Read the Docs build information Build id: 1645530 Project: institute-for-disease-modeling-emodpy-malaria Version: latest Commit: c605e47561053c11089b453f8f109ecac6c0854d Date: 2023-08-07T17:30:02.021535Z State: cancelled Success: False [rtd-command-info] start-time: 2023-08-07T17:30:06.512553Z, end-time: 2023-08-07T17:30:09.393668Z, duration: 2, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/emodpy-malaria.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2023-08-07T17:30:09.652350Z, end-time: 2023-08-07T17:30:12.779274Z, duration: 3, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/emodpy-malaria * [new tag] 3.1.1 -> 3.1.1 * [new tag] v3.1.12 -> v3.1.12 [rtd-command-info] start-time: 2023-08-07T17:30:13.022893Z, end-time: 2023-08-07T17:30:13.386693Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at c605e47 adding_needed_changes_for_snt_work (#614) [rtd-command-info] start-time: 2023-08-07T17:30:13.698275Z, end-time: 2023-08-07T17:30:13.775854Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-07T17:30:14.130243Z, end-time: 2023-08-07T17:30:14.178756Z, 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 # 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 - pdf # Optionally set the version of Python and requirements required to build your docs python: version: 3.8 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: 2023-08-07T17:30:17.742279Z, end-time: 2023-08-07T17:30:32.537537Z, duration: 14, exit-code: 0 python3.8 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2023-08-07T17:30:32.917042Z, end-time: 2023-08-07T17:30:35.302556Z, duration: 2, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages (23.2.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 24.7 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 68.0.0 Uninstalling setuptools-68.0.0: Successfully uninstalled setuptools-68.0.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2023-08-07T17:30:35.806017Z, end-time: 2023-08-07T17:30:46.711335Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Collecting pillow Obtaining dependency information for pillow from https://files.pythonhosted.org/packages/8b/b3/d7b6ee16358d829ca482c74a96e2b9079bf33f8d7d37d16f8ebb19ddf5a4/Pillow-10.0.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading Pillow-10.0.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.5 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 23.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading 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snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4 [rtd-command-info] start-time: 2023-08-07T17:30:46.948762Z, end-time: 2023-08-07T17:31:31.315343Z, duration: 44, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: 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pyproj-3.5.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.8/7.8 MB 194.8 MB/s eta 0:00:00 Collecting geographiclib (from emod-api~=1.24->emodpy~=1.16->-r requirements.txt (line 1)) Downloading geographiclib-2.0-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.3/40.3 kB 107.3 MB/s eta 0:00:00 Collecting scikit-learn (from emod-api~=1.24->emodpy~=1.16->-r requirements.txt (line 1)) Obtaining dependency information for scikit-learn from https://files.pythonhosted.org/packages/bf/15/d1b649fc7685d11b806b4546a5438191fb2ad761de70da95ff676189dcec/scikit_learn-1.3.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading scikit_learn-1.3.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Collecting lz4 (from emod-api~=1.24->emodpy~=1.16->-r requirements.txt (line 1)) Downloading lz4-4.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB) 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xdg, urllib3, tzdata, tqdm, threadpoolctl, tabulate, soupsieve, pyyaml, python-dateutil, pyproj, pyparsing, pycparser, pluggy, numpy, natsort, more-itertools, lz4, kiwisolver, joblib, jinja2, jeepney, humanfriendly, graphviz, geographiclib, future, fonttools, filelock, diskcache, cycler, click, backoff, astunparse, astor, shapely, scipy, requests, pandas, packaging, jaraco.classes, importlib-resources, importlib-metadata, contourpy, coloredlogs, cffi, beautifulsoup4, yarg, scikit-learn, pygit2, pyCOMPS, matplotlib, cryptography, bs4, SecretStorage, pipreqs, emod-api, keyring, idmtools, idmtools-platform-comps, idmtools-models, emodpy Attempting uninstall: urllib3 Found existing installation: urllib3 2.0.4 Uninstalling urllib3-2.0.4: Successfully uninstalled urllib3-2.0.4 Attempting uninstall: jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: requests Found existing installation: requests 2.31.0 Uninstalling requests-2.31.0: Successfully uninstalled requests-2.31.0 Attempting uninstall: packaging Found existing installation: packaging 23.1 Uninstalling packaging-23.1: Successfully uninstalled packaging-23.1 Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 beautifulsoup4-4.12.2 bs4-0.0.1 cffi-1.15.1 click-7.1.2 coloredlogs-15.0.1 contourpy-1.1.0 cryptography-41.0.3 cycler-0.11.0 diskcache-5.4.0 docopt-0.6.2 emod-api-1.29.7 emod-malaria-0.0.54 emodpy-1.21.1 filelock-3.12.2 fonttools-4.42.0 future-0.18.3 geographiclib-2.0 graphviz-0.20.1 humanfriendly-10.0 idmtools-1.7.8 idmtools-models-1.7.8 idmtools-platform-comps-1.7.8 importlib-metadata-6.8.0 importlib-resources-6.0.1 jaraco.classes-3.3.0 jeepney-0.8.0 jinja2-3.1.2 joblib-1.3.1 keyring-24.2.0 kiwisolver-1.4.4 lz4-4.3.2 matplotlib-3.7.2 more-itertools-9.0.0 natsort-8.2.0 numpy-1.24.4 packaging-21.3 pandas-2.0.3 parse-1.19.1 pipreqs-0.4.13 pluggy-1.0.