Read the Docs build information Build id: 1968133 Project: institute-for-disease-modeling-emodpy-typhoid Version: latest Commit: 99a597aecad8b54a6b4fb73a817f913642ce277c Date: 2024-01-23T20:28:01.096111Z State: finished Success: True [rtd-command-info] start-time: 2024-01-23T20:28:02.320035Z, end-time: 2024-01-23T20:28:02.887152Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/emodpy-typhoid.git . Cloning into '.'... [rtd-command-info] start-time: 2024-01-23T20:28:02.970065Z, end-time: 2024-01-23T20:28:03.992259Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/InstituteforDiseaseModeling/emodpy-typhoid * [new tag] v0.0.5 -> v0.0.5 * [new tag] v0.0.6 -> v0.0.6 [rtd-command-info] start-time: 2024-01-23T20:28:04.116456Z, end-time: 2024-01-23T20:28:04.204248Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to '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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 99a597a Age base hint SFTs (#32) [rtd-command-info] start-time: 2024-01-23T20:28:04.273496Z, end-time: 2024-01-23T20:28:04.328110Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-01-23T20:28:04.398623Z, end-time: 2024-01-23T20:28:04.458801Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip # Optionally set the version of Python and requirements required to build your docs python: install: - requirements: requirements.txt - requirements: docs/requirements.txt - method: setuptools path: . # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank # search: # ranking: [rtd-command-info] start-time: 2024-01-23T20:28:09.869430Z, end-time: 2024-01-23T20:28:09.942976Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-01-23T20:28:10.292625Z, end-time: 2024-01-23T20:28:11.528164Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 910ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-01-23T20:28:11.597061Z, end-time: 2024-01-23T20:28:21.203340Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Looking in indexes: https://pypi.org/simple, 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-typhoid/envs/latest/lib/python3.9/site-packages (23.1) Collecting pip Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/15/aa/3f4c7bcee2057a76562a5b33ecbd199be08cdb4443a02e26bd2c3cf6fc39/pip-23.3.2-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 16.9 MB/s eta 0:00:00 Requirement already 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Jinja2-3.1.3 MarkupSafe-2.1.4 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.1.0 zipp-3.17.0 [rtd-command-info] start-time: 2024-01-23T20:28:29.922827Z, end-time: 2024-01-23T20:29:17.143124Z, duration: 47, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting emodpy==1.22.0.dev3 (from -r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.22.0.dev3/emodpy-1.22.0.dev3-py3-none-any.whl (135 kB) 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idmtools~=1.7 (from emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.7.9/idmtools-1.7.9-py3-none-any.whl (168 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 168.6/168.6 kB 30.8 MB/s eta 0:00:00 Collecting idmtools-platform-comps~=1.7 (from emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-platform-comps/1.7.9/idmtools_platform_comps-1.7.9-py3-none-any.whl (188 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 188.5/188.5 kB 31.3 MB/s eta 0:00:00 Collecting idmtools-models~=1.7 (from emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.7.9/idmtools_models-1.7.9.tar.gz (12 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting matplotlib (from emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading 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(setup.py): finished with status 'done' Collecting networkx (from emod_api==1.31.0.dev5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d5/f0/8fbc882ca80cf077f1b246c0e3c3465f7f415439bdea6b899f6b19f61f70/networkx-3.2.1-py3-none-any.