeb5c7dd3 Best match: ipykernel 5.3.4 Processing ipykernel-5.3.4-py3-none-any.whl Installing ipykernel-5.3.4-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/ipykernel-5.3.4-py3.7.egg/EGG-INFO/requires.txt Adding ipykernel 5.3.4 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/ipykernel-5.3.4-py3.7.egg Searching for retrying>=1.3.3 Reading https://pypi.org/simple/retrying/ Downloading https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz#sha256=08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b Best match: retrying 1.3.3 Processing retrying-1.3.3.tar.gz Writing /tmp/easy_install-7ter1b4c/retrying-1.3.3/setup.cfg Running retrying-1.3.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-7ter1b4c/retrying-1.3.3/egg-dist-tmp-svaz87m7 zip_safe flag not set; analyzing archive contents... Moving retrying-1.3.3-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding retrying 1.3.3 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/retrying-1.3.3-py3.7.egg Searching for werkzeug Reading https://pypi.org/simple/werkzeug/ Downloading https://files.pythonhosted.org/packages/cc/94/5f7079a0e00bd6863ef8f1da638721e9da21e5bacee597595b318f71d62e/Werkzeug-1.0.1-py2.py3-none-any.whl#sha256=2de2a5db0baeae7b2d2664949077c2ac63fbd16d98da0ff71837f7d1dea3fd43 Best match: Werkzeug 1.0.1 Processing Werkzeug-1.0.1-py2.py3-none-any.whl Installing Werkzeug-1.0.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Werkzeug-1.0.1-py3.7.egg/EGG-INFO/requires.txt Adding Werkzeug 1.0.1 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/Werkzeug-1.0.1-py3.7.egg Searching for twisted>=18.4.0 Reading https://pypi.org/simple/twisted/ Downloading https://files.pythonhosted.org/packages/b8/f9/489416dda6de8ae6419356bf003c10d1ce6fb8377b6a3207b02b3a39c42a/Twisted-20.3.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=894f6f3cfa57a15ea0d0714e4283913a5f2511dbd18653dd148eba53b3919797 Best match: Twisted 20.3.0 Processing Twisted-20.3.0-cp37-cp37m-manylinux1_x86_64.whl Installing Twisted-20.3.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Twisted-20.3.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Twisted-20.3.0-py3.7-linux-x86_64.egg Searching for sqlalchemy Reading https://pypi.org/simple/sqlalchemy/ Downloading https://files.pythonhosted.org/packages/24/66/962298533cb599e7c4c27791189b750b0ac12140043e48848811fbd82b8d/SQLAlchemy-1.3.20-cp37-cp37m-manylinux1_x86_64.whl#sha256=9e379674728f43a0cd95c423ac0e95262500f9bfd81d33b999daa8ea1756d162 Best match: SQLAlchemy 1.3.20 Processing SQLAlchemy-1.3.20-cp37-cp37m-manylinux1_x86_64.whl Installing SQLAlchemy-1.3.20-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/SQLAlchemy-1.3.20-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding SQLAlchemy 1.3.20 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/SQLAlchemy-1.3.20-py3.7-linux-x86_64.egg Searching for service-identity Reading https://pypi.org/simple/service-identity/ Downloading https://files.pythonhosted.org/packages/e9/7c/2195b890023e098f9618d43ebc337d83c8b38d414326685339eb024db2f6/service_identity-18.1.0-py2.py3-none-any.whl#sha256=001c0707759cb3de7e49c078a7c0c9cd12594161d3bf06b9c254fdcb1a60dc36 Best match: service-identity 18.1.0 Processing service_identity-18.1.0-py2.py3-none-any.whl Installing service_identity-18.1.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/service_identity-18.1.0-py3.7.egg/EGG-INFO/requires.txt Adding service-identity 18.1.0 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/service_identity-18.1.0-py3.7.egg Searching for redis==2.10.6 Reading https://pypi.org/simple/redis/ Downloading https://files.pythonhosted.org/packages/3b/f6/7a76333cf0b9251ecf49efff635015171843d9b977e4ffcf59f9c4428052/redis-2.10.6-py2.py3-none-any.whl#sha256=8a1900a9f2a0a44ecf6e8b5eb3e967a9909dfed219ad66df094f27f7d6f330fb Best match: redis 2.10.6 Processing redis-2.10.6-py2.py3-none-any.whl Installing redis-2.10.6-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding redis 2.10.6 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/redis-2.10.6-py3.7.egg Searching for pyasn1 Reading https://pypi.org/simple/pyasn1/ Downloading https://files.pythonhosted.org/packages/62/1e/a94a8d635fa3ce4cfc7f506003548d0a2447ae76fd5ca53932970fe3053f/pyasn1-0.4.8-py2.py3-none-any.whl#sha256=39c7e2ec30515947ff4e87fb6f456dfc6e84857d34be479c9d4a4ba4bf46aa5d Best match: pyasn1 0.4.8 Processing pyasn1-0.4.8-py2.py3-none-any.whl Installing pyasn1-0.4.8-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding pyasn1 0.4.8 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/pyasn1-0.4.8-py3.7.egg Searching for mpld3 Reading https://pypi.org/simple/mpld3/ Downloading https://files.pythonhosted.org/packages/66/31/89bd2afd21b920e3612996623e7b3aac14d741537aa77600ea5102a34be0/mpld3-0.5.1.tar.gz#sha256=1677a314125ff2984e2f291d595188d5ee8ca66ac21b0c2c8633961bc33a7bf8 Best match: mpld3 0.5.1 Processing mpld3-0.5.1.tar.gz Writing /tmp/easy_install-_7_lx_36/mpld3-0.5.1/setup.cfg Running mpld3-0.5.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-_7_lx_36/mpld3-0.5.1/egg-dist-tmp-3afecgn0 warning: no files found matching 'visual_tests.py' zip_safe flag not set; analyzing archive contents... mpld3.__pycache__.__init__.cpython-37: module references __file__ mpld3.__pycache__.urls.cpython-37: module references __path__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/mpld3-0.5.1-py3.7.egg Extracting mpld3-0.5.1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding mpld3 0.5.1 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/mpld3-0.5.1-py3.7.egg Searching for flask>=1.0.0 Reading https://pypi.org/simple/flask/ Downloading https://files.pythonhosted.org/packages/f2/28/2a03252dfb9ebf377f40fba6a7841b47083260bf8bd8e737b0c6952df83f/Flask-1.1.2-py2.py3-none-any.whl#sha256=8a4fdd8936eba2512e9c85df320a37e694c93945b33ef33c89946a340a238557 Best match: Flask 1.1.2 Processing Flask-1.1.2-py2.py3-none-any.whl Installing Flask-1.1.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Flask-1.1.2-py3.7.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Flask-1.1.2-py3.7.egg Searching for flask-session>=0.3.1 Reading https://pypi.org/simple/flask-session/ Downloading https://files.pythonhosted.org/packages/32/6a/c1cf600a14b98347a35b1142bb5f2674f356c261a6de4a36c88fc8a47620/Flask_Session-0.3.2-py2.py3-none-any.whl#sha256=d75eb27f918421ccaf1ba86353348b84ecf07fc64ce40ff7ad05a190c4bf50f1 Best match: Flask-Session 0.3.2 Processing Flask_Session-0.3.2-py2.py3-none-any.whl Installing Flask_Session-0.3.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Flask_Session-0.3.2-py3.7.egg/EGG-INFO/requires.txt Adding Flask-Session 0.3.2 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/Flask_Session-0.3.2-py3.7.egg Searching for flask-login>=0.4.1 Reading https://pypi.org/simple/flask-login/ Downloading https://files.pythonhosted.org/packages/2b/83/ac5bf3279f969704fc1e63f050c50e10985e50fd340e6069ec7e09df5442/Flask_Login-0.5.0-py2.py3-none-any.whl#sha256=7451b5001e17837ba58945aead261ba425fdf7b4f0448777e597ddab39f4fba0 Best match: Flask-Login 0.5.0 Processing Flask_Login-0.5.0-py2.py3-none-any.whl Installing Flask_Login-0.5.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Flask_Login-0.5.0-py3.7.egg/EGG-INFO/requires.txt Adding Flask-Login 0.5.0 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/Flask_Login-0.5.0-py3.7.egg Searching for decorator>=4.1.2 Reading https://pypi.org/simple/decorator/ Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760 Best match: decorator 4.4.2 Processing decorator-4.4.2-py2.py3-none-any.whl Installing decorator-4.4.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding decorator 4.4.2 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/decorator-4.4.2-py3.7.egg Searching for celery>=4.2 Reading https://pypi.org/simple/celery/ Downloading https://files.pythonhosted.org/packages/a7/a1/bd9fb8e546344b0a7fa2b986b15ec281a68387aea101b0e557887c5a1d17/celery-5.0.1-py3-none-any.whl#sha256=7aa4ee46ed318bc177900ae7c01500354aee62d723255b0925db0754bcd4d390 Best match: celery 5.0.1 Processing celery-5.0.1-py3-none-any.whl Installing celery-5.0.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/celery-5.0.1-py3.7.egg/EGG-INFO/requires.txt Adding celery 5.0.1 to easy-install.pth file Installing celery script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/celery-5.0.1-py3.7.egg Searching for xlsxwriter Reading https://pypi.org/simple/xlsxwriter/ Downloading https://files.pythonhosted.org/packages/6b/41/bf1aae04932d1eaffee1fc5f8b38ca47bbbf07d765129539bc4bcce1ce0c/XlsxWriter-1.3.7-py2.py3-none-any.whl#sha256=b807c2d3e379bf6a925f472955beef3e07495c1bac708640696876e68675b49b Best match: XlsxWriter 1.3.7 Processing XlsxWriter-1.3.7-py2.py3-none-any.whl Installing XlsxWriter-1.3.7-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding XlsxWriter 1.3.7 to easy-install.pth file Installing vba_extract.