Read the Docs build information Build id: 2640581 Project: institute-for-disease-modeling-emodpy-malaria Version: 10 Commit: 6cd0bb1c69f8a522509271828f402ec5558252f0 Date: 2024-11-25T19:21:56.887025Z State: finished Success: True [rtd-command-info] start-time: 2024-11-25T19:24:49.026272Z, end-time: 2024-11-25T19:24:53.529342Z, duration: 4, exit-code: 0 git clone --depth 1 https://github.com/EMOD-Hub/emodpy-malaria.git . Cloning into '.'... [rtd-command-info] start-time: 2024-11-25T19:24:53.598885Z, end-time: 2024-11-25T19:24:55.178163Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/10/head:external-10 From https://github.com/EMOD-Hub/emodpy-malaria * [new ref] refs/pull/10/head -> external-10 * [new tag] v4.0.0 -> v4.0.0 [rtd-command-info] start-time: 2024-11-25T19:24:55.307388Z, end-time: 2024-11-25T19:24:55.786222Z, duration: 0, exit-code: 0 git checkout --force 6cd0bb1c69f8a522509271828f402ec5558252f0 Note: switching to '6cd0bb1c69f8a522509271828f402ec5558252f0'. 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 6cd0bb1 fixing parasetemia_bins dependency and adding a test to verify it's gone [rtd-command-info] start-time: 2024-11-25T19:24:55.851897Z, end-time: 2024-11-25T19:24:55.913556Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip # Optionally set the version of Python and requirements required to build your docs python: install: - requirements: requirements.txt - requirements: docs/requirements.txt - method: setuptools path: . # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank # search: # ranking: [rtd-command-info] start-time: 2024-11-25T19:25:00.990925Z, end-time: 2024-11-25T19:25:01.073237Z, duration: 0, exit-code: 0 asdf global python 3.9.20 [rtd-command-info] start-time: 2024-11-25T19:25:01.482410Z, end-time: 2024-11-25T19:25:02.472808Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.20.final.0-64 in 649ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-11-25T19:25:02.545511Z, end-time: 2024-11-25T19:25:16.462628Z, duration: 13, 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/10/lib/python3.9/site-packages (23.1) Collecting pip Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ef/7d/500c9ad20238fcfcb4cb9243eede163594d7020ce87bd9610c9e02771876/pip-24.3.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 10.6 MB/s eta 0:00:00 Requirement already satisfied: setuptools in 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charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 importlib-metadata-8.5.0 packaging-24.2 requests-2.32.3 snowballstemmer-2.2.0 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-2.1.0 urllib3-2.2.3 zipp-3.21.0 [rtd-command-info] start-time: 2024-11-25T19:25:29.265653Z, end-time: 2024-11-25T19:26:30.551252Z, duration: 61, 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==0.0.72 (from -r requirements.txt (line 2)) Downloading 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finished with status 'done' Created wheel for xmlrunner: filename=xmlrunner-1.7.7-py3-none-any.whl size=6222 sha256=c7fdb02323ef6617db67538c1652af92023795c31a964e3684a0315965477f8e Stored in directory: /tmp/pip-ephem-wheel-cache-xtbh9cs0/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=3917 sha256=afd2e3ea5e8e37ecc2a892650ce64d2aa6a177d1a7ffc603403a4e0c6f1b6f0b Stored in directory: /tmp/pip-ephem-wheel-cache-xtbh9cs0/wheels/b1/d2/34/e78c711b3a006c0865ac4a8e82dc78c1b5a017cc3edb109a37 Successfully built xmlrunner prodict Installing collected packages: xmlrunner, pytz, parse, emod-malaria, xdg, urllib3, tzdata, tqdm, threadpoolctl, tabulate, soupsieve, six, pyyaml, pyproj, pyparsing, pycparser, prodict, pluggy, pillow, numpy, natsort, more-itertools, lz4, kiwisolver, joblib, jeepney, iniconfig, importlib-resources, humanfriendly, graphviz, geographiclib, future, fonttools, filelock, exceptiongroup, diskcache, cycler, click, backports.tarfile, backoff, astor, shapely, scipy, requests, python-dateutil, pytest, jaraco.functools, jaraco.context, jaraco.classes, contourpy, coloredlogs, cffi, beautifulsoup4, astunparse, scikit-learn, pyCOMPS, pandas, matplotlib, cryptography, bs4, SecretStorage, idmtools, emod-api, keyring, idmtools-platform-comps, idmtools-models, emodpy Attempting uninstall: urllib3 Found existing installation: urllib3 2.2.3 Uninstalling urllib3-2.2.3: Successfully uninstalled urllib3-2.2.3 Attempting uninstall: requests Found existing installation: requests 2.32.3 Uninstalling requests-2.32.3: Successfully uninstalled requests-2.32.3 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 beautifulsoup4-4.12.3 bs4-0.0.2 cffi-1.17.1 click-7.1.2 coloredlogs-15.0.1 contourpy-1.3.0 cryptography-43.0.3 cycler-0.12.1 diskcache-5.4.0 emod-api-1.33.3 emod-malaria-0.0.72 emodpy-1.22.1 exceptiongroup-1.2.2 filelock-3.16.1 fonttools-4.55.0 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-6.4.5 iniconfig-2.0.0 jaraco.classes-3.4.0 jaraco.context-6.0.1 jaraco.functools-4.1.0 jeepney-0.8.0 joblib-1.4.2 keyring-25.5.0 kiwisolver-1.4.7 lz4-4.3.3 matplotlib-3.9.2 more-itertools-9.1.0 natsort-8.4.0 numpy-2.0.2 pandas-2.2.3 parse-1.20.2 pillow-11.0.0 pluggy-1.5.0 prodict-0.8.20 pyCOMPS-2.11.0 pycparser-2.22 pyparsing-3.2.0 pyproj-3.6.1 pytest-8.1.2 python-dateutil-2.9.0.post0 pytz-2024.2 pyyaml-6.0.2 requests-2.29.0 scikit-learn-1.5.2 scipy-1.13.1 shapely-2.0.6 six-1.16.0 soupsieve-2.6 tabulate-0.9.0 threadpoolctl-3.5.0 tqdm-4.67.1 tzdata-2024.2 urllib3-1.26.20 xdg-6.0.0 