Read the Docs build information Build id: 3109419 Project: institute-for-disease-modeling-emodpy-malaria Version: latest Commit: 2d39e09700e371c68d04f92513d6654fcae2637f Date: 2025-06-10T19:26:26.014029Z State: cancelled Success: False [rtd-command-info] start-time: 2025-06-10T19:26:26.746874Z, end-time: 2025-06-10T19:26:29.067865Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/EMOD-Hub/emodpy-malaria.git . Cloning into '.'... [rtd-command-info] start-time: 2025-06-10T19:26:29.104955Z, end-time: 2025-06-10T19:26:30.719127Z, 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/EMOD-Hub/emodpy-malaria * [new tag] v.4.0.0 -> v.4.0.0 * [new tag] v4.0.0 -> v4.0.0 [rtd-command-info] start-time: 2025-06-10T19:26:30.809547Z, end-time: 2025-06-10T19:26:30.941154Z, 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 2d39e09 GF New Name - Update LICENSE (#26) [rtd-command-info] start-time: 2025-06-10T19:26:30.976420Z, end-time: 2025-06-10T19:26:31.019288Z, 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: 2025-06-10T19:26:35.923412Z, end-time: 2025-06-10T19:26:35.991193Z, duration: 0, exit-code: 0 asdf global python 3.9.22 [rtd-command-info] start-time: 2025-06-10T19:26:36.395759Z, end-time: 2025-06-10T19:26:37.604085Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.22.final.0-64 in 886ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/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: 2025-06-10T19:26:37.647817Z, end-time: 2025-06-10T19:26:46.707236Z, 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-malaria/envs/latest/lib/python3.9/site-packages (23.1) Collecting pip Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/29/a2/d40fb2460e883eca5199c62cfc2463fd261f760556ae6290f88488c362c0/pip-25.1.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 11.1 MB/s eta 0:00:00 Requirement already satisfied: setuptools in 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(70 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6b/11/cc635220681e93a0183390e26485430ca2c7b5f9d33b15c74c2861cb8091/urllib3-2.4.0-py3-none-any.whl (128 kB) Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4a/7e/3db2bd1b1f9e95f7cddca6d6e75e2f2bd9f51b1246e546d88addca0106bd/certifi-2025.4.26-py3-none-any.whl (159 kB) Installing collected packages: zipp, urllib3, tomli, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-0.7.16 babel-2.17.0 certifi-2025.4.26 charset_normalizer-3.4.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 importlib-metadata-8.7.0 packaging-25.0 requests-2.32.4 snowballstemmer-3.0.1 sphinx-7.4.7 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 tomli-2.2.1 urllib3-2.4.0 zipp-3.23.0 [rtd-command-info] start-time: 2025-06-10T19:26:56.289982Z, end-time: 2025-06-10T19:27:49.501106Z, duration: 53, 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~=1.16 (from -r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.22.1/emodpy-1.22.1-py3-none-any.whl (122 kB) Collecting emod-malaria==0.0.73 (from -r requirements.txt (line 2)) Downloading 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matplotlib->emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/0b/532e31abc7389617ddff12551af625a9b03cd61d2989fa595e43c470ec67/pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 16.7 MB/s eta 0:00:00 Collecting pyparsing>=2.3.1 (from matplotlib->emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/e7/df2285f3d08fee213f2d041540fa4fc9ca6c2d44cf36d3a035bf2a8d2bcc/pyparsing-3.2.3-py3-none-any.whl (111 kB) Collecting importlib-resources>=3.2.0 (from matplotlib->emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a4/ed/1f1afb2e9e7f38a545d628f864d562a5ae64fe6f7a10e28ffb9b185b4e89/importlib_resources-6.5.2-py3-none-any.whl (37 kB) Collecting joblib>=1.2.0 (from scikit-learn->emod-api~=1.30->emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7d/4f/1195bbac8e0c2acc5f740661631d8d750dc38d4a32b23ee5df3cde6f4e0d/joblib-1.5.1-py3-none-any.whl (307 kB) Collecting threadpoolctl>=3.1.0 (from scikit-learn->emod-api~=1.30->emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/32/d5/f9a850d79b0851d1d4ef6456097579a9005b31fea68726a4ae5f2d82ddd9/threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Building wheels for collected packages: xmlrunner, prodict DEPRECATION: Building 'xmlrunner' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'xmlrunner'. Discussion can be found at https://github.com/pypa/pip/issues/6334 Building wheel for xmlrunner (setup.py): started Building wheel for xmlrunner (setup.py): finished with status 'done' Created wheel for xmlrunner: filename=xmlrunner-1.7.7-py3-none-any.whl size=6270 sha256=4d038976192e19489824a9244099e9c92354d0fb0aeaabb1c2a5a1084f49bfec Stored in directory: /tmp/pip-ephem-wheel-cache-z5vha6rq/wheels/a4/a4/74/ecccb934115344497d64c4f2580518f026a59db2b252531496 Building wheel for prodict (pyproject.toml): started Building wheel for prodict (pyproject.toml): finished with status 'done' Created wheel for prodict: filename=prodict-0.8.20-py3-none-any.whl size=3919 sha256=5892ae318a4c5ca1fd8017ed5bd4ca73e14abe0c92bfc768aa5bfdb92afcff7f Stored in directory: /tmp/pip-ephem-wheel-cache-z5vha6rq/wheels/b1/d2/34/e78c711b3a006c0865ac4a8e82dc78c1b5a017cc3edb109a37 Successfully built xmlrunner prodict Installing collected packages: xmlrunner, pytz, parse, emod-malaria, xdg, urllib3, tzdata, typing-extensions, tqdm, threadpoolctl, tabulate, soupsieve, six, pyyaml, pyproj, pyparsing, pycparser, prodict, pluggy, pillow, packaging, numpy, natsort, more-itertools, lz4, kiwisolver, joblib, jeepney, iniconfig, importlib-resources, humanfriendly, graphviz, geographiclib, future, fonttools, filelock, diskcache, cycler, click, backports.tarfile, backoff, astor, shapely, scipy, requests, python-dateutil, jaraco.functools, jaraco.context, jaraco.classes, exceptiongroup, contourpy, coloredlogs, cffi, beautifulsoup4, astunparse, scikit-learn, pytest, pyCOMPS, pandas, matplotlib, cryptography, bs4, SecretStorage, idmtools, emod-api, keyring, idmtools-platform-comps, idmtools-models, emodpy