Read the Docs build information Build id: 505487 Project: institute-for-disease-modeling-emodpy-malaria Version: latest Commit: f75a5780215b157bcadff6755e87753712aad2ee Date: 2020-12-12T00:20:58.247128Z State: finished Success: True [rtd-command-info] start-time: 2020-12-12T00:20:59.744863Z, end-time: 2020-12-12T00:21:01.474829Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emodpy-malaria.git . Cloning into '.'... Warning: Permanently added 'github.com,140.82.113.3' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2020-12-12T00:21:02.037909Z, end-time: 2020-12-12T00:21:02.111800Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: checking out 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at f75a578 fixed indentation in docstrings causing sphinx build errors [rtd-command-info] start-time: 2020-12-12T00:21:02.309501Z, end-time: 2020-12-12T00:21:02.367850Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-12-12T00:21:03.759572Z, end-time: 2020-12-12T00:21:09.139019Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-12-12T00:21:09.356493Z, end-time: 2020-12-12T00:21:11.136123Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (20.3.1) [rtd-command-info] start-time: 2020-12-12T00:21:11.277982Z, end-time: 2020-12-12T00:21:27.514231Z, duration: 16, exit-code: 0 python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading 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(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=db0975e3bc56e003dfff213435d5ed85f91f6c2057f4a647398bc7b7e5ebd1e2 Stored in directory: /tmp/pip-ephem-wheel-cache-onrqeinz/wheels/39/db/d5/e22e622f3ac6beb40ab992464b2b5ae38526942ed4ffff7c05 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=491058 sha256=8db3bd1addcbee7346e94e1442883ed8db3ae83630c28ae2766e2ba81c30b248 Stored in directory: /tmp/pip-ephem-wheel-cache-onrqeinz/wheels/59/f9/bf/01e56e422aee5062f2ae1890a7f6593443981ae37e18fecbfb Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 51.0.0 Uninstalling setuptools-51.0.0: Successfully uninstalled setuptools-51.0.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.3 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 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-20.7 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2 [rtd-command-info] start-time: 2020-12-12T00:21:27.624438Z, end-time: 2020-12-12T00:21:58.238852Z, duration: 30, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking 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astunparse->emodpy~=1.8.2->-r requirements.txt (line 2)) (0.36.1) Requirement already satisfied: six<2.0,>=1.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from astunparse->emodpy~=1.8.2->-r requirements.txt (line 2)) (1.15.0) Collecting bs4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/ed/7e8b97591f6f456174139ec089c769f89a94a1a4025fe967691de971f314/bs4-0.0.1.tar.gz (1.1 kB) Collecting beautifulsoup4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d1/41/e6495bd7d3781cee623ce23ea6ac73282a373088fcd0ddc809a047b18eae/beautifulsoup4-4.9.3-py3-none-any.whl (115 kB) Collecting click~=7.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting geopy Downloading 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sha256=c0f0285842aa576efe00e1970e4401ac8ae3aaa7b6ff5fd34896a2c512e2009f Stored in directory: /tmp/pip-ephem-wheel-cache-h60_qkgk/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c Building wheel for pyyaml (setup.py): started Building wheel for pyyaml (setup.py): finished with status 'done' Created wheel for pyyaml: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44621 sha256=b60313c45cde456cd291cddb6a1ea6a683b6d150efd1f9466765d8433a98504d Stored in directory: /tmp/pip-ephem-wheel-cache-h60_qkgk/wheels/a7/32/27/98ea868164aa8ce9798f7dedbae1b456b4edf247f860a0ab51 Successfully built bs4 docopt pyyaml Installing collected packages: zipp, pycparser, yarg, python-dateutil, numpy, importlib-metadata, humanfriendly, docopt, cffi, xdg, tqdm, tabulate, soupsieve, pyyaml, pluggy, pipreqs, pillow, pandas, more-itertools, kiwisolver, jeepney, geographiclib, diskcache, cycler, cryptography, coloredlogs, backoff, shapely, SecretStorage, scipy, pyproj, pyCOMPS, matplotlib, lz4, idmtools, geopy, beautifulsoup4, keyring, idmtools-platform-comps, idmtools-models, emod-api, click, bs4, astunparse, astor, emodpy Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed SecretStorage-3.3.0 astor-0.8.1 astunparse-1.6.3 backoff-1.10.0 beautifulsoup4-4.9.3 bs4-0.0.1 cffi-1.14.4 click-7.1.2 coloredlogs-14.3 cryptography-3.3.1 cycler-0.10.0 diskcache-5.1.0 docopt-0.6.2 