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/XlsxWriter-1.3.7-py3.7.egg Searching for xlrd Reading https://pypi.org/simple/xlrd/ Downloading https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl#sha256=e551fb498759fa3a5384a94ccd4c3c02eb7c00ea424426e212ac0c57be9dfbde Best match: xlrd 1.2.0 Processing xlrd-1.2.0-py2.py3-none-any.whl Installing xlrd-1.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding xlrd 1.2.0 to easy-install.pth file Installing runxlrd.py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/xlrd-1.2.0-py3.7.egg Searching for psutil Reading https://pypi.org/simple/psutil/ Downloading https://files.pythonhosted.org/packages/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz#sha256=90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb Best match: psutil 5.7.2 Processing psutil-5.7.2.tar.gz Writing /tmp/easy_install-p0ao8rv1/psutil-5.7.2/setup.cfg Running psutil-5.7.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-p0ao8rv1/psutil-5.7.2/egg-dist-tmp-b5p8cjis creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/psutil-5.7.2-py3.7-linux-x86_64.egg Extracting psutil-5.7.2-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding psutil 5.7.2 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/psutil-5.7.2-py3.7-linux-x86_64.egg Searching for openpyexcel>=2.5 Reading https://pypi.org/simple/openpyexcel/ Downloading https://files.pythonhosted.org/packages/32/e1/722047fae7a46b658d7fa038cf5b952fbbb150c3c8a31012e4fb76eba27d/openpyexcel-2.5.14-py2.py3-none-any.whl#sha256=f18f4efadbc25a26870885f342e14b6cd6862ca1f4b8195b394fc2681ccdbaab Best match: openpyexcel 2.5.14 Processing openpyexcel-2.5.14-py2.py3-none-any.whl Installing openpyexcel-2.5.14-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/openpyexcel-2.5.14-py3.7.egg/EGG-INFO/requires.txt Adding openpyexcel 2.5.14 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/openpyexcel-2.5.14-py3.7.egg Searching for memory-profiler Reading https://pypi.org/simple/memory-profiler/ Downloading https://files.pythonhosted.org/packages/8f/fd/d92b3295657f8837e0177e7b48b32d6651436f0293af42b76d134c3bb489/memory_profiler-0.58.0.tar.gz#sha256=01385ac0fec944fcf7969814ec4406c6d8a9c66c079d09276723c5a7680f44e5 Best match: memory-profiler 0.58.0 Processing memory_profiler-0.58.0.tar.gz Writing /tmp/easy_install-sr3ynf33/memory_profiler-0.58.0/setup.cfg Running memory_profiler-0.58.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-sr3ynf33/memory_profiler-0.58.0/egg-dist-tmp-zbl_m77r warning: no files found matching 'mprof.bat' zip_safe flag not set; analyzing archive contents... __pycache__.memory_profiler.cpython-37: module MAY be using inspect.getsourcefile __pycache__.memory_profiler.cpython-37: module MAY be using inspect.stack __pycache__.memory_profiler.cpython-37: module MAY be using inspect.trace creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/memory_profiler-0.58.0-py3.7.egg Extracting memory_profiler-0.58.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding memory-profiler 0.58.0 to easy-install.pth file Installing mprof script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/memory_profiler-0.58.0-py3.7.egg Searching for line-profiler Reading https://pypi.org/simple/line-profiler/ Downloading https://files.pythonhosted.org/packages/a3/c7/8c3af643c203c1e481043caca821dce9cb0b14e1cbff20e06d117be2713c/line_profiler-3.0.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=e095430561ae8166d698a02ec9c08a30a7018baceda423e8919e390e0ba9acda Best match: line-profiler 3.0.2 Processing line_profiler-3.0.2-cp37-cp37m-manylinux1_x86_64.whl Installing line_profiler-3.0.2-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/line_profiler-3.0.2-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/line_profiler-3.0.2-py3.7-linux-x86_64.egg Searching for jsonpickle Reading https://pypi.org/simple/jsonpickle/ Downloading https://files.pythonhosted.org/packages/af/ca/4fee219cc4113a5635e348ad951cf8a2e47fed2e3342312493f5b73d0007/jsonpickle-1.4.1-py2.py3-none-any.whl#sha256=8919c166bac0574e3d74425c7559434062002d9dfc0ac2afa6dc746ba4a19439 Best match: jsonpickle 1.4.1 Processing jsonpickle-1.4.1-py2.py3-none-any.whl Installing jsonpickle-1.4.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jsonpickle-1.4.1-py3.7.egg/EGG-INFO/requires.txt Adding jsonpickle 1.4.1 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/jsonpickle-1.4.1-py3.7.egg Searching for jellyfish Reading https://pypi.org/simple/jellyfish/ Downloading https://files.pythonhosted.org/packages/04/3f/d03cb056f407ef181a45569255348457b1a0915fc4eb23daeceb930a68a4/jellyfish-0.8.2.tar.gz#sha256=a499741401512d05bbd3556e448e960bc908eba3879fb73d450e8e91566a030b Best match: jellyfish 0.8.2 Processing jellyfish-0.8.2.tar.gz Writing /tmp/easy_install-ry20y7o2/jellyfish-0.8.2/setup.cfg Running jellyfish-0.8.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ry20y7o2/jellyfish-0.8.2/egg-dist-tmp-czcg8as0 warning: no previously-included files matching '.git' found anywhere in distribution cjellyfish/soundex.c: In function ‘soundex’: cjellyfish/soundex.c:8:10: warning: ‘c’ may be used uninitialized in this function [-Wmaybe-uninitialized] char c, prev; ^ cjellyfish/porter.c: In function ‘m’: cjellyfish/porter.c:127:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (! cons(z, i)) break; i++; ^~ cjellyfish/porter.c:127:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (! cons(z, i)) break; i++; ^ cjellyfish/porter.c: In function ‘step4’: cjellyfish/porter.c:339:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ends(z, 4, "ence")) break; return; ^~ cjellyfish/porter.c:339:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ends(z, 4, "ence")) break; return; ^~~~~~ cjellyfish/porter.c:343:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ends(z, 4, "ible")) break; return; ^~ cjellyfish/porter.c:343:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ends(z, 4, "ible")) break; return; ^~~~~~ cjellyfish/porter.c:347:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ends(z, 3, "ent")) break; return; ^~ cjellyfish/porter.c:347:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ends(z, 3, "ent")) break; return; ^~~~~~ cjellyfish/porter.c:349:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ends(z, 2, "ou")) break; return; ^~ cjellyfish/porter.c:349:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ends(z, 2, "ou")) break; return; ^~~~~~ cjellyfish/porter.c:353:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ends(z, 3, "iti")) break; return; ^~ cjellyfish/porter.c:353:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ends(z, 3, "iti")) break; return; ^~~~~~ zip_safe flag not set; analyzing archive contents... jellyfish.__pycache__.cjellyfish.cpython-37: module references __file__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jellyfish-0.8.2-py3.7-linux-x86_64.egg Extracting jellyfish-0.8.2-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding jellyfish 0.8.2 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/jellyfish-0.8.2-py3.7-linux-x86_64.egg Searching for gitpython Reading https://pypi.org/simple/gitpython/ Downloading https://files.pythonhosted.org/packages/24/d1/a7f8fe3df258549b303415157328bfcc63e9b11d06a7ad7a3327f3d32606/GitPython-3.1.11-py3-none-any.whl#sha256=6eea89b655917b500437e9668e4a12eabdcf00229a0df1762aabd692ef9b746b Best match: GitPython 3.1.11 Processing GitPython-3.1.11-py3-none-any.whl Installing GitPython-3.1.11-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/GitPython-3.1.11-py3.7.egg/EGG-INFO/requires.txt Adding GitPython 3.1.11 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/GitPython-3.1.11-py3.7.egg Searching for dill Reading https://pypi.org/simple/dill/ Downloading https://files.pythonhosted.org/packages/e2/96/518a8ea959a734b70d2e95fef98bcbfdc7adad1c1e5f5dd9148c835205a5/dill-0.3.2.zip#sha256=6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e Best match: dill 0.3.2 Processing dill-0.3.2.zip Writing /tmp/easy_install-gfnozu5y/dill-0.3.2/setup.cfg Running dill-0.3.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-gfnozu5y/dill-0.3.2/egg-dist-tmp-tqz4oc29 no previously-included directories found matching '.git' no previously-included directories found matching '.coverage' creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/dill-0.3.2-py3.7.egg Extracting dill-0.3.2-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding dill 0.3.2 to easy-install.pth file Installing undill script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing get_objgraph script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/dill-0.3.2-py3.7.egg Searching for patsy>=0.5 Reading https://pypi.org/simple/patsy/ Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl#sha256=5465be1c0e670c3a965355ec09e9a502bf2c4cbe4875e8528b0221190a8a5d40 Best match: patsy 0.5.1 Processing patsy-0.5.1-py2.py3-none-any.whl Installing patsy-0.5.