Read the Docs build information Build id: 598228 Project: institute-for-disease-modeling-covasim Version: latest Commit: 7f38b18c57967ce60fe286c985ef06a0bd3821e4 Date: 2021-03-24T07:35:02.192682Z State: finished Success: False [rtd-command-info] start-time: 2021-03-24T07:35:04.216672Z, end-time: 2021-03-24T07:35:07.257960Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/covasim.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-03-24T07:35:07.420626Z, end-time: 2021-03-24T07:35:07.507369Z, 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 7f38b18 Merge pull request #859 from amath-idm/rc2.0.5 [rtd-command-info] start-time: 2021-03-24T07:35:07.642289Z, end-time: 2021-03-24T07:35:07.725998Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-03-24T07:35:08.714426Z, end-time: 2021-03-24T07:35:14.151563Z, duration: 5, exit-code: 0 python3.8 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin/python3.8 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: 2021-03-24T07:35:14.293247Z, end-time: 2021-03-24T07:35:15.916743Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (21.0.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (54.2.0) [rtd-command-info] start-time: 2021-03-24T07:35:16.047362Z, end-time: 2021-03-24T07:35:43.937012Z, duration: 27, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 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<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting setuptools Downloading setuptools-54.2.0-py3-none-any.whl (785 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 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-2.8.1-py3-none-any.whl (983 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp38-cp38-manylinux2010_x86_64.whl (32 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.4-py2.py3-none-any.whl (153 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 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) Building wheels for collected packages: mock, pillow, 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=23755 sha256=4907b521d1523f2c4e2aee0b4dd2ce7e3cf11a1dd98fa5923d15c0dbe4a3eef0 Stored in directory: /tmp/pip-ephem-wheel-cache-xvkfz3c8/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65 Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260039 sha256=57d1e8513871db8b8077be08019d0b3d22db159533dec6671505350d4179834e Stored in directory: /tmp/pip-ephem-wheel-cache-xvkfz3c8/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d 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=dce1e2b7ab5b9850a8f920758797c9b424e69b4957d489d4ecf2c10a8d3524c4 Stored in directory: /tmp/pip-ephem-wheel-cache-xvkfz3c8/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow 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 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.16 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 setuptools-54.2.0 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4 [rtd-command-info] start-time: 2021-03-24T07:35:44.068455Z, end-time: 2021-03-24T07:36:14.865652Z, duration: 30, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pytest Downloading pytest-6.2.2-py3-none-any.whl (280 kB) Requirement already satisfied: sphinx-rtd-theme in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3) Collecting sphinxcontrib-napoleon Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from -r docs/requirements.txt (line 4)) (1.8.5) Collecting plantweb Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting ipykernel Downloading ipykernel-5.5.0-py3-none-any.whl (120 kB) Collecting nbsphinx Downloading nbsphinx-0.8.2-py3-none-any.whl (24 kB) Collecting pandoc Downloading pandoc-1.0.2.tar.gz (488 kB) Collecting pypandoc Downloading pypandoc-1.5.tar.gz (26 kB) Collecting optuna Downloading optuna-2.6.0-py3-none-any.whl (293 kB) Collecting numba==0.48 Downloading numba-0.48.0-1-cp38-cp38-manylinux2014_x86_64.whl (3.6 MB) Collecting llvmlite<0.32.0,>=0.31.0dev0 Downloading llvmlite-0.31.0-cp38-cp38-manylinux1_x86_64.whl (20.2 MB) Requirement already satisfied: setuptools in 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Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting decorator Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Requirement already satisfied: pygments in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from ipython>=5.0.0->ipykernel->-r docs/requirements.txt (line 6)) (2.8.1) Collecting jedi>=0.16 Downloading jedi-0.18.0-py2.py3-none-any.whl (1.4 MB) Collecting parso<0.9.0,>=0.8.0 Downloading parso-0.8.1-py2.py3-none-any.whl (93 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting wcwidth Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from nbsphinx->-r docs/requirements.txt (line 7)) (0.16) Collecting nbconvert!