Attempting uninstall: urllib3 Found existing installation: urllib3 2.4.0 Uninstalling urllib3-2.4.0: Successfully uninstalled urllib3-2.4.0 Attempting uninstall: packaging Found existing installation: packaging 25.0 Uninstalling packaging-25.0: Successfully uninstalled packaging-25.0 Attempting uninstall: requests Found existing installation: requests 2.32.4 Uninstalling requests-2.32.4: Successfully uninstalled requests-2.32.4 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. sphinx 7.4.7 requires requests>=2.30.0, but you have requests 2.29.0 which is incompatible. Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 backports.tarfile-1.2.0 beautifulsoup4-4.13.4 bs4-0.0.2 cffi-1.17.1 click-7.1.2 coloredlogs-15.0.1 contourpy-1.3.0 cryptography-45.0.4 cycler-0.12.1 diskcache-5.4.0 emod-api-1.33.4 emod-malaria-0.0.73 emodpy-1.22.1 exceptiongroup-1.3.0 filelock-3.18.0 fonttools-4.58.2 future-1.0.0 geographiclib-2.0 graphviz-0.20.3 humanfriendly-10.0 idmtools-1.7.11 idmtools-models-1.7.11 idmtools-platform-comps-1.7.11 importlib-resources-6.5.2 iniconfig-2.1.0 jaraco.classes-3.4.0 jaraco.context-6.0.1 jaraco.functools-4.1.0 jeepney-0.9.0 joblib-1.5.1 keyring-25.6.0 kiwisolver-1.4.7 lz4-4.4.4 matplotlib-3.9.4 more-itertools-9.1.0 natsort-8.4.0 numpy-2.0.2 packaging-24.2 pandas-2.3.0 parse-1.20.2 pillow-11.2.1 pluggy-1.6.0 prodict-0.8.20 pyCOMPS-2.11.0 pycparser-2.22 pyparsing-3.2.3 pyproj-3.6.1 pytest-8.1.2 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.2 requests-2.29.0 scikit-learn-1.6.1 scipy-1.13.1 shapely-2.0.7 six-1.17.0 soupsieve-2.7 tabulate-0.9.0 threadpoolctl-3.6.0 tqdm-4.67.1 typing-extensions-4.14.0 tzdata-2025.2 urllib3-1.26.20 xdg-6.0.0 xmlrunner-1.7.7 [rtd-command-info] start-time: 2025-06-10T19:27:49.542216Z, end-time: 2025-06-10T19:28:08.846858Z, duration: 19, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting sphinxext.remoteliteralinclude~=0.4.0 (from -r docs/requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/13/0d/7e5009f48c33d5fd533dda80b42c4a79fce8dfdd1b617d0a9df9a9836145/sphinxext_remoteliteralinclude-0.4.0-py3-none-any.whl (6.4 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages (from -r docs/requirements.txt (line 2)) (7.4.7) Collecting pydata-sphinx-theme (from -r docs/requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e2/0d/8ba33fa83a7dcde13eb3c1c2a0c1cc29950a048bfed6d9b0d8b6bd710b4c/pydata_sphinx_theme-0.16.1-py3-none-any.whl (6.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.7/6.7 MB 16.1 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon (from -r docs/requirements.txt (line 4)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/75/f2/6b7627dfe7b4e418e295e254bb15c3a6455f11f8c0ad0d43113f678049c3/sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting plantweb~=1.2.1 (from -r docs/requirements.txt (line 5)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d6/6f/9ab1a1c3e33aaa0c0931983578c09336b092c75dce777ea666d3032f756e/plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.17 (from -r docs/requirements.txt (line 6)) Downloading 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https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1d/f6/6d61a023d758f488e36638076e8a4ec4447a2cdf86938cf6c60cf1c860e6/myst_parser-2.0.0-py3-none-any.whl (77 kB) Collecting readthedocs-sphinx-search~=0.3.1 (from -r docs/requirements.txt (line 10)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/04/3c/41bc9d7d4d936a73e380423f23996bee1691e17598d8a03c062be6aac640/readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB) Collecting sphinx-copybutton~=0.5.2 (from -r docs/requirements.txt (line 11)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9e/48/1ea60e74949eecb12cdd6ac43987f9fd331156388dcc2319b45e2ebb81bf/sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB) Collecting pygithub~=1.57 (from -r docs/requirements.txt (line 12)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2c/71/aff5465d9e3d448a5d4beab1dc7c8dec72037e3ae7e0d856ee08538dc934/PyGithub-1.59.1-py3-none-any.whl (342 kB) Collecting sphinxcontrib-jquery~=4.1 (from -r docs/requirements.txt (line 13)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/76/85/749bd22d1a68db7291c89e2ebca53f4306c3f205853cf31e9de279034c3c/sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages (from sphinxext.remoteliteralinclude~=0.4.0->-r docs/requirements.txt (line 1)) (1.17.0) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 5)) (2.29.0) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 5)) (0.21.2) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) (3.1.6) Collecting nbconvert!