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/patsy-0.5.1-py3.7.egg/EGG-INFO/requires.txt Adding patsy 0.5.1 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/patsy-0.5.1-py3.7.egg Searching for ipython-genutils Reading https://pypi.org/simple/ipython-genutils/ Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl#sha256=72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8 Best match: ipython-genutils 0.2.0 Processing ipython_genutils-0.2.0-py2.py3-none-any.whl Installing ipython_genutils-0.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding ipython-genutils 0.2.0 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/ipython_genutils-0.2.0-py3.7.egg Searching for jupyter-core Reading https://pypi.org/simple/jupyter-core/ Downloading https://files.pythonhosted.org/packages/63/0d/df2d17cdf389cea83e2efa9a4d32f7d527ba78667e0153a8e676e957b2f7/jupyter_core-4.6.3-py2.py3-none-any.whl#sha256=a4ee613c060fe5697d913416fc9d553599c05e4492d58fac1192c9a6844abb21 Best match: jupyter-core 4.6.3 Processing jupyter_core-4.6.3-py2.py3-none-any.whl Installing jupyter_core-4.6.3-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_core-4.6.3-py3.7.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_core-4.6.3-py3.7.egg Searching for jsonschema!=2.5.0,>=2.4 Reading https://pypi.org/simple/jsonschema/ Downloading https://files.pythonhosted.org/packages/c5/8f/51e89ce52a085483359217bc72cdbf6e75ee595d5b1d4b5ade40c7e018b8/jsonschema-3.2.0-py2.py3-none-any.whl#sha256=4e5b3cf8216f577bee9ce139cbe72eca3ea4f292ec60928ff24758ce626cd163 Best match: jsonschema 3.2.0 Processing jsonschema-3.2.0-py2.py3-none-any.whl Installing jsonschema-3.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jsonschema-3.2.0-py3.7.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jsonschema-3.2.0-py3.7.egg Searching for prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Reading https://pypi.org/simple/prompt-toolkit/ Downloading https://files.pythonhosted.org/packages/8a/aa/198e6a857e83ea8b711a6ae0c37717c0eb1b23ff52e3732a644fcd389cb3/prompt_toolkit-3.0.8-py3-none-any.whl#sha256=7debb9a521e0b1ee7d2fe96ee4bd60ef03c6492784de0547337ca4433e46aa63 Best match: prompt-toolkit 3.0.8 Processing prompt_toolkit-3.0.8-py3-none-any.whl Installing prompt_toolkit-3.0.8-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/prompt_toolkit-3.0.8-py3.7.egg/EGG-INFO/requires.txt Adding prompt-toolkit 3.0.8 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/prompt_toolkit-3.0.8-py3.7.egg Searching for pickleshare Reading https://pypi.org/simple/pickleshare/ Downloading https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl#sha256=9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56 Best match: pickleshare 0.7.5 Processing pickleshare-0.7.5-py2.py3-none-any.whl Installing pickleshare-0.7.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding pickleshare 0.7.5 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/pickleshare-0.7.5-py3.7.egg Searching for pexpect>4.3 Reading https://pypi.org/simple/pexpect/ Downloading https://files.pythonhosted.org/packages/39/7b/88dbb785881c28a102619d46423cb853b46dbccc70d3ac362d99773a78ce/pexpect-4.8.0-py2.py3-none-any.whl#sha256=0b48a55dcb3c05f3329815901ea4fc1537514d6ba867a152b581d69ae3710937 Best match: pexpect 4.8.0 Processing pexpect-4.8.0-py2.py3-none-any.whl Installing pexpect-4.8.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/pexpect-4.8.0-py3.7.egg/EGG-INFO/requires.txt Adding pexpect 4.8.0 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/pexpect-4.8.0-py3.7.egg Searching for jedi>=0.10 Reading https://pypi.org/simple/jedi/ Downloading https://files.pythonhosted.org/packages/c3/d4/36136b18daae06ad798966735f6c3fb96869c1be9f8245d2a8f556e40c36/jedi-0.17.2-py2.py3-none-any.whl#sha256=98cc583fa0f2f8304968199b01b6b4b94f469a1f4a74c1560506ca2a211378b5 Best match: jedi 0.17.2 Processing jedi-0.17.2-py2.py3-none-any.whl Installing jedi-0.17.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jedi-0.17.2-py3.7.egg/EGG-INFO/requires.txt Adding jedi 0.17.2 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/jedi-0.17.2-py3.7.egg Searching for backcall Reading https://pypi.org/simple/backcall/ Downloading https://files.pythonhosted.org/packages/4c/1c/ff6546b6c12603d8dd1070aa3c3d273ad4c07f5771689a7b69a550e8c951/backcall-0.2.0-py2.py3-none-any.whl#sha256=fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255 Best match: backcall 0.2.0 Processing backcall-0.2.0-py2.py3-none-any.whl Installing backcall-0.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding backcall 0.2.0 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/backcall-0.2.0-py3.7.egg Searching for tornado>=4.2 Reading https://pypi.org/simple/tornado/ Downloading https://files.pythonhosted.org/packages/3c/97/e3c09fac8be818099c886d660a0616674c82d6a56f203187a2ccb66bfdc4/tornado-6.1b1-cp37-cp37m-manylinux1_x86_64.whl#sha256=c1f366cfaa051e59d24cee3466c03f3c990afb322c06c56bf3c13092b722c7b8 Best match: tornado 6.1b1 Processing tornado-6.1b1-cp37-cp37m-manylinux1_x86_64.whl Installing tornado-6.1b1-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding tornado 6.1b1 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/tornado-6.1b1-py3.7-linux-x86_64.egg Searching for jupyter-client Reading https://pypi.org/simple/jupyter-client/ Downloading https://files.pythonhosted.org/packages/dc/41/9fa443d5ae8907dd8f7d12146cb0092dc053afd67b5b57e7e8786a328547/jupyter_client-6.1.7-py3-none-any.whl#sha256=c958d24d6eacb975c1acebb68ac9077da61b5f5c040f22f6849928ad7393b950 Best match: jupyter-client 6.1.7 Processing jupyter_client-6.1.7-py3-none-any.whl Installing jupyter_client-6.1.7-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client-6.1.7-py3.7.egg/EGG-INFO/requires.txt Adding jupyter-client 6.1.7 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/jupyter_client-6.1.7-py3.7.egg Searching for zope.interface>=4.4.2 Reading https://pypi.org/simple/zope.interface/ Downloading https://files.pythonhosted.org/packages/e5/62/f4c6e60a4cbbfb85afcb83402ba8fea5301d5049af10a089a8679a8d4870/zope.interface-5.1.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=a1cdd7390d7f66ddcebf545203ca3728c4890d605f9f2697bc8e31437906e8e7 Best match: zope.interface 5.1.2 Processing zope.interface-5.1.2-cp37-cp37m-manylinux1_x86_64.whl Installing zope.interface-5.1.2-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/zope.interface-5.1.2-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding zope.interface 5.1.2 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/zope.interface-5.1.2-py3.7-linux-x86_64.egg Searching for incremental>=16.10.1 Reading https://pypi.org/simple/incremental/ Downloading https://files.pythonhosted.org/packages/f5/1d/c98a587dc06e107115cf4a58b49de20b19222c83d75335a192052af4c4b7/incremental-17.5.0-py2.py3-none-any.whl#sha256=717e12246dddf231a349175f48d74d93e2897244939173b01974ab6661406b9f Best match: incremental 17.5.0 Processing incremental-17.5.0-py2.py3-none-any.whl Installing incremental-17.5.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/incremental-17.5.0-py3.7.egg/EGG-INFO/requires.txt Adding incremental 17.5.0 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/incremental-17.5.0-py3.7.egg Searching for hyperlink>=17.1.1 Reading https://pypi.org/simple/hyperlink/ Downloading https://files.pythonhosted.org/packages/88/a5/74f77547e9b175eb894d4fec5c76b0c8176c045e5bf3ac6a4d4d3feab4bb/hyperlink-20.0.1-py2.py3-none-any.whl#sha256=c528d405766f15a2c536230de7e160b65a08e20264d8891b3eb03307b0df3c63 Best match: hyperlink 20.0.1 Processing hyperlink-20.0.1-py2.py3-none-any.whl Installing hyperlink-20.0.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/hyperlink-20.0.1-py3.7.egg/EGG-INFO/requires.txt Adding hyperlink 20.0.1 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/hyperlink-20.0.1-py3.7.egg Searching for constantly>=15.1 Reading https://pypi.org/simple/constantly/ Downloading https://files.pythonhosted.org/packages/b9/65/48c1909d0c0aeae6c10213340ce682db01b48ea900a7d9fce7a7910ff318/constantly-15.1.0-py2.py3-none-any.whl#sha256=dd2fa9d6b1a51a83f0d7dd76293d734046aa176e384bf6e33b7e44880eb37c5d Best match: constantly 15.1.0 Processing constantly-15.1.0-py2.py3-none-any.whl Installing constantly-15.1.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding constantly 15.1.0 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/constantly-15.1.0-py3.7.egg Searching for PyHamcrest!=1.10.0,>=1.9.0 Reading https://pypi.org/simple/PyHamcrest/ Downloading https://files.pythonhosted.org/packages/40/16/e54cc65891f01cb62893540f44ffd3e8dab0a22443e1b438f1a9f5574bee/PyHamcrest-2.0.2-py3-none-any.whl#sha256=7ead136e03655af85069b6f47b23eb7c3e5c221aa9f022a4fbb499f5b7308f29 Best match: PyHamcrest 2.0.2 Processing PyHamcrest-2.0.2-py3-none-any.whl Installing PyHamcrest-2.0.2-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding PyHamcrest 2.0.2 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/PyHamcrest-2.0.2-py3.7.egg Searching for Automat>=0.3.0 Reading https://pypi.org/simple/Automat/ Downloading https://files.pythonhosted.org/packages/dd/83/5f6f3c1a562674d65efc320257bdc0873ec53147835aeef7762fe7585273/Automat-20.2.0-py2.py3-none-any.whl#sha256=b6feb6455337df834f6c9962d6ccf771515b7d939bca142b29c20c2376bc6111 Best match: Automat 20.2.0 Processing Automat-20.2.0-py2.py3-none-any.whl Installing Automat-20.2.