xmlrunner-1.7.7 [rtd-command-info] start-time: 2024-11-25T19:26:30.669906Z, end-time: 2024-11-25T19:26:52.718900Z, duration: 22, 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/10/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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Collecting jsonpointer>1.13 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/71/92/5e77f98553e9e75130c78900d000368476aed74276eb8ae8796f65f00918/jsonpointer-3.0.0-py2.py3-none-any.whl (7.6 kB) Collecting uri-template (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e7/00/3fca040d7cf8a32776d3d81a00c8ee7457e00f80c649f1e4a863c8321ae9/uri_template-1.3.0-py3-none-any.whl (11 kB) Collecting webcolors>=24.6.0 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading 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arrow>=0.15.0->isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/35/d6/ba5f61958f358028f2e2ba1b8e225b8e263053bd57d3a79e2d2db64c807b/types_python_dateutil-2.9.0.20241003-py3-none-any.whl (9.7 kB) Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, typing-extensions, 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, asttokens, accessible-pygments, terminado, stack-data, sphinxcontrib-napoleon, referencing, pynacl, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, async-lru, arrow, argon2-cffi-bindings, anyio, sphinxcontrib-programoutput, sphinxcontrib-jquery, sphinx-copybutton, 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 2.32.3 which is incompatible. Successfully installed accessible-pygments-0.0.5 anyio-4.6.2.post1 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-24.2.0 bleach-6.2.0 comm-0.2.2 debugpy-1.8.9 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.15 docutils-0.20.1 executing-2.1.0 fastjsonschema-2.20.0 fqdn-1.5.1 ipykernel-6.29.5 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.2 json5-0.9.28 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.2 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-3.0.2 myst-parser-2.0.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 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-4.3.6 pockets-0.9.1 prometheus-client-0.21.0 prompt-toolkit-3.0.48 psutil-6.1.0 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.0 pygithub-1.59.1 pyjwt-2.10.0 pynacl-1.5.0 python-json-logger-2.0.7 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.21.0 send2trash-1.8.3 sniffio-1.3.1 sphinx-copybutton-0.5.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.4.0 tornado-6.4.2 traitlets-5.14.3 types-python-dateutil-2.9.0.20241003 typing-extensions-4.12.2 uri-template-1.3.0 wcwidth-0.2.13 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.8.0 wrapt-1.17.0 [rtd-command-info] start-time: 2024-11-25T19:26:52.808474Z, end-time: 2024-11-25T19:26:54.633229Z, duration: 1, exit-code: 0 python ./setup.py install --force /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() running bdist_egg running egg_info creating emodpy_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' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/lib/emodpy_malaria copying emodpy_malaria/malaria_config.py -> build/lib/emodpy_malaria copying emodpy_malaria/malaria_vector_species_params.py -> build/lib/emodpy_malaria copying emodpy_malaria/__init__.py -> build/lib/emodpy_malaria copying emodpy_malaria/vector_config.py -> build/lib/emodpy_malaria creating build/lib/tests copying tests/create_auth_token_args.py -> build/lib/tests copying tests/run_all_sft_tests.py -> build/lib/tests copying tests/__init__.py -> build/lib/tests copying tests/add_itn.py -> build/lib/tests creating build/lib/emodpy_malaria/reporters copying emodpy_malaria/reporters/__init__.py -> build/lib/emodpy_malaria/reporters copying emodpy_malaria/reporters/builtin.py -> build/lib/emodpy_malaria/reporters creating build/lib/emodpy_malaria/demographics copying emodpy_malaria/demographics/MalariaDemographics.py -> build/lib/emodpy_malaria/demographics copying emodpy_malaria/demographics/__init__.py -> build/lib/emodpy_malaria/demographics creating build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_utils.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_set.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_variable.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/data_sources.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_request.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_metadata.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/__init__.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_data.py -> build/lib/emodpy_malaria/weather creating build/lib/emodpy_malaria/vector_migration copying emodpy_malaria/vector_migration/vector_migration.py -> build/lib/emodpy_malaria/vector_migration copying emodpy_malaria/vector_migration/__init__.py -> build/lib/emodpy_malaria/vector_migration creating build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/zero_infections.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/serialization_support.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/replace_genomes.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/__init__.py -> build/lib/emodpy_malaria/serialization copying emodpy_malaria/serialization/replace_genomes_get_next_barcode.py -> build/lib/emodpy_malaria/serialization creating build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/bednet.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/mosquitorelease.