=5.4 Downloading nbconvert-6.0.7-py3-none-any.whl (552 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from nbsphinx->-r docs/requirements.txt (line 7)) (2.11.3) Collecting nbformat Downloading nbformat-5.1.2-py3-none-any.whl (113 kB) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (1.2.4) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (1.2.0) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.25.1) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (20.9) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (0.7.12) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.9.0) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (1.15.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinx->-r docs/requirements.txt (line 4)) (2.1.0) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from babel!=2.0,>=1.3->sphinx->-r docs/requirements.txt (line 4)) (2021.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from jinja2->nbsphinx->-r docs/requirements.txt (line 7)) (1.1.1) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) 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tqdm-4.59.0-py2.py3-none-any.whl (74 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from packaging->sphinx->-r docs/requirements.txt (line 4)) (2.4.7) Collecting greenlet!=0.4.17 Downloading greenlet-1.0.0-cp38-cp38-manylinux2010_x86_64.whl (165 kB) Collecting ply Downloading ply-3.11-py2.py3-none-any.whl (49 kB) Requirement already satisfied: pip>=8.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from pypandoc->-r docs/requirements.txt (line 9)) (21.0.1) Requirement already satisfied: wheel>=0.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from pypandoc->-r docs/requirements.txt (line 9)) (0.36.2) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting py>=1.8.2 Downloading py-1.10.0-py2.py3-none-any.whl (97 kB) Collecting pluggy<1.0.0a1,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Collecting python-editor>=0.3 Downloading python_editor-1.0.4-py3-none-any.whl (4.9 kB) Collecting Mako Downloading Mako-1.1.4-py2.py3-none-any.whl (75 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting PrettyTable>=0.7.2 Downloading prettytable-2.1.0-py3-none-any.whl (22 kB) Collecting pbr!=2.1.0,>=2.0.0 Downloading pbr-5.5.1-py2.py3-none-any.whl (106 kB) Collecting stevedore>=2.0.1 Downloading stevedore-3.3.0-py3-none-any.whl (49 kB) Collecting PyYAML>=3.12 Downloading PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl (662 kB) Collecting cmd2>=1.0.0 Downloading cmd2-1.5.0-py3-none-any.whl (133 kB) Collecting colorama>=0.3.7 Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB) Collecting pyperclip>=1.6 Downloading pyperclip-1.8.2.tar.gz (20 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages (from sphinxcontrib-websupport->sphinx->-r docs/requirements.txt (line 4)) (1.1.4) Building wheels for collected packages: pandocfilters, pyrsistent, pandoc, pypandoc, pyperclip Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7992 sha256=62b5c6a9daa14b926d376857ffbe72ae2be1451f943a00393ed34f0a721e2ded Stored in directory: /tmp/pip-ephem-wheel-cache-27z4gors/wheels/fc/39/52/8d6f3cec1cca4ceb44d658427c35711b19d89dbc4914af657f Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp38-cp38-linux_x86_64.whl size=119667 sha256=3d01243d6b5e1346bc293eab8c3c5c51c6d6a2e3ac099ab2f0132cbab38d34bb Stored in directory: /tmp/pip-ephem-wheel-cache-27z4gors/wheels/3d/22/08/7042eb6309c650c7b53615d5df5cc61f1ea9680e7edd3a08d2 Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-1.0.2-py3-none-any.whl size=19992 sha256=e486f9dd6375bdf42d385c4826f7521e1e1569842e2a82834168f99c2e561ba7 Stored in directory: /tmp/pip-ephem-wheel-cache-27z4gors/wheels/a4/b9/34/3e82b9444401c2199d721240a388499a262d2e2ad37f6f3fa7 Building wheel for pypandoc (setup.py): started Building wheel for pypandoc (setup.py): finished with status 'done' Created wheel for pypandoc: filename=pypandoc-1.5-py3-none-any.whl size=17037 sha256=52064c5a3daa8d24926575bc1858ca27b13aee59a6ecfbfae8830aa6c761e338 Stored in directory: /tmp/pip-ephem-wheel-cache-27z4gors/wheels/27/01/d8/dde8d4ae5c2a6e6dda11cee8c4fb855c9f60f1f8cdc1332cef Building wheel for pyperclip (setup.py): started Building wheel for pyperclip (setup.py): finished with status 'done' Created wheel for pyperclip: filename=pyperclip-1.8.2-py3-none-any.whl size=11107 sha256=4afcd553e71dd0c7201980baaebdbd26fce6a4debd268c982c510f91b0886a42 Stored in directory: /tmp/pip-ephem-wheel-cache-27z4gors/wheels/7f/1a/65/84ff8c386bec21fca6d220ea1f5498a0367883a78dd5ba6122 Successfully built pandocfilters pyrsistent pandoc pypandoc pyperclip Installing collected packages: ipython-genutils, traitlets, pyrsistent, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, wcwidth, pyperclip, ptyprocess, pbr, parso, nest-asyncio, nbformat, jupyter-client, greenlet, colorama, async-generator, testpath, stevedore, sqlalchemy, PyYAML, python-editor, prompt-toolkit, PrettyTable, pickleshare, pexpect, pandocfilters, nbclient, mistune, Mako, jupyterlab-pygments, jedi, entrypoints, defusedxml, decorator, cmd2, bleach, backcall, tqdm, toml, scipy, py, pockets, ply, pluggy, nbconvert, llvmlite, ipython, iniconfig, colorlog, cmaes, cliff, alembic, sphinxcontrib-napoleon, pytest, pypandoc, plantweb, pandoc, optuna, numba, nbsphinx, ipykernel