emod-api-1.4.1 emodpy-1.8.2 geographiclib-1.50 geopy-2.0.0 humanfriendly-8.2 idmtools-1.6.2 idmtools-models-1.6.2 idmtools-platform-comps-1.6.2 importlib-metadata-3.1.1 jeepney-0.6.0 keyring-21.5.0 kiwisolver-1.3.1 lz4-3.1.1 matplotlib-3.3.3 more-itertools-8.6.0 numpy-1.19.3 pandas-1.1.5 pillow-8.0.1 pipreqs-0.4.10 pluggy-0.13.1 pyCOMPS-2.4.1 pycparser-2.20 pyproj-3.0.0.post1 python-dateutil-2.8.1 pyyaml-5.3.1 scipy-1.5.4 shapely-1.7.1 soupsieve-2.1 tabulate-0.8.7 tqdm-4.54.1 xdg-5.0.1 yarg-0.1.9 zipp-3.4.0 [rtd-command-info] start-time: 2020-12-12T00:21:58.412840Z, end-time: 2020-12-12T00:22:08.432205Z, duration: 10, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple Collecting plantweb~=1.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d6/6f/9ab1a1c3e33aaa0c0931983578c09336b092c75dce777ea666d3032f756e/plantweb-1.2.1-py3-none-any.whl (20 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (1.15.0) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 4)) (0.14) 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[rtd-command-info] start-time: 2020-12-12T00:22:08.592169Z, end-time: 2020-12-12T00:22:09.606187Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating emodpy_malaria.egg-info writing emodpy_malaria.egg-info/PKG-INFO writing dependency_links to emodpy_malaria.egg-info/dependency_links.txt writing requirements to emodpy_malaria.egg-info/requires.txt writing top-level names to emodpy_malaria.egg-info/top_level.txt writing manifest file 'emodpy_malaria.egg-info/SOURCES.txt' reading manifest file 'emodpy_malaria.egg-info/SOURCES.txt' writing manifest file 'emodpy_malaria.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/tests copying tests/__init__.py -> build/lib/tests creating build/lib/emodpy_malaria copying emodpy_malaria/__init__.py -> build/lib/emodpy_malaria copying emodpy_malaria/config.py -> build/lib/emodpy_malaria creating build/lib/emodpy_malaria/reporters copying emodpy_malaria/reporters/builtin.py -> build/lib/emodpy_malaria/reporters copying emodpy_malaria/reporters/__init__.py -> build/lib/emodpy_malaria/reporters creating build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/spacespraying.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/sugartrap.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/__init__.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/bednet.py -> build/lib/emodpy_malaria/interventions creating build/lib/emodpy_malaria/demographics copying emodpy_malaria/demographics/MalariaDemographics.py -> build/lib/emodpy_malaria/demographics copying emodpy_malaria/demographics/__init__.py -> build/lib/emodpy_malaria/demographics creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/tests copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/emodpy_malaria copying build/lib/emodpy_malaria/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria copying build/lib/emodpy_malaria/config.py -> build/bdist.linux-x86_64/egg/emodpy_malaria creating build/bdist.linux-x86_64/egg/emodpy_malaria/reporters copying build/lib/emodpy_malaria/reporters/builtin.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/reporters copying build/lib/emodpy_malaria/reporters/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/reporters creating build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/spacespraying.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/sugartrap.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/bednet.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions creating build/bdist.linux-x86_64/egg/emodpy_malaria/demographics copying build/lib/emodpy_malaria/demographics/MalariaDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/demographics copying build/lib/emodpy_malaria/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/demographics byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/config.py to config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/builtin.py to builtin.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/spacespraying.py to spacespraying.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/sugartrap.py to sugartrap.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/bednet.py to bednet.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/MalariaDemographics.py to MalariaDemographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/__init__.py to __init__.