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 19.0 MB/s eta 0:00:00 Collecting parse (from emod_api==1.31.0.dev5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/27/da/2c9c45c3cca6ef6ebf8b4974bf211b523ad8064a315448372f3088a2193e/parse-1.20.0-py2.py3-none-any.whl (19 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages (from requests==2.29.0->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages (from requests==2.29.0->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) (3.6) Collecting urllib3<1.27,>=1.21.1 (from requests==2.29.0->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b0/53/aa91e163dcfd1e5b82d8a890ecf13314e3e149c05270cc644581f77f17fd/urllib3-1.26.18-py2.py3-none-any.whl (143 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.8/143.8 kB 26.3 MB/s eta 0:00:00 Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages (from requests==2.29.0->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) (2023.11.17) Collecting backoff<2.3,>=1.10.0 (from idmtools~=1.7->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/df/73/b6e24bd22e6720ca8ee9a85a0c4a2971af8497d8f3193fa05390cbd46e09/backoff-2.2.1-py3-none-any.whl (15 kB) Collecting coloredlogs~=15.0 (from idmtools~=1.7->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 163.8 MB/s eta 0:00:00 Collecting diskcache~=5.4.0 (from idmtools~=1.7->emodpy==1.22.0.dev3->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a1/c4/80d38cf6852ba87f8b506a91f18b3a485c668f452700689add960d7e2ecc/diskcache-5.4.0-py3-none-any.whl (44 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.0/45.0 kB 169.1 MB/s eta 0:00:00 Collecting filelock (from idmtools~=1.7->emodpy==1.22.0.dev3->-r requirements.txt 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packages: idmtools-models, prodict, future, docopt Building wheel for idmtools-models (setup.py): started Building wheel for idmtools-models (setup.py): finished with status 'done' Created wheel for idmtools-models: filename=idmtools_models-1.7.9-py3-none-any.whl size=18203 sha256=b0eb7006cdc3930018552d23b2e66955e415e8b56a963d83af002dd3535bc46c Stored in directory: /tmp/pip-ephem-wheel-cache-ic5lemji/wheels/45/89/0f/d22c2ae7e95145614a035133233281200ff8036033c3e183a7 Building wheel for prodict (setup.py): started Building wheel for prodict (setup.py): finished with status 'done' Created wheel for prodict: filename=prodict-0.8.18-py3-none-any.whl size=4203 sha256=29c26f9a6a56b071cb5813b7bb15c68e2552fefd87ebe83cdb9a8661ba33611b Stored in directory: /tmp/pip-ephem-wheel-cache-ic5lemji/wheels/b0/9c/b9/694dc9fa35b338adf315c91781d2150a3bccd224174d897720 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492022 sha256=f7c8c5da30d7cd6055e3cca86d1ff6f86e2027650628fa61ad57024d6f362dfe Stored in directory: /tmp/pip-ephem-wheel-cache-ic5lemji/wheels/2f/cc/b7/c2afbd9aa308238e24770b186ce812c515ff12207dd4d176b4 Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13707 sha256=530de66256d7f6cd97947b2ea3c5b0baf68d4bc827b5f692513327bc4b09ef73 Stored in directory: /tmp/pip-ephem-wheel-cache-ic5lemji/wheels/8d/59/3a/894ec22b85063f7b617ea5956e702fa119c6b14d7e6208a419 Successfully built idmtools-models prodict future docopt Installing collected packages: pytz, prodict, parse, emod-typhoid, docopt, xdg, urllib3, tzdata, tqdm, threadpoolctl, tabulate, soupsieve, six, pyyaml, pyproj, pyparsing, pycparser, pluggy, pillow, numpy, networkx, natsort, more-itertools, lz4, kiwisolver, joblib, jeepney, importlib-resources, humanfriendly, geographiclib, future, fonttools, filelock, diskcache, cycler, click, backoff, astor, shapely, scipy, requests, python-dateutil, packaging, jaraco.classes, contourpy, coloredlogs, cffi, beautifulsoup4, astunparse, yarg, scikit-learn, pygit2, pyCOMPS, pandas, matplotlib, cryptography, bs4, SecretStorage, pipreqs, emod_api, keyring, idmtools, idmtools-platform-comps, idmtools-models, emodpy Attempting uninstall: urllib3 Found existing installation: urllib3 2.1.0 Uninstalling urllib3-2.1.0: Successfully uninstalled urllib3-2.1.0 Attempting uninstall: requests Found existing installation: requests 2.31.0 Uninstalling requests-2.31.0: Successfully uninstalled requests-2.31.0 Attempting uninstall: packaging Found existing installation: packaging 23.2 Uninstalling packaging-23.2: Successfully uninstalled packaging-23.2 Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 beautifulsoup4-4.12.3 bs4-0.0.2 cffi-1.16.0 click-7.1.2 coloredlogs-15.0.1 contourpy-1.2.0 cryptography-42.0.0 cycler-0.12.1 diskcache-5.4.0 docopt-0.6.2 emod-typhoid-0.0.7.dev3 emod_api-1.31.0.dev5 emodpy-1.22.0.dev3 filelock-3.13.1 fonttools-4.47.2 future-0.18.3 geographiclib-2.0 humanfriendly-10.0 idmtools-1.7.9 idmtools-models-1.7.9 idmtools-platform-comps-1.7.9 importlib-resources-6.1.1 jaraco.classes-3.3.0 jeepney-0.8.0 joblib-1.3.2 keyring-24.3.0 kiwisolver-1.4.5 lz4-4.3.3 matplotlib-3.8.2 more-itertools-9.1.0 natsort-8.4.0 networkx-3.2.1 numpy-1.26.3 packaging-21.3 pandas-2.2.0 parse-1.20.0 pillow-10.2.0 pipreqs-0.4.13 pluggy-1.2.