Successfully installed Mako-1.1.4 PrettyTable-2.1.0 PyYAML-5.4.1 alembic-1.5.8 async-generator-1.10 attrs-20.3.0 backcall-0.2.0 bleach-3.3.0 cliff-3.7.0 cmaes-0.8.2 cmd2-1.5.0 colorama-0.4.4 colorlog-4.8.0 decorator-4.4.2 defusedxml-0.7.1 entrypoints-0.3 greenlet-1.0.0 iniconfig-1.1.1 ipykernel-5.5.0 ipython-7.21.0 ipython-genutils-0.2.0 jedi-0.18.0 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 llvmlite-0.31.0 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.2 nbsphinx-0.8.2 nest-asyncio-1.5.1 numba-0.48.0 optuna-2.6.0 pandoc-1.0.2 pandocfilters-1.4.3 parso-0.8.1 pbr-5.5.1 pexpect-4.8.0 pickleshare-0.7.5 plantweb-1.2.1 pluggy-0.13.1 ply-3.11 pockets-0.9.1 prompt-toolkit-3.0.18 ptyprocess-0.7.0 py-1.10.0 pypandoc-1.5 pyperclip-1.8.2 pyrsistent-0.17.3 pytest-6.2.2 python-editor-1.0.4 pyzmq-22.0.3 scipy-1.6.1 sphinxcontrib-napoleon-0.7 sqlalchemy-1.4.2 stevedore-3.3.0 testpath-0.4.4 toml-0.10.2 tornado-6.1 tqdm-4.59.0 traitlets-5.0.5 wcwidth-0.2.5 webencodings-0.5.1 [rtd-command-info] start-time: 2021-03-24T07:36:14.996152Z, end-time: 2021-03-24T07:36:21.608652Z, duration: 6, 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: 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/interventions.py -> build/lib/covasim copying covasim/utils.py -> build/lib/covasim copying covasim/parameters.py -> build/lib/covasim copying covasim/settings.py -> build/lib/covasim copying covasim/population.py -> build/lib/covasim copying covasim/version.py -> build/lib/covasim copying covasim/people.py -> build/lib/covasim copying covasim/analysis.py -> build/lib/covasim copying covasim/misc.py -> build/lib/covasim copying covasim/plotting.py -> build/lib/covasim copying covasim/base.py -> build/lib/covasim copying covasim/defaults.py -> build/lib/covasim copying covasim/run.py -> build/lib/covasim copying covasim/sim.py -> build/lib/covasim copying covasim/requirements.py -> build/lib/covasim copying covasim/__init__.py -> build/lib/covasim creating build/lib/covasim/data copying covasim/data/household_size_data.py -> build/lib/covasim/data copying covasim/data/state_age_data.py -> build/lib/covasim/data copying covasim/data/loaders.py -> build/lib/covasim/data copying covasim/data/country_age_data.py -> build/lib/covasim/data copying covasim/data/__init__.py -> build/lib/covasim/data copying covasim/README.rst -> build/lib/covasim creating build/lib/covasim/regression copying covasim/regression/README.rst -> build/lib/covasim/regression copying covasim/regression/pars_v0.30.4.json -> build/lib/covasim/regression copying covasim/regression/pars_v0.31.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v0.32.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.0.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.0.1.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.1.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.1.1.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.1.3.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.2.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.3.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.4.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.5.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.6.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v1.7.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v2.0.0.json -> build/lib/covasim/regression copying covasim/regression/pars_v2.1.0.json -> build/lib/covasim/regression 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/interventions.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/utils.py -> build/bdist.linux-x86_64/egg/covasim creating 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/state_age_data.py -> 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/country_age_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/parameters.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/settings.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/version.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/people.py -> build/bdist.linux-x86_64/egg/covasim creating build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.5.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.6.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v0.31.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.0.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.1.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v2.1.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v2.0.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.0.1.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.1.1.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.4.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.7.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.1.3.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.3.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v1.2.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v0.32.0.