=5.4,>=5.3 (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/cc/9a/cd673b2f773a12c992f41309ef81b99da1690426bd2f96957a7ade0d3ed7/nbconvert-7.16.6-py3-none-any.whl (258 kB) Collecting traitlets>=5 (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl (85 kB) Collecting nbformat (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading 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https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8e/37/efad0257dc6e593a18957422533ff0f87ede7c9c6ea010a2177d738fb82f/pure_eval-0.2.3-py3-none-any.whl (11 kB) Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, types-python-dateutil, traitlets, tornado, 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, json5, fqdn, executing, docutils, defusedxml, decorator, debugpy, bleach, attrs, async-lru, asttokens, accessible-pygments, terminado, stack-data, sphinxcontrib-napoleon, referencing, pynacl, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, arrow, argon2-cffi-bindings, anyio, sphinxcontrib-programoutput, sphinxcontrib-jquery, sphinx-copybutton, pydata-sphinx-theme, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, isoduration, ipython, argon2-cffi, 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 0.21.2 Uninstalling docutils-0.21.2: Successfully uninstalled docutils-0.21.2 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 1.22.1 requires requests==2.29.0, but you have requests 2.32.4 which is incompatible. Successfully installed accessible-pygments-0.0.5 anyio-4.9.0 argon2-cffi-25.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-3.0.0 async-lru-2.0.5 attrs-25.3.0 bleach-6.2.0 comm-0.2.2 debugpy-1.8.14 decorator-5.2.1 defusedxml-0.7.1 deprecated-1.2.18 docutils-0.20.1 executing-2.2.0 fastjsonschema-2.21.1 fqdn-1.5.1 ipykernel-6.29.5 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.2 json5-0.12.0 jsonpointer-3.0.0 jsonschema-4.24.0 jsonschema-specifications-2025.4.1 jupyter-client-8.6.3 jupyter-core-5.8.1 jupyter-events-0.12.0 jupyter-lsp-2.2.5 jupyter-server-2.16.0 jupyter-server-terminals-0.5.3 jupyterlab-4.0.13 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.3 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.1.3 myst-parser-2.0.0 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.7 nest-asyncio-1.6.0 notebook-shim-0.2.4 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.3.8 pockets-0.9.1 prometheus-client-0.22.1 prompt-toolkit-3.0.51 psutil-7.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 pygithub-1.59.1 pyjwt-2.10.1 pynacl-1.5.0 python-json-logger-3.3.0 pyzmq-26.4.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 requests-2.32.4 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.25.1 send2trash-1.8.3 sniffio-1.3.1 sphinx-copybutton-0.5.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.18 sphinxext.remoteliteralinclude-0.4.0 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.4.0 tornado-6.5.1 traitlets-5.14.3 types-python-dateutil-2.9.0.20250516 uri-template-1.3.0 wcwidth-0.2.13 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.8.0 wrapt-1.17.2 [rtd-command-info] start-time: 2025-06-10T19:28:08.895806Z, end-time: 2025-06-10T19:28:09.523811Z, duration: 0, exit-code: 0 python ./setup.py install --force /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/setuptools/__init__.py:92: _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`. By 2025-Oct-31, you need to update your project and remove deprecated calls or your builds will no longer be supported. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. By 2025-Oct-31, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py creating build/lib/tests copying tests/create_auth_token_args.py -> build/lib/tests copying tests/add_itn.py -> build/lib/tests copying tests/run_all_sft_tests.py -> build/lib/tests copying tests/__init__.py -> build/lib/tests creating build/lib/emodpy_malaria copying emodpy_malaria/malaria_config.py -> build/lib/emodpy_malaria copying emodpy_malaria/vector_config.py -> build/lib/emodpy_malaria copying emodpy_malaria/__init__.py -> build/lib/emodpy_malaria copying emodpy_malaria/malaria_vector_species_params.py -> build/lib/emodpy_malaria creating build/lib/tests/unittests copying tests/unittests/test_demog.py -> build/lib/tests/unittests copying tests/unittests/test_import.py -> build/lib/tests/unittests copying tests/unittests/test_campaign_common.py -> build/lib/tests/unittests copying tests/unittests/manifest.py -> build/lib/tests/unittests copying tests/unittests/test_treatment_seeking.py -> build/lib/tests/unittests copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_reporters.py -> build/lib/tests/unittests copying tests/unittests/get_unittest_coverage.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_interventions.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_interventions_as_files.py -> build/lib/tests/unittests copying tests/unittests/__init__.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_config.py -> build/lib/tests/unittests copying tests/unittests/coverage_check.py -> build/lib/tests/unittests creating build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_scenarios.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/__init__.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_e2e.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_request.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_e2e_comps.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_set.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_data.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_metadata.py -> build/lib/tests/unittests/weather creating build/lib/emodpy_malaria/migration copying emodpy_malaria/migration/convert_json_to_bin.py -> build/lib/emodpy_malaria/migration copying emodpy_malaria/migration/convert_csv_to_bin_vector_migration.py -> build/lib/emodpy_malaria/migration copying emodpy_malaria/migration/__main__.py -> build/lib/emodpy_malaria/migration copying emodpy_malaria/migration/__init__.py -> build/lib/emodpy_malaria/migration copying emodpy_malaria/migration/vector_migration.py -> build/lib/emodpy_malaria/migration copying emodpy_malaria/migration/convert_txt_to_bin.py -> build/lib/emodpy_malaria/migration creating build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/diag_survey.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/malaria_challenge.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outdoorrestkill.