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.21 pygit2-1.10.1 pyparsing-3.1.1 pyproj-3.6.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 requests-2.29.0 scikit-learn-1.4.0 scipy-1.12.0 shapely-2.0.2 six-1.16.0 soupsieve-2.5 tabulate-0.9.0 threadpoolctl-3.2.0 tqdm-4.66.1 tzdata-2023.4 urllib3-1.26.18 xdg-6.0.0 yarg-0.1.9 [rtd-command-info] start-time: 2024-01-23T20:29:17.234470Z, end-time: 2024-01-23T20:29:47.088778Z, 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https://packages.idmod.org/api/pypi/pypi-production/packages/packages/45/86/4736ac618d82a20d87d2f92ae19441ebc7ac9e7a581d7e58bbe79233b24a/asttokens-2.4.1-py2.py3-none-any.whl (27 kB) Collecting pure-eval (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/27/77f9d5684e6bce929f5cfe18d6cfbe5133013c06cb2fbf5933670e60761d/pure_eval-0.2.2-py3-none-any.whl (11 kB) Collecting arrow>=0.15.0 (from isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f8/ed/e97229a566617f2ae958a6b13e7cc0f585470eac730a73e9e82c32a3cdd2/arrow-1.3.0-py3-none-any.whl (66 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.4/66.4 kB 204.8 MB/s eta 0:00:00 Collecting types-python-dateutil>=2.8.10 (from arrow>=0.15.0->isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/28/50/8ed67814241e2684369f4b8b881c7d31a0816e76c8690ea8518017a35b7e/types_python_dateutil-2.8.19.20240106-py3-none-any.whl (9.7 kB) Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, json5, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tomli, tinycss2, sphinxext.remoteliteralinclude, sniffio, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, requests, readthedocs-sphinx-search, pyzmq, python-json-logger, pyjwt, psutil, prompt-toolkit, prometheus-client, pockets, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, bleach, attrs, asttokens, terminado, stack-data, sphinxcontrib-napoleon, sphinx, referencing, pynacl, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, async-lru, arrow, argon2-cffi-bindings, anyio, sphinxcontrib-programoutput, sphinxcontrib-jquery, sphinx-copybutton, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, isoduration, ipython, argon2-cffi, sphinx-rtd-theme, pygithub, myst-parser, jsonschema, ipykernel, nbformat, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab Attempting uninstall: requests Found existing installation: requests 2.29.0 Uninstalling requests-2.29.0: Successfully uninstalled requests-2.29.0 Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 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. emodpy 1.22.0.dev3 requires requests==2.29.0, but you have requests 2.31.0 which is incompatible. Successfully installed anyio-4.2.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 bleach-6.1.0 comm-0.2.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docutils-0.18.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.1 fqdn-1.5.1 ipykernel-6.29.0 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyter-events-0.9.0 jupyter-lsp-2.2.2 jupyter-server-2.12.5 jupyter-server-terminals-0.5.2 jupyterlab-4.0.11 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.9.0 nbconvert-7.14.2 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 notebook-shim-0.2.3 overrides-7.6.0 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.1.0 pockets-0.9.1 prometheus-client-0.19.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-json-logger-2.0.7 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.32.1 requests-2.31.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.17.1 send2trash-1.8.2 sniffio-1.3.0 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinx-rtd-theme-1.2.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0 stack-data-0.6.3 terminado-0.18.0 tinycss2-1.2.1 tomli-2.0.1 tornado-6.4 traitlets-5.14.1 types-python-dateutil-2.8.19.20240106 typing-extensions-4.9.0 uri-template-1.3.0 wcwidth-0.2.13 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 wrapt-1.16.0 [rtd-command-info] start-time: 2024-01-23T20:29:47.183749Z, end-time: 2024-01-23T20:29:48.481578Z, duration: 1, exit-code: 0 python ./setup.py install --force /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() running bdist_egg running egg_info creating emodpy_typhoid.egg-info writing emodpy_typhoid.egg-info/PKG-INFO writing dependency_links to emodpy_typhoid.egg-info/dependency_links.txt writing requirements to emodpy_typhoid.egg-info/requires.txt writing top-level names to emodpy_typhoid.egg-info/top_level.txt writing manifest file 'emodpy_typhoid.egg-info/SOURCES.txt' reading manifest file 'emodpy_typhoid.