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/README.rst -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/regression/pars_v0.30.4.json -> build/bdist.linux-x86_64/egg/covasim/regression copying build/lib/covasim/analysis.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/misc.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/plotting.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/base.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/defaults.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/run.py -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/README.rst -> build/bdist.linux-x86_64/egg/covasim copying build/lib/covasim/sim.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/__init__.py -> build/bdist.linux-x86_64/egg/covasim byte-compiling build/bdist.linux-x86_64/egg/covasim/interventions.py to interventions.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/utils.py to utils.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/household_size_data.py to household_size_data.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/state_age_data.py to state_age_data.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/loaders.py to loaders.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/country_age_data.py to country_age_data.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/data/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/parameters.py to parameters.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/settings.py to settings.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/population.py to population.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/version.py to version.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/people.py to people.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/analysis.py to analysis.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/misc.py to misc.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/plotting.py to plotting.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/base.py to base.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/defaults.py to defaults.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/run.py to run.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/sim.py to sim.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/requirements.py to requirements.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/covasim/__init__.py to __init__.cpython-38.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-38: module MAY be using inspect.getouterframes covasim.__pycache__.misc.cpython-38: module references __file__ creating dist creating 'dist/covasim-2.1.0-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing covasim-2.1.0-py3.8.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim-2.1.0-py3.8.egg Extracting covasim-2.1.0-py3.8.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding covasim 2.1.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/covasim-2.1.0-py3.8.egg Processing dependencies for covasim==2.1.0 Searching for sciris>=1.0.0 Reading https://pypi.org/simple/sciris/ Downloading https://files.pythonhosted.org/packages/a5/8d/bf0545ef25a10d52c78f1aa08548eab729ce967fe2f782d6315f5454d5a1/sciris-1.1.1-py3-none-any.whl#sha256=a344f9d185aef89912e029d5f0236ceeb9cf59642325f9516469de1e2da4ba6b Best match: sciris 1.1.1 Processing sciris-1.1.1-py3-none-any.whl Installing sciris-1.1.1-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding sciris 1.1.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sciris-1.1.1-py3.8.egg Searching for xlrd==1.2.0 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/python3.8/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/python3.8/site-packages/xlrd-1.2.0-py3.8.egg Searching for statsmodels Reading https://pypi.org/simple/statsmodels/ Downloading https://files.pythonhosted.org/packages/bc/75/95096c520c34169244e5a3b488e282acae2c2aece99909d57dee45360c82/statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl#sha256=587deb788e7f8f3f866d28e812cf5c082b4d4a2d3f5beea94d0e9699ea71ef22 Best match: statsmodels 0.12.2 Processing statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl Installing statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding statsmodels 0.12.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/statsmodels-0.12.2-py3.8-linux-x86_64.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/python3.8/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/python3.8/site-packages/XlsxWriter-1.3.7-py3.8.egg Searching for psutil Reading https://pypi.org/simple/psutil/ Downloading https://files.pythonhosted.org/packages/3b/c2/78109a12da9febb2f965abf29da6f81b0a3f2b89a7b59d88b759e68dc6db/psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl#sha256=28ff7c95293ae74bf1ca1a79e8805fcde005c18a122ca983abf676ea3466362b Best match: psutil 5.8.0 Processing psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl Installing psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding psutil 5.8.