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Automat-20.2.0-py3.7.egg/EGG-INFO/requires.txt 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 Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/Automat-20.2.0-py3.7.egg Searching for pyasn1-modules Reading https://pypi.org/simple/pyasn1-modules/ Downloading https://files.pythonhosted.org/packages/95/de/214830a981892a3e286c3794f41ae67a4495df1108c3da8a9f62159b9a9d/pyasn1_modules-0.2.8-py2.py3-none-any.whl#sha256=a50b808ffeb97cb3601dd25981f6b016cbb3d31fbf57a8b8a87428e6158d0c74 Best match: pyasn1-modules 0.2.8 Processing pyasn1_modules-0.2.8-py2.py3-none-any.whl Installing pyasn1_modules-0.2.8-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/pyasn1_modules-0.2.8-py3.7.egg/EGG-INFO/requires.txt Adding pyasn1-modules 0.2.8 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/pyasn1_modules-0.2.8-py3.7.egg Searching for cryptography Reading https://pypi.org/simple/cryptography/ Downloading https://files.pythonhosted.org/packages/70/d2/ae380f16d025459d282878e094518664a13a0e740cc957b1ada59590991d/cryptography-3.1.1-cp35-abi3-manylinux1_x86_64.whl#sha256=a7597ffc67987b37b12e09c029bd1dc43965f75d328076ae85721b84046e9ca7 Best match: cryptography 3.1.1 Processing cryptography-3.1.1-cp35-abi3-manylinux1_x86_64.whl Installing cryptography-3.1.1-cp35-abi3-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/cryptography-3.1.1-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding cryptography 3.1.1 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/cryptography-3.1.1-py3.7-linux-x86_64.egg Searching for itsdangerous>=0.24 Reading https://pypi.org/simple/itsdangerous/ Downloading https://files.pythonhosted.org/packages/93/95/e61aeeaeb9b343373bb1d9e160551a33babb30c4a2a12ef0a29be77284b0/itsdangerous-2.0.0a1-py3-none-any.whl#sha256=26ba8fb99157bbd5a1016f9d9dc5ed5ff1325f6f6f2c10b18107199470676b4d Best match: itsdangerous 2.0.0a1 Processing itsdangerous-2.0.0a1-py3-none-any.whl Installing itsdangerous-2.0.0a1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding itsdangerous 2.0.0a1 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/itsdangerous-2.0.0a1-py3.7.egg Searching for click>=5.1 Reading https://pypi.org/simple/click/ Downloading https://files.pythonhosted.org/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl#sha256=dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc Best match: click 7.1.2 Processing click-7.1.2-py2.py3-none-any.whl Installing click-7.1.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding click 7.1.2 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/click-7.1.2-py3.7.egg Searching for cachelib Reading https://pypi.org/simple/cachelib/ Downloading https://files.pythonhosted.org/packages/e6/fc/9c5571cf72ac3ea64ad5cd9d704c1000452cb483a6a3233357d8f3da6991/cachelib-0.1.1-py3-none-any.whl#sha256=7df6e05b8dfccdeb869e171575580e5606cf1e82a166633b3cb406bc4f113fd0 Best match: cachelib 0.1.1 Processing cachelib-0.1.1-py3-none-any.whl Installing cachelib-0.1.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding cachelib 0.1.1 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/cachelib-0.1.1-py3.7.egg Searching for vine<6.0,>=5.0.0 Reading https://pypi.org/simple/vine/ Downloading https://files.pythonhosted.org/packages/8d/61/a7badb48186919a9fd7cf0ef427cab6d16e0ed474035c36fa64ddd72bfa2/vine-5.0.0-py2.py3-none-any.whl#sha256=4c9dceab6f76ed92105027c49c823800dd33cacce13bdedc5b914e3514b7fb30 Best match: vine 5.0.0 Processing vine-5.0.0-py2.py3-none-any.whl Installing vine-5.0.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding vine 5.0.0 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/vine-5.0.0-py3.7.egg Searching for kombu<6.0,>=5.0.0 Reading https://pypi.org/simple/kombu/ Downloading https://files.pythonhosted.org/packages/22/6e/69bc1061633a88aa47beaa8bbecff1c3c555a005603cfbebcec4aa37f183/kombu-5.0.2-py2.py3-none-any.whl#sha256=6dc509178ac4269b0e66ab4881f70a2035c33d3a622e20585f965986a5182006 Best match: kombu 5.0.2 Processing kombu-5.0.2-py2.py3-none-any.whl Installing kombu-5.0.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/kombu-5.0.2-py3.7.egg/EGG-INFO/requires.txt Adding kombu 5.0.2 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/kombu-5.0.2-py3.7.egg Searching for click-repl>=0.1.6 Reading https://pypi.org/simple/click-repl/ Downloading https://files.pythonhosted.org/packages/6c/4e/577214ee76a5a36af485ae9ec01b4a47ee607b5d413b2063dafccf41f3ad/click_repl-0.1.6-py3-none-any.whl#sha256=9c4c3d022789cae912aad8a3f5e1d7c2cdd016ee1225b5212ad3e8691563cda5 Best match: click-repl 0.1.6 Processing click_repl-0.1.6-py3-none-any.whl Installing click_repl-0.1.6-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/click_repl-0.1.6-py3.7.egg/EGG-INFO/requires.txt Adding click-repl 0.1.6 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/click_repl-0.1.6-py3.7.egg Searching for click-didyoumean>=0.0.3 Reading https://pypi.org/simple/click-didyoumean/ Downloading https://files.pythonhosted.org/packages/9f/79/d265d783dd022541b744d002745d9e55d84c04a41930e35d8795934f6526/click-didyoumean-0.0.3.tar.gz#sha256=112229485c9704ff51362fe34b2d4f0b12fc71cc20f6d2b3afabed4b8bfa6aeb Best match: click-didyoumean 0.0.3 Processing click-didyoumean-0.0.3.tar.gz Writing /tmp/easy_install-1f4rnv5v/click-didyoumean-0.0.3/setup.cfg Running click-didyoumean-0.0.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-1f4rnv5v/click-didyoumean-0.0.3/egg-dist-tmp-1v_iwqlt zip_safe flag not set; analyzing archive contents... Moving click_didyoumean-0.0.3-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding click-didyoumean 0.0.3 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/click_didyoumean-0.0.3-py3.7.egg Searching for billiard<4.0,>=3.6.3.0 Reading https://pypi.org/simple/billiard/ Downloading https://files.pythonhosted.org/packages/e8/5e/7591866ff45b370354bd20291cb6f87ddb2eef1f1c88c890a38412037e11/billiard-3.6.3.0-py3-none-any.whl#sha256=bff575450859a6e0fbc2f9877d9b715b0bbc07c3565bb7ed2280526a0cdf5ede Best match: billiard 3.6.3.0 Processing billiard-3.6.3.0-py3-none-any.whl Installing billiard-3.6.3.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding billiard 3.6.3.0 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/billiard-3.6.3.0-py3.7.egg Searching for jdcal Reading https://pypi.org/simple/jdcal/ Downloading https://files.pythonhosted.org/packages/f0/da/572cbc0bc582390480bbd7c4e93d14dc46079778ed915b505dc494b37c57/jdcal-1.4.1-py2.py3-none-any.whl#sha256=1abf1305fce18b4e8aa248cf8fe0c56ce2032392bc64bbd61b5dff2a19ec8bba Best match: jdcal 1.4.1 Processing jdcal-1.4.1-py2.py3-none-any.whl Installing jdcal-1.4.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding jdcal 1.4.1 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/jdcal-1.4.1-py3.7.egg Searching for et-xmlfile Reading https://pypi.org/simple/et-xmlfile/ Downloading https://files.pythonhosted.org/packages/22/28/a99c42aea746e18382ad9fb36f64c1c1f04216f41797f2f0fa567da11388/et_xmlfile-1.0.1.tar.gz#sha256=614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b Best match: et-xmlfile 1.0.1 Processing et_xmlfile-1.0.1.tar.gz Writing /tmp/easy_install-5ukt60qz/et_xmlfile-1.0.1/setup.cfg Running et_xmlfile-1.0.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-5ukt60qz/et_xmlfile-1.0.1/egg-dist-tmp-qmmbdmvo zip_safe flag not set; analyzing archive contents... et_xmlfile.tests.__pycache__.common_imports.cpython-37: module references __file__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/et_xmlfile-1.0.1-py3.7.egg Extracting et_xmlfile-1.0.1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding et-xmlfile 1.0.1 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/et_xmlfile-1.0.1-py3.7.egg Searching for gitdb<5,>=4.0.1 Reading https://pypi.org/simple/gitdb/ Downloading https://files.pythonhosted.org/packages/48/11/d1800bca0a3bae820b84b7d813ad1eff15a48a64caea9c823fc8c1b119e8/gitdb-4.0.5-py3-none-any.whl#sha256=91f36bfb1ab7949b3b40e23736db18231bf7593edada2ba5c3a174a7b23657ac Best match: gitdb 4.0.5 Processing gitdb-4.0.5-py3-none-any.whl Installing gitdb-4.0.5-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/gitdb-4.0.5-py3.7.egg/EGG-INFO/requires.txt Adding gitdb 4.0.5 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/gitdb-4.0.5-py3.7.egg Searching for pyrsistent>=0.14.0 Reading https://pypi.org/simple/pyrsistent/ Downloading https://files.pythonhosted.org/packages/4d/70/fd441df751ba8b620e03fd2d2d9ca902103119616f0f6cc42e6405035062/pyrsistent-0.17.3.tar.gz#sha256=2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e Best match: pyrsistent 0.17.3 Processing pyrsistent-0.17.3.tar.gz Writing /tmp/easy_install-054tiws4/pyrsistent-0.17.3/setup.cfg Running pyrsistent-0.17.