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.21 pygit2-1.10.1 pyparsing-3.0.9 pyproj-3.5.0 python-dateutil-2.8.2 pyyaml-6.0.1 requests-2.29.0 scikit-learn-1.3.0 scipy-1.10.1 shapely-2.0.1 soupsieve-2.4.1 tabulate-0.9.0 threadpoolctl-3.2.0 tqdm-4.65.0 tzdata-2023.3 urllib3-1.26.16 xdg-6.0.0 yarg-0.1.9 zipp-3.16.2 [rtd-command-info] start-time: 2023-08-07T17:31:31.582168Z, end-time: 2023-08-07T17:31:39.570738Z, duration: 7, 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/artifactory/api/pypi/idm-pypi-production/simple Collecting plantweb~=1.2.1 (from -r docs/requirements.txt (line 1)) Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinx-copybutton~=0.3.1 (from -r docs/requirements.txt (line 2)) Downloading sphinx_copybutton-0.3.3-py3-none-any.whl (12 kB) Collecting sphinx-rtd-theme~=0.5.0 (from -r docs/requirements.txt (line 3)) Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 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(line 6)) (3.0.9) Downloading typing_extensions-4.7.1-py3-none-any.whl (33 kB) Installing collected packages: typing-extensions, sphinxext.remoteliteralinclude, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, readthedocs-sphinx-search, pockets, mdurl, docutils, sphinxcontrib-napoleon, sphinx, plantweb, markdown-it-py, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, mdit-py-plugins, myst-parser Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed docutils-0.16 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 myst-parser-0.18.1 plantweb-1.2.1 pockets-0.9.1 readthedocs-sphinx-search-0.3.1 sphinx-4.4.0 sphinx-copybutton-0.3.3 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxcontrib-qthelp-1.0.3 sphinxext.remoteliteralinclude-0.4.0 typing-extensions-4.7.1 [rtd-command-info] start-time: 2023-08-07T17:31:39.918590Z, end-time: 2023-08-07T17:31:42.586078Z, duration: 2, exit-code: 0 python ./setup.py install --force running install 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 creating build/lib creating build/lib/emodpy_malaria copying emodpy_malaria/malaria_vector_species_params.py -> build/lib/emodpy_malaria copying emodpy_malaria/vector_config.py -> build/lib/emodpy_malaria copying emodpy_malaria/malaria_config.py -> build/lib/emodpy_malaria copying emodpy_malaria/__init__.py -> build/lib/emodpy_malaria creating build/lib/tests copying tests/run_all_sft_tests.py -> build/lib/tests copying tests/add_itn.py -> build/lib/tests copying tests/__init__.py -> build/lib/tests copying tests/create_auth_token_args.py -> build/lib/tests creating build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_utils.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_request.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/data_sources.py -> build/lib/emodpy_malaria/weather copying emodpy_malaria/weather/weather_metadata.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 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/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/vector_migration copying emodpy_malaria/vector_migration/__init__.py -> build/lib/emodpy_malaria/vector_migration copying emodpy_malaria/vector_migration/vector_migration.py -> build/lib/emodpy_malaria/vector_migration creating build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/common.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/adherentdrug.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/sugartrap.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/usage_dependent_bednet.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/vaccine.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/malaria_challenge.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/larvicide.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outbreak.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/outdoorrestkill.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/irs.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/community_health_worker.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/__init__.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/inputeir.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/spacespraying.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/diag_survey.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/drug_campaign.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/ivermectin.py -> build/lib/emodpy_malaria/interventions copying emodpy_malaria/interventions/bednet.py -> build/lib/emodpy_malaria/interventions creating build/lib/tests/unittests copying tests/unittests/test_treatment_seeking.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_reporters.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_config.py -> build/lib/tests/unittests copying tests/unittests/manifest.py -> build/lib/tests/unittests copying tests/unittests/test_import.