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/psutil-5.8.0-py3.8-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/python3.8/site-packages 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/python3.8/site-packages/openpyexcel-2.5.14-py3.8.egg Searching for multiprocess Reading https://pypi.org/simple/multiprocess/ Downloading https://files.pythonhosted.org/packages/db/20/458ac043a57322365ac2ed86a911bf7598fc2e49bccb3f94ea810fbb6b9b/multiprocess-0.70.11.1-py37-none-any.whl#sha256=164c77448e357ebee0dc6abc7ee8c823e40e295e629a5fc6d31725109a3a7ee9 Best match: multiprocess 0.70.11.1 Processing multiprocess-0.70.11.1-py37-none-any.whl Installing multiprocess-0.70.11.1-py37-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding multiprocess 0.70.11.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/multiprocess-0.70.11.1-py3.8.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-kfilkhyi/memory_profiler-0.58.0/setup.cfg Running memory_profiler-0.58.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-kfilkhyi/memory_profiler-0.58.0/egg-dist-tmp-hmlg4mmu warning: no files found matching 'mprof.bat' build/bdist.linux-x86_64/egg/mprof.py:76: SyntaxWarning: "is" with a literal. Did you mean "=="? if args is "all": zip_safe flag not set; analyzing archive contents... __pycache__.memory_profiler.cpython-38: module MAY be using inspect.getsourcefile __pycache__.memory_profiler.cpython-38: module MAY be using inspect.stack __pycache__.memory_profiler.cpython-38: module MAY be using inspect.trace creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/memory_profiler-0.58.0-py3.8.egg Extracting memory_profiler-0.58.0-py3.8.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/site-packages/memory_profiler-0.58.0-py3.8.egg Searching for line-profiler Reading https://pypi.org/simple/line-profiler/ Downloading https://files.pythonhosted.org/packages/57/bb/090216d371e6faea7960d03cbdbcbc1b53d6d675fcaae5078a7ac5d4a437/line_profiler-3.1.0-cp38-cp38-manylinux1_x86_64.whl#sha256=a66e089e6d98ab8a70b5f89c0367c6780abad0f0b1d624dbe5edd8f0083986c7 Best match: line-profiler 3.1.0 Processing line_profiler-3.1.0-cp38-cp38-manylinux1_x86_64.whl Installing line_profiler-3.1.0-cp38-cp38-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding line-profiler 3.1.0 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/python3.8/site-packages/line_profiler-3.1.0-py3.8-linux-x86_64.egg Searching for jsonpickle Reading https://pypi.org/simple/jsonpickle/ Downloading https://files.pythonhosted.org/packages/bb/1a/f2db026d4d682303793559f1c2bb425ba3ec0d6fd7ac63397790443f2461/jsonpickle-2.0.0-py2.py3-none-any.whl#sha256=c1010994c1fbda87a48f8a56698605b598cb0fc6bb7e7927559fc1100e69aeac Best match: jsonpickle 2.0.0 Processing jsonpickle-2.0.0-py2.py3-none-any.whl Installing jsonpickle-2.0.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding jsonpickle 2.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/jsonpickle-2.0.0-py3.8.egg Searching for jellyfish Reading https://pypi.org/simple/jellyfish/ Downloading https://files.pythonhosted.org/packages/11/50/52dc08e011620516462e3c23d9c0d174d8bb56dbdc2c9b623946f6c125ea/jellyfish-0.8.2-cp38-cp38-manylinux2014_x86_64.whl#sha256=288727bac0cef5817640d1d0d3655dabb9906d1f7b3e31eb1bd0b005bdf0eaf2 Best match: jellyfish 0.8.2 Processing jellyfish-0.8.2-cp38-cp38-manylinux2014_x86_64.whl Installing jellyfish-0.8.2-cp38-cp38-manylinux2014_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/site-packages/jellyfish-0.8.2-py3.8-linux-x86_64.egg Searching for gitpython Reading https://pypi.org/simple/gitpython/ Downloading https://files.pythonhosted.org/packages/a6/99/98019716955ba243657daedd1de8f3a88ca1f5b75057c38e959db22fb87b/GitPython-3.1.14-py3-none-any.whl#sha256=3283ae2fba31c913d857e12e5ba5f9a7772bbc064ae2bb09efafa71b0dd4939b Best match: GitPython 3.1.14 Processing GitPython-3.1.14-py3-none-any.whl Installing GitPython-3.1.14-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding GitPython 3.1.14 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/GitPython-3.1.14-py3.8.egg Searching for dill Reading https://pypi.org/simple/dill/ Downloading https://files.pythonhosted.org/packages/52/d6/79f40d230895fa1ce3b6af0d22e0ac79c65175dc069c194b79cc8e05a033/dill-0.3.3-py2.py3-none-any.whl#sha256=78370261be6ea49037ace8c17e0b7dd06d0393af6513cc23f9b222d9367ce389 Best match: dill 0.3.3 Processing dill-0.3.3-py2.py3-none-any.whl Installing dill-0.3.3-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding dill 0.3.3 to easy-install.pth file Installing get_objgraph script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing undill 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/python3.8/site-packages/dill-0.3.3-py3.8.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/python3.8/site-packages 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/python3.8/site-packages/patsy-0.5.1-py3.8.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/python3.8/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/python3.8/site-packages/jdcal-1.4.1-py3.8.