Read the Docs build information Build id: 3765880 Project: institute-for-disease-modeling-emodpy-malaria Version: latest Commit: cf2956bec435d5e3482af753ac6ae9bb638f0f5d Date: 2026-02-19T21:52:47.851232Z State: finished Success: True [rtd-command-info] start-time: 2026-02-19T21:52:48.715904Z, end-time: 2026-02-19T21:52:50.639601Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/EMOD-Hub/emodpy-malaria.git . Cloning into '.'... [rtd-command-info] start-time: 2026-02-19T21:52:50.761073Z, end-time: 2026-02-19T21:52:52.138144Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 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 * [new tag] v4.2.0 -> v4.2.0 * [new tag] v4.2.1 -> v4.2.1 * [new tag] v4.2.2 -> v4.2.2 * [new tag] v4.3.1 -> v4.3.1 * [new tag] v4.3.2 -> v4.3.2 * [new tag] v4.3.2.dev2 -> v4.3.2.dev2 [rtd-command-info] start-time: 2026-02-19T21:52:52.869793Z, end-time: 2026-02-19T21:52:52.910470Z, 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: 2026-02-19T21:52:57.751513Z, end-time: 2026-02-19T21:52:57.817381Z, duration: 0, exit-code: 0 asdf global python 3.9.22 [rtd-command-info] start-time: 2026-02-19T21:52:58.263301Z, end-time: 2026-02-19T21:52:59.552039Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.22.final.0-64 in 946ms 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: 2026-02-19T21:52:59.653991Z, end-time: 2026-02-19T21:53:22.435694Z, duration: 22, 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 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Uninstalling pip-23.1: Successfully uninstalled pip-23.1 Successfully installed pip-26.0.1 setuptools-82.0.0 [rtd-command-info] start-time: 2026-02-19T21:53:22.537775Z, end-time: 2026-02-19T21:54:36.250448Z, duration: 73, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting sphinx Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0d/ef/153f6803c5d5f8917dbb7f7fcf6d34a871ede3296fa89c2c703f5f8a6c8e/sphinx-7.4.7-py3-none-any.whl (3.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 240.2 kB/s 0:00:14 Collecting sphinxcontrib-applehelp (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5d/85/9ebeae2f76e9e77b952f4b274c27238156eae7979c5421fba91a28f4970d/sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB) Collecting sphinxcontrib-devhelp (from sphinx) Downloading 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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-3.0.3 Pygments-2.19.2 alabaster-0.7.16 babel-2.18.0 certifi-2026.1.4 charset_normalizer-3.4.4 docutils-0.21.2 idna-3.11 imagesize-1.4.1 importlib-metadata-8.7.1 packaging-26.0 requests-2.32.5 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-2.4.0 urllib3-2.6.3 zipp-3.23.0 [rtd-command-info] start-time: 2026-02-19T21:54:36.371881Z, end-time: 2026-02-19T22:00:31.531971Z, duration: 355, 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==0.0.78 (from -r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-malaria/0.0.78/emod_malaria-0.0.78-py3-none-any.whl (3.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.8/3.8 MB 439.0 kB/s 0:00:08 Collecting requests==2.29.0 (from -r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/cf/e1/2aa539876d9ed0ddc95882451deb57cfd7aa8dbf0b8dbce68e045549ba56/requests-2.29.0-py3-none-any.whl (62 kB) Requirement already satisfied: charset-normalizer<4,>=2 in 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(from emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting idmtools~=1.7 (from emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.7.11/idmtools-1.7.11-py3-none-any.whl (171 kB) Collecting idmtools-platform-comps~=1.7 (from emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-platform-comps/1.7.11/idmtools_platform_comps-1.7.11-py3-none-any.whl (134 kB) Collecting idmtools-models~=1.7 (from emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.7.11/idmtools_models-1.7.11-py3-none-any.whl (18 kB) Collecting emod-api~=1.30 (from emodpy~=1.16->-r requirements.txt (line 1)) Downloading 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dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting pytest==8.1.2 (from emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/d7/a812a0bd0f5160823e647524488cc9734f93782f2c273b8f77e8afc60a37/pytest-8.1.2-py3-none-any.whl (337 kB) Collecting iniconfig (from pytest==8.1.2->emodpy~=1.16->-r requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2c/e1/e6716421ea10d38022b952c159d5161ca1193197fb744506875fbb87ea7b/iniconfig-2.1.0-py3-none-any.whl (6.0 kB) Requirement already satisfied: packaging in 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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 