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'emodpy_typhoid.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/emodpy_typhoid copying emodpy_typhoid/config.py -> build/lib/emodpy_typhoid copying emodpy_typhoid/__init__.py -> build/lib/emodpy_typhoid creating build/lib/emodpy_typhoid/demographics copying emodpy_typhoid/demographics/TyphoidDemographics.py -> build/lib/emodpy_typhoid/demographics copying emodpy_typhoid/demographics/__init__.py -> build/lib/emodpy_typhoid/demographics creating build/lib/emodpy_typhoid/interventions copying emodpy_typhoid/interventions/tcc.py -> build/lib/emodpy_typhoid/interventions copying emodpy_typhoid/interventions/outbreak.py -> build/lib/emodpy_typhoid/interventions copying emodpy_typhoid/interventions/tcd.py -> build/lib/emodpy_typhoid/interventions copying emodpy_typhoid/interventions/__init__.py -> build/lib/emodpy_typhoid/interventions copying emodpy_typhoid/interventions/typhoid_wash.py -> build/lib/emodpy_typhoid/interventions copying emodpy_typhoid/interventions/typhoid_vaccine.py -> build/lib/emodpy_typhoid/interventions creating build/lib/emodpy_typhoid/utility copying emodpy_typhoid/utility/sweeping.py -> build/lib/emodpy_typhoid/utility copying emodpy_typhoid/utility/__init__.py -> build/lib/emodpy_typhoid/utility creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/emodpy_typhoid creating build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics copying build/lib/emodpy_typhoid/demographics/TyphoidDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics copying build/lib/emodpy_typhoid/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics creating build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/interventions/tcc.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/interventions/tcd.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/interventions/typhoid_wash.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/interventions/typhoid_vaccine.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions copying build/lib/emodpy_typhoid/config.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid copying build/lib/emodpy_typhoid/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid creating build/bdist.linux-x86_64/egg/emodpy_typhoid/utility copying build/lib/emodpy_typhoid/utility/sweeping.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/utility copying build/lib/emodpy_typhoid/utility/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_typhoid/utility byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics/TyphoidDemographics.py to TyphoidDemographics.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/demographics/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/tcc.py to tcc.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/outbreak.py to outbreak.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/tcd.py to tcd.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/typhoid_wash.py to typhoid_wash.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/interventions/typhoid_vaccine.py to typhoid_vaccine.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/config.py to config.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/utility/sweeping.py to sweeping.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_typhoid/utility/__init__.py to __init__.cpython-39.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_typhoid.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_typhoid.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_typhoid.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_typhoid.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_typhoid.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_typhoid-0.1.0-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emodpy_typhoid-0.1.0-py3.9.egg Copying emodpy_typhoid-0.1.0-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Adding emodpy-typhoid 0.1.