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-ulke2zi6/et_xmlfile-1.0.1/setup.cfg Running et_xmlfile-1.0.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ulke2zi6/et_xmlfile-1.0.1/egg-dist-tmp-xst3pk40 /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/memory_profiler-0.58.0-py3.8.egg/mprof.py:76: SyntaxWarning: "is" with a literal. Did you mean "=="? if args is "all": zip_safe flag not set; analyzing archive contents... et_xmlfile.tests.__pycache__.common_imports.cpython-38: module references __file__ creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/et_xmlfile-1.0.1-py3.8.egg Extracting et_xmlfile-1.0.1-py3.8.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/site-packages/et_xmlfile-1.0.1-py3.8.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/python3.8/site-packages 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/python3.8/site-packages/gitdb-4.0.5-py3.8.egg Searching for smmap<4,>=3.0.1 Reading https://pypi.org/simple/smmap/ Downloading https://files.pythonhosted.org/packages/d5/1e/6130925131f639b2acde0f7f18b73e33ce082ff2d90783c436b52040af5a/smmap-3.0.5-py2.py3-none-any.whl#sha256=7bfcf367828031dc893530a29cb35eb8c8f2d7c8f2d0989354d75d24c8573714 Best match: smmap 3.0.5 Processing smmap-3.0.5-py2.py3-none-any.whl Installing smmap-3.0.5-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Adding smmap 3.0.5 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/smmap-3.0.5-py3.8.egg Searching for pandas==1.1.3 Best match: pandas 1.1.3 Adding pandas 1.1.3 to easy-install.pth file Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for matplotlib==3.3.2 Best match: matplotlib 3.3.2 matplotlib 3.3.2 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for scipy==1.6.1 Best match: scipy 1.6.1 Adding scipy 1.6.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for numba==0.48.0 Best match: numba 0.48.0 Adding numba 0.48.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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 f2py3.8 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for pytz==2021.1 Best match: pytz 2021.1 Adding pytz 2021.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/3.8.6/lib/python3.8/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/3.8.6/lib/python3.8/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-covasim/envs/latest/lib/python3.8/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/python3.8/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/3.8.6/lib/python3.8/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/3.8.6/lib/python3.8/site-packages Searching for setuptools==54.2.0 Best match: setuptools 54.2.0 Adding setuptools 54.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/site-packages Searching for ipython==7.21.0 Best match: ipython 7.21.0 Adding ipython 7.21.0 to easy-install.pth file Installing iptest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing iptest3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/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/python3.8/site-packages Searching for pexpect==4.8.0 Best match: pexpect 4.8.0 Adding pexpect 4.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for Pygments==2.8.1 Best match: Pygments 2.8.1 Adding Pygments 2.8.1 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/python3.8/site-packages Searching for jedi==0.18.0 Best match: jedi 0.18.0 Adding jedi 0.18.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for prompt-toolkit==3.0.18 Best match: prompt-toolkit 3.0.18 Adding prompt-toolkit 3.0.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for pickleshare==0.7.5 Best match: pickleshare 0.7.5 Adding pickleshare 0.7.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for decorator==4.4.2 Best match: decorator 4.4.2 Adding decorator 4.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for backcall==0.2.0 Best match: backcall 0.2.0 Adding backcall 0.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for traitlets==5.0.5 Best match: traitlets 5.0.5 Adding traitlets 5.0.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for ptyprocess==0.7.0 Best match: ptyprocess 0.7.0 Adding ptyprocess 0.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for parso==0.8.1 Best match: parso 0.8.1 Adding parso 0.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for wcwidth==0.2.5 Best match: wcwidth 0.2.5 Adding wcwidth 0.2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Searching for ipython-genutils==0.2.0 Best match: ipython-genutils 0.2.0 Adding ipython-genutils 0.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages Finished processing dependencies for covasim==2.1.0 [rtd-command-info] start-time: 2021-03-24T07:36:22.568899Z, end-time: 2021-03-24T07:36:22.639925Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # 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 from datetime import datetime import covasim as cv 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', 'sphinx.ext.viewcode', # Add a link to the Python source code for classes, functions etc. 