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_interventions.py -> build/lib/tests/unittests copying tests/unittests/test_demog.py -> build/lib/tests/unittests copying tests/unittests/test_malaria_interventions_as_files.py -> build/lib/tests/unittests copying tests/unittests/__init__.py -> build/lib/tests/unittests copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests copying tests/unittests/test_campaign_common.py -> build/lib/tests/unittests copying tests/unittests/get_unittest_coverage.py -> build/lib/tests/unittests creating build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_metadata.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_e2e_comps.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_e2e.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/__init__.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_data.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_request.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_set.py -> build/lib/tests/unittests/weather copying tests/unittests/weather/test_weather_scenarios.py -> build/lib/tests/unittests/weather copying emodpy_malaria/malaria_drug_params.csv -> build/lib/emodpy_malaria creating build/bdist.linux-x86_64 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/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_request.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/weather_set.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_metadata.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/weather/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_malaria/weather 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/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 copying build/lib/emodpy_malaria/vector_config.py -> build/bdist.linux-x86_64/egg/emodpy_malaria 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/reporters copying build/lib/emodpy_malaria/reporters/builtin.py -> 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 creating 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 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/malaria_drug_params.csv -> build/bdist.linux-x86_64/egg/emodpy_malaria copying build/lib/emodpy_malaria/__init__.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/common.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/sugartrap.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/drug.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/vaccine.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/larvicide.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/outdoorrestkill.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/community_health_worker.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/inputeir.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/treatment_seeking.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/diag_survey.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/interventions/ivermectin.py -> 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 creating build/bdist.linux-x86_64/egg/tests copying build/lib/tests/run_all_sft_tests.py -> build/bdist.linux-x86_64/egg/tests copying build/lib/tests/add_itn.py -> build/bdist.linux-x86_64/egg/tests copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests creating 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_metadata.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/test_e2e.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_data.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_set.py -> 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/test_treatment_seeking.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_config.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_import.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_demog.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_malaria_interventions_as_files.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/schema_path_file.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/get_unittest_coverage.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/create_auth_token_args.py -> build/bdist.linux-x86_64/egg/tests byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_utils.py to weather_utils.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_request.py to weather_request.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_variable.py to weather_variable.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_set.py to weather_set.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/data_sources.py to data_sources.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_metadata.py to weather_metadata.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/weather_data.py to weather_data.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/weather/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/malaria_vector_species_params.py to malaria_vector_species_params.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/MalariaDemographics.py to MalariaDemographics.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/demographics/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/vector_config.py to vector_config.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/malaria_config.py to malaria_config.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/builtin.py to builtin.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/reporters/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/vector_migration/vector_migration.py to vector_migration.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/common.py to common.