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/spacespraying.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/bednet.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/community_health_worker.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/larvicide.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/adherentdrug.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/usage_dependent_bednet.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/vector_surveillance.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/vaccine.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/common.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/irs.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/drug_campaign.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/mosquitorelease.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/treatment_seeking.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/__init__.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/scale_larval_habitats.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/drug.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outbreak.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/ivermectin.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/inputeir.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/sugartrap.py -> build/lib/emodpy_malaria/interventions creating build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/replace_genomes.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/zero_infections.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/replace_genomes_get_next_barcode.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/__init__.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/serialization_support.py -> build/lib/emodpy_malaria/serialization creating build/lib/emodpy_malaria/reporters copying emodpy_malaria/reporters/builtin.py -> build/lib/emodpy_malaria/reporters copying emodpy_malaria/reporters/__init__.py -> build/lib/emodpy_malaria/reporters creating build/lib/emodpy_malaria/demographics copying emodpy_malaria/demographics/__init__.py -> build/lib/emodpy_malaria/demographics copying emodpy_malaria/demographics/MalariaDemographics.py -> build/lib/emodpy_malaria/demographics creating build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_metadata.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_request.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_utils.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_variable.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_set.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_data.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/__init__.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/data_sources.py -> build/lib/emodpy_malaria/weather running egg_info creating emodpy_malaria.egg-info writing emodpy_malaria.egg-info/PKG-INFO writing dependency_links to emodpy_malaria.egg-info/dependency_links.txt writing requirements to emodpy_malaria.egg-info/requires.txt writing top-level names to emodpy_malaria.egg-info/top_level.txt writing manifest file 'emodpy_malaria.egg-info/SOURCES.txt' reading manifest file 'emodpy_malaria.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'emodpy_malaria.egg-info/SOURCES.txt' copying emodpy_malaria/malaria_drug_params.csv -> build/lib/emodpy_malaria running install_lib copying build/lib/tests/unittests/test_demog.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_import.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_campaign_common.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/manifest.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_treatment_seeking.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/schema_path_file.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_malaria_reporters.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/get_unittest_coverage.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_malaria_interventions.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_malaria_interventions_as_files.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/test_malaria_config.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests copying build/lib/tests/unittests/coverage_check.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_scenarios.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_e2e.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_request.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_e2e_comps.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_set.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_data.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_metadata.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather copying build/lib/tests/create_auth_token_args.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests copying build/lib/tests/add_itn.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests copying build/lib/tests/run_all_sft_tests.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests copying build/lib/tests/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/migration/convert_json_to_bin.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/migration/convert_csv_to_bin_vector_migration.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/migration/__main__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/migration/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/migration/vector_migration.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/migration/convert_txt_to_bin.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration copying build/lib/emodpy_malaria/malaria_drug_params.csv -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria copying build/lib/emodpy_malaria/malaria_config.