'nbsphinx', ] autodoc_default_options = { 'member-order': 'bysource', 'members': None } autodoc_mock_imports = [] napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autoclass_content = "both" # Add __init__ doc (ie. params) to class summaries html_show_sourcelink = False # Remove 'view source code' from top of page (for html, not python) autodoc_member_order = 'bysource' # Keep original ordering add_module_names = False # NB, does not work autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes # 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' master_doc = 'index' # General information about the project. project = 'Covasim' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for Covasim version {cv.__version__}.\n' 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. version = cv.__version__ # The full version, including alpha/beta/rc tags. release = cv.__version__ # 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 # 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'] pygments_style = 'sphinx' # 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' # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] html_logo = "images/IDM_white.png" 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 = '%Y-%b-%d' # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_show_sphinx = False # 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' # 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 # -- 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'), ] # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} # Configure nbsphinx nbsphinx_kernel_name = "python" nbsphinx_timeout = 60 # Time in seconds; use -1 for no timeout nbsphinx_execute_arguments = [ "--InlineBackend.figure_formats={'svg', 'pdf'}", "--InlineBackend.rc=figure.dpi=96", ] # Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs nb_ex_default = ['auto', 'never'][0] nb_ex = os.getenv('NBSPHINX_EXECUTE') if not nb_ex: nb_ex = nb_ex_default print(f'\n\nBuilding Jupyter notebooks with build option: {nb_ex}\n\n') nbsphinx_execute = nb_ex ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file should't rely on extra depencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/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': '7f38b18c', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-covasim/builds/598228/' 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: 2021-03-24T07:36:22.768831Z, end-time: 2021-03-24T07:40:24.521449Z, duration: 241, exit-code: 2 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.5 Matplotlib is building the font cache; this may take a moment. Covasim 2.1.0 (2021-03-23) — © 2021 by IDM Building Jupyter notebooks with build option: auto loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [html]: targets for 42 source files that are out of date updating environment: 42 added, 0 changed, 0 removed reading sources... [ 2%] conduct reading sources... [ 4%] contributing reading sources... [ 7%] covasim.analysis reading sources... [ 9%] covasim.base reading sources... [ 11%] covasim.data reading sources... [ 14%] covasim.data.country_age_data reading sources... [ 16%] covasim.data.household_size_data reading sources... [ 19%] covasim.data.loaders reading sources... [ 21%] covasim.data.state_age_data reading sources... [ 23%] covasim.defaults reading sources... [ 26%] covasim.interventions reading sources... [ 28%] covasim.misc reading sources... [ 30%] covasim.parameters reading sources... [ 33%] covasim.people reading sources... 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[ 90%] tutorials/t07 /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/jupyter_client/localinterfaces.py:245: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) warn("Unexpected error discovering local network interfaces: %s" % e) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/jupyter_client/localinterfaces.py:245: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) warn("Unexpected error discovering local network interfaces: %s" % e) Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 622, in _async_poll_for_reply msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/util.py", line 85, in ensure_async result = await obj File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/jupyter_client/asynchronous/channels.py", line 48, in get_msg raise Empty _queue.Empty During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbsphinx.py", line 1021, in parse rststring, resources = exporter.from_notebook_node(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbsphinx.py", line 832, in from_notebook_node nb, resources = pp.preprocess(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 79, in preprocess self.execute() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped return just_run(coro(*args, **kwargs)) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run return loop.run_until_complete(coro) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nest_asyncio.py", line 