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/drug.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outdoorrestkill.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outbreak.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/diag_survey.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/malaria_challenge.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/common.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/spacespraying.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/vaccine.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/sugartrap.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/__init__.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/adherentdrug.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/treatment_seeking.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/scale_larval_habitats.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/irs.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/drug_campaign.py -> build/lib/emodpy_malaria/interventions creating build/lib/tests/unittests copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_interventions_as_files.py -> build/lib/tests/unittests copying tests/unittests/test_demog.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_reporters.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_interventions.py -> build/lib/tests/unittests copying tests/unittests/test_campaign_common.py -> build/lib/tests/unittests copying tests/unittests/test_import.py -> build/lib/tests/unittests copying tests/unittests/coverage_check.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/get_unittest_coverage.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 creating build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_scenarios.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_request.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_data.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_e2e_comps.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/__init__.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_set.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_e2e.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_metadata.py -> build/lib/tests/unittests/weather copying emodpy_malaria/malaria_drug_params.csv -> build/lib/emodpy_malaria creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/emodpy_malaria creating build/bdist.linux-x86_64/egg/emodpy_malaria/reporters copying build/lib/emodpy_malaria/reporters/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/reporters copying build/lib/emodpy_malaria/reporters/builtin.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/reporters creating build/bdist.linux-x86_64/egg/emodpy_malaria/demographics copying build/lib/emodpy_malaria/demographics/MalariaDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/demographics copying build/lib/emodpy_malaria/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/demographics creating build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_utils.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_set.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_variable.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/data_sources.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_request.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_metadata.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/weather/weather_data.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather copying build/lib/emodpy_malaria/malaria_config.py -> build/bdist.linux-x86_64/egg/emodpy_malaria creating build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration copying build/lib/emodpy_malaria/vector_migration/vector_migration.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration copying build/lib/emodpy_malaria/vector_migration/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration creating build/bdist.linux-x86_64/egg/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/zero_infections.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/serialization_support.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/replace_genomes.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/serialization copying build/lib/emodpy_malaria/serialization/replace_genomes_get_next_barcode.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/serialization copying build/lib/emodpy_malaria/malaria_vector_species_params.py -> build/bdist.linux-x86_64/egg/emodpy_malaria creating build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/bednet.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/mosquitorelease.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/drug.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/outdoorrestkill.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/diag_survey.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/usage_dependent_bednet.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/vector_surveillance.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/malaria_challenge.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/common.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/spacespraying.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/vaccine.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/community_health_worker.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/larvicide.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/sugartrap.