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/adherentdrug.py to adherentdrug.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/sugartrap.py to sugartrap.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/scale_larval_habitats.py to scale_larval_habitats.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/drug.py to drug.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/usage_dependent_bednet.py to usage_dependent_bednet.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/vaccine.py to vaccine.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/malaria_challenge.py to malaria_challenge.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/larvicide.py to larvicide.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/outbreak.py to outbreak.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/outdoorrestkill.py to outdoorrestkill.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/irs.py to irs.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/community_health_worker.py to community_health_worker.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/inputeir.py to inputeir.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/mosquitorelease.py to mosquitorelease.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/treatment_seeking.py to treatment_seeking.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/spacespraying.py to spacespraying.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/diag_survey.py to diag_survey.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/drug_campaign.py to drug_campaign.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/ivermectin.py to ivermectin.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_malaria/interventions/bednet.py to bednet.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/run_all_sft_tests.py to run_all_sft_tests.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/add_itn.py to add_itn.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_metadata.py to test_weather_metadata.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_e2e_comps.py to test_e2e_comps.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_e2e.py to test_e2e.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_data.py to test_weather_data.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_request.py to test_weather_request.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_set.py to test_weather_set.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/weather/test_weather_scenarios.py to test_weather_scenarios.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_treatment_seeking.py to test_treatment_seeking.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_reporters.py to test_malaria_reporters.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_config.py to test_malaria_config.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/manifest.py to manifest.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_import.py to test_import.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_interventions.py to test_malaria_interventions.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demog.py to test_demog.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_malaria_interventions_as_files.py to test_malaria_interventions_as_files.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/schema_path_file.py to schema_path_file.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_campaign_common.py to test_campaign_common.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/get_unittest_coverage.py to get_unittest_coverage.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/create_auth_token_args.py to create_auth_token_args.cpython-38.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-38: module references __file__ tests.__pycache__.run_all_sft_tests.cpython-38: module references __file__ tests.unittests.__pycache__.manifest.cpython-38: module references __file__ tests.unittests.__pycache__.schema_path_file.cpython-38: module references __file__ tests.unittests.__pycache__.test_campaign_common.cpython-38: module references __file__ tests.unittests.__pycache__.test_demog.cpython-38: module references __file__ tests.unittests.__pycache__.test_malaria_config.cpython-38: module references __file__ tests.unittests.__pycache__.test_malaria_interventions.cpython-38: module references __file__ tests.unittests.__pycache__.test_malaria_reporters.cpython-38: module references __file__ tests.unittests.__pycache__.test_treatment_seeking.cpython-38: module references __file__ tests.unittests.weather.__pycache__.__init__.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_e2e.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_e2e_comps.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_weather_data.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_weather_metadata.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_weather_request.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_weather_scenarios.cpython-38: module references __file__ tests.unittests.weather.__pycache__.test_weather_set.cpython-38: module references __file__ creating dist creating 'dist/emodpy_malaria-3.1.20.dev0-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emodpy_malaria-3.1.20.dev0-py3.8.