70, in run_until_complete return f.result() File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/futures.py", line 178, in result raise self._exception File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/tasks.py", line 280, in __step result = coro.send(None) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 553, in async_execute await self.async_execute_cell( File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 123, in async_execute_cell cell, resources = self.preprocess_cell(cell, self.resources, cell_index) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 146, in preprocess_cell cell = run_sync(NotebookClient.async_execute_cell)(self, cell, index, store_history=self.store_history) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped return just_run(coro(*args, **kwargs)) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run return loop.run_until_complete(coro) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nest_asyncio.py", line 70, in run_until_complete return f.result() File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/futures.py", line 178, in result raise self._exception File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/tasks.py", line 282, in __step result = coro.throw(exc) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 841, in async_execute_cell exec_reply = await self.task_poll_for_reply File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/futures.py", line 260, in __await__ yield self # This tells Task to wait for completion. File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/tasks.py", line 349, in __wakeup future.result() File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/futures.py", line 178, in result raise self._exception File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/asyncio/tasks.py", line 280, in __step result = coro.send(None) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 646, in _async_poll_for_reply await self._async_handle_timeout(timeout, cell) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbclient/client.py", line 696, in _async_handle_timeout raise CellTimeoutError.error_from_timeout_and_cell( nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 60 seconds. The message was: Cell execution timed out. Here is a preview of the cell contents: ------------------- ["'''", 'Example for running Optuna', "'''", '', 'import os'] ... [' run_workers()', ' study = op.load_study(storage=g.storage, study_name=g.name)', ' best_pars = study.best_params', ' T = sc.toc(t0, output=True)', " print(f'\\n\\nOutput: {best_pars}, time: {T:0.1f} s')"] ------------------- During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/cmd/build.py", line 304, in build_main app.build(args.force_all, filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/application.py", line 341, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 345, in build_update self.build(to_build, File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 360, in build updated_docnames = set(self.read()) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 468, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 490, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 534, in read_doc doctree = read_doc(self.app, self.env, self.env.doc2path(docname)) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/sphinx/io.py", line 318, in read_doc pub.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/docutils/core.py", line 217, in publish self.document = self.reader.read(self.source, self.parser, File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/docutils/readers/__init__.py", line 71, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/docutils/readers/__init__.py", line 77, in parse self.parser.parse(self.input, document) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-covasim/envs/latest/lib/python3.8/site-packages/nbsphinx.py", line 1030, in parse raise NotebookError(type(e).__name__ + ' in ' + nbsphinx.NotebookError: CellTimeoutError in tutorials/t07.ipynb: A cell timed out while it was being executed, after 60 seconds. The message was: Cell execution timed out. Here is a preview of the cell contents: ------------------- ["'''", 'Example for running Optuna', "'''", '', 'import os'] ... [' run_workers()', ' study = op.load_study(storage=g.storage, study_name=g.name)', ' best_pars = study.best_params', ' T = sc.toc(t0, output=True)', " print(f'\\n\\nOutput: {best_pars}, time: {T:0.1f} s')"] ------------------- Notebook error: CellTimeoutError in tutorials/t07.ipynb: A cell timed out while it was being executed, after 60 seconds. The message was: Cell execution timed out. Here is a preview of the cell contents: ------------------- ["'''", 'Example for running Optuna', "'''", '', 'import os'] ... [' run_workers()', ' study = op.load_study(storage=g.storage, study_name=g.name)', ' best_pars = study.best_params', ' T = sc.toc(t0, output=True)', " print(f'\\n\\nOutput: {best_pars}, time: {T:0.1f} s')"] -------------------