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-054tiws4/pyrsistent-0.17.3/egg-dist-tmp-kdy9wpu2 pvectorcmodule.c: In function ‘nodeFor’: pvectorcmodule.c:152:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if((i >= 0) && (i < self->count)) { ^ pvectorcmodule.c:153:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i >= TAIL_OFF(self)) { ^~ pvectorcmodule.c: In function ‘PVector_repeat’: pvectorcmodule.c:428:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(j=0; jcount; j++) { ^ pvectorcmodule.c: In function ‘extendWithItem’: pvectorcmodule.c:145:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] #define ROOT_NODE_FULL(vec) ((vec->count >> SHIFT) > (1 << vec->shift)) ^ pvectorcmodule.c:769:8: note: in expansion of macro ‘ROOT_NODE_FULL’ if(ROOT_NODE_FULL(newVec)) { ^~~~~~~~~~~~~~ pvectorcmodule.c: In function ‘PVector_append’: pvectorcmodule.c:145:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] #define ROOT_NODE_FULL(vec) ((vec->count >> SHIFT) > (1 << vec->shift)) ^ pvectorcmodule.c:919:6: note: in expansion of macro ‘ROOT_NODE_FULL’ if(ROOT_NODE_FULL(self)) { ^~~~~~~~~~~~~~ /home/docs/.pyenv/versions/3.7.9/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'license_files' warnings.warn(msg) zip_safe flag not set; analyzing archive contents... __pycache__.pvectorc.cpython-37: module references __file__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/pyrsistent-0.17.3-py3.7-linux-x86_64.egg Extracting pyrsistent-0.17.3-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding pyrsistent 0.17.3 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/pyrsistent-0.17.3-py3.7-linux-x86_64.egg Searching for wcwidth Reading https://pypi.org/simple/wcwidth/ Downloading https://files.pythonhosted.org/packages/59/7c/e39aca596badaf1b78e8f547c807b04dae603a433d3e7a7e04d67f2ef3e5/wcwidth-0.2.5-py2.py3-none-any.whl#sha256=beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784 Best match: wcwidth 0.2.5 Processing wcwidth-0.2.5-py2.py3-none-any.whl Installing wcwidth-0.2.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding wcwidth 0.2.5 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/wcwidth-0.2.5-py3.7.egg Searching for ptyprocess>=0.5 Reading https://pypi.org/simple/ptyprocess/ Downloading https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl#sha256=d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f Best match: ptyprocess 0.6.0 Processing ptyprocess-0.6.0-py2.py3-none-any.whl Installing ptyprocess-0.6.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding ptyprocess 0.6.0 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/ptyprocess-0.6.0-py3.7.egg Searching for parso<0.8.0,>=0.7.0 Reading https://pypi.org/simple/parso/ Downloading https://files.pythonhosted.org/packages/93/d1/e635bdde32890db5aeb2ffbde17e74f68986305a4466b0aa373b861e3f00/parso-0.7.1-py2.py3-none-any.whl#sha256=97218d9159b2520ff45eb78028ba8b50d2bc61dcc062a9682666f2dc4bd331ea Best match: parso 0.7.1 Processing parso-0.7.1-py2.py3-none-any.whl Installing parso-0.7.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/parso-0.7.1-py3.7.egg/EGG-INFO/requires.txt Adding parso 0.7.1 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/parso-0.7.1-py3.7.egg Searching for pyzmq>=13 Reading https://pypi.org/simple/pyzmq/ Downloading https://files.pythonhosted.org/packages/cd/ba/144b5f68fcd643937a4a953017abf1527ff34d43d2d912206fed962efde0/pyzmq-19.0.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=5d9fc809aa8d636e757e4ced2302569d6e60e9b9c26114a83f0d9d6519c40493 Best match: pyzmq 19.0.2 Processing pyzmq-19.0.2-cp37-cp37m-manylinux1_x86_64.whl Installing pyzmq-19.0.2-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding pyzmq 19.0.2 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/pyzmq-19.0.2-py3.7-linux-x86_64.egg Searching for cffi!=1.11.3,>=1.8 Reading https://pypi.org/simple/cffi/ Downloading https://files.pythonhosted.org/packages/26/d7/1c485a42d59d45f14f27bb93769e56142518c85ddf379dbdad7e42d0ffcd/cffi-1.14.3-cp37-cp37m-manylinux1_x86_64.whl#sha256=22399ff4870fb4c7ef19fff6eeb20a8bbf15571913c181c78cb361024d574579 Best match: cffi 1.14.3 Processing cffi-1.14.3-cp37-cp37m-manylinux1_x86_64.whl Installing cffi-1.14.3-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/cffi-1.14.3-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding cffi 1.14.3 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/cffi-1.14.3-py3.7-linux-x86_64.egg Searching for amqp<6.0.0,>=5.0.0 Reading https://pypi.org/simple/amqp/ Downloading https://files.pythonhosted.org/packages/6a/10/2d781823dd1366d7609148714e1a81af402c3c4d0ef52c1a1ac0716da9d0/amqp-5.0.1-py2.py3-none-any.whl#sha256=a8fb8151eb9d12204c9f1784c0da920476077609fa0a70f2468001e3a4258484 Best match: amqp 5.0.1 Processing amqp-5.0.1-py2.py3-none-any.whl Installing amqp-5.0.1-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages/amqp-5.0.1-py3.7.egg/EGG-INFO/requires.txt Adding amqp 5.0.1 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/amqp-5.0.1-py3.7.egg Searching for smmap<4,>=3.0.1 Reading https://pypi.org/simple/smmap/ Downloading https://files.pythonhosted.org/packages/b0/9a/4d409a6234eb940e6a78dfdfc66156e7522262f5f2fecca07dc55915952d/smmap-3.0.4-py2.py3-none-any.whl#sha256=54c44c197c819d5ef1991799a7e30b662d1e520f2ac75c9efbeb54a742214cf4 Best match: smmap 3.0.4 Processing smmap-3.0.4-py2.py3-none-any.whl Installing smmap-3.0.4-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding smmap 3.0.4 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/smmap-3.0.4-py3.7.egg Searching for pycparser Reading https://pypi.org/simple/pycparser/ Downloading https://files.pythonhosted.org/packages/ae/e7/d9c3a176ca4b02024debf82342dab36efadfc5776f9c8db077e8f6e71821/pycparser-2.20-py2.py3-none-any.whl#sha256=7582ad22678f0fcd81102833f60ef8d0e57288b6b5fb00323d101be910e35705 Best match: pycparser 2.20 Processing pycparser-2.20-py2.py3-none-any.whl Installing pycparser-2.20-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.7/site-packages Adding pycparser 2.20 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/pycparser-2.20-py3.7.egg 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 matplotlib==3.3.2 Best match: matplotlib 3.3.2 Adding matplotlib 3.3.2 to easy-install.pth file Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for scipy==1.5.3 Best match: scipy 1.5.3 scipy 1.5.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for pandas==1.1.3 Best match: pandas 1.1.3 pandas 1.1.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for numpy==1.19.2 Best match: numpy 1.19.2 numpy 1.19.2 is already the active version in easy-install.pth 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/.pyenv/versions/3.7.9/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 setuptools==50.3.2 Best match: setuptools 50.3.2 Adding setuptools 50.3.2 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-3.8 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 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 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 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 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 kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 kiwisolver 1.2.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 cycler 0.10.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for Pillow==8.0.0 Best match: Pillow 8.0.0 Pillow 8.0.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages Searching for 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 Pygments==2.7.1 Best match: Pygments 2.7.1 Adding Pygments 2.7.1 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 attrs==20.2.0 Best match: attrs 20.2.0 Adding attrs 20.2.0 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 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 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 urllib3==1.25.11 Best match: urllib3 1.25.11 Adding urllib3 1.25.11 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 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==2.0.0 Best match: importlib-metadata 2.0.0 Adding importlib-metadata 2.0.0 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 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 zipp==3.3.1 Best match: zipp 3.3.1 Adding zipp 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 Finished processing dependencies for covasim==1.7.6 [rtd-command-info] start-time: 2020-10-23T23:17:40.249158Z, end-time: 2020-10-23T23:17:40.327018Z, 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 on_rtd = os.environ.get('READTHEDOCS') == 'True' if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "covasim package" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read exitsting file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ # If your 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.mathjax', '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 = '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 = { 'rtd_url': 'https://docs.idmod.org/projects/covasim/en/latest', 'theme_vcs_pageview_mode': 'edit', '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. # if not on_rtd: html_extra_path = ['robots.txt'] # 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 = 'docs.idmod.org/projects/covasim/en/latest' # 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': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/covasim/en/latest/pdf/"), ("html", "//docs.idmod.org/_/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://docs.idmod.org/projects/covasim/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'covasim', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': 'a55a849b', } 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: 2020-10-23T23:17:40.436273Z, end-time: 2020-10-23T23:18:18.898569Z, duration: 38, exit-code: 0 python sphinx-build -T -E -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.2.1 Covasim 1.7.6 (2020-10-23) — © 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 30 source files that are out of date updating environment: [new config] 30 added, 0 changed, 0 removed reading sources... [ 3%] conduct reading sources... [ 6%] contributing reading sources... [ 10%] covasim.analysis reading sources... [ 13%] covasim.base reading sources... [ 16%] covasim.data reading sources... [ 20%] covasim.data.country_age_data reading sources... [ 23%] covasim.data.household_size_data reading sources... [ 26%] covasim.data.loaders reading sources... [ 30%] covasim.data.state_age_data reading sources... [ 33%] covasim.defaults reading sources... [ 36%] covasim.interventions reading sources... [ 40%] covasim.misc reading sources... [ 43%] covasim.parameters reading sources... [ 46%] covasim.people reading sources... [ 50%] covasim.plotting reading sources... [ 53%] covasim.population reading sources... [ 56%] covasim.requirements reading sources... [ 60%] covasim.run reading sources... [ 63%] covasim.sim reading sources... [ 66%] covasim.utils reading sources... [ 70%] covasim.version reading sources... [ 73%] covasim.webapp reading sources... [ 76%] covasim.webapp.cova_app reading sources... [ 80%] data reading sources... [ 83%] docker reading sources... [ 86%] index reading sources... [ 90%] modules reading sources... [ 93%] parameters reading sources... [ 96%] webapp reading sources... [100%] whatsnew looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 3%] conduct writing output... [ 6%] contributing writing output... [ 10%] covasim.analysis writing output... [ 13%] covasim.base writing output... [ 16%] covasim.data writing output... [ 20%] covasim.data.country_age_data writing output... [ 23%] covasim.data.household_size_data writing output... [ 26%] covasim.data.loaders writing output... [ 30%] covasim.data.state_age_data writing output... [ 33%] covasim.defaults writing output... [ 36%] covasim.interventions writing output... [ 40%] covasim.misc writing output... [ 43%] covasim.parameters writing output... [ 46%] covasim.people writing output... [ 50%] covasim.plotting writing output... [ 53%] covasim.population writing output... [ 56%] covasim.requirements writing output... [ 60%] covasim.run writing output... [ 63%] covasim.sim writing output... [ 66%] covasim.utils writing output... [ 70%] covasim.version writing output... [ 73%] covasim.webapp writing output... [ 76%] covasim.webapp.cova_app writing output... [ 80%] data writing output... [ 83%] docker writing output... [ 86%] index writing output... [ 90%] modules writing output... [ 93%] parameters writing output... [ 96%] 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: 2020-10-23T23:18:19.183947Z, end-time: 2020-10-23T23:18:29.447223Z, duration: 10, exit-code: 0 python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.2.1 Covasim 1.7.6 (2020-10-23) — © 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] 30 added, 0 changed, 0 removed reading sources... [ 3%] conduct reading sources... [ 6%] contributing reading sources... [ 10%] covasim.analysis reading sources... [ 13%] covasim.base reading sources... [ 16%] covasim.data reading sources... [ 20%] covasim.data.country_age_data reading sources... [ 23%] covasim.data.household_size_data reading sources... [ 26%] covasim.data.loaders reading sources... [ 30%] covasim.data.state_age_data reading sources... [ 33%] covasim.defaults reading sources... [ 36%] covasim.interventions reading sources... [ 40%] covasim.misc reading sources... [ 43%] covasim.parameters reading sources... [ 46%] covasim.people reading sources... [ 50%] covasim.plotting reading sources... [ 53%] covasim.population reading sources... [ 56%] covasim.requirements reading sources... [ 60%] covasim.run reading sources... [ 63%] covasim.sim reading sources... [ 66%] covasim.utils reading sources... [ 70%] covasim.version reading sources... [ 73%] covasim.webapp reading sources... [ 76%] covasim.webapp.cova_app reading sources... [ 80%] data reading sources... [ 83%] docker reading sources... [ 86%] index reading sources... [ 90%] modules reading sources... [ 93%] parameters reading sources... [ 96%] webapp reading sources... [100%] whatsnew looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... whatsnew parameters contributing conduct webapp docker data modules covasim.data covasim.data.country_age_data covasim.data.household_size_data covasim.data.loaders covasim.data.state_age_data covasim.webapp covasim.webapp.cova_app covasim.analysis covasim.base covasim.defaults covasim.interventions covasim.misc covasim.parameters covasim.people covasim.plotting covasim.population covasim.requirements covasim.run covasim.sim covasim.utils covasim.version 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: 2020-10-23T23:18:29.646611Z, end-time: 2020-10-23T23:18:40.204080Z, duration: 10, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 Covasim 1.7.6 (2020-10-23) — © 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] 30 added, 0 changed, 0 removed reading sources... [ 3%] conduct reading sources... [ 6%] contributing reading sources... [ 10%] covasim.analysis reading sources... [ 13%] covasim.base reading sources... [ 16%] covasim.data reading sources... [ 20%] covasim.data.country_age_data reading sources... [ 23%] covasim.data.household_size_data reading sources... [ 26%] covasim.data.loaders reading sources... [ 30%] covasim.data.state_age_data reading sources... [ 33%] covasim.defaults reading sources... 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[100%] whatsnew looking for now-outdated files... none found pickling environment... done checking consistency... done processing covasim-docs.tex... index whatsnew parameters contributing conduct webapp docker data modules covasim.data covasim.data.country_age_data covasim.data.household_size_data covasim.data.loaders covasim.data.state_age_data covasim.webapp covasim.webapp.cova_app covasim.analysis covasim.base covasim.defaults covasim.interventions covasim.misc covasim.parameters covasim.people covasim.plotting covasim.population covasim.requirements covasim.run covasim.sim covasim.utils covasim.version 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: 2020-10-23T23:18:40.592436Z, end-time: 2020-10-23T23:18:40.662253Z, 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: 2020-10-23T23:18:40.769300Z, end-time: 2020-10-23T23:18:43.915238Z, duration: 3, 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. 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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.analysis:module-covasim.analysis' on page 105 undefined on input line 9559 Reference `covasim.base:module-covasim.base' on page 105 undefined on input line 9560 Reference `covasim.data.country_age_data:module-covasim.data.country_age_data' on page 105 undefined on input line 9562 Reference `covasim.data.household_size_data:module-covasim.data.household_size_data' on page 105 undefined on input line 9563 Reference `covasim.data.loaders:module-covasim.data.loaders' on page 105 undefined on input line 9564 Reference `covasim.data.state_age_data:module-covasim.data.state_age_data' on page 105 undefined on input line 9565 Reference `covasim.data:module-covasim.data' on page 105 undefined on input line 9561 Reference `covasim.defaults:module-covasim.defaults' on page 105 undefined on input line 9566 Reference `covasim.interventions:module-covasim.interventions' on page 105 undefined on input line 9567 Reference `covasim.misc:module-covasim.misc' on page 105 undefined on input line 9568 Reference `covasim.parameters:module-covasim.parameters' on page 105 undefined on input line 9569 Reference `covasim.people:module-covasim.people' on page 105 undefined on input line 9570 Reference `covasim.plotting:module-covasim.plotting' on page 105 undefined on input line 9571 Reference `covasim.population:module-covasim.population' on page 105 undefined on input line 9572 Reference `covasim.requirements:module-covasim.requirements' on page 105 undefined on input line 9573 Reference `covasim.run:module-covasim.run' on page 105 undefined on input line 9574 Reference `covasim.sim:module-covasim.sim' on page 105 undefined on input line 9575 Reference `covasim.utils:module-covasim.utils' on page 105 undefined on input line 9576 Reference `covasim.version:module-covasim.version' on page 105 undefined on input line 9577 Reference `covasim.webapp.cova_app:module-covasim.webapp.cova_app' on page 105 undefined on input line 9579 Reference `covasim.webapp:module-covasim.webapp' on page 105 undefined on input line 9578 Reference `modules:module-covasim' on page 105 undefined on input line 9558 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'... 