Read the Docs build information Build id: 621978 Project: institute-for-disease-modeling-idmtools-calibra Version: latest Commit: ca39949d461d75ba6a9ced3e5a6c869bb9504bee Date: 2021-04-28T17:16:26.861370Z State: finished Success: True [rtd-command-info] start-time: 2021-04-28T17:16:28.320920Z, end-time: 2021-04-28T17:16:30.981254Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/idmtools_calibra.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-04-28T17:16:31.110844Z, end-time: 2021-04-28T17:16:31.296037Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. 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 performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at ca39949 Merge pull request #99 from ZDu-IDM/calibra_update [rtd-command-info] start-time: 2021-04-28T17:16:31.450369Z, end-time: 2021-04-28T17:16:31.530895Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-04-28T17:16:32.527662Z, end-time: 2021-04-28T17:16:36.987150Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-04-28T17:16:37.097436Z, end-time: 2021-04-28T17:16:38.509005Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools 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-idmtools-calibra/envs/latest/lib/python3.7/site-packages (21.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (56.0.0) [rtd-command-info] start-time: 2021-04-28T17:16:38.621865Z, end-time: 2021-04-28T17:16:47.608980Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting Pygments>=2.0 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directory: /tmp/pip-ephem-wheel-cache-u_25xb5t/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=44c5a5b9c1da530fab511e6b9a05e03c293783c228643f31d93221dd335c92d6 Stored in directory: /tmp/pip-ephem-wheel-cache-u_25xb5t/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4 [rtd-command-info] start-time: 2021-04-28T17:16:47.720959Z, end-time: 2021-04-28T17:17:19.878554Z, duration: 32, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple Collecting fasteners~=0.15 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/78/20/c862d765287e9e8b29f826749ebae8775bdca50b2cb2ca079346d5fbfd76/fasteners-0.16-py2.py3-none-any.whl (28 kB) Collecting geopy~=2.0.0 Downloading 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filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=b19aa6fca5bb5838872df451dfdd37d2e006f908232d6ab57041c537e1859963 Stored in directory: /tmp/pip-ephem-wheel-cache-t5mpasfl/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c Successfully built sklearn docopt Installing collected packages: zipp, typing-extensions, pycparser, numpy, yarg, threadpoolctl, scipy, python-dateutil, pillow, kiwisolver, joblib, importlib-metadata, humanfriendly, docopt, cycler, cffi, cached-property, tqdm, tabulate, scikit-learn, PyYaml, pygit2, pluggy, pipreqs, patsy, pandas, more-itertools, matplotlib, geographiclib, diskcache, coloredlogs, backoff, statsmodels, sklearn, seaborn, idmtools, geopy, fasteners Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed PyYaml-5.4.1 backoff-1.10.0 cached-property-1.5.2 cffi-1.14.5 coloredlogs-15.0 cycler-0.10.0 diskcache-5.1.0 docopt-0.6.2 fasteners-0.16 geographiclib-1.50 geopy-2.0.0 humanfriendly-9.1 idmtools-1.6.3 importlib-metadata-4.0.1 joblib-1.0.1 kiwisolver-1.3.1 matplotlib-3.4.1 more-itertools-8.7.0 numpy-1.20.2 pandas-1.1.5 patsy-0.5.1 pillow-8.2.0 pipreqs-0.4.10 pluggy-0.13.1 pycparser-2.20 pygit2-1.5.0 python-dateutil-2.8.1 scikit-learn-0.24.2 scipy-1.5.4 seaborn-0.11.1 sklearn-0.0 statsmodels-0.12.2 tabulate-0.8.9 threadpoolctl-2.1.0 tqdm-4.60.0 typing-extensions-3.7.4.3 yarg-0.1.9 zipp-3.4.1 [rtd-command-info] start-time: 2021-04-28T17:17:19.985302Z, end-time: 2021-04-28T17:17:25.977518Z, duration: 5, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r dev_requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/artifactory/api/pypi/idm-pypi-production/simple Collecting allure-pytest~=2.8.19 Downloading allure_pytest-2.8.40-py3-none-any.whl (9.6 kB) Collecting junitparser~=1.6.2 Downloading junitparser-1.6.3-py2.py3-none-any.whl (10 kB) Collecting livereload~=2.6.3 Downloading livereload-2.6.3.tar.gz (25 kB) Collecting pytest-cache~=1.0 Downloading pytest-cache-1.0.tar.gz (16 kB) Collecting pytest-cov~=2.10.1 Downloading pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB) Collecting pytest-html~=2.1.1 Downloading pytest_html-2.1.1-py2.py3-none-any.whl (16 kB) Collecting pytest-runner~=5.2 Downloading pytest_runner-5.3.0-py3-none-any.whl (7.1 kB) Collecting pytest-timeout~=1.4.2 Downloading pytest_timeout-1.4.2-py2.py3-none-any.whl (10 kB) Collecting pytest-xdist~=2.1 Downloading pytest_xdist-2.2.1-py3-none-any.whl (37 kB) Collecting pytest~=6.1.2 Downloading pytest-6.1.2-py3-none-any.whl (272 kB) Collecting xmlrunner~=1.7.7 Downloading xmlrunner-1.7.7.tar.gz (5.6 kB) Requirement already satisfied: six>=1.9.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from allure-pytest~=2.8.19->-r dev_requirements.txt (line 1)) (1.15.0) Collecting allure-python-commons==2.8.40 Downloading allure_python_commons-2.8.40-py3-none-any.whl (15 kB) Requirement already satisfied: pluggy>=0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from allure-python-commons==2.8.40->allure-pytest~=2.8.19->-r dev_requirements.txt (line 1)) (0.13.1) Collecting attrs>=16.0.0 Downloading attrs-20.3.0-py2.py3-none-any.whl (49 kB) Requirement already satisfied: future in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from junitparser~=1.6.2->-r dev_requirements.txt (line 2)) (0.18.2) Collecting tornado Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting execnet>=1.1.dev1 Downloading execnet-1.8.0-py2.py3-none-any.whl (39 kB) Collecting coverage>=4.4 Downloading coverage-5.5-cp37-cp37m-manylinux2010_x86_64.whl (242 kB) Collecting pytest-metadata Downloading pytest_metadata-1.11.0-py2.py3-none-any.whl (10 kB) Collecting pytest-forked Downloading pytest_forked-1.3.0-py2.py3-none-any.whl (4.7 kB) Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Requirement already satisfied: importlib-metadata>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from pytest~=6.1.2->-r dev_requirements.txt (line 10)) (4.0.1) Collecting py>=1.8.2 Downloading py-1.10.0-py2.py3-none-any.whl (97 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from pytest~=6.1.2->-r dev_requirements.txt (line 10)) (20.9) Collecting apipkg>=1.4 Downloading apipkg-1.5-py2.py3-none-any.whl (4.9 kB) Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=0.12->pytest~=6.1.2->-r dev_requirements.txt (line 10)) (3.7.4.3) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=0.12->pytest~=6.1.2->-r dev_requirements.txt (line 10)) (3.4.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from packaging->pytest~=6.1.2->-r dev_requirements.txt (line 10)) (2.4.7) Building wheels for collected packages: livereload, pytest-cache, xmlrunner Building wheel for livereload (setup.py): started Building wheel for livereload (setup.py): finished with status 'done' Created wheel for livereload: filename=livereload-2.6.3-py2.py3-none-any.whl size=24713 sha256=5a150680e1bf83d61098581dd6b0bbcad7f7be67d66ca10c196ec7bff0854395 Stored in directory: /tmp/pip-ephem-wheel-cache-6yjbo3r6/wheels/d4/f2/03/55f37093eb8cb0c89d7efb206f792dba55cd5bd67b1c5b1ce1 Building wheel for pytest-cache (setup.py): started Building wheel for pytest-cache (setup.py): finished with status 'done' Created wheel for pytest-cache: filename=pytest_cache-1.0-py3-none-any.whl size=6933 sha256=7c8ed74d6006c3656a945a8f0cbe16c27789437b4e2ccd84a550d50cf41f1efc Stored in directory: /tmp/pip-ephem-wheel-cache-6yjbo3r6/wheels/76/fb/36/4304dce3f49d3aecf92d63f079db516641a8061a83a0b5a292 Building wheel for xmlrunner (setup.py): started Building wheel for xmlrunner (setup.py): finished with status 'done' Created wheel for xmlrunner: filename=xmlrunner-1.7.7-py3-none-any.whl size=6235 sha256=36e9e515270b5c5966ed6842af1d213eecc794d2c1deaaa6d4c267098c8c8046 Stored in directory: /tmp/pip-ephem-wheel-cache-6yjbo3r6/wheels/bb/ae/64/7394a8365bd8e7bf4c49b01d80c0260d1c1ec975183ac1ce37 Successfully built livereload pytest-cache xmlrunner Installing collected packages: toml, py, iniconfig, attrs, pytest, apipkg, tornado, pytest-metadata, pytest-forked, execnet, coverage, allure-python-commons, xmlrunner, pytest-xdist, pytest-timeout, pytest-runner, pytest-html, pytest-cov, pytest-cache, livereload, junitparser, allure-pytest Successfully installed allure-pytest-2.8.40 allure-python-commons-2.8.40 apipkg-1.5 attrs-20.3.0 coverage-5.5 execnet-1.8.0 iniconfig-1.1.1 junitparser-1.6.3 livereload-2.6.3 py-1.10.0 pytest-6.1.2 pytest-cache-1.0 pytest-cov-2.10.1 pytest-forked-1.3.0 pytest-html-2.1.1 pytest-metadata-1.11.0 pytest-runner-5.3.0 pytest-timeout-1.4.2 pytest-xdist-2.2.1 toml-0.10.2 tornado-6.1 xmlrunner-1.7.7 [rtd-command-info] start-time: 2021-04-28T17:17:26.084785Z, end-time: 2021-04-28T17:17:30.248533Z, duration: 4, 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 sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.0 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting docutils<0.17 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 2)) (1.15.0) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.1.4) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.25.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.11.3) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (56.0.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (20.9) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.9.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.1.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.8.1) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.2.0) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2021.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.1.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.10) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r docs/requirements.txt (line 3)) (2.4.7) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, docutils, sphinx, pockets, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinx-rtd-theme, plantweb 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 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 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 plantweb-1.2.1 pockets-0.9.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxcontrib-qthelp-1.0.3 [rtd-command-info] start-time: 2021-04-28T17:17:30.350279Z, end-time: 2021-04-28T17:17:31.888274Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating idmtools_calibra.egg-info writing idmtools_calibra.egg-info/PKG-INFO writing dependency_links to idmtools_calibra.egg-info/dependency_links.txt writing requirements to idmtools_calibra.egg-info/requires.txt writing top-level names to idmtools_calibra.egg-info/top_level.txt writing manifest file 'idmtools_calibra.egg-info/SOURCES.txt' reading manifest file 'idmtools_calibra.