2.6.3 Uninstalling urllib3-2.6.3: Successfully uninstalled urllib3-2.6.3 Attempting uninstall: packaging Found existing installation: packaging 26.0 Uninstalling packaging-26.0: Successfully uninstalled packaging-26.0 Attempting uninstall: requests Found existing installation: requests 2.32.5 Uninstalling requests-2.32.5: Successfully uninstalled requests-2.32.5 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 PyYaml-6.0.3 SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 backports.tarfile-1.2.0 beautifulsoup4-4.14.3 bs4-0.0.2 cffi-2.0.0 click-7.1.2 coloredlogs-15.0.1 contourpy-1.3.0 cryptography-46.0.5 cycler-0.12.1 diskcache-5.4.0 emod-api-1.33.7 emod-malaria-0.0.78 emodpy-1.22.1 exceptiongroup-1.3.1 filelock-3.19.1 fonttools-4.60.2 future-1.0.0 geographiclib-2.1 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-6.1.0 jaraco.functools-4.4.0 jeepney-0.9.0 joblib-1.5.3 keyring-25.7.0 kiwisolver-1.4.7 lz4-4.4.5 matplotlib-3.9.4 more-itertools-9.1.0 natsort-8.4.0 numpy-2.0.2 packaging-24.2 pandas-2.3.3 pillow-11.3.0 pluggy-1.6.0 pyCOMPS-2.11.0 pycparser-2.23 pyparsing-3.3.2 pyproj-3.6.1 pytest-8.1.2 python-dateutil-2.9.0.post0 pytz-2025.2 requests-2.29.0 scikit-learn-1.6.1 scipy-1.13.1 shapely-2.0.7 six-1.17.0 soupsieve-2.8.3 tabulate-0.9.0 threadpoolctl-3.6.0 tqdm-4.67.3 typing-extensions-4.15.0 tzdata-2025.3 urllib3-1.26.20 xdg-6.0.0 xmlrunner-1.7.7 [rtd-command-info] start-time: 2026-02-19T22:00:31.649646Z, end-time: 2026-02-19T22:02:36.456533Z, duration: 124, 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 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(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 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stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading 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, pure-eval, ptyprocess, fastjsonschema, wrapt, websocket-client, webcolors, wcwidth, uri-template, traitlets, tornado, tinycss2, sphinxext.remoteliteralinclude, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, requests, readthedocs-sphinx-search, pyzmq, python-json-logger, pyjwt, psutil, prometheus-client, pockets, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, lark, jupyterlab-pygments, jsonpointer, json5, fqdn, executing, docutils, defusedxml, decorator, debugpy, comm, bleach, attrs, async-lru, asttokens, accessible-pygments, terminado, stack-data, sphinxcontrib-napoleon, rfc3987-syntax, referencing, pynacl, prompt-toolkit, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, 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 2.32.5 which is incompatible. Successfully installed accessible-pygments-0.0.5 anyio-4.12.1 argon2-cffi-25.1.0 argon2-cffi-bindings-25.1.0 arrow-1.4.0 asttokens-3.0.1 async-lru-2.0.5 attrs-25.4.0 bleach-6.2.0 comm-0.2.3 debugpy-1.8.20 decorator-5.2.1 defusedxml-0.7.1 deprecated-1.3.1 docutils-0.20.1 executing-2.2.1 fastjsonschema-2.21.2 fqdn-1.5.1 ipykernel-6.31.0 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.2 json5-0.13.0 jsonpointer-3.0.0 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 jupyter-client-8.6.3 jupyter-core-5.8.1 jupyter-events-0.12.0 jupyter-lsp-2.3.0 jupyter-server-2.17.0 jupyter-server-terminals-0.5.4 jupyterlab-4.0.13 jupyterlab-pygments-0.3.0 jupyterlab-server-2.28.0 lark-1.3.1 markdown-it-py-3.0.0 matplotlib-inline-0.2.1 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.2.0 myst-parser-2.0.0 nbclient-0.10.2 nbconvert-7.17.0 nbformat-5.10.4 nbsphinx-0.9.8 nest-asyncio-1.6.0 notebook-shim-0.2.4 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.6 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.4.0 pockets-0.9.1 prometheus-client-0.24.1 prompt-toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 pygithub-1.59.1 pyjwt-2.11.0 pynacl-1.6.2 python-json-logger-4.0.0 pyzmq-27.1.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 requests-2.32.5 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rfc3987-syntax-1.1.0 rpds-py-0.27.1 send2trash-2.1.0 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-6.5.4 traitlets-5.14.3 uri-template-1.3.0 wcwidth-0.6.0 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.9.0 wrapt-2.1.1 [rtd-command-info] start-time: 2026-02-19T22:02:36.566815Z, end-time: 2026-02-19T22:02:37.136094Z, duration: 0, exit-code: 0 python ./setup.py install --force 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. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. 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/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/utils.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/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/indoor_individual_emanator.