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria copying build/lib/emodpy_malaria/vector_config.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/diag_survey.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/malaria_challenge.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/outdoorrestkill.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/spacespraying.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/bednet.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/community_health_worker.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/larvicide.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/adherentdrug.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/usage_dependent_bednet.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/vector_surveillance.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/vaccine.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/common.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/irs.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/drug_campaign.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/mosquitorelease.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/treatment_seeking.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/scale_larval_habitats.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/drug.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/outbreak.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/ivermectin.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/inputeir.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/sugartrap.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/replace_genomes.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/zero_infections.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/replace_genomes_get_next_barcode.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/serialization_support.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/reporters copying build/lib/emodpy_malaria/reporters/builtin.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/reporters copying build/lib/emodpy_malaria/reporters/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/reporters copying build/lib/emodpy_malaria/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/demographics copying build/lib/emodpy_malaria/demographics/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/demographics copying build/lib/emodpy_malaria/demographics/MalariaDemographics.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/demographics copying build/lib/emodpy_malaria/malaria_vector_species_params.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_metadata.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_request.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_utils.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_variable.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_set.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_data.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/data_sources.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_demog.py to test_demog.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_import.py to test_import.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_campaign_common.py to test_campaign_common.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/manifest.py to manifest.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_treatment_seeking.py to test_treatment_seeking.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/schema_path_file.py to schema_path_file.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_malaria_reporters.py to test_malaria_reporters.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/get_unittest_coverage.py to get_unittest_coverage.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_malaria_interventions.py to test_malaria_interventions.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_malaria_interventions_as_files.py to test_malaria_interventions_as_files.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/test_malaria_config.py to test_malaria_config.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/coverage_check.py to coverage_check.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_weather_scenarios.py to test_weather_scenarios.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_e2e.py to test_e2e.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_weather_request.py to test_weather_request.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_e2e_comps.py to test_e2e_comps.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_weather_set.py to test_weather_set.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_weather_data.py to test_weather_data.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/unittests/weather/test_weather_metadata.py to test_weather_metadata.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/create_auth_token_args.py to create_auth_token_args.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/add_itn.py to add_itn.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/run_all_sft_tests.py to run_all_sft_tests.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration/convert_json_to_bin.py to convert_json_to_bin.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration/convert_csv_to_bin_vector_migration.py to convert_csv_to_bin_vector_migration.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration/__main__.py to __main__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration/vector_migration.py to vector_migration.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/migration/convert_txt_to_bin.py to convert_txt_to_bin.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/malaria_config.py to malaria_config.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/vector_config.py to vector_config.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/diag_survey.py to diag_survey.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/malaria_challenge.py to malaria_challenge.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/outdoorrestkill.py to outdoorrestkill.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/spacespraying.py to spacespraying.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/bednet.py to bednet.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/community_health_worker.py to community_health_worker.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/larvicide.py to larvicide.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/adherentdrug.py to adherentdrug.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/usage_dependent_bednet.py to usage_dependent_bednet.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/vector_surveillance.py to vector_surveillance.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/vaccine.py to vaccine.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/common.py to common.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/irs.py to irs.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/drug_campaign.py to drug_campaign.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/mosquitorelease.py to mosquitorelease.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/treatment_seeking.py to treatment_seeking.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/scale_larval_habitats.py to scale_larval_habitats.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/drug.py to drug.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/outbreak.py to outbreak.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/ivermectin.py to ivermectin.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/inputeir.py to inputeir.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/interventions/sugartrap.py to sugartrap.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization/replace_genomes.py to replace_genomes.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization/zero_infections.py to zero_infections.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization/replace_genomes_get_next_barcode.py to replace_genomes_get_next_barcode.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/serialization/serialization_support.py to serialization_support.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/reporters/builtin.py to builtin.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/reporters/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/demographics/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/demographics/MalariaDemographics.py to MalariaDemographics.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/malaria_vector_species_params.py to malaria_vector_species_params.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/weather_metadata.py to weather_metadata.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/weather_request.py to weather_request.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/weather_utils.py to weather_utils.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/weather_variable.py to weather_variable.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/weather_set.py to weather_set.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/weather_data.py to weather_data.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria/weather/data_sources.py to data_sources.cpython-39.pyc running install_egg_info Copying emodpy_malaria.egg-info to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.9/site-packages/emodpy_malaria-4.1.0-py3.9.egg-info running install_scripts [rtd-command-info] start-time: 2025-06-10T19:28:09.665982Z, end-time: 2025-06-10T19:28:09.708846Z, 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-malaria" 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 ------------------------------------------------ tags.add('emodpymalaria') # 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', 'sphinx_search.extension', 'sphinx.ext.viewcode', # link to view source code 'myst_parser', # source files written in MD or RST ] 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'] # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'emodpy-malaria' copyright = 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 = 'pydata_sphinx_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 = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "IDM docs", "url": "https://docs.idmod.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/institutefordiseasemodeling/emodpy-malaria", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/idm-logo-transparent.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/emodpy-malaria/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/emodpy-malaria/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # 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-malaria' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emodpy-malaria-docs.tex', u'emodpy-malaria', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria', author, 'Institute for Disease Modeling', 'How to use emodpy for malaria simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'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), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None), 'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None), 'emod': ('https://docs.idmod.org/projects/emod/en/latest/', None) }