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/adherentdrug.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/treatment_seeking.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/scale_larval_habitats.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/ivermectin.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/inputeir.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/irs.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/interventions/drug_campaign.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/interventions copying build/lib/emodpy_malaria/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria copying build/lib/emodpy_malaria/malaria_drug_params.csv -> build/bdist.linux-x86_64/egg/emodpy_malaria copying build/lib/emodpy_malaria/vector_config.py -> build/bdist.linux-x86_64/egg/emodpy_malaria creating build/bdist.linux-x86_64/egg/tests copying build/lib/tests/create_auth_token_args.py -> build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/schema_path_file.py -> build/bdist.linux-x86_64/egg/tests/unittests creating build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_scenarios.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_request.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_data.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_e2e_comps.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_set.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_e2e.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/weather/test_weather_metadata.py -> build/bdist.linux-x86_64/egg/tests/unittests/weather copying build/lib/tests/unittests/test_malaria_interventions_as_files.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_demog.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_malaria_reporters.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_malaria_interventions.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_campaign_common.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_import.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/coverage_check.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_malaria_config.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/get_unittest_coverage.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/manifest.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_treatment_seeking.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/run_all_sft_tests.py -> build/bdist.linux-x86_64/egg/tests copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests copying build/lib/tests/add_itn.py -> build/bdist.linux-x86_64/egg/tests byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/builtin.py to builtin.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/MalariaDemographics.py to MalariaDemographics.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_utils.py to weather_utils.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_set.py to weather_set.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_variable.py to weather_variable.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/data_sources.py to data_sources.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_request.py to weather_request.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_metadata.py to weather_metadata.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_data.py to weather_data.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/malaria_config.py to malaria_config.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration/vector_migration.py to vector_migration.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/serialization/zero_infections.py to zero_infections.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/serialization/serialization_support.py to serialization_support.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/serialization/replace_genomes.py to replace_genomes.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/serialization/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/serialization/replace_genomes_get_next_barcode.py to replace_genomes_get_next_barcode.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/malaria_vector_species_params.py to malaria_vector_species_params.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/bednet.py to bednet.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/mosquitorelease.py to mosquitorelease.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/drug.py to drug.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/outdoorrestkill.py to outdoorrestkill.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/outbreak.py to outbreak.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/diag_survey.py to diag_survey.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/usage_dependent_bednet.py to usage_dependent_bednet.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/vector_surveillance.py to vector_surveillance.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/malaria_challenge.py to malaria_challenge.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/common.py to common.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/spacespraying.py to spacespraying.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/vaccine.py to vaccine.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/community_health_worker.py to community_health_worker.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/larvicide.py to larvicide.