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outbreak.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outdoor_node_emanator.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 copying emodpy_malaria/migration/README.md -> build/lib/emodpy_malaria/migration copying emodpy_malaria/weather/README.md -> build/lib/emodpy_malaria/weather copying emodpy_malaria/migration/README.md -> build/lib/emodpy_malaria/migration copying emodpy_malaria/weather/README.md -> build/lib/emodpy_malaria/weather running install_lib 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/README.md -> /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/indoor_individual_emanator.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/outdoor_node_emanator.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/utils.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/__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/README.md -> /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/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/indoor_individual_emanator.py to indoor_individual_emanator.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/outdoor_node_emanator.py to outdoor_node_emanator.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/utils.py to 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/__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-4.3.3-py3.9.egg-info running install_scripts [rtd-command-info] start-time: 2026-02-19T22:02:37.300612Z, end-time: 2026-02-19T22:02:37.346655Z, 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), '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) } [rtd-command-info] start-time: 2026-02-19T22:02:37.424769Z, end-time: 2026-02-19T22:03:56.244121Z, duration: 78, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = ['.rst', '.md']` to `source_suffix = {'.rst': 'restructuredtext', '.md': 'restructuredtext'}`. loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv... loading intersphinx inventory 'idmtools' from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory 'pycomps' from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... loading intersphinx inventory 'emod-generic' from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory 'emod' from https://docs.idmod.org/projects/emod/en/latest/objects.inv... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_admonition', 'deflist', 'amsmath', 'dollarmath', 'html_image', 'smartquotes', 'attrs_inline', 'replacements', 'strikethrough', 'linkify', 'colon_fence', 'tasklist', 'fieldlist', 'substitution'}, 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 254 source files that are out of date updating environment: [new config] 254 added, 0 changed, 0 removed reading sources... 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The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2026-02-19T22:03:56.369032Z, end-time: 2026-02-19T22:04:31.842012Z, duration: 35, exit-code: 0 python -m sphinx -T -W --keep-going -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = ['.rst', '.md']` to `source_suffix = {'.rst': 'restructuredtext', '.md': 'restructuredtext'}`. loading pickled environment... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'substitution', 'html_admonition', 'html_image', 'dollarmath', 'replacements', 'amsmath', 'linkify', 'tasklist', 'strikethrough', 'fieldlist', 'colon_fence', 'smartquotes', 'attrs_inline', 'deflist'}, 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 [singlehtml]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation emod/install-overview emod/install-windows emod/install-linux installation-basic overview emod/software-overview emod/software-inputs emod/software-demographics emod/software-demographics-overlay emod/software-configuration emod/software-configuration-overlay emod/software-parameter-sweep emod/software-campaign emod/software-campaign-overlay emod/software-migration emod/software-migration-creation emod/software-migration-vector emod/software-migration-creation-vector emod/software-climate emod/software-load-balancing emod/software-serialized emod/software-run-simulation emod/software-simulation-cli emod/software-simulation-mpiexec emod/software-simulation-performance emod/software-serializing-pops emod/software-serializing-create emod/software-serializing-change-config emod/software-serializing-change-campaign emod/software-serializing-change-demog emod/software-serializing-change-climate emod/software-serializing-change-migration emod/software-serializing-change-reports emod/software-outputs emod/software-custom-reporter