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages/emodpy_malaria-3.1.20.dev0-py3.8.egg Extracting emodpy_malaria-3.1.20.dev0-py3.8.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Adding emodpy-malaria 3.1.20.dev0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages/emodpy_malaria-3.1.20.dev0-py3.8.egg Processing dependencies for emodpy-malaria==3.1.20.dev0 Searching for requests==2.29.0 Best match: requests 2.29.0 Adding requests 2.29.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for emod-malaria==0.0.54 Best match: emod-malaria 0.0.54 Adding emod-malaria 0.0.54 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for emodpy==1.21.1 Best match: emodpy 1.21.1 Adding emodpy 1.21.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for certifi==2023.7.22 Best match: certifi 2023.7.22 Adding certifi 2023.7.22 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for idna==3.4 Best match: idna 3.4 Adding idna 3.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for charset-normalizer==3.2.0 Best match: charset-normalizer 3.2.0 Adding charset-normalizer 3.2.0 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for urllib3==1.26.16 Best match: urllib3 1.26.16 Adding urllib3 1.26.16 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for keyring==24.2.0 Best match: keyring 24.2.0 Adding keyring 24.2.0 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for matplotlib==3.7.2 Best match: matplotlib 3.7.2 Adding matplotlib 3.7.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for idmtools-platform-comps==1.7.8 Best match: idmtools-platform-comps 1.7.8 Adding idmtools-platform-comps 1.7.8 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for emod-api==1.29.7 Best match: emod-api 1.29.7 Adding emod-api 1.29.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for pyCOMPS==2.10.0 Best match: pyCOMPS 2.10.0 Adding pyCOMPS 2.10.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for bs4==0.0.1 Best match: bs4 0.0.1 Adding bs4 0.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for idmtools-models==1.7.8 Best match: idmtools-models 1.7.8 Adding idmtools-models 1.7.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for idmtools==1.7.8 Best match: idmtools 1.7.8 Adding idmtools 1.7.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for importlib-resources==6.0.1 Best match: importlib-resources 6.0.1 Adding importlib-resources 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for jaraco.classes==3.3.0 Best match: jaraco.classes 3.3.0 Adding jaraco.classes 3.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for importlib-metadata==6.8.0 Best match: importlib-metadata 6.8.0 Adding importlib-metadata 6.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for packaging==21.3 Best match: packaging 21.3 Adding packaging 21.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for Pillow==10.0.0 Best match: Pillow 10.0.0 Adding Pillow 10.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for python-dateutil==2.8.2 Best match: python-dateutil 2.8.2 Adding python-dateutil 2.8.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for numpy==1.24.4 Best match: numpy 1.24.4 Adding numpy 1.24.4 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing f2py3.8 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pyparsing==3.0.9 Best match: pyparsing 3.0.9 Adding pyparsing 3.0.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for fonttools==4.42.0 Best match: fonttools 4.42.0 Adding fonttools 4.42.0 to easy-install.pth file Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for contourpy==1.1.0 Best match: contourpy 1.1.0 Adding contourpy 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for cycler==0.11.0 Best match: cycler 0.11.0 Adding cycler 0.11.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for kiwisolver==1.4.4 Best match: kiwisolver 1.4.4 Adding kiwisolver 1.4.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for tqdm==4.65.0 Best match: tqdm 4.65.0 Adding tqdm 4.65.0 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for Jinja2==3.1.2 Best match: Jinja2 3.1.2 Adding Jinja2 3.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for natsort==8.2.0 Best match: natsort 8.2.0 Adding natsort 8.2.0 to easy-install.pth file Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for prodict==0.8.18 Best match: prodict 0.8.18 Adding prodict 0.8.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for shapely==2.0.1 Best match: shapely 2.0.1 Adding shapely 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for graphviz==0.20.1 Best match: graphviz 0.20.1 Adding graphviz 0.20.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for parse==1.19.1 Best match: parse 1.19.1 Adding parse 1.19.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for scipy==1.10.1 Best match: scipy 1.10.1 Adding scipy 1.10.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pandas==2.0.3 Best match: pandas 2.0.3 Adding pandas 2.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pyproj==3.5.0 Best match: pyproj 3.5.0 Adding pyproj 3.5.0 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for scikit-learn==1.3.0 Best match: scikit-learn 1.3.0 Adding scikit-learn 1.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for PyYAML==6.0.1 Best match: PyYAML 6.0.1 Adding PyYAML 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for lz4==4.3.2 Best match: lz4 4.3.2 Adding lz4 4.3.