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'tests' writing manifest file 'idmtools_calibra.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/idmtools_emodpy_malaria copying idmtools_emodpy_malaria/__init__.py -> build/lib/idmtools_emodpy_malaria creating build/lib/malaria copying malaria/symptoms.py -> build/lib/malaria copying malaria/immunity.py -> build/lib/malaria copying malaria/infection.py -> build/lib/malaria copying malaria/params.py -> build/lib/malaria copying malaria/__init__.py -> build/lib/malaria creating build/lib/examples copying examples/helper.py -> build/lib/examples copying examples/__init__.py -> build/lib/examples creating build/lib/idmtools_calibra copying idmtools_calibra/prior.py -> build/lib/idmtools_calibra copying idmtools_calibra/calib_manager.py -> build/lib/idmtools_calibra copying idmtools_calibra/utils.py -> build/lib/idmtools_calibra copying idmtools_calibra/iteration_state.py -> build/lib/idmtools_calibra copying idmtools_calibra/resample_manager.py -> build/lib/idmtools_calibra copying idmtools_calibra/ll_calculators.py -> build/lib/idmtools_calibra copying idmtools_calibra/calib_site.py -> build/lib/idmtools_calibra copying idmtools_calibra/__init__.py -> build/lib/idmtools_calibra copying idmtools_calibra/parameter_set.py -> build/lib/idmtools_calibra creating build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/prevalence_by_round_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/base_summary_calibration_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/channel_by_season_cohort_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/helpers.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/channel_by_season_spatial_cohort_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/channel_by_season_age_density_cohort_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/positive_fraction_by_distance_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/channel_by_age_cohort_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/channel_by_season_analyzer.py -> build/lib/idmtools_emodpy_malaria/analyzers copying idmtools_emodpy_malaria/analyzers/__init__.py -> build/lib/idmtools_emodpy_malaria/analyzers creating build/lib/idmtools_emodpy_malaria/emod_220 copying idmtools_emodpy_malaria/emod_220/__init__.py -> build/lib/idmtools_emodpy_malaria/emod_220 creating build/lib/idmtools_emodpy_malaria/emod_le_218 copying idmtools_emodpy_malaria/emod_le_218/__init__.py -> build/lib/idmtools_emodpy_malaria/emod_le_218 creating build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DapelogoCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MoinespatialCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeSeasonCalibSiteBabies.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/NdiopCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/AjuraEntoCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/IncidenceCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DapelogoInfCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MagudeMultiYearEntoCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DapelogoInfectiousnessCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MatsariCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/TororoEntoCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DielmoCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/NamawalaCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeDateSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeSeasonCalibSiteBabies.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DapelogoAgeDateSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DapelogoSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/entomology_calib_site.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/GarkiSites.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MagudeEntoCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeSeasonCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeSeasonCalibSiteBabies.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/GarkiEntoCalibSites.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeDateSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/entomology_spatial_calib_site.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/HouseholdCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/LayeAgeDateSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/LayeSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/LayeCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/site_setup_functions.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MapatizyaCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/DensityCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeDateSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/PrevalenceCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeSeasonCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeSeasonCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/SugungumCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/LayeInfectiousnessCalibSite.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites copying idmtools_emodpy_malaria/emod_220/study_sites/__init__.py -> build/lib/idmtools_emodpy_malaria/emod_220/study_sites creating build/lib/idmtools_emodpy_malaria/emod_220/reports copying idmtools_emodpy_malaria/emod_220/reports/malaria_report.py -> build/lib/idmtools_emodpy_malaria/emod_220/reports copying idmtools_emodpy_malaria/emod_220/reports/__init__.py -> build/lib/idmtools_emodpy_malaria/emod_220/reports creating build/lib/malaria/analyzers copying malaria/analyzers/prevalence_by_round_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/base_summary_calibration_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/channel_by_season_cohort_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/helpers.py -> build/lib/malaria/analyzers copying malaria/analyzers/channel_by_season_spatial_cohort_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/channel_by_season_age_density_cohort_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/positive_fraction_by_distance_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/channel_by_age_cohort_analyzer.py -> build/lib/malaria/analyzers copying malaria/analyzers/__init__.py -> build/lib/malaria/analyzers creating build/lib/malaria/site copying malaria/site/input_eir_by_site.py -> build/lib/malaria/site copying malaria/site/__init__.py -> build/lib/malaria/site creating build/lib/malaria/interventions copying malaria/interventions/malaria_drugs.py -> build/lib/malaria/interventions copying malaria/interventions/adherent_drug.py -> build/lib/malaria/interventions copying malaria/interventions/health_seeking.py -> build/lib/malaria/interventions copying malaria/interventions/irs.py -> build/lib/malaria/interventions copying malaria/interventions/malaria_diagnostic.py -> build/lib/malaria/interventions copying malaria/interventions/animal_feed_kill.py -> build/lib/malaria/interventions copying malaria/interventions/malaria_vaccine.py -> build/lib/malaria/interventions copying malaria/interventions/malaria_drug_campaigns.py -> build/lib/malaria/interventions copying malaria/interventions/malaria_challenge.py -> build/lib/malaria/interventions copying malaria/interventions/__init__.py -> build/lib/malaria/interventions creating build/lib/malaria/study_sites copying malaria/study_sites/sugungum_age_season_calib_site_babies.py -> build/lib/malaria/study_sites copying malaria/study_sites/dapelogo_age_date_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/namawala_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/rafin_marke_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/dapelogo_infectiousness_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/rafin_marke_age_season_calib_site_babies.py -> build/lib/malaria/study_sites copying malaria/study_sites/magude_ento_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/prevalence_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/dapelogo_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/sugungum_age_date_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/household_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/mapatizya_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/ajura_ento_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/matsari_age_date_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/magude_multi_year_ento_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/laye_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/ndiop_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/sugungum_age_season_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/moinespatial_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/matsari_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/matsari_age_season_calib_site_babies.py -> build/lib/malaria/study_sites copying malaria/study_sites/dapelogo_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/garki_sites.py -> build/lib/malaria/study_sites copying malaria/study_sites/matsari_age_season_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/incidence_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/density_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/laye_age_date_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/garki_ento_calib_sites.py -> build/lib/malaria/study_sites copying malaria/study_sites/dielmo_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/site_setup_functions.py -> build/lib/malaria/study_sites copying malaria/study_sites/sugungum_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/rafin_marke_age_date_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/dapelogo_inf_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/rafin_marke_age_season_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/laye_infectiousness_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/tororo_ento_calib_site.py -> build/lib/malaria/study_sites copying malaria/study_sites/__init__.py -> build/lib/malaria/study_sites copying malaria/study_sites/laye_site.py -> build/lib/malaria/study_sites creating build/lib/malaria/reports copying malaria/reports/malaria_report.py -> build/lib/malaria/reports copying malaria/reports/__init__.py -> build/lib/malaria/reports creating build/lib/examples/inputs copying examples/inputs/__init__.py -> build/lib/examples/inputs creating build/lib/examples/inputs/bamboo copying examples/inputs/bamboo/__init__.py -> build/lib/examples/inputs/bamboo creating build/lib/examples/inputs/demographics copying examples/inputs/demographics/__init__.py -> build/lib/examples/inputs/demographics creating build/lib/examples/inputs/assets copying examples/inputs/assets/__init__.py -> build/lib/examples/inputs/assets creating build/lib/examples/inputs/bamboo/reporter_plugins copying examples/inputs/bamboo/reporter_plugins/__init__.py -> build/lib/examples/inputs/bamboo/reporter_plugins creating build/lib/idmtools_calibra/analyzers copying idmtools_calibra/analyzers/malaria_summary.py -> build/lib/idmtools_calibra/analyzers copying idmtools_calibra/analyzers/base_calibration_analyzer.py -> build/lib/idmtools_calibra/analyzers copying idmtools_calibra/analyzers/helpers.py -> build/lib/idmtools_calibra/analyzers copying idmtools_calibra/analyzers/__init__.py -> build/lib/idmtools_calibra/analyzers creating build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/emod_malaria_sim.py -> build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/helper.py -> build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/encoding.py -> build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/distro.py -> build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/mod_fn.py -> build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/display.py -> build/lib/idmtools_calibra/utilities copying idmtools_calibra/utilities/__init__.py -> build/lib/idmtools_calibra/utilities creating build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/sirs_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/sir_vaccinations_a_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/irs.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/itn.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/property_change.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/novel_vector_control.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/incidence_counter.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/dengue_bednets_irs_vaccines.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/habitat_scale.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/mosquito_release.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/sir_vaccinations_c_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/sir_vaccinations_b_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/outbreakindividualdengue.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/sir_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/migrate_to.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/sis_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/seir_vitaldynamics.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/heg.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/si_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/empty_campaign.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/seir_initial_seeding.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/support_scripts.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/outbreakindividual.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/seirs.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/biting_risk.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/ivermectin.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/itn_age_season.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/__init__.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/triggered_campaign_delay_event.py -> build/lib/idmtools_calibra/interventions copying idmtools_calibra/interventions/input_EIR.py -> build/lib/idmtools_calibra/interventions creating build/lib/idmtools_calibra/resamplers copying idmtools_calibra/resamplers/random_perturbation_resampler.py -> build/lib/idmtools_calibra/resamplers copying idmtools_calibra/resamplers/base_resampler.py -> build/lib/idmtools_calibra/resamplers copying idmtools_calibra/resamplers/calibration_point.py -> build/lib/idmtools_calibra/resamplers copying idmtools_calibra/resamplers/calibration_points.py -> build/lib/idmtools_calibra/resamplers copying idmtools_calibra/resamplers/cramer_rao_resampler.py -> build/lib/idmtools_calibra/resamplers copying idmtools_calibra/resamplers/__init__.py -> build/lib/idmtools_calibra/resamplers creating build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/optim_tool_spsa_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/optim_tool_pbnb_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/base_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/separatrix_bhm_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/optim_tool_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/site_data_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/likelihood_plotter.py -> build/lib/idmtools_calibra/plotters copying idmtools_calibra/plotters/__init__.py -> build/lib/idmtools_calibra/plotters creating build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/generic_iterative_next_point.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/gpc.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/separatrix_bhm.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/next_point_algorithm.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/imis.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/optim_tool.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/optim_tools_pspo.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/optim_tools_spsa.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/fisher_inf_matrix.py -> build/lib/idmtools_calibra/algorithms copying idmtools_calibra/algorithms/__init__.py -> build/lib/idmtools_calibra/algorithms creating build/lib/idmtools_calibra/output copying idmtools_calibra/output/spatial_output.py -> build/lib/idmtools_calibra/output copying idmtools_calibra/output/output_parser.py -> build/lib/idmtools_calibra/output copying idmtools_calibra/output/__init__.py -> build/lib/idmtools_calibra/output creating build/lib/idmtools_calibra/utilities/vector copying idmtools_calibra/utilities/vector/larval_habitat.py -> build/lib/idmtools_calibra/utilities/vector copying idmtools_calibra/utilities/vector/study_sites.py -> build/lib/idmtools_calibra/utilities/vector copying idmtools_calibra/utilities/vector/params.py -> build/lib/idmtools_calibra/utilities/vector copying idmtools_calibra/utilities/vector/__init__.py -> build/lib/idmtools_calibra/utilities/vector copying idmtools_calibra/utilities/vector/species.py -> build/lib/idmtools_calibra/utilities/vector creating build/lib/idmtools_calibra/utilities/demographics copying idmtools_calibra/utilities/demographics/node.py -> build/lib/idmtools_calibra/utilities/demographics copying idmtools_calibra/utilities/demographics/__init__.py -> build/lib/idmtools_calibra/utilities/demographics creating build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/geography.py -> build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/demographics.py -> build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/disease.py -> build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/climate.py -> build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/migration.py -> build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/params.py -> build/lib/idmtools_calibra/utilities/generic copying idmtools_calibra/utilities/generic/__init__.py -> build/lib/idmtools_calibra/utilities/generic creating build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/malaria_summary.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/np2pd.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/np2json.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/JSON.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/pd2csv.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/bin2np.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/dict2pd.py -> build/lib/idmtools_calibra/utilities/parsers copying idmtools_calibra/utilities/parsers/__init__.py -> build/lib/idmtools_calibra/utilities/parsers creating build/lib/idmtools_calibra/utilities/reports copying idmtools_calibra/utilities/reports/custom_report.py -> build/lib/idmtools_calibra/utilities/reports copying idmtools_calibra/utilities/reports/vector_report.py -> build/lib/idmtools_calibra/utilities/reports copying idmtools_calibra/utilities/reports/base_age_hist_report.py -> build/lib/idmtools_calibra/utilities/reports copying idmtools_calibra/utilities/reports/__init__.py -> build/lib/idmtools_calibra/utilities/reports creating build/lib/idmtools_calibra/algorithms/pbnb copying idmtools_calibra/algorithms/pbnb/c_sub_region.py -> build/lib/idmtools_calibra/algorithms/pbnb copying idmtools_calibra/algorithms/pbnb/fun_pbnb_support_functions.py -> build/lib/idmtools_calibra/algorithms/pbnb copying idmtools_calibra/algorithms/pbnb/m_intial_paramters_setting.py -> build/lib/idmtools_calibra/algorithms/pbnb copying idmtools_calibra/algorithms/pbnb/optim_tool_pbnb.py -> build/lib/idmtools_calibra/algorithms/pbnb copying idmtools_calibra/algorithms/pbnb/__init__.py -> build/lib/idmtools_calibra/algorithms/pbnb creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria creating build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/prevalence_by_round_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/base_summary_calibration_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/channel_by_season_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/helpers.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/channel_by_season_spatial_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/channel_by_season_age_density_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/positive_fraction_by_distance_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/channel_by_age_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/channel_by_season_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers copying build/lib/idmtools_emodpy_malaria/analyzers/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers creating build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220 creating build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MoinespatialCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeSeasonCalibSiteBabies.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/NdiopCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/AjuraEntoCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/IncidenceCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoInfCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MagudeMultiYearEntoCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoInfectiousnessCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MatsariCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/TororoEntoCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DielmoCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/NamawalaCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeDateSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeSeasonCalibSiteBabies.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoAgeDateSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/entomology_calib_site.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/GarkiSites.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MagudeEntoCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeSeasonCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeSeasonCalibSiteBabies.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/GarkiEntoCalibSites.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeDateSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/entomology_spatial_calib_site.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/HouseholdCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/LayeAgeDateSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/LayeSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/LayeCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/site_setup_functions.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MapatizyaCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/DensityCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeDateSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/PrevalenceCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeSeasonCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeSeasonCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/SugungumCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/LayeInfectiousnessCalibSite.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/study_sites/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites copying build/lib/idmtools_emodpy_malaria/emod_220/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220 creating build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/reports copying build/lib/idmtools_emodpy_malaria/emod_220/reports/malaria_report.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/reports copying build/lib/idmtools_emodpy_malaria/emod_220/reports/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/reports creating build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_le_218 copying build/lib/idmtools_emodpy_malaria/emod_le_218/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_le_218 copying build/lib/idmtools_emodpy_malaria/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria creating build/bdist.linux-x86_64/egg/malaria creating build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/prevalence_by_round_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/base_summary_calibration_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/channel_by_season_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/helpers.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/channel_by_season_spatial_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/channel_by_season_age_density_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/positive_fraction_by_distance_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/channel_by_age_cohort_analyzer.py -> build/bdist.linux-x86_64/egg/malaria/analyzers copying build/lib/malaria/analyzers/__init__.py -> build/bdist.linux-x86_64/egg/malaria/analyzers creating build/bdist.linux-x86_64/egg/malaria/site copying build/lib/malaria/site/input_eir_by_site.py -> build/bdist.linux-x86_64/egg/malaria/site copying build/lib/malaria/site/__init__.py -> build/bdist.linux-x86_64/egg/malaria/site copying build/lib/malaria/symptoms.py -> build/bdist.linux-x86_64/egg/malaria copying build/lib/malaria/immunity.py -> build/bdist.linux-x86_64/egg/malaria creating build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/malaria_drugs.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/adherent_drug.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/health_seeking.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/irs.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/malaria_diagnostic.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/animal_feed_kill.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/malaria_vaccine.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/malaria_drug_campaigns.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/malaria_challenge.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/interventions/__init__.py -> build/bdist.linux-x86_64/egg/malaria/interventions copying build/lib/malaria/infection.py -> build/bdist.linux-x86_64/egg/malaria copying build/lib/malaria/params.py -> build/bdist.linux-x86_64/egg/malaria creating build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/sugungum_age_season_calib_site_babies.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/dapelogo_age_date_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/namawala_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/rafin_marke_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/dapelogo_infectiousness_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/rafin_marke_age_season_calib_site_babies.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/magude_ento_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/prevalence_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/dapelogo_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/sugungum_age_date_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/household_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/mapatizya_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/ajura_ento_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/matsari_age_date_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/magude_multi_year_ento_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/laye_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/ndiop_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/sugungum_age_season_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/moinespatial_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/matsari_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/matsari_age_season_calib_site_babies.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/dapelogo_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/garki_sites.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/matsari_age_season_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/incidence_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/density_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/laye_age_date_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/garki_ento_calib_sites.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/dielmo_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/site_setup_functions.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/sugungum_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/rafin_marke_age_date_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/dapelogo_inf_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/rafin_marke_age_season_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/laye_infectiousness_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/tororo_ento_calib_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/__init__.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/study_sites/laye_site.py -> build/bdist.linux-x86_64/egg/malaria/study_sites copying build/lib/malaria/__init__.py -> build/bdist.linux-x86_64/egg/malaria creating build/bdist.linux-x86_64/egg/malaria/reports copying build/lib/malaria/reports/malaria_report.py -> build/bdist.linux-x86_64/egg/malaria/reports copying build/lib/malaria/reports/__init__.py -> build/bdist.linux-x86_64/egg/malaria/reports creating build/bdist.linux-x86_64/egg/examples copying build/lib/examples/helper.py -> build/bdist.linux-x86_64/egg/examples creating build/bdist.linux-x86_64/egg/examples/inputs creating build/bdist.linux-x86_64/egg/examples/inputs/bamboo creating build/bdist.linux-x86_64/egg/examples/inputs/bamboo/reporter_plugins copying build/lib/examples/inputs/bamboo/reporter_plugins/__init__.py -> build/bdist.linux-x86_64/egg/examples/inputs/bamboo/reporter_plugins copying build/lib/examples/inputs/bamboo/__init__.py -> build/bdist.linux-x86_64/egg/examples/inputs/bamboo creating build/bdist.linux-x86_64/egg/examples/inputs/demographics copying build/lib/examples/inputs/demographics/__init__.py -> build/bdist.linux-x86_64/egg/examples/inputs/demographics creating build/bdist.linux-x86_64/egg/examples/inputs/assets copying build/lib/examples/inputs/assets/__init__.py -> build/bdist.linux-x86_64/egg/examples/inputs/assets copying build/lib/examples/inputs/__init__.py -> build/bdist.linux-x86_64/egg/examples/inputs copying build/lib/examples/__init__.py -> build/bdist.linux-x86_64/egg/examples creating build/bdist.linux-x86_64/egg/idmtools_calibra creating build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers copying build/lib/idmtools_calibra/analyzers/malaria_summary.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers copying build/lib/idmtools_calibra/analyzers/base_calibration_analyzer.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers copying build/lib/idmtools_calibra/analyzers/helpers.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers copying build/lib/idmtools_calibra/analyzers/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers creating build/bdist.linux-x86_64/egg/idmtools_calibra/utilities copying build/lib/idmtools_calibra/utilities/emod_malaria_sim.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities creating build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector copying build/lib/idmtools_calibra/utilities/vector/larval_habitat.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector copying build/lib/idmtools_calibra/utilities/vector/study_sites.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector copying build/lib/idmtools_calibra/utilities/vector/params.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector copying build/lib/idmtools_calibra/utilities/vector/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector copying build/lib/idmtools_calibra/utilities/vector/species.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector creating build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/demographics copying build/lib/idmtools_calibra/utilities/demographics/node.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/demographics copying build/lib/idmtools_calibra/utilities/demographics/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/demographics creating build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/geography.