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(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-covasim.idx (./institute-for-disease-modeling-covasim.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-covasim.out) (./institute-for-disease-modeling-covasim.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./institute-for-disease-modeling-covasim.toc) [1] [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [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. [17] [18] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [19] [20] Underfull \hbox (badness 6910) in paragraph at lines 676--677 []\T1/ptm/m/n/10 If the sim-u-la-tion has reached the end, \T1/pcr/m/n/10 sim.r un() \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 sim.step()\T1/ptm/m/n/10 ) will now rai se an [21] [22] [23] [24] [25] [26] [27] [28] Underfull \hbox (badness 6792) in paragraph at lines 1230--1231 []\T1/ptm/m/n/10 Interventions now have a \T1/pcr/m/n/10 label \T1/ptm/m/n/10 a t-tribute, which can be help-ful for find-ing them if many Underfull \hbox (badness 10000) in paragraph at lines 1230--1231 \T1/ptm/m/n/10 are used, e.g. \T1/pcr/m/n/10 [interv if interv.label==\TS1/pcr/ m/n/10 '\T1/pcr/m/n/10 Close schools\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 for interv in Underfull \hbox (badness 7832) in paragraph at lines 1271--1272 []\T1/ptm/m/n/10 An ^^Poverview^^Q plot-ting fea-ture has been added for sims a nd sce-nar-ios: sim-ply use \T1/pcr/m/n/10 sim. [29] Underfull \hbox (badness 6300) in paragraph at lines 1294--1295 []\T1/ptm/m/n/10 Moved \T1/pcr/m/n/10 transtree \T1/ptm/m/n/10 from \T1/pcr/m/n /10 sim.people \T1/ptm/m/n/10 into its own class: thus in-stead of \T1/pcr/m/n/ 10 sim.people. [30] [31] [32] Underfull \hbox (badness 6526) in paragraph at lines 1585--1586 []\T1/ptm/m/n/10 Updated \T1/pcr/m/n/10 r_eff \T1/ptm/m/n/10 to use a new metho d based on daily new in-fec-tions. 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lines 3408--3408 []\T1/ptm/m/n/10 221.0| Overfull \hbox (7.50366pt too wide) in paragraph at lines 3408--3408 []\T1/ptm/m/n/10 221.0| Overfull \hbox (5.00366pt too wide) in paragraph at lines 3408--3408 []\T1/ptm/m/n/10 1605| Overfull \hbox (8.07166pt too wide) in paragraph at lines 3408--3408 []\T1/ptm/m/n/10 2020- Underfull \hbox (badness 10000) in paragraph at lines 3408--3408 \T1/ptm/m/n/10 03- Overfull \hbox (0.83572pt too wide) in paragraph at lines 3408--3408 []\T1/ptm/m/n/10 963.0| Overfull \hbox (2.11104pt too wide) in paragraph at lines 3408--3408 []\T1/ptm/m/n/10 750.0| Overfull \hbox (12.50366pt too wide) in paragraph at lines 3408--3408 []\T1/ptm/m/n/10 1713.0| [48] Underfull \hbox (badness 10000) in paragraph at lines 1--3466 [][][]$\T1/ptm/m/n/10 https : / / population . un . org / household / exceldata / population _ division _ UN _ Houseshold _ Size _ and _ Composition _ [49] [50] Underfull \hbox (badness 10000) in paragraph at lines 3667--3667 []\T1/ptm/m/it/10 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 , [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 6775) in paragraph at lines 4376--4376 []\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 , [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Underfull \hbox (badness 10000) in paragraph at lines 5730--5730 []\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 5730--5730 \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 5730--5730 \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 , [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 5822--5822 []\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 5822--5822 \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 5822--5822 \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 5822--5822 \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 , [69] Underfull \hbox (badness 10000) in paragraph at lines 5901--5901 []\T1/ptm/m/it/10 trace_probs=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 trace_time=N one\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5901--5901 \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 pre-sump- [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6596--6596 []\T1/ptm/m/it/10 sim\T1/ptm/m/n/10 , \T1/ptm/m/it/10 se-ries=None\T1/ptm/m/n/1 0 , \T1/ptm/m/it/10 in-ter-val=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day=N one\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6596--6596 \T1/ptm/m/it/10 end_day=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mov-ing_window=Non e\T1/ptm/m/n/10 , \T1/ptm/m/it/10 exp_approx=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6612--6612 []\T1/ptm/m/it/10 count1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 count2\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex-po-sure1=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex-po-sure2=1\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 ra-tio_null=1\T1/ptm/m/n/10 , [76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7186--7186 \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 7186--7186 \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 7186--7186 \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 7186--7186 \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 7194--7194 []\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 7194--7194 \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 7194--7194 \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 7194--7194 \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 7194--7194 \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 7194--7194 \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 7194--7194 \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 , [81] Underfull \hbox (badness 10000) in paragraph at lines 7210--7210 []\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 7210--7210 \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 7218--7218 []\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 , [82] Underfull \hbox (badness 10000) in paragraph at lines 7299--7299 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 7352--7352 []\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 7392--7392 []\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 , [83] Underfull \hbox (badness 10000) in paragraph at lines 7485--7485 []\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 , [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 8238--8238 \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 , [91] [92] [93] Underfull \hbox (badness 10000) in paragraph at lines 8483--8483 []\T1/ptm/m/it/10 save_pop=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 load_pop=False \T1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-file=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-set=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=None\T1/ptm/m/n/10 , [94] [95] [96] [97] ! 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.8998 ...