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for wheel==0.41.1 Best match: wheel 0.41.1 Adding wheel 0.41.1 to easy-install.pth file Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for future==0.18.3 Best match: future 0.18.3 Adding future 0.18.3 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for pytz==2023.3 Best match: pytz 2023.3 Adding pytz 2023.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for beautifulsoup4==4.12.2 Best match: beautifulsoup4 4.12.2 Adding beautifulsoup4 4.12.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for more-itertools==9.0.0 Best match: more-itertools 9.0.0 Adding more-itertools 9.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pygit2==1.10.1 Best match: pygit2 1.10.1 Adding pygit2 1.10.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for filelock==3.12.2 Best match: filelock 3.12.2 Adding filelock 3.12.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pluggy==1.0.0 Best match: pluggy 1.0.0 Adding pluggy 1.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/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/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pipreqs==0.4.13 Best match: pipreqs 0.4.13 Adding pipreqs 0.4.13 to easy-install.pth file Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/lib/python3.8/site-packages Searching for zipp==3.16.2 Best match: zipp 3.16.2 Adding zipp 3.16.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for cryptography==41.0.3 Best match: cryptography 41.0.3 Adding cryptography 41.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for MarkupSafe==2.1.3 Best match: MarkupSafe 2.1.3 Adding MarkupSafe 2.1.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for tzdata==2023.3 Best match: tzdata 2023.3 Adding tzdata 2023.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for joblib==1.3.1 Best match: joblib 1.3.1 Adding joblib 1.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for threadpoolctl==3.2.0 Best match: threadpoolctl 3.2.0 Adding threadpoolctl 3.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for soupsieve==2.4.1 Best match: soupsieve 2.4.1 Adding soupsieve 2.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for cffi==1.15.1 Best match: cffi 1.15.1 Adding cffi 1.15.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/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/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for docopt==0.6.2 Best match: docopt 0.6.2 Adding docopt 0.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for yarg==0.1.9 Best match: yarg 0.1.9 Adding yarg 0.1.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Searching for pycparser==2.21 Best match: pycparser 2.21 Adding pycparser 2.21 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/envs/latest/lib/python3.8/site-packages Finished processing dependencies for emodpy-malaria==3.1.20.dev0 [rtd-command-info] start-time: 2023-08-07T17:31:47.629616Z, end-time: 2023-08-07T17:31:47.709001Z, 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' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = [] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'emodpy-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 = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css', '_static/copy_button.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_parent}/{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), 'emod-malaria': ('https://docs.idmod.org/projects/emod-malaria/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("v3.1.12", "/en/v3.1.12/"), ("3.1.1", "/en/3.1.1/"), ("2.4.3", "/en/2.4.3/"), ("2.3.6", "/en/2.3.6/"), ("v2.3.1", "/en/v2.3.1/"), ("2.2.1", "/en/2.2.1/"), ("v2.1.1", "/en/v2.1.1/"), ("v2.0.2", "/en/v2.0.2/"), ("v2.0.1", "/en/v2.0.1/"), ("v1.20.2", "/en/v1.20.2/"), ("v1.1.19", "/en/v1.1.19/"), ("v1.1.0", "/en/v1.1.0/"), ("v1.0.10", "/en/v1.0.10/"), ("v1.0.9", "/en/v1.0.9/"), ("v1.0.2", "/en/v1.0.2/"), ("v3.0.1release", "/en/v3.0.1release/"), ("v.2.2.0", "/en/v.2.2.0/"), ("2.3.6release", "/en/2.3.6release/"), ("v0.0.61", "/en/v0.0.61/"), ("v0.0.50", "/en/v0.0.50/"), ("0.0.50", "/en/0.0.50/"), ("v0.0.48", "/en/v0.0.48/"), ("v0.0.45", "/en/v0.0.45/"), ("v0.0.44", "/en/v0.0.44/"), ("v0.0.29", "/en/v0.0.29/"), ("v0.0.18", "/en/v0.0.18/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/emodpy-malaria/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/emodpy-malaria/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emodpy-malaria', 'name': u'emodpy-malaria', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': '', 'analytics_code': 'G-SVDSQH04EM', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emodpy-malaria', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': 'c605e475', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-emodpy-malaria/builds/1645530/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-08-07T17:31:47.946691Z, end-time: 2023-08-07T17:32:03.233172Z, duration: 15, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), 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') building [mo]: targets for 0 po files that are out of date building [html]: targets for 45 source files that are out of date updating environment: [new config] 45 added, 0 changed, 0 removed reading sources... 