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating dist creating 'dist/emodpy_malaria-0.0.7-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emodpy_malaria-0.0.7-py3.7.egg Copying emodpy_malaria-0.0.7-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Adding emodpy-malaria 0.0.7 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages/emodpy_malaria-0.0.7-py3.7.egg Processing dependencies for emodpy-malaria==0.0.7 Searching for emodpy==1.8.2 Best match: emodpy 1.8.2 Adding emodpy 1.8.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for emod-api==1.4.1 Best match: emod-api 1.4.1 Adding emod-api 1.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for idmtools-models==1.6.2 Best match: idmtools-models 1.6.2 Adding idmtools-models 1.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for astunparse==1.6.3 Best match: astunparse 1.6.3 Adding astunparse 1.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for astor==0.8.1 Best match: astor 0.8.1 Adding astor 0.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for keyring==21.5.0 Best match: keyring 21.5.0 Adding keyring 21.5.0 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for click==7.1.2 Best match: click 7.1.2 Adding click 7.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for bs4==0.0.1 Best match: bs4 0.0.1 Adding bs4 0.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for matplotlib==3.3.3 Best match: matplotlib 3.3.3 Adding matplotlib 3.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for idmtools-platform-comps==1.6.2 Best match: idmtools-platform-comps 1.6.2 Adding idmtools-platform-comps 1.6.2 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for idmtools==1.6.2 Best match: idmtools 1.6.2 Adding idmtools 1.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for lz4==3.1.1 Best match: lz4 3.1.1 Adding lz4 3.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pyproj==3.0.0.post1 Best match: pyproj 3.0.0.post1 Adding pyproj 3.0.0.post1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for Shapely==1.7.1 Best match: Shapely 1.7.1 Adding Shapely 1.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pandas==1.1.5 Best match: pandas 1.1.5 Adding pandas 1.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for PyYAML==5.3.1 Best match: PyYAML 5.3.1 Adding PyYAML 5.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for numpy==1.19.3 Best match: numpy 1.19.3 Adding numpy 1.19.3 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for scipy==1.5.4 Best match: scipy 1.5.4 Adding scipy 1.5.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for geopy==2.0.0 Best match: geopy 2.0.0 Adding geopy 2.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for wheel==0.36.1 Best match: wheel 0.36.1 Adding wheel 0.36.1 to easy-install.pth file Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for jeepney==0.6.0 Best match: jeepney 0.6.0 Adding jeepney 0.6.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for importlib-metadata==3.1.1 Best match: importlib-metadata 3.1.1 Adding importlib-metadata 3.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for SecretStorage==3.3.0 Best match: SecretStorage 3.3.0 Adding SecretStorage 3.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for beautifulsoup4==4.9.3 Best match: beautifulsoup4 4.9.3 Adding beautifulsoup4 4.9.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 Adding cycler 0.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 Adding python-dateutil 2.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for kiwisolver==1.3.1 Best match: kiwisolver 1.3.1 Adding kiwisolver 1.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for Pillow==8.0.1 Best match: Pillow 8.0.1 Adding Pillow 8.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for tqdm==4.54.1 Best match: tqdm 4.54.1 Adding tqdm 4.54.1 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pyCOMPS==2.4.1 Best match: pyCOMPS 2.4.1 Adding pyCOMPS 2.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for coloredlogs==14.3 Best match: coloredlogs 14.3 Adding coloredlogs 14.3 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for backoff==1.10.0 Best match: backoff 1.10.0 Adding backoff 1.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for diskcache==5.1.0 Best match: diskcache 5.1.0 Adding diskcache 5.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pluggy==0.13.1 Best match: pluggy 0.13.1 Adding pluggy 0.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for tabulate==0.8.7 Best match: tabulate 0.8.7 Adding tabulate 0.8.7 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pipreqs==0.4.10 Best match: pipreqs 0.4.10 Adding pipreqs 0.4.10 to easy-install.pth file Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for humanfriendly==8.2 Best match: humanfriendly 8.2 Adding humanfriendly 8.2 to easy-install.pth file Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for packaging==20.7 Best match: packaging 20.7 Adding packaging 20.