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/sugartrap.py to sugartrap.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/adherentdrug.py to adherentdrug.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/treatment_seeking.py to treatment_seeking.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/scale_larval_habitats.py to scale_larval_habitats.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/ivermectin.py to ivermectin.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/inputeir.py to inputeir.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/irs.py to irs.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/drug_campaign.py to drug_campaign.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/vector_config.py to vector_config.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/create_auth_token_args.py to create_auth_token_args.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/schema_path_file.py to schema_path_file.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_scenarios.py to test_weather_scenarios.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_request.py to test_weather_request.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_data.py to test_weather_data.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_e2e_comps.py to test_e2e_comps.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_set.py to test_weather_set.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_e2e.py to test_e2e.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_metadata.py to test_weather_metadata.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_interventions_as_files.py to test_malaria_interventions_as_files.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demog.py to test_demog.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_reporters.py to test_malaria_reporters.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_interventions.py to test_malaria_interventions.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_campaign_common.py to test_campaign_common.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_import.py to test_import.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/coverage_check.py to coverage_check.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_config.py to test_malaria_config.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/get_unittest_coverage.py to get_unittest_coverage.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/manifest.py to manifest.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_treatment_seeking.py to test_treatment_seeking.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/run_all_sft_tests.py to run_all_sft_tests.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/add_itn.py to add_itn.cpython-39.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_malaria.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... emodpy_malaria.__pycache__.malaria_config.cpython-39: module references __file__ tests.__pycache__.run_all_sft_tests.cpython-39: module references __file__ tests.unittests.__pycache__.manifest.cpython-39: module references __file__ tests.unittests.__pycache__.schema_path_file.cpython-39: module references __file__ tests.unittests.__pycache__.test_campaign_common.cpython-39: module references __file__ tests.unittests.__pycache__.test_demog.cpython-39: module references __file__ tests.unittests.__pycache__.test_malaria_config.cpython-39: module references __file__ tests.unittests.__pycache__.test_malaria_interventions.cpython-39: module references __file__ tests.unittests.__pycache__.test_malaria_reporters.cpython-39: module references __file__ tests.unittests.__pycache__.test_treatment_seeking.cpython-39: module references __file__ tests.unittests.weather.__pycache__.__init__.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_e2e.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_e2e_comps.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_weather_data.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_weather_metadata.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_weather_request.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_weather_scenarios.cpython-39: module references __file__ tests.unittests.weather.__pycache__.test_weather_set.cpython-39: module references __file__ creating dist creating 'dist/emodpy_malaria-4.0.0-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emodpy_malaria-4.0.0-py3.9.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/emodpy_malaria-4.0.0-py3.9.egg Extracting emodpy_malaria-4.0.0-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Adding emodpy-malaria 4.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/emodpy_malaria-4.0.0-py3.9.egg Processing dependencies for emodpy-malaria==4.0.0 Searching for requests==2.29.0 Reading https://pypi.org/simple/requests/ Downloading https://files.pythonhosted.org/packages/cf/e1/2aa539876d9ed0ddc95882451deb57cfd7aa8dbf0b8dbce68e045549ba56/requests-2.29.0-py3-none-any.whl#sha256=e8f3c9be120d3333921d213eef078af392fba3933ab7ed2d1cba3b56f2568c3b Best match: requests 2.29.0 Processing requests-2.29.0-py3-none-any.whl Installing requests-2.29.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Adding requests 2.29.0 to easy-install.pth file detected new path './emodpy_malaria-4.0.0-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/requests-2.29.0-py3.9.egg Searching for emod-malaria==0.0.72 Best match: emod-malaria 0.0.72 Adding emod-malaria 0.0.72 to easy-install.pth file detected new path './requests-2.29.0-py3.9.