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/emodpy_typhoid-0.1.0-py3.9.egg Processing dependencies for emodpy-typhoid==0.1.0 Searching for requests==2.29.0 Reading https://pypi.org/simple/requests/ Downloading https://files.pythonhosted.org/packages/cf/e1/2aa539876d9ed0ddc95882451deb57cfd7aa8dbf0b8dbce68e045549ba56/requests-2.29.0-py3-none-any.whl#sha256=e8f3c9be120d3333921d213eef078af392fba3933ab7ed2d1cba3b56f2568c3b Best match: requests 2.29.0 Processing requests-2.29.0-py3-none-any.whl Installing requests-2.29.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Adding requests 2.29.0 to easy-install.pth file detected new path './emodpy_typhoid-0.1.0-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages/requests-2.29.0-py3.9.egg Searching for emod-typhoid==0.0.7.dev3 Best match: emod-typhoid 0.0.7.dev3 Adding emod-typhoid 0.0.7.dev3 to easy-install.pth file detected new path './requests-2.29.0-py3.9.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for emod-api==1.31.0.dev5 Best match: emod-api 1.31.0.dev5 Adding emod-api 1.31.0.dev5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for emodpy==1.22.0.dev3 Best match: emodpy 1.22.0.dev3 Adding emodpy 1.22.0.dev3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for matplotlib==3.8.2 Best match: matplotlib 3.8.2 Adding matplotlib 3.8.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for parse==1.20.0 Best match: parse 1.20.0 Adding parse 1.20.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for networkx==3.2.1 Best match: networkx 3.2.1 Adding networkx 3.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for prodict==0.8.18 Best match: prodict 0.8.18 Adding prodict 0.8.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for lz4==4.3.3 Best match: lz4 4.3.3 Adding lz4 4.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for scikit-learn==1.4.0 Best match: scikit-learn 1.4.0 Adding scikit-learn 1.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for geographiclib==2.0 Best match: geographiclib 2.0 Adding geographiclib 2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pyproj==3.6.1 Best match: pyproj 3.6.1 Adding pyproj 3.6.1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for shapely==2.0.2 Best match: shapely 2.0.2 Adding shapely 2.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for scipy==1.12.0 Best match: scipy 1.12.0 Adding scipy 1.12.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pandas==2.2.0 Best match: pandas 2.2.0 Adding pandas 2.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for PyYAML==6.0.1 Best match: PyYAML 6.0.1 Adding PyYAML 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for numpy==1.26.3 Best match: numpy 1.26.3 Adding numpy 1.26.3 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pyCOMPS==2.10.0 Best match: pyCOMPS 2.10.0 Adding pyCOMPS 2.10.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for keyring==24.3.0 Best match: keyring 24.3.0 Adding keyring 24.3.0 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for bs4==0.0.2 Best match: bs4 0.0.2 Adding bs4 0.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/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-typhoid/envs/latest/lib/python3.9/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-typhoid/envs/latest/lib/python3.9/site-packages Searching for idmtools-models==1.7.9 Best match: idmtools-models 1.7.9 Adding idmtools-models 1.7.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for idmtools-platform-comps==1.7.9 Best match: idmtools-platform-comps 1.7.9 Adding idmtools-platform-comps 1.7.9 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for idmtools==1.7.9 Best match: idmtools 1.7.9 Adding idmtools 1.7.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/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-typhoid/envs/latest/lib/python3.9/site-packages Searching for importlib-resources==6.1.1 Best match: importlib-resources 6.1.1 Adding importlib-resources 6.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for python-dateutil==2.8.2 Best match: python-dateutil 2.8.2 Adding python-dateutil 2.8.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pyparsing==3.1.1 Best match: pyparsing 3.1.1 Adding pyparsing 3.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pillow==10.2.0 Best match: pillow 10.2.0 Adding pillow 10.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for packaging==21.3 Best match: packaging 21.3 Adding packaging 21.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for kiwisolver==1.4.5 Best match: kiwisolver 1.4.5 Adding kiwisolver 1.4.