{\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.8998 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 9301--9303 [][][]$\T1/ptm/m/n/10 https : / / stackover^^]ow . com / questions / 19045971 / [101] [102] [103] [104] [105] (./institute-for-disease-modeling-covasim.ind [106] Underfull \hbox (badness 10000) in paragraph at lines 20--21 []\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 21--22 []\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 41--42 []\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 43--44 []\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 48--49 []\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 50--51 []\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 51--52 []\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 67--68 []\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 71--73 []\T1/pcr/m/n/10 compute_windows() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v- [107] Underfull \hbox (badness 10000) in paragraph at lines 79--80 []\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 158--159 []\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 168--170 []\T1/pcr/m/n/10 get_age_distribution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 173--174 []\T1/pcr/m/n/10 get_country_aliases() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le co-v- Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 get_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v - [108] Underfull \hbox (badness 10000) in paragraph at lines 177--178 []\T1/pcr/m/n/10 get_household_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e co-v- Underfull \hbox (badness 10000) in paragraph at lines 178--179 []\T1/pcr/m/n/10 get_interventions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim. base.BaseSim Underfull \hbox (badness 10000) in paragraph at lines 179--180 []\T1/pcr/m/n/10 get_licenses() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v - Underfull \hbox (badness 10000) in paragraph at lines 180--182 []\T1/pcr/m/n/10 get_location_options() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 182--184 []\T1/pcr/m/n/10 get_output_files() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 190--191 []\T1/pcr/m/n/10 get_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 195--196 []\T1/pcr/m/n/10 healthcheck() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 201--203 []\T1/pcr/m/n/10 identify_contacts() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v- Underfull \hbox (badness 10000) in paragraph at lines 201--203 \T1/ptm/m/it/10 asim.interventions.contact_tracing method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 208--209 []\T1/pcr/m/n/10 init_contacts() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.base .BasePeople Underfull \hbox (badness 10000) in paragraph at lines 213--214 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.analysi s.age_histogram Underfull \hbox (badness 10000) in paragraph at lines 217--218 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.change_beta Underfull \hbox (badness 10000) in paragraph at lines 218--219 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.clip_edges Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v- Underfull \hbox (badness 10000) in paragraph at lines 219--221 \T1/ptm/m/it/10 asim.interventions.contact_tracing method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 221--222 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.Intervention Underfull \hbox (badness 10000) in paragraph at lines 222--223 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.sequence Underfull \hbox (badness 10000) in paragraph at lines 223--224 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.test_num Underfull \hbox (badness 10000) in paragraph at lines 224--225 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.test_prob Underfull \hbox (badness 10000) in paragraph at lines 225--226 []\T1/pcr/m/n/10 initialize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interve ntions.vaccine Underfull \hbox (badness 10000) in paragraph at lines 230--231 []\T1/pcr/m/n/10 InterventionDict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 257--258 []\T1/pcr/m/n/10 make_detailed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.anal ysis.TransTree Underfull \hbox (badness 10000) in paragraph at lines 258--259 []\T1/pcr/m/n/10 make_edgelist() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.base .BasePeople Underfull \hbox (badness 10000) in paragraph 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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> Output written on institute-for-disease-modeling-covasim.pdf (115 pages, 434597 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 , [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 6775) in paragraph at lines 4376--4376 []\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 , [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Underfull \hbox (badness 10000) in paragraph at lines 5730--5730 []\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 5730--5730 \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 5730--5730 \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 , [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 5822--5822 []\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 5822--5822 \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 5822--5822 \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 5822--5822 \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 , [69] Underfull \hbox (badness 10000) in paragraph at lines 5901--5901 []\T1/ptm/m/it/10 trace_probs=None\T1/ptm/m/n/10 , 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[76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7186--7186 \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 7186--7186 \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 7186--7186 \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 7186--7186 \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 7194--7194 []\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 7194--7194 \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 7194--7194 \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 7194--7194 \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 7194--7194 \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 7194--7194 \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 7194--7194 \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 , [81] Underfull \hbox (badness 10000) in paragraph at lines 7210--7210 []\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 7210--7210 \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 7218--7218 []\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 , [82] Underfull \hbox (badness 10000) in paragraph at lines 7299--7299 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 7352--7352 []\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 7392--7392 []\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 , [83] Underfull \hbox (badness 10000) in paragraph at lines 7485--7485 []\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 , [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 8238--8238 \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 , [91] [92] [93] Underfull \hbox (badness 10000) in paragraph at lines 8483--8483 []\T1/ptm/m/it/10 save_pop=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 load_pop=False \T1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-file=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-set=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=None\T1/ptm/m/n/10 , [94] [95] [96] [97] ! 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Type H for immediate help. ... l.8998 ...{\PYGZsh{} returns Normal(μ=3, σ=0.5)} [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 9301--9303 [][][]$\T1/ptm/m/n/10 https : / / stackover^^]ow . com / questions / 19045971 / [101] [102] [103] [104] [105] (./institute-for-disease-modeling-covasim.ind [106] Underfull \hbox (badness 10000) in paragraph at lines 20--21 []\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 21--22 []\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 41--42 []\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 43--44 []\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 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387--389 []\T1/pcr/m/n/10 select_cases() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v- Underfull \hbox (badness 10000) in paragraph at lines 387--389 \T1/ptm/m/it/10 asim.interventions.contact_tracing method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 418--419 []\T1/pcr/m/n/10 to_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.interventi ons.Intervention Underfull \hbox (badness 10000) in paragraph at lines 432--433 []\T1/pcr/m/n/10 update_contacts() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim.pe ople.People Underfull \hbox (badness 10000) in paragraph at lines 435--436 []\T1/pcr/m/n/10 update_states_post() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim .people.People Underfull \hbox (badness 10000) in paragraph at lines 436--437 []\T1/pcr/m/n/10 update_states_pre() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asim. people.People Underfull \hbox (badness 10000) in paragraph at lines 437--438 []\T1/pcr/m/n/10 upload_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 438--439 []\T1/pcr/m/n/10 upload_pars() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule co-v- Underfull \hbox (badness 10000) in paragraph at lines 445--446 []\T1/pcr/m/n/10 validate_layer_pars() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 co-v-asi m.sim.Sim [111]) (./institute-for-disease-modeling-covasim.aux) ) (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> Output written on institute-for-disease-modeling-covasim.pdf (115 pages, 434717 bytes). 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