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for emodpy==1.22.1 Best match: emodpy 1.22.1 Adding emodpy 1.22.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for certifi==2024.8.30 Best match: certifi 2024.8.30 Adding certifi 2024.8.30 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for urllib3==1.26.20 Best match: urllib3 1.26.20 Adding urllib3 1.26.20 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for idna==3.10 Best match: idna 3.10 Adding idna 3.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for charset-normalizer==3.4.0 Best match: charset-normalizer 3.4.0 Adding charset-normalizer 3.4.0 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pytest==8.1.2 Best match: pytest 8.1.2 Adding pytest 8.1.2 to easy-install.pth file Installing py.test script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Installing pytest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for xmlrunner==1.7.7 Best match: xmlrunner 1.7.7 Adding xmlrunner 1.7.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pyCOMPS==2.11.0 Best match: pyCOMPS 2.11.0 Adding pyCOMPS 2.11.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for keyring==25.5.0 Best match: keyring 25.5.0 Adding keyring 25.5.0 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for bs4==0.0.2 Best match: bs4 0.0.2 Adding bs4 0.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for astunparse==1.6.3 Best match: astunparse 1.6.3 Adding astunparse 1.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for astor==0.8.1 Best match: astor 0.8.1 Adding astor 0.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for matplotlib==3.9.2 Best match: matplotlib 3.9.2 Adding matplotlib 3.9.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for emod-api==1.33.3 Best match: emod-api 1.33.3 Adding emod-api 1.33.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for idmtools-models==1.7.11 Best match: idmtools-models 1.7.11 Adding idmtools-models 1.7.11 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for idmtools-platform-comps==1.7.11 Best match: idmtools-platform-comps 1.7.11 Adding idmtools-platform-comps 1.7.11 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for idmtools==1.7.11 Best match: idmtools 1.7.11 Adding idmtools 1.7.11 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for click==7.1.2 Best match: click 7.1.2 Adding click 7.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for tomli==2.1.0 Best match: tomli 2.1.0 Adding tomli 2.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for exceptiongroup==1.2.2 Best match: exceptiongroup 1.2.2 Adding exceptiongroup 1.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pluggy==1.5.0 Best match: pluggy 1.5.0 Adding pluggy 1.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for packaging==24.2 Best match: packaging 24.2 Adding packaging 24.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/setuptools/_vendor Searching for iniconfig==2.0.0 Best match: iniconfig 2.0.0 Adding iniconfig 2.0.0 to easy-install.pth file detected new path './setuptools/_vendor' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for xdg==6.0.0 Best match: xdg 6.0.0 Adding xdg 6.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for future==1.0.0 Best match: future 1.0.0 Adding future 1.0.0 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pytz==2024.2 Best match: pytz 2024.2 Adding pytz 2024.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for jeepney==0.8.0 Best match: jeepney 0.8.0 Adding jeepney 0.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for SecretStorage==3.3.3 Best match: SecretStorage 3.3.3 Adding SecretStorage 3.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for importlib-metadata==8.5.0 Best match: importlib-metadata 8.5.0 Adding importlib-metadata 8.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for jaraco.context==6.0.1 Best match: jaraco.context 6.0.1 Adding jaraco.context 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for jaraco.functools==4.1.0 Best match: jaraco.functools 4.1.0 Adding jaraco.functools 4.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for jaraco.classes==3.4.0 Best match: jaraco.classes 3.4.0 Adding jaraco.classes 3.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for beautifulsoup4==4.12.3 Best match: beautifulsoup4 4.12.3 Adding beautifulsoup4 4.12.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for wheel==0.43.0 Best match: wheel 0.43.0 wheel 0.43.0 is already the active version in easy-install.pth Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/setuptools/_vendor Searching for importlib-resources==6.4.5 Best match: importlib-resources 6.4.5 Adding importlib-resources 6.4.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for python-dateutil==2.9.0.post0 Best match: python-dateutil 2.9.0.post0 Adding python-dateutil 2.9.0.post0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pyparsing==3.2.0 Best match: pyparsing 3.2.0 Adding pyparsing 3.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pillow==11.0.0 Best match: pillow 11.0.0 Adding pillow 11.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for numpy==2.0.2 Best match: numpy 2.0.2 Adding numpy 2.0.2 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Installing numpy-config script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for kiwisolver==1.4.7 Best match: kiwisolver 1.4.7 Adding kiwisolver 1.4.