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/demographics.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/disease.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/climate.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/migration.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/params.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/generic/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic copying build/lib/idmtools_calibra/utilities/helper.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities copying build/lib/idmtools_calibra/utilities/encoding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities creating build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/malaria_summary.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/np2pd.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/np2json.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/JSON.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/pd2csv.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/bin2np.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/dict2pd.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/parsers/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers copying build/lib/idmtools_calibra/utilities/distro.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities copying build/lib/idmtools_calibra/utilities/mod_fn.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities copying build/lib/idmtools_calibra/utilities/display.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities copying build/lib/idmtools_calibra/utilities/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities creating build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports copying build/lib/idmtools_calibra/utilities/reports/custom_report.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports copying build/lib/idmtools_calibra/utilities/reports/vector_report.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports copying build/lib/idmtools_calibra/utilities/reports/base_age_hist_report.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports copying build/lib/idmtools_calibra/utilities/reports/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports copying build/lib/idmtools_calibra/prior.py -> build/bdist.linux-x86_64/egg/idmtools_calibra copying build/lib/idmtools_calibra/calib_manager.py -> build/bdist.linux-x86_64/egg/idmtools_calibra copying build/lib/idmtools_calibra/utils.py -> build/bdist.linux-x86_64/egg/idmtools_calibra copying build/lib/idmtools_calibra/iteration_state.py -> build/bdist.linux-x86_64/egg/idmtools_calibra creating build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/sirs_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/sir_vaccinations_a_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/irs.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/itn.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/property_change.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/novel_vector_control.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/incidence_counter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/dengue_bednets_irs_vaccines.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/habitat_scale.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/mosquito_release.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/sir_vaccinations_c_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/sir_vaccinations_b_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/outbreakindividualdengue.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/sir_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/migrate_to.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/sis_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/seir_vitaldynamics.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/heg.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/si_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/empty_campaign.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/seir_initial_seeding.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/support_scripts.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/outbreakindividual.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/seirs.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/biting_risk.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/ivermectin.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/itn_age_season.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/triggered_campaign_delay_event.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/interventions/input_EIR.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/interventions copying build/lib/idmtools_calibra/resample_manager.py -> build/bdist.linux-x86_64/egg/idmtools_calibra copying build/lib/idmtools_calibra/ll_calculators.py -> build/bdist.linux-x86_64/egg/idmtools_calibra creating build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers copying build/lib/idmtools_calibra/resamplers/random_perturbation_resampler.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers copying build/lib/idmtools_calibra/resamplers/base_resampler.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers copying build/lib/idmtools_calibra/resamplers/calibration_point.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers copying build/lib/idmtools_calibra/resamplers/calibration_points.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers copying build/lib/idmtools_calibra/resamplers/cramer_rao_resampler.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers copying build/lib/idmtools_calibra/resamplers/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers creating build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/optim_tool_spsa_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/optim_tool_pbnb_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/base_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/separatrix_bhm_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/optim_tool_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/site_data_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/likelihood_plotter.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/plotters/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/plotters copying build/lib/idmtools_calibra/calib_site.py -> build/bdist.linux-x86_64/egg/idmtools_calibra creating build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/generic_iterative_next_point.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/gpc.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/separatrix_bhm.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/next_point_algorithm.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/imis.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms creating build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/pbnb copying build/lib/idmtools_calibra/algorithms/pbnb/c_sub_region.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/pbnb copying build/lib/idmtools_calibra/algorithms/pbnb/fun_pbnb_support_functions.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/pbnb copying build/lib/idmtools_calibra/algorithms/pbnb/m_intial_paramters_setting.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/pbnb copying build/lib/idmtools_calibra/algorithms/pbnb/optim_tool_pbnb.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/pbnb copying build/lib/idmtools_calibra/algorithms/pbnb/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/pbnb copying build/lib/idmtools_calibra/algorithms/optim_tool.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/optim_tools_pspo.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/optim_tools_spsa.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/fisher_inf_matrix.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/algorithms/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms copying build/lib/idmtools_calibra/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra creating build/bdist.linux-x86_64/egg/idmtools_calibra/output copying build/lib/idmtools_calibra/output/spatial_output.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/output copying build/lib/idmtools_calibra/output/output_parser.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/output copying build/lib/idmtools_calibra/output/__init__.py -> build/bdist.linux-x86_64/egg/idmtools_calibra/output copying build/lib/idmtools_calibra/parameter_set.py -> build/bdist.linux-x86_64/egg/idmtools_calibra byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/prevalence_by_round_analyzer.py to prevalence_by_round_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/base_summary_calibration_analyzer.py to base_summary_calibration_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/channel_by_season_cohort_analyzer.py to channel_by_season_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/helpers.py to helpers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/channel_by_season_spatial_cohort_analyzer.py to channel_by_season_spatial_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/channel_by_season_age_density_cohort_analyzer.py to channel_by_season_age_density_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/positive_fraction_by_distance_analyzer.py to positive_fraction_by_distance_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/channel_by_age_cohort_analyzer.py to channel_by_age_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/channel_by_season_analyzer.py to channel_by_season_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/analyzers/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoCalibSite.py to DapelogoCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MoinespatialCalibSite.py to MoinespatialCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeSeasonCalibSiteBabies.py to MatsariAgeSeasonCalibSiteBabies.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/NdiopCalibSite.py to NdiopCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/AjuraEntoCalibSite.py to AjuraEntoCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/IncidenceCalibSite.py to IncidenceCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoInfCalibSite.py to DapelogoInfCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MagudeMultiYearEntoCalibSite.py to MagudeMultiYearEntoCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoInfectiousnessCalibSite.py to DapelogoInfectiousnessCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MatsariCalibSite.py to MatsariCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/TororoEntoCalibSite.py to TororoEntoCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DielmoCalibSite.py to DielmoCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/NamawalaCalibSite.py to NamawalaCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeDateSite.py to SugungumAgeDateSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeSeasonCalibSiteBabies.py to RafinMarkeAgeSeasonCalibSiteBabies.