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for fonttools==4.47.2 Best match: fonttools 4.47.2 Adding fonttools 4.47.2 to easy-install.pth file Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for cycler==0.12.1 Best match: cycler 0.12.1 Adding cycler 0.12.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for contourpy==1.2.0 Best match: contourpy 1.2.0 Adding contourpy 1.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for threadpoolctl==3.2.0 Best match: threadpoolctl 3.2.0 Adding threadpoolctl 3.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for joblib==1.3.2 Best match: joblib 1.3.2 Adding joblib 1.3.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for certifi==2023.11.17 Best match: certifi 2023.11.17 Adding certifi 2023.11.17 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for tzdata==2023.4 Best match: tzdata 2023.4 Adding tzdata 2023.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pytz==2023.3.post1 Best match: pytz 2023.3.post1 Adding pytz 2023.3.post1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for urllib3==1.26.18 Best match: urllib3 1.26.18 Adding urllib3 1.26.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for idna==3.6 Best match: idna 3.6 Adding idna 3.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for charset-normalizer==3.3.2 Best match: charset-normalizer 3.3.2 Adding charset-normalizer 3.3.2 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for xdg==6.0.0 Best match: xdg 6.0.0 Adding xdg 6.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for future==0.18.3 Best match: future 0.18.3 Adding future 0.18.3 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for jeepney==0.8.0 Best match: jeepney 0.8.0 Adding jeepney 0.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for SecretStorage==3.3.3 Best match: SecretStorage 3.3.3 Adding SecretStorage 3.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for importlib-metadata==7.0.1 Best match: importlib-metadata 7.0.1 Adding importlib-metadata 7.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for jaraco.classes==3.3.0 Best match: jaraco.classes 3.3.0 Adding jaraco.classes 3.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for beautifulsoup4==4.12.3 Best match: beautifulsoup4 4.12.3 Adding beautifulsoup4 4.12.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for wheel==0.40.0 Best match: wheel 0.40.0 Adding wheel 0.40.0 to easy-install.pth file Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for Jinja2==3.1.3 Best match: Jinja2 3.1.3 Adding Jinja2 3.1.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for natsort==8.4.0 Best match: natsort 8.4.0 Adding natsort 8.4.0 to easy-install.pth file Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for tqdm==4.66.1 Best match: tqdm 4.66.1 Adding tqdm 4.66.1 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pygit2==1.10.1 Best match: pygit2 1.10.1 Adding pygit2 1.10.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for tabulate==0.9.0 Best match: tabulate 0.9.0 Adding tabulate 0.9.0 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pluggy==1.2.0 Best match: pluggy 1.2.0 Adding pluggy 1.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pipreqs==0.4.13 Best match: pipreqs 0.4.13 Adding pipreqs 0.4.13 to easy-install.pth file Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for more-itertools==9.1.0 Best match: more-itertools 9.1.0 Adding more-itertools 9.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for filelock==3.13.1 Best match: filelock 3.13.1 Adding filelock 3.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for diskcache==5.4.0 Best match: diskcache 5.4.0 Adding diskcache 5.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for coloredlogs==15.0.1 Best match: coloredlogs 15.0.1 Adding coloredlogs 15.0.1 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for backoff==2.2.1 Best match: backoff 2.2.1 Adding backoff 2.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for zipp==3.17.0 Best match: zipp 3.17.0 Adding zipp 3.17.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for cryptography==42.0.0 Best match: cryptography 42.0.0 Adding cryptography 42.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for soupsieve==2.5 Best match: soupsieve 2.5 Adding soupsieve 2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for MarkupSafe==2.1.4 Best match: MarkupSafe 2.1.4 Adding MarkupSafe 2.1.