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[ 97%] installation-basic reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] emodpy_malaria writing output... [ 4%] emodpy_malaria.demographics writing output... [ 6%] emodpy_malaria.demographics.MalariaDemographics writing output... [ 8%] emodpy_malaria.interventions writing output... [ 11%] emodpy_malaria.interventions.adherentdrug writing output... [ 13%] emodpy_malaria.interventions.bednet writing output... [ 15%] emodpy_malaria.interventions.common writing output... [ 17%] emodpy_malaria.interventions.community_health_worker writing output... [ 20%] emodpy_malaria.interventions.diag_survey writing output... [ 22%] emodpy_malaria.interventions.drug writing output... [ 24%] emodpy_malaria.interventions.drug_campaign writing output... [ 26%] emodpy_malaria.interventions.inputeir writing output... [ 28%] emodpy_malaria.interventions.irs writing output... [ 31%] emodpy_malaria.interventions.ivermectin writing output... [ 33%] emodpy_malaria.interventions.larvicide writing output... [ 35%] emodpy_malaria.interventions.malaria_challenge writing output... [ 37%] emodpy_malaria.interventions.mosquitorelease writing output... [ 40%] emodpy_malaria.interventions.outbreak writing output... [ 42%] emodpy_malaria.interventions.outdoorrestkill writing output... [ 44%] emodpy_malaria.interventions.scale_larval_habitats writing output... [ 46%] emodpy_malaria.interventions.spacespraying writing output... [ 48%] emodpy_malaria.interventions.sugartrap writing output... [ 51%] emodpy_malaria.interventions.treatment_seeking writing output... [ 53%] emodpy_malaria.interventions.usage_dependent_bednet writing output... [ 55%] emodpy_malaria.interventions.vaccine writing output... [ 57%] emodpy_malaria.malaria_config writing output... [ 60%] emodpy_malaria.malaria_vector_species_params writing output... [ 62%] emodpy_malaria.reporters writing output... [ 64%] emodpy_malaria.reporters.builtin writing output... [ 66%] emodpy_malaria.vector_config writing output... [ 68%] emodpy_malaria.vector_migration writing output... [ 71%] emodpy_malaria.vector_migration.vector_migration writing output... [ 73%] emodpy_malaria.weather writing output... [ 75%] emodpy_malaria.weather.data_sources writing output... [ 77%] emodpy_malaria.weather.weather_data writing output... [ 80%] emodpy_malaria.weather.weather_metadata writing output... [ 82%] emodpy_malaria.weather.weather_request writing output... [ 84%] emodpy_malaria.weather.weather_set writing output... [ 86%] emodpy_malaria.weather.weather_utils writing output... [ 88%] emodpy_malaria.weather.weather_variable writing output... [ 91%] faq writing output... [ 93%] index writing output... [ 95%] installation writing output... [ 97%] installation-basic writing output... [100%] modules generating indices... genindex py-modindex done writing additional pages... search opensearch done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in ../_readthedocs/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-08-07T17:32:03.494745Z, end-time: 2023-08-07T17:32:16.333070Z, duration: 12, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), 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') building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 45 added, 0 changed, 0 removed reading sources... [ 2%] emodpy_malaria reading sources... [ 4%] emodpy_malaria.demographics reading sources... [ 6%] emodpy_malaria.demographics.MalariaDemographics reading sources... [ 8%] emodpy_malaria.interventions reading sources... [ 11%] emodpy_malaria.interventions.adherentdrug reading sources... [ 13%] emodpy_malaria.interventions.bednet reading sources... [ 15%] emodpy_malaria.interventions.common reading sources... [ 17%] emodpy_malaria.interventions.community_health_worker reading sources... [ 20%] emodpy_malaria.interventions.diag_survey reading sources... [ 22%] emodpy_malaria.interventions.drug reading sources... [ 24%] emodpy_malaria.interventions.drug_campaign reading sources... [ 26%] emodpy_malaria.interventions.inputeir reading sources... [ 28%] emodpy_malaria.interventions.irs reading sources... [ 31%] emodpy_malaria.interventions.ivermectin reading sources... [ 33%] emodpy_malaria.interventions.larvicide reading sources... [ 35%] emodpy_malaria.interventions.malaria_challenge reading sources... [ 37%] emodpy_malaria.interventions.mosquitorelease reading sources... [ 40%] emodpy_malaria.interventions.outbreak reading sources... [ 42%] emodpy_malaria.interventions.outdoorrestkill reading sources... [ 44%] emodpy_malaria.interventions.scale_larval_habitats reading sources... [ 46%] emodpy_malaria.interventions.spacespraying reading sources... [ 48%] emodpy_malaria.interventions.sugartrap reading sources... [ 51%] emodpy_malaria.interventions.treatment_seeking reading sources... [ 53%] emodpy_malaria.interventions.usage_dependent_bednet reading sources... [ 55%] emodpy_malaria.interventions.vaccine reading sources... [ 57%] emodpy_malaria.malaria_config reading sources... [ 60%] emodpy_malaria.malaria_vector_species_params reading sources... [ 62%] emodpy_malaria.reporters reading sources... [ 64%] emodpy_malaria.reporters.builtin /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.7.8/configuration.html for details on how to configure idmtools. reading sources... [ 66%] emodpy_malaria.vector_config reading