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for more-itertools==8.6.0 Best match: more-itertools 8.6.0 Adding more-itertools 8.6.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for certifi==2020.12.5 Best match: certifi 2020.12.5 Adding certifi 2020.12.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pytz==2020.4 Best match: pytz 2020.4 Adding pytz 2020.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for geographiclib==1.50 Best match: geographiclib 1.50 Adding geographiclib 1.50 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for zipp==3.4.0 Best match: zipp 3.4.0 Adding zipp 3.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for cryptography==3.3.1 Best match: cryptography 3.3.1 Adding cryptography 3.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for soupsieve==2.1 Best match: soupsieve 2.1 Adding soupsieve 2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for future==0.18.2 Best match: future 0.18.2 Adding future 0.18.2 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for xdg==5.0.1 Best match: xdg 5.0.1 Adding xdg 5.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for yarg==0.1.9 Best match: yarg 0.1.9 Adding yarg 0.1.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for docopt==0.6.2 Best match: docopt 0.6.2 Adding docopt 0.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for cffi==1.14.4 Best match: cffi 1.14.4 Adding cffi 1.14.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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-emodpy-malaria/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-emodpy-malaria/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-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Searching for pycparser==2.20 Best match: pycparser 2.20 Adding pycparser 2.20 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.7/site-packages Finished processing dependencies for emodpy-malaria==0.0.7 [rtd-command-info] start-time: 2020-12-12T00:22:10.965773Z, end-time: 2020-12-12T00:22:11.047343Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = [] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'emodpy-malaria' copyright = u'2020, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'emodpy-malaria' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emodpy-malaria-docs.tex', u'emodpy-malaria', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria', author, 'Institute for Disease Modeling', 'How to use emodpy for malaria simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/emodpy-malaria/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/emodpy-malaria/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emodpy-malaria', 'name': u'emodpy-malaria', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/emodpy-malaria/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': 'emodpy-malaria', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': 'f75a5780', } 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: 2020-12-12T00:22:11.192032Z, end-time: 2020-12-12T00:23:12.595401Z, duration: 61, 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 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) rm: cannot remove 'emodpy_malaria_index.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 13 source files that are out of date updating environment: [new config] 13 added, 0 changed, 0 removed reading sources... [ 7%] emodpy_malaria reading sources... [ 15%] emodpy_malaria.config reading sources... [ 23%] emodpy_malaria.demographics reading sources... [ 30%] emodpy_malaria.demographics.MalariaDemographics Matplotlib is building the font cache; this may take a moment. reading sources... [ 38%] emodpy_malaria.interventions reading sources... [ 46%] emodpy_malaria.interventions.bednet reading sources... [ 53%] emodpy_malaria.interventions.spacespraying reading sources... [ 61%] emodpy_malaria.interventions.sugartrap reading sources... [ 69%] emodpy_malaria.reporters reading sources... [ 76%] emodpy_malaria.reporters.builtin /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.6.2/configuration.html for details on how to configure idmtools. reading sources... [ 84%] emodpy_malaria_index reading sources... [ 92%] index reading sources... [100%] installation looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 7%] emodpy_malaria writing output... [ 15%] emodpy_malaria.config writing output... [ 23%] emodpy_malaria.demographics writing output... [ 30%] emodpy_malaria.demographics.MalariaDemographics writing output... [ 38%] emodpy_malaria.interventions writing output... [ 46%] emodpy_malaria.interventions.bednet writing output... [ 53%] emodpy_malaria.interventions.spacespraying writing output... [ 61%] emodpy_malaria.interventions.sugartrap writing output... [ 69%] emodpy_malaria.reporters writing output... [ 76%] emodpy_malaria.reporters.builtin writing output... [ 84%] emodpy_malaria_index writing output... [ 92%] index writing output... [100%] installation generating indices... genindex py-modindexdone writing additional pages... search opensearchdone copying static files... ... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2020-12-12T00:23:12.787520Z, end-time: 2020-12-12T00:23:15.265984Z, duration: 2, 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 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) 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] 13 added, 0 changed, 0 removed reading sources... [ 7%] emodpy_malaria reading sources... [ 15%] emodpy_malaria.config reading sources... [ 23%] emodpy_malaria.demographics reading sources... [ 30%] emodpy_malaria.demographics.MalariaDemographics reading sources... [ 38%] emodpy_malaria.interventions reading sources... [ 46%] emodpy_malaria.interventions.bednet reading sources... [ 53%] emodpy_malaria.interventions.spacespraying reading sources... [ 61%] emodpy_malaria.interventions.sugartrap reading sources... [ 69%] emodpy_malaria.reporters reading sources... [ 76%] emodpy_malaria.reporters.builtin /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.6.2/configuration.html for details on how to configure idmtools. reading sources... [ 84%] emodpy_malaria_index reading sources... [ 92%] index reading sources... [100%] installation looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation emodpy_malaria_index emodpy_malaria emodpy_malaria.demographics emodpy_malaria.demographics.MalariaDemographics emodpy_malaria.interventions emodpy_malaria.interventions.bednet emodpy_malaria.interventions.spacespraying emodpy_malaria.interventions.sugartrap emodpy_malaria.reporters emodpy_malaria.reporters.builtin emodpy_malaria.config done writing... done writing additional files... opensearchdone copying static files... ... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2020-12-12T00:23:15.463827Z, end-time: 2020-12-12T00:23:17.868163Z, duration: 2, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) 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] 13 added, 0 changed, 0 removed reading sources... [ 7%] emodpy_malaria reading sources... [ 15%] emodpy_malaria.config reading sources... [ 23%] emodpy_malaria.demographics reading sources... [ 30%] emodpy_malaria.demographics.MalariaDemographics reading sources... [ 38%] emodpy_malaria.interventions reading sources... [ 46%] emodpy_malaria.interventions.bednet reading sources... [ 53%] emodpy_malaria.interventions.spacespraying reading sources... [ 61%] emodpy_malaria.interventions.sugartrap reading sources... [ 69%] emodpy_malaria.reporters reading sources... [ 76%] emodpy_malaria.reporters.builtin /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.6.2/configuration.html for details on how to configure idmtools. reading sources... [ 84%] emodpy_malaria_index reading sources... [ 92%] index reading sources... [100%] installation looking for now-outdated files... none found pickling environment... done checking consistency... done processing emodpy-malaria-docs.tex... index installation emodpy_malaria_index emodpy_malaria emodpy_malaria.demographics emodpy_malaria.demographics.MalariaDemographics emodpy_malaria.interventions emodpy_malaria.interventions.bednet emodpy_malaria.interventions.spacespraying emodpy_malaria.interventions.sugartrap emodpy_malaria.reporters emodpy_malaria.reporters.builtin emodpy_malaria.config resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/checkouts/latest/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2020-12-12T00:23:18.079319Z, end-time: 2020-12-12T00:23:18.138649Z, 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: 2020-12-12T00:23:18.278125Z, end-time: 2020-12-12T00:23:36.251407Z, duration: 17, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emodpy-malaria -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' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emodpy-malaria" "emodpy-malaria-docs.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emodpy-malaria-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[3] [4] Chapter 2. 