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for fonttools==4.55.0 Best match: fonttools 4.55.0 Adding fonttools 4.55.0 to easy-install.pth file Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for cycler==0.12.1 Best match: cycler 0.12.1 Adding cycler 0.12.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for contourpy==1.3.0 Best match: contourpy 1.3.0 Adding contourpy 1.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for parse==1.20.2 Best match: parse 1.20.2 Adding parse 1.20.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for graphviz==0.20.3 Best match: graphviz 0.20.3 Adding graphviz 0.20.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for prodict==0.8.20 Best match: prodict 0.8.20 Adding prodict 0.8.20 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for lz4==4.3.3 Best match: lz4 4.3.3 Adding lz4 4.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for scikit-learn==1.5.2 Best match: scikit-learn 1.5.2 Adding scikit-learn 1.5.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for geographiclib==2.0 Best match: geographiclib 2.0 Adding geographiclib 2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pyproj==3.6.1 Best match: pyproj 3.6.1 Adding pyproj 3.6.1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for shapely==2.0.6 Best match: shapely 2.0.6 Adding shapely 2.0.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for scipy==1.13.1 Best match: scipy 1.13.1 Adding scipy 1.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pandas==2.2.3 Best match: pandas 2.2.3 Adding pandas 2.2.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for PyYAML==6.0.2 Best match: PyYAML 6.0.2 Adding PyYAML 6.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for jinja2==3.1.4 Best match: jinja2 3.1.4 Adding jinja2 3.1.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for natsort==8.4.0 Best match: natsort 8.4.0 Adding natsort 8.4.0 to easy-install.pth file Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for tqdm==4.67.1 Best match: tqdm 4.67.1 Adding tqdm 4.67.1 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for tabulate==0.9.0 Best match: tabulate 0.9.0 Adding tabulate 0.9.0 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for more-itertools==9.1.0 Best match: more-itertools 9.1.0 Adding more-itertools 9.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for filelock==3.16.1 Best match: filelock 3.16.1 Adding filelock 3.16.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for diskcache==5.4.0 Best match: diskcache 5.4.0 Adding diskcache 5.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for coloredlogs==15.0.1 Best match: coloredlogs 15.0.1 Adding coloredlogs 15.0.1 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for backoff==2.2.1 Best match: backoff 2.2.1 Adding backoff 2.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for cryptography==43.0.3 Best match: cryptography 43.0.3 Adding cryptography 43.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for zipp==3.21.0 Best match: zipp 3.21.0 Adding zipp 3.21.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for backports.tarfile==1.2.0 Best match: backports.tarfile 1.2.0 backports.tarfile 1.2.0 is already the active version in easy-install.pth Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages/setuptools/_vendor Searching for soupsieve==2.6 Best match: soupsieve 2.6 Adding soupsieve 2.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for threadpoolctl==3.5.0 Best match: threadpoolctl 3.5.0 Adding threadpoolctl 3.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for joblib==1.4.2 Best match: joblib 1.4.2 Adding joblib 1.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for tzdata==2024.2 Best match: tzdata 2024.2 Adding tzdata 2024.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for MarkupSafe==3.0.2 Best match: MarkupSafe 3.0.2 Adding MarkupSafe 3.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for humanfriendly==10.0 Best match: humanfriendly 10.0 Adding humanfriendly 10.0 to easy-install.pth file Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for cffi==1.17.1 Best match: cffi 1.17.1 Adding cffi 1.17.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Searching for pycparser==2.22 Best match: pycparser 2.22 Adding pycparser 2.22 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/10/lib/python3.9/site-packages Finished processing dependencies for emodpy-malaria==4.0.0 [rtd-command-info] start-time: 2024-11-25T19:26:54.821335Z, end-time: 2024-11-25T19:26:54.877398Z, 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) } [rtd-command-info] start-time: 2024-11-25T19:26:54.950846Z, end-time: 2024-11-25T19:28:01.685479Z, duration: 66, 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 'emod_api' from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory 'emodpy' from https://docs.idmod.org/projects/emodpy/en/latest/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={'smartquotes', 'fieldlist', 'linkify', 'colon_fence', 'dollarmath', 'substitution', 'html_image', 'amsmath', 'strikethrough', 'tasklist', 'deflist', 'html_admonition', 'attrs_inline', 'replacements'}, 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 243 source files that are out of date updating environment: [new config] 243 added, 0 changed, 0 removed reading sources... 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