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for cffi==1.16.0 Best match: cffi 1.16.0 Adding cffi 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/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-typhoid/envs/latest/lib/python3.9/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-typhoid/envs/latest/lib/python3.9/site-packages Searching for humanfriendly==10.0 Best match: humanfriendly 10.0 Adding humanfriendly 10.0 to easy-install.pth file Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Searching for pycparser==2.21 Best match: pycparser 2.21 Adding pycparser 2.21 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-typhoid/envs/latest/lib/python3.9/site-packages Finished processing dependencies for emodpy-typhoid==0.1.0 [rtd-command-info] start-time: 2024-01-23T20:29:49.085348Z, end-time: 2024-01-23T20:29:49.148235Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser from datetime import datetime from urllib.request import urlretrieve 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 "emodpy-typhoid" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx_copybutton', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude', 'myst_parser', # source files written in MD or RST 'sphinx_search.extension', # search across entire IDM docs domain 'sphinx.ext.viewcode' # link to view source code ] myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "linkify", "replacements", "smartquotes", "strikethrough", "substitution", "tasklist", ] 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-typhoid' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = 'en' # 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_css_files = ['theme_overrides.css'] html_js_files = ['show_block_by_os.js'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # -- RTD Sphinx search for searching across the entire domain ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } # 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-typhoid' # -- 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-typhoid-docs.tex', u'emodpy-typhoid', 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-typhoid-docs', u'emodpy-typhoid', [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-typhoid-docs', u'emodpy-typhoid', author, 'Institute for Disease Modeling', 'How to use emodpy for typhoid 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 = {'python': ('https://docs.python.org/3', None), 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'emod-typhoid': ('https://docs.idmod.org/projects/emod-typhoid/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { '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", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("v0.1.0", "/en/v0.1.0/"), ("v0.0.6", "/en/v0.0.6/"), ("v0.0.5", "/en/v0.0.5/"), ("v0.0.4", "/en/v0.0.4/"), ], 'downloads': [ ("html", "//docs.idmod.org/_/downloads/emodpy-typhoid/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emodpy-typhoid', 'name': u'emodpy-typhoid', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': '', 'analytics_code': 'G-SVDSQH04EM', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emodpy-typhoid', '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': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': '99a597ae', } # 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(): for key in context: if key not in html_context: html_context[key] = context[key] 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-emodpy-typhoid/builds/1968133/' 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: 2024-01-23T20:29:49.224440Z, end-time: 2024-01-23T20:29:53.838818Z, duration: 4, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [Makefile:58: generate-api] Error 1 (ignored) making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-typhoid/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'linkify', 'dollarmath', 'substitution', 'tasklist', 'html_image', 'colon_fence', 'amsmath', 'attrs_inline', 'html_admonition', 'smartquotes', 'replacements', 'fieldlist', 'deflist', 'strikethrough'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 17 source files that are out of date updating environment: [new config] 17 added, 0 changed, 0 removed reading sources... [ 5%] emodpy_typhoid reading sources... [ 11%] emodpy_typhoid.config reading sources... [ 17%] emodpy_typhoid.demographics reading sources... [ 