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoAgeDateSite.py to DapelogoAgeDateSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DapelogoSite.py to DapelogoSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/entomology_calib_site.py to entomology_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/GarkiSites.py to GarkiSites.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MagudeEntoCalibSite.py to MagudeEntoCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeSeasonCalibSite.py to MatsariAgeSeasonCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeSeasonCalibSiteBabies.py to SugungumAgeSeasonCalibSiteBabies.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/GarkiEntoCalibSites.py to GarkiEntoCalibSites.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeDateSite.py to RafinMarkeAgeDateSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/entomology_spatial_calib_site.py to entomology_spatial_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/HouseholdCalibSite.py to HouseholdCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/LayeAgeDateSite.py to LayeAgeDateSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/LayeSite.py to LayeSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/LayeCalibSite.py to LayeCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/site_setup_functions.py to site_setup_functions.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MapatizyaCalibSite.py to MapatizyaCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/DensityCalibSite.py to DensityCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/MatsariAgeDateSite.py to MatsariAgeDateSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/PrevalenceCalibSite.py to PrevalenceCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeAgeSeasonCalibSite.py to RafinMarkeAgeSeasonCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/RafinMarkeCalibSite.py to RafinMarkeCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/SugungumAgeSeasonCalibSite.py to SugungumAgeSeasonCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/SugungumCalibSite.py to SugungumCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/LayeInfectiousnessCalibSite.py to LayeInfectiousnessCalibSite.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/study_sites/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/reports/malaria_report.py to malaria_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_220/reports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/emod_le_218/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_emodpy_malaria/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/prevalence_by_round_analyzer.py to prevalence_by_round_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/base_summary_calibration_analyzer.py to base_summary_calibration_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/channel_by_season_cohort_analyzer.py to channel_by_season_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/helpers.py to helpers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/channel_by_season_spatial_cohort_analyzer.py to channel_by_season_spatial_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/channel_by_season_age_density_cohort_analyzer.py to channel_by_season_age_density_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/positive_fraction_by_distance_analyzer.py to positive_fraction_by_distance_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/channel_by_age_cohort_analyzer.py to channel_by_age_cohort_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/analyzers/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/site/input_eir_by_site.py to input_eir_by_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/site/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/symptoms.py to symptoms.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/immunity.py to immunity.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/malaria_drugs.py to malaria_drugs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/adherent_drug.py to adherent_drug.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/health_seeking.py to health_seeking.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/irs.py to irs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/malaria_diagnostic.py to malaria_diagnostic.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/animal_feed_kill.py to animal_feed_kill.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/malaria_vaccine.py to malaria_vaccine.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/malaria_drug_campaigns.py to malaria_drug_campaigns.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/malaria_challenge.py to malaria_challenge.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/infection.py to infection.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/params.py to params.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/sugungum_age_season_calib_site_babies.py to sugungum_age_season_calib_site_babies.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/dapelogo_age_date_site.py to dapelogo_age_date_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/namawala_calib_site.py to namawala_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/rafin_marke_calib_site.py to rafin_marke_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/dapelogo_infectiousness_calib_site.py to dapelogo_infectiousness_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/rafin_marke_age_season_calib_site_babies.py to rafin_marke_age_season_calib_site_babies.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/magude_ento_calib_site.py to magude_ento_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/prevalence_calib_site.py to prevalence_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/dapelogo_calib_site.py to dapelogo_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/sugungum_age_date_site.py to sugungum_age_date_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/household_calib_site.py to household_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/mapatizya_calib_site.py to mapatizya_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/ajura_ento_calib_site.py to ajura_ento_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/matsari_age_date_site.py to matsari_age_date_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/magude_multi_year_ento_calib_site.py to magude_multi_year_ento_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/laye_calib_site.py to laye_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/ndiop_calib_site.py to ndiop_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/sugungum_age_season_calib_site.py to sugungum_age_season_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/moinespatial_calib_site.py to moinespatial_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/matsari_calib_site.py to matsari_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/matsari_age_season_calib_site_babies.py to matsari_age_season_calib_site_babies.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/dapelogo_site.py to dapelogo_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/garki_sites.py to garki_sites.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/matsari_age_season_calib_site.py to matsari_age_season_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/incidence_calib_site.py to incidence_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/density_calib_site.py to density_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/laye_age_date_site.py to laye_age_date_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/garki_ento_calib_sites.py to garki_ento_calib_sites.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/dielmo_calib_site.py to dielmo_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/site_setup_functions.py to site_setup_functions.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/sugungum_calib_site.py to sugungum_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/rafin_marke_age_date_site.py to rafin_marke_age_date_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/dapelogo_inf_calib_site.py to dapelogo_inf_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/rafin_marke_age_season_calib_site.py to rafin_marke_age_season_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/laye_infectiousness_calib_site.py to laye_infectiousness_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/tororo_ento_calib_site.py to tororo_ento_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/study_sites/laye_site.py to laye_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/reports/malaria_report.py to malaria_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/malaria/reports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/helper.py to helper.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/inputs/bamboo/reporter_plugins/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/inputs/bamboo/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/inputs/demographics/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/inputs/assets/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/inputs/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/examples/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers/malaria_summary.py to malaria_summary.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers/base_calibration_analyzer.py to base_calibration_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers/helpers.py to helpers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/analyzers/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/emod_malaria_sim.py to emod_malaria_sim.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector/larval_habitat.py to larval_habitat.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector/study_sites.py to study_sites.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector/params.py to params.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/vector/species.py to species.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/demographics/node.py to node.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/demographics/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/geography.py to geography.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/demographics.py to demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/disease.py to disease.