emod/software-error-logging emod/software-report-binned emod/software-report-demographic-summary emod/software-report-inset-chart emod/software-report-property emod/software-report-event-counter emod/software-report-event-recorder emod/software-report-human-migration emod/software-report-node-demographics emod/software-report-spatial emod/software-report-vector-genetics emod/software-report-vector-migration emod/software-report-vector-stats emod/software-report-vector-habitat emod/software-report-vector-species emod/software-report-malaria-immunity emod/software-report-malaria-patient emod/software-report-malaria-sql emod/software-report-malaria-summary emod/software-report-malaria-survey emod/software-report-drug-status emod/software-report-filtered-malaria emod/software-report-fpg-new-infections emod/software-report-malaria-node-demographics emod/software-report-malaria-node-demographics-genetics emod/software-report-simple-malaria-transmission emod/software-report-vector-stats-malaria-genetics emod/software-report-malaria-spatial emod/software-report-intervention-population-average emod/software-report-antibodies emod/model-overview emod/vector-model-overview emod/vector-model-climate-demographics emod/vector-model-larval-habitat emod/vector-model-transmission emod/malaria-model-overview emod/malaria-model-infection-immunity emod/malaria-model-symptoms-diagnosis emod/malaria-model-antimalarial-drugs emod/model-outbreak emod/model-heterogeneity emod/model-population-density emod/model-properties emod/model-migration emod/model-campaign emod/model-targeted-interventions emod/model-vaccination emod/model-care-cascade emod/malaria-overview emod/tutorials emod/vector-scenarios emod/malaria-scenarios reference emod/parameter-overview emod/parameter-demographics emod/parameter-configuration emod/parameter-configuration-drugs emod/parameter-configuration-enable emod/parameter-configuration-general-disease emod/parameter-configuration-env emod/parameter-configuration-immunity emod/parameter-configuration-incubation emod/parameter-configuration-infectivity emod/parameter-configuration-input emod/parameter-configuration-larval emod/parameter-configuration-migration emod/parameter-configuration-mortality emod/parameter-configuration-output emod/parameter-configuration-parasite emod/parameter-configuration-population emod/parameter-configuration-sampling emod/parameter-configuration-scalars emod/parameter-configuration-setup emod/parameter-configuration-symptoms emod/parameter-configuration-vector-control emod/parameter-configuration-vector-lifecycle emod/parameter-campaign emod/parameter-campaign-event-coordinators emod/parameter-campaign-event-broadcastcoordinatorevent emod/parameter-campaign-event-calendareventcoordinator emod/parameter-campaign-event-campaignevent emod/parameter-campaign-event-communityhealthworkereventcoordinator emod/parameter-campaign-event-coveragebynodeeventcoordinator emod/parameter-campaign-event-delayeventcoordinator emod/parameter-campaign-event-incidenceeventcoordinator emod/parameter-campaign-event-nchoosereventcoordinator emod/parameter-campaign-event-standardinterventiondistributioneventcoordinator emod/parameter-campaign-event-surveillanceeventcoordinator emod/parameter-campaign-event-triggeredeventcoordinator emod/parameter-campaign-node-interventions emod/parameter-campaign-node-animalfeedkill emod/parameter-campaign-node-artificialdiet emod/parameter-campaign-node-broadcastcoordinatoreventfromnode emod/parameter-campaign-node-broadcastnodeevent emod/parameter-campaign-node-firstnodewithnodepropertyeventcoordinator emod/parameter-campaign-node-indoorspacespraying emod/parameter-campaign-node-inputeir emod/parameter-campaign-node-larvicides emod/parameter-campaign-node-malariachallenge emod/parameter-campaign-node-migratefamily emod/parameter-campaign-node-mosquitorelease emod/parameter-campaign-node-multiinsecticideindoorspacespraying emod/parameter-campaign-node-multiinsecticidespacespraying emod/parameter-campaign-node-multinodeinterventiondistributor emod/parameter-campaign-node-nlhtivnode emod/parameter-campaign-node-nodelevelhealthtriggerediv emod/parameter-campaign-node-nodepropertyvaluechanger emod/parameter-campaign-node-outbreak emod/parameter-campaign-node-outdoorrestkill emod/parameter-campaign-node-outdoornodeemanator emod/parameter-campaign-node-ovipositiontrap emod/parameter-campaign-node-scalelarvalhabitat emod/parameter-campaign-node-spacespraying emod/parameter-campaign-node-spatialrepellent emod/parameter-campaign-node-sugartrap emod/parameter-campaign-individual-interventions emod/parameter-campaign-individual-adherentdrug emod/parameter-campaign-individual-antimalarialdrug emod/parameter-campaign-individual-bitingrisk emod/parameter-campaign-individual-broadcastevent emod/parameter-campaign-individual-broadcasteventtoothernodes emod/parameter-campaign-individual-controlledvaccine emod/parameter-campaign-individual-delayedintervention emod/parameter-campaign-individual-humanhostseekingtrap emod/parameter-campaign-individual-immunitybloodtest emod/parameter-campaign-individual-indoorindividualemanator emod/parameter-campaign-individual-individualimmunitychanger emod/parameter-campaign-individual-individualnondiseasedeathratemodifier emod/parameter-campaign-individual-irshousingmodification emod/parameter-campaign-individual-ivcalendar emod/parameter-campaign-individual-ivermectin emod/parameter-campaign-individual-malariadiagnostic emod/parameter-campaign-individual-migrateindividuals emod/parameter-campaign-individual-multieffectboostervaccine emod/parameter-campaign-individual-multieffectvaccine emod/parameter-campaign-individual-multiinsecticideirshousingmodification emod/parameter-campaign-individual-multiinsecticideusagedependentbednet emod/parameter-campaign-individual-multiinterventiondistributor emod/parameter-campaign-individual-multipackcombodrug emod/parameter-campaign-individual-outbreakindividual emod/parameter-campaign-individual-outbreakindividualmalariagenetics emod/parameter-campaign-individual-outbreakindividualmalariavargenes emod/parameter-campaign-individual-propertyvaluechanger emod/parameter-campaign-individual-rtssvaccine emod/parameter-campaign-individual-screeninghousingmodification emod/parameter-campaign-individual-simplebednet emod/parameter-campaign-individual-simpleboostervaccine emod/parameter-campaign-individual-simplediagnostic emod/parameter-campaign-individual-simplehealthseekingbehavior emod/parameter-campaign-individual-simplehousingmodification emod/parameter-campaign-individual-simpleindividualrepellent emod/parameter-campaign-individual-simplevaccine emod/parameter-campaign-individual-spatialrepellenthousingmodification emod/parameter-campaign-individual-standarddiagnostic emod/parameter-campaign-individual-usagedependentbednet emod/parameter-campaign-waningeffects emod/parameter-campaign-targeting-config emod/parameter-campaign-event-list emod/parameter-schema modules emodpy_malaria emodpy_malaria.demographics emodpy_malaria.demographics.MalariaDemographics emodpy_malaria.interventions emodpy_malaria.interventions.adherentdrug emodpy_malaria.interventions.bednet emodpy_malaria.interventions.common emodpy_malaria.interventions.community_health_worker emodpy_malaria.interventions.diag_survey emodpy_malaria.interventions.drug emodpy_malaria.interventions.drug_campaign emodpy_malaria.interventions.indoor_individual_emanator emodpy_malaria.interventions.inputeir emodpy_malaria.interventions.irs emodpy_malaria.interventions.ivermectin emodpy_malaria.interventions.larvicide emodpy_malaria.interventions.malaria_challenge emodpy_malaria.interventions.mosquitorelease emodpy_malaria.interventions.outbreak emodpy_malaria.interventions.outdoor_node_emanator emodpy_malaria.interventions.outdoorrestkill emodpy_malaria.interventions.scale_larval_habitats emodpy_malaria.interventions.spacespraying emodpy_malaria.interventions.sugartrap emodpy_malaria.interventions.treatment_seeking emodpy_malaria.interventions.usage_dependent_bednet emodpy_malaria.interventions.vaccine emodpy_malaria.interventions.vector_surveillance emodpy_malaria.migration emodpy_malaria.migration.convert_csv_to_bin_vector_migration emodpy_malaria.migration.convert_json_to_bin emodpy_malaria.migration.convert_txt_to_bin emodpy_malaria.migration.vector_migration emodpy_malaria.reporters emodpy_malaria.reporters.builtin emodpy_malaria.serialization emodpy_malaria.serialization.replace_genomes emodpy_malaria.serialization.replace_genomes_get_next_barcode emodpy_malaria.serialization.serialization_support emodpy_malaria.serialization.zero_infections emodpy_malaria.weather emodpy_malaria.weather.data_sources emodpy_malaria.weather.weather_data emodpy_malaria.weather.weather_metadata emodpy_malaria.weather.weather_request emodpy_malaria.weather.weather_set emodpy_malaria.weather.weather_utils emodpy_malaria.weather.weather_variable emodpy_malaria.malaria_config emodpy_malaria.malaria_vector_species_params emodpy_malaria.utils emodpy_malaria.vector_config faq emod/troubleshooting emod/tips-tricks emod/tips-biting-risk glossary done writing... done writing additional files... opensearchdone copying images... 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