23%] emodpy_typhoid.demographics.TyphoidDemographics reading sources... [ 29%] emodpy_typhoid.interventions reading sources... [ 35%] emodpy_typhoid.interventions.outbreak reading sources... [ 41%] emodpy_typhoid.interventions.tcc reading sources... [ 47%] emodpy_typhoid.interventions.tcd reading sources... [ 52%] emodpy_typhoid.interventions.typhoid_vaccine reading sources... [ 58%] emodpy_typhoid.interventions.typhoid_wash reading sources... [ 64%] emodpy_typhoid.utility reading sources... [ 70%] emodpy_typhoid.utility.sweeping reading sources... [ 76%] faq reading sources... [ 82%] index reading sources... [ 88%] installation reading sources... [ 94%] installation-basic reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 5%] emodpy_typhoid writing output... [ 11%] emodpy_typhoid.config writing output... [ 17%] emodpy_typhoid.demographics writing output... [ 23%] emodpy_typhoid.demographics.TyphoidDemographics writing output... [ 29%] emodpy_typhoid.interventions writing output... [ 35%] emodpy_typhoid.interventions.outbreak writing output... [ 41%] emodpy_typhoid.interventions.tcc writing output... [ 47%] emodpy_typhoid.interventions.tcd writing output... [ 52%] emodpy_typhoid.interventions.typhoid_vaccine writing output... [ 58%] emodpy_typhoid.interventions.typhoid_wash writing output... [ 64%] emodpy_typhoid.utility writing output... [ 70%] emodpy_typhoid.utility.sweeping writing output... [ 76%] faq writing output... [ 82%] index writing output... [ 88%] installation writing output... [ 94%] installation-basic writing output... [100%] modules generating indices... genindex py-modindex done highlighting module code... [ 12%] emodpy_typhoid.config highlighting module code... [ 25%] emodpy_typhoid.demographics.TyphoidDemographics highlighting module code... [ 37%] emodpy_typhoid.interventions.outbreak highlighting module code... [ 50%] emodpy_typhoid.interventions.tcc highlighting module code... [ 62%] emodpy_typhoid.interventions.tcd highlighting module code... [ 75%] emodpy_typhoid.interventions.typhoid_vaccine highlighting module code... [ 87%] emodpy_typhoid.interventions.typhoid_wash highlighting module code... [100%] emodpy_typhoid.utility.sweeping writing additional pages... search opensearch done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2024-01-23T20:29:53.915183Z, end-time: 2024-01-23T20:29:57.907412Z, duration: 3, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v6.2.1 making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-typhoid/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'substitution', 'html_image', 'strikethrough', 'deflist', 'smartquotes', 'linkify', 'fieldlist', 'colon_fence', 'attrs_inline', 'dollarmath', 'html_admonition', 'amsmath', 'replacements', 'tasklist'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 17 added, 0 changed, 0 removed reading sources... [ 5%] emodpy_typhoid reading sources... [ 11%] emodpy_typhoid.config reading sources... [ 17%] emodpy_typhoid.demographics reading sources... [ 23%] emodpy_typhoid.demographics.TyphoidDemographics reading sources... [ 29%] emodpy_typhoid.interventions reading sources... [ 35%] emodpy_typhoid.interventions.outbreak reading sources... [ 41%] emodpy_typhoid.interventions.tcc reading sources... [ 47%] emodpy_typhoid.interventions.tcd reading sources... [ 52%] emodpy_typhoid.interventions.typhoid_vaccine reading sources... [ 58%] emodpy_typhoid.interventions.typhoid_wash reading sources... [ 64%] emodpy_typhoid.utility reading sources... [ 70%] emodpy_typhoid.utility.sweeping reading sources... [ 76%] faq reading sources... [ 82%] index reading sources... [ 88%] installation reading sources... [ 94%] installation-basic reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation installation-basic modules emodpy_typhoid emodpy_typhoid.demographics emodpy_typhoid.demographics.TyphoidDemographics emodpy_typhoid.interventions emodpy_typhoid.interventions.outbreak emodpy_typhoid.interventions.tcc emodpy_typhoid.interventions.tcd emodpy_typhoid.interventions.typhoid_vaccine emodpy_typhoid.interventions.typhoid_wash emodpy_typhoid.utility emodpy_typhoid.utility.sweeping emodpy_typhoid.config faq done writing... done writing additional files... opensearchdone copying static files... done copying extra files... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML page is in ../_readthedocs/htmlzip.