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/climate.py to climate.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/migration.py to migration.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/params.py to params.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/generic/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/helper.py to helper.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/encoding.py to encoding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/malaria_summary.py to malaria_summary.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/np2pd.py to np2pd.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/np2json.py to np2json.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/JSON.py to JSON.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/pd2csv.py to pd2csv.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/bin2np.py to bin2np.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/dict2pd.py to dict2pd.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/parsers/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/distro.py to distro.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/mod_fn.py to mod_fn.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/display.py to display.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports/custom_report.py to custom_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports/vector_report.py to vector_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports/base_age_hist_report.py to base_age_hist_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utilities/reports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/prior.py to prior.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/calib_manager.py to calib_manager.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/utils.py to utils.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/iteration_state.py to iteration_state.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/sirs_initial_seeding.py to sirs_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/sir_vaccinations_a_initial_seeding.py to sir_vaccinations_a_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/irs.py to irs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/itn.py to itn.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/property_change.py to property_change.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/novel_vector_control.py to novel_vector_control.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/incidence_counter.py to incidence_counter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/dengue_bednets_irs_vaccines.py to dengue_bednets_irs_vaccines.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/habitat_scale.py to habitat_scale.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/mosquito_release.py to mosquito_release.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/sir_vaccinations_c_initial_seeding.py to sir_vaccinations_c_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/sir_vaccinations_b_initial_seeding.py to sir_vaccinations_b_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/outbreakindividualdengue.py to outbreakindividualdengue.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/sir_initial_seeding.py to sir_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/migrate_to.py to migrate_to.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/sis_initial_seeding.py to sis_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/seir_vitaldynamics.py to seir_vitaldynamics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/heg.py to heg.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/si_initial_seeding.py to si_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/empty_campaign.py to empty_campaign.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/seir_initial_seeding.py to seir_initial_seeding.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/support_scripts.py to support_scripts.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/outbreakindividual.py to outbreakindividual.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/seirs.py to seirs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/biting_risk.py to biting_risk.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/ivermectin.py to ivermectin.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/itn_age_season.py to itn_age_season.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/triggered_campaign_delay_event.py to triggered_campaign_delay_event.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/interventions/input_EIR.py to input_EIR.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resample_manager.py to resample_manager.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/ll_calculators.py to ll_calculators.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers/random_perturbation_resampler.py to random_perturbation_resampler.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers/base_resampler.py to base_resampler.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers/calibration_point.py to calibration_point.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers/calibration_points.py to calibration_points.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers/cramer_rao_resampler.py to cramer_rao_resampler.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/resamplers/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/optim_tool_spsa_plotter.py to optim_tool_spsa_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/optim_tool_pbnb_plotter.py to optim_tool_pbnb_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/base_plotter.py to base_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/separatrix_bhm_plotter.py to separatrix_bhm_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/optim_tool_plotter.py to optim_tool_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/site_data_plotter.py to site_data_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/likelihood_plotter.py to likelihood_plotter.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/plotters/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/calib_site.py to calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/generic_iterative_next_point.py to generic_iterative_next_point.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/gpc.py to gpc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/separatrix_bhm.py to separatrix_bhm.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/next_point_algorithm.py to next_point_algorithm.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/imis.py to imis.cpython-37.pyc 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build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/optim_tools_spsa.py to optim_tools_spsa.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/fisher_inf_matrix.py to fisher_inf_matrix.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/algorithms/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/output/spatial_output.py to spatial_output.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/output/output_parser.py to output_parser.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/output/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/idmtools_calibra/parameter_set.py to parameter_set.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying idmtools_calibra.egg-info/PKG-INFO -> 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references __file__ malaria.study_sites.__pycache__.tororo_ento_calib_site.cpython-37: module references __file__ creating dist creating 'dist/idmtools_calibra-1.0.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing idmtools_calibra-1.0.0-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages/idmtools_calibra-1.0.0-py3.7.egg Extracting idmtools_calibra-1.0.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Adding idmtools-calibra 1.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages/idmtools_calibra-1.0.0-py3.7.egg Processing dependencies for idmtools-calibra==1.0.0 Searching for statsmodels==0.12.2 Best match: statsmodels 0.12.2 Adding statsmodels 0.12.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for numpy==1.20.2 Best match: numpy 1.20.2 Adding numpy 1.20.2 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for sklearn==0.0 Best match: sklearn 0.0 Adding sklearn 0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for seaborn==0.11.1 Best match: seaborn 0.11.1 Adding seaborn 0.11.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for scipy==1.5.4 Best match: scipy 1.5.4 Adding scipy 1.5.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for idmtools==1.6.3 Best match: idmtools 1.6.3 Adding idmtools 1.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for geopy==2.0.0 Best match: geopy 2.0.0 Adding geopy 2.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for fasteners==0.16 Best match: fasteners 0.16 Adding fasteners 0.16 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for patsy==0.5.1 Best match: patsy 0.5.1 Adding patsy 0.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pandas==1.1.5 Best match: pandas 1.1.5 Adding pandas 1.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for scikit-learn==0.24.2 Best match: scikit-learn 0.24.2 Adding scikit-learn 0.24.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for matplotlib==3.4.1 Best match: matplotlib 3.4.1 Adding matplotlib 3.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for more-itertools==8.7.0 Best match: more-itertools 8.7.0 Adding more-itertools 8.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pipreqs==0.4.10 Best match: pipreqs 0.4.10 Adding pipreqs 0.4.10 to easy-install.pth file Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for packaging==20.9 Best match: packaging 20.9 Adding packaging 20.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pygit2==1.5.0 Best match: pygit2 1.5.0 Adding pygit2 1.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for tqdm==4.60.0 Best match: tqdm 4.60.0 Adding tqdm 4.60.0 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for backoff==1.10.0 Best match: backoff 1.10.0 Adding backoff 1.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for diskcache==5.1.0 Best match: diskcache 5.1.0 Adding diskcache 5.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for tabulate==0.8.9 Best match: tabulate 0.8.9 Adding tabulate 0.8.9 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for coloredlogs==15.0 Best match: coloredlogs 15.0 Adding coloredlogs 15.0 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pluggy==0.13.1 Best match: pluggy 0.13.1 Adding pluggy 0.