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paragraph at lines 278--278 \T1/ptm/m/it/10 Pretty_Format: [7] [8] LaTeX Warning: Reference `emodpy_malaria:module-emodpy_malaria' on page 9 undef ined on input line 379. LaTeX Warning: Reference `emodpy_malaria.config:module-emodpy_malaria.config' o n page 9 undefined on input line 380. LaTeX Warning: Reference `emodpy_malaria.demographics:module-emodpy_malaria.dem ographics' on page 9 undefined on input line 381. LaTeX Warning: Reference `emodpy_malaria.demographics.MalariaDemographics:modul e-emodpy_malaria.demographics.MalariaDemographics' on page 9 undefined on input line 382. Overfull \hbox (54.6225pt too wide) in paragraph at lines 382--383 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 , LaTeX Warning: Reference `emodpy_malaria.interventions:module-emodpy_malaria.in terventions' on page 9 undefined on input line 383. LaTeX Warning: Reference `emodpy_malaria.interventions.bednet:module-emodpy_mal aria.interventions.bednet' on page 9 undefined on input line 384. 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(./institute-for-disease-modeling-emodpy-malaria.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-emodpy-mal aria.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emodpy-malaria.pdf (13 pages, 91851 bytes). Transcript written on institute-for-disease-modeling-emodpy-malaria.log. Latexmk: Index file 'institute-for-disease-modeling-emodpy-malaria.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-emodpy-malaria.ind' from line 'No file institute-for-disease-modeling-emodpy-malaria.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-malaria.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-malaria.pdf' Latexmk: List of undefined refs and citations: Reference `emodpy_malaria.config:module-emodpy_malaria.config' on page 9 undefined on input line 380 Reference `emodpy_malaria.demographics.MalariaDemographics:module-emodpy_malaria.demographics.MalariaDemographics' on page 9 undefined on input line 382 Reference `emodpy_malaria.demographics:module-emodpy_malaria.demographics' on page 9 undefined on input line 381 Reference `emodpy_malaria.interventions.bednet:module-emodpy_malaria.interventions.bednet' on page 9 undefined on input line 384 Reference `emodpy_malaria.interventions.spacespraying:module-emodpy_malaria.interventions.spacespraying' on page 9 undefined on input line 385 Reference `emodpy_malaria.interventions.sugartrap:module-emodpy_malaria.interventions.sugartrap' on page 9 undefined on input line 386 Reference `emodpy_malaria.interventions:module-emodpy_malaria.interventions' on page 9 undefined on input line 383 Reference `emodpy_malaria.reporters.builtin:module-emodpy_malaria.reporters.builtin' on page 9 undefined on input line 388 Reference `emodpy_malaria.reporters:module-emodpy_malaria.reporters' on page 9 undefined on input line 387 Reference `emodpy_malaria:module-emodpy_malaria' on page 9 undefined on input line 379 Latexmk: Summary of warnings: Latex failed to resolve 11 reference(s) Rule 'makeindex institute-for-disease-modeling-emodpy-malaria.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-emodpy-malaria.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-emodpy-malaria.idx' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-emodpy-malaria.idx'... ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-emodpy-malaria.ind" "institute-for-disease-modeling-emodpy-malaria.idx"' ------------ This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-emodpy-malaria.idx....done (45 entries accepted, 0 rejected). Sorting entries....done (275 comparisons). Generating output file institute-for-disease-modeling-emodpy-malaria.ind....done (110 lines written, 0 warnings). Output written in institute-for-disease-modeling-emodpy-malaria.ind. Transcript written in institute-for-disease-modeling-emodpy-malaria.ilg. 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[3] [4] Chapter 2. 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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emodpy-malaria.out) (./institute-for-disease-modeling-emodpy-malaria.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-emodpy-malaria.toc) [1] [2] [1] [2] Chapter 1. [3] [4] Chapter 2. 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\T1/ptm/m/it/10 name=None\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 201--201 []\T1/ptm/m/it/10 camp\T1/ptm/m/n/10 , \T1/ptm/m/it/10 start_day\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cov-er-age=1.0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 201--201 \T1/ptm/m/it/10 killing_eff=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-sec-ti-cide=No ne\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 224--224 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pa-ram-e-ters: Underfull \hbox (badness 10000) in paragraph at lines 224--224 \T1/ptm/m/it/10 dict = \T1/ptm/m/n/10 , Underfull \hbox (badness 6348) in paragraph at lines 224--224 \T1/ptm/m/it/10 En-abled: bool = [6] Underfull \hbox (badness 10000) in paragraph at lines 264--264 []\T1/ptm/m/it/10 class_name: str Underfull \hbox (badness 10000) in paragraph at lines 264--264 \T1/ptm/m/it/10 = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 Malar-i-a-Sum- Underfull \hbox (badness 10000) in paragraph 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paragraph at lines 278--278 \T1/ptm/m/it/10 Pretty_Format: [7] [8] Overfull \hbox (54.6225pt too wide) in paragraph at lines 382--383 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 385--386 []\T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 386--387 []\T1/pcr/m/n/10 emodpy_malaria.interventions.sugartrap\T1/ptm/m/n/10 , [9] (./institute-for-disease-modeling-emodpy-malaria.ind [10] Underfull \hbox (badness 10000) in paragraph at lines 9--10 []\T1/pcr/m/n/10 add_mutation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 add_resistance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 15--16 []\T1/pcr/m/n/10 Bednet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (84.70978pt too wide) in paragraph at lines 19--21 []\T1/pcr/m/n/10 class_name \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.repo rters.builtin.MalariaPatientJSONReport Overfull \hbox (71.06006pt too wide) in paragraph at lines 21--23 []\T1/pcr/m/n/10 class_name \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.repo rters.builtin.MalariaSummaryReport Overfull \hbox (49.04977pt too wide) in paragraph at lines 23--25 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportVectorGenetics Overfull \hbox (33.50998pt too wide) in paragraph at lines 25--27 []\T1/pcr/m/n/10 config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.report ers.builtin.ReportVectorStats Overfull \hbox (52.1225pt too wide) in paragraph at lines 36--37 []\T1/pcr/m/n/10 emodpy_malaria.demographics.MalariaDemographics Overfull \hbox (22.1225pt too wide) in paragraph at lines 42--43 []\T1/pcr/m/n/10 emodpy_malaria.interventions.spacespraying Underfull \hbox (badness 10000) in paragraph at lines 53--55 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82--84 \T1/ptm/m/it/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 84--86 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (61.04977pt too wide) in paragraph at lines 89--91 []\T1/pcr/m/n/10 parameters \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.repo rters.builtin.ReportVectorGenetics [11] Overfull \hbox (45.50998pt too wide) in paragraph at lines 91--93 []\T1/pcr/m/n/10 parameters \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emodpy_malaria.repo rters.builtin.ReportVectorStats Underfull \hbox (badness 10000) in paragraph at lines 96--98 []\T1/pcr/m/n/10 ReportVectorGenetics \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/pcr/m/n/10 ReportVectorStats \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 103--104 []\T1/pcr/m/n/10 set_genetics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 104--105 []\T1/pcr/m/n/10 set_resistances() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 105--107 []\T1/pcr/m/n/10 SpaceSpraying() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 105--107 \T1/ptm/m/it/10 emodpy_malaria.interventions.spacespraying\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 107--109 []\T1/pcr/m/n/10 SugarTrap() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 107--109 \T1/ptm/m/it/10 emodpy_malaria.interventions.sugartrap\T1/ptm/m/n/10 ), [12]) (./institute-for-disease-modeling-emodpy-malaria.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emodpy-malaria.pdf (16 pages, 104250 bytes). Transcript written on institute-for-disease-modeling-emodpy-malaria.log. Latexmk: Index file 'institute-for-disease-modeling-emodpy-malaria.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-malaria.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emodpy-malaria.pdf' Latexmk: All targets (institute-for-disease-modeling-emodpy-malaria.pdf) are up-to-date [rtd-command-info] start-time: 2020-12-12T00:23:36.373092Z, end-time: 2020-12-12T00:23:36.428537Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/checkouts/latest/docs/_build/latex/institute-for-disease-modeling-emodpy-malaria.pdf /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/artifacts/latest/sphinx_pdf/institute-for-disease-modeling-emodpy-malaria.pdf