sources... [ 68%] emodpy_malaria.vector_migration reading sources... [ 71%] emodpy_malaria.vector_migration.vector_migration reading sources... [ 73%] emodpy_malaria.weather reading sources... [ 75%] emodpy_malaria.weather.data_sources reading sources... [ 77%] emodpy_malaria.weather.weather_data reading sources... [ 80%] emodpy_malaria.weather.weather_metadata reading sources... [ 82%] emodpy_malaria.weather.weather_request reading sources... [ 84%] emodpy_malaria.weather.weather_set reading sources... [ 86%] emodpy_malaria.weather.weather_utils reading sources... [ 88%] emodpy_malaria.weather.weather_variable reading sources... [ 91%] faq reading sources... [ 93%] index reading sources... [ 95%] installation reading sources... [ 97%] installation-basic reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation installation-basic modules emodpy_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.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.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.reporters emodpy_malaria.reporters.builtin emodpy_malaria.vector_migration emodpy_malaria.vector_migration.vector_migration 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.vector_config faq done writing... done writing additional files... opensearchdone copying static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-08-07T17:32:18.089323Z, end-time: 2023-08-07T17:32:30.684602Z, duration: 12, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), 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') building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 45 added, 0 changed, 0 removed reading sources... [ 2%] emodpy_malaria reading sources... [ 4%] emodpy_malaria.demographics reading sources... [ 6%] emodpy_malaria.demographics.MalariaDemographics reading sources... [ 8%] emodpy_malaria.interventions reading sources... [ 11%] emodpy_malaria.interventions.adherentdrug reading sources... [ 13%] emodpy_malaria.interventions.bednet reading sources... [ 15%] emodpy_malaria.interventions.common reading sources... [ 17%] emodpy_malaria.interventions.community_health_worker reading sources... [ 20%] emodpy_malaria.interventions.diag_survey reading sources... [ 22%] emodpy_malaria.interventions.drug reading sources... [ 24%] emodpy_malaria.interventions.drug_campaign reading sources... [ 26%] emodpy_malaria.interventions.inputeir reading sources... [ 28%] emodpy_malaria.interventions.irs reading sources... [ 31%] emodpy_malaria.interventions.ivermectin reading sources... [ 33%] emodpy_malaria.interventions.larvicide reading sources... [ 35%] emodpy_malaria.interventions.malaria_challenge reading sources... [ 37%] emodpy_malaria.interventions.mosquitorelease reading sources... [ 40%] emodpy_malaria.interventions.outbreak reading sources... [ 42%] emodpy_malaria.interventions.outdoorrestkill reading sources... [ 44%] emodpy_malaria.interventions.scale_larval_habitats reading sources... [ 46%] emodpy_malaria.interventions.spacespraying reading sources... [ 48%] emodpy_malaria.interventions.sugartrap reading sources... [ 51%] emodpy_malaria.interventions.treatment_seeking reading sources... [ 53%] emodpy_malaria.interventions.usage_dependent_bednet reading sources... [ 55%] emodpy_malaria.interventions.vaccine reading sources... [ 57%] emodpy_malaria.malaria_config reading sources... [ 60%] emodpy_malaria.malaria_vector_species_params reading sources... [ 62%] emodpy_malaria.reporters reading sources... [ 64%] emodpy_malaria.reporters.builtin /!\ WARNING: File 'idmtools.ini' Not Found! For details on how to configure idmtools, see https://docs.idmod.org/projects/idmtools/en/v1.7.8/configuration.html for details on how to configure idmtools. reading sources... [ 66%] emodpy_malaria.vector_config reading sources... [ 68%] emodpy_malaria.vector_migration reading sources... [ 71%] emodpy_malaria.vector_migration.vector_migration reading sources... [ 73%] emodpy_malaria.weather reading sources... [ 75%] emodpy_malaria.weather.data_sources reading sources... [ 77%] emodpy_malaria.weather.weather_data reading sources... [ 80%] emodpy_malaria.weather.weather_metadata reading sources... [ 82%] emodpy_malaria.weather.weather_request reading sources... [ 84%] emodpy_malaria.weather.weather_set reading sources... [ 86%] emodpy_malaria.weather.weather_utils reading sources... [ 88%] emodpy_malaria.weather.weather_variable reading sources... [ 91%] faq reading sources... [ 93%] index reading sources... [ 95%] installation reading sources... [ 97%] installation-basic reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done processing emodpy-malaria-docs.tex... index installation installation-basic 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.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.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.reporters emodpy_malaria.reporters.builtin emodpy_malaria.vector_migration emodpy_malaria.vector_migration.vector_migration 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.vector_config faq resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-malaria/checkouts/latest/_readthedocs/pdf/_static/searchtools.js [rtd-command-info] start-time: 2023-08-07T17:32:30.967588Z, end-time: 2023-08-07T17:32:31.056093Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); }