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for PyYAML==5.4.1 Best match: PyYAML 5.4.1 Adding PyYAML 5.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for geographiclib==1.50 Best match: geographiclib 1.50 Adding geographiclib 1.50 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 Adding python-dateutil 2.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pytz==2021.1 Best match: pytz 2021.1 Adding pytz 2021.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for threadpoolctl==2.1.0 Best match: threadpoolctl 2.1.0 Adding threadpoolctl 2.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for joblib==1.0.1 Best match: joblib 1.0.1 Adding joblib 1.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for Pillow==8.2.0 Best match: Pillow 8.2.0 Adding Pillow 8.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pyparsing==2.4.7 Best match: pyparsing 2.4.7 Adding pyparsing 2.4.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for kiwisolver==1.3.1 Best match: kiwisolver 1.3.1 Adding kiwisolver 1.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for cycler==0.10.0 Best match: cycler 0.10.0 Adding cycler 0.10.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/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-idmtools-calibra/envs/latest/lib/python3.7/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-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for cffi==1.14.5 Best match: cffi 1.14.5 Adding cffi 1.14.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for cached-property==1.5.2 Best match: cached-property 1.5.2 Adding cached-property 1.5.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for humanfriendly==9.1 Best match: humanfriendly 9.1 Adding humanfriendly 9.1 to easy-install.pth file Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for importlib-metadata==4.0.1 Best match: importlib-metadata 4.0.1 Adding importlib-metadata 4.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for requests==2.25.1 Best match: requests 2.25.1 Adding requests 2.25.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for pycparser==2.20 Best match: pycparser 2.20 Adding pycparser 2.20 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for typing-extensions==3.7.4.3 Best match: typing-extensions 3.7.4.3 Adding typing-extensions 3.7.4.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for zipp==3.4.1 Best match: zipp 3.4.1 Adding zipp 3.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for certifi==2020.12.5 Best match: certifi 2020.12.5 Adding certifi 2020.12.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for urllib3==1.26.4 Best match: urllib3 1.26.4 Adding urllib3 1.26.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for idna==2.10 Best match: idna 2.10 Adding idna 2.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Searching for chardet==4.0.0 Best match: chardet 4.0.0 Adding chardet 4.0.0 to easy-install.pth file Installing chardetect script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/site-packages Finished processing dependencies for idmtools-calibra==1.0.0 [rtd-command-info] start-time: 2021-04-28T17:17:32.832588Z, end-time: 2021-04-28T17:17:32.905783Z, 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 from datetime import datetime 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__))) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx.ext.intersphinx' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = ['history_matching', 'pycuda', 'COMPS', 'gpc', 'skcuda', 'calibmanager', 'idmtools.utils.json', 'idmtools_calibra.output.output_parser', 'simtools', 'dtk', 'idmtools_calibra.interventions', 'idmtools_calibra.utilities'] 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'idmtools_calibra' 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. import idmtools_calibra version = idmtools_calibra.__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 = None # 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' ] } # 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 # 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 = 'idmtools_calibra' # -- 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, 'idmtools_calibra.tex', u'idmtools_calibra', 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, 'idmtools_calibra-docs', u'idmtools_calibra', [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, 'idmtools_calibra-docs', u'idmtools_calibra', author, 'Institute for Disease Modeling', 'How to use idmtools_calibra for calibration', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'python': ('https://docs.python.org/3', None), 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # 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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file should't rely on extra depencies. 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: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] 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", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/idmtools_calibra/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/idmtools_calibra/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-idmtools-calibra', 'name': u'idmtools_calibra', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/idmtools_calibra/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'idmtools_calibra', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', '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': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': 'ca39949d', } # 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(): html_context.update(context) 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-idmtools-calibra/builds/621978/' 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: 2021-04-28T17:17:33.012566Z, end-time: 2021-04-28T17:17:48.543272Z, duration: 15, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) 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/pycomps/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 112 source files that are out of date updating environment: [new config] 112 added, 0 changed, 0 removed reading sources... [ 0%] idmtools_calibra reading sources... [ 1%] idmtools_calibra.algorithms reading sources... [ 2%] idmtools_calibra.algorithms.fisher_inf_matrix reading sources... [ 3%] idmtools_calibra.algorithms.generic_iterative_next_point reading sources... [ 4%] idmtools_calibra.algorithms.gpc reading sources... [ 5%] idmtools_calibra.algorithms.imis reading sources... [ 6%] idmtools_calibra.algorithms.next_point_algorithm reading sources... [ 7%] idmtools_calibra.algorithms.optim_tool reading sources... [ 8%] idmtools_calibra.algorithms.optim_tools_pspo reading sources... [ 8%] idmtools_calibra.algorithms.optim_tools_spsa reading sources... [ 9%] idmtools_calibra.algorithms.pbnb reading sources... [ 10%] idmtools_calibra.algorithms.pbnb.c_sub_region reading sources... [ 11%] idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions reading sources... [ 12%] idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting reading sources... 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[100%] overview looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 0%] idmtools_calibra writing output... [ 1%] idmtools_calibra.algorithms writing output... [ 2%] idmtools_calibra.algorithms.fisher_inf_matrix writing output... [ 3%] idmtools_calibra.algorithms.generic_iterative_next_point writing output... [ 4%] idmtools_calibra.algorithms.gpc writing output... [ 5%] idmtools_calibra.algorithms.imis writing output... [ 6%] idmtools_calibra.algorithms.next_point_algorithm writing output... [ 7%] idmtools_calibra.algorithms.optim_tool writing output... [ 8%] idmtools_calibra.algorithms.optim_tools_pspo writing output... [ 8%] idmtools_calibra.algorithms.optim_tools_spsa writing output... [ 9%] idmtools_calibra.algorithms.pbnb writing output... [ 10%] idmtools_calibra.algorithms.pbnb.c_sub_region writing output... [ 11%] idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions writing output... [ 12%] idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting writing output... [ 13%] idmtools_calibra.algorithms.pbnb.optim_tool_pbnb writing output... [ 14%] idmtools_calibra.algorithms.separatrix_bhm writing output... [ 15%] idmtools_calibra.analyzers writing output... [ 16%] idmtools_calibra.analyzers.base_calibration_analyzer writing output... [ 16%] idmtools_calibra.analyzers.helpers writing output... [ 17%] idmtools_calibra.analyzers.malaria_summary writing output... [ 18%] idmtools_calibra.calib_manager writing output... [ 19%] idmtools_calibra.calib_site writing output... [ 20%] idmtools_calibra.interventions writing output... [ 21%] idmtools_calibra.interventions.biting_risk writing output... [ 22%] idmtools_calibra.interventions.dengue_bednets_irs_vaccines writing output... [ 23%] idmtools_calibra.interventions.empty_campaign writing output... [ 24%] idmtools_calibra.interventions.habitat_scale writing output... [ 25%] idmtools_calibra.interventions.heg writing output... [ 25%] idmtools_calibra.interventions.incidence_counter writing output... [ 26%] idmtools_calibra.interventions.input_EIR writing output... [ 27%] idmtools_calibra.interventions.irs writing output... [ 28%] idmtools_calibra.interventions.itn writing output... [ 29%] idmtools_calibra.interventions.itn_age_season writing output... [ 30%] idmtools_calibra.interventions.ivermectin writing output... [ 31%] idmtools_calibra.interventions.migrate_to writing output... [ 32%] idmtools_calibra.interventions.mosquito_release writing output... [ 33%] idmtools_calibra.interventions.novel_vector_control writing output... [ 33%] idmtools_calibra.interventions.outbreakindividual writing output... [ 34%] idmtools_calibra.interventions.outbreakindividualdengue writing output... [ 35%] idmtools_calibra.interventions.property_change writing output... [ 36%] idmtools_calibra.interventions.seir_initial_seeding writing output... [ 37%] idmtools_calibra.interventions.seir_vitaldynamics writing output... [ 38%] idmtools_calibra.interventions.seirs writing output... [ 39%] idmtools_calibra.interventions.si_initial_seeding writing output... [ 40%] idmtools_calibra.interventions.sir_initial_seeding writing output... [ 41%] idmtools_calibra.interventions.sir_vaccinations_a_initial_seeding writing output... [ 41%] idmtools_calibra.interventions.sir_vaccinations_b_initial_seeding writing output... [ 42%] idmtools_calibra.interventions.sir_vaccinations_c_initial_seeding writing output... [ 43%] idmtools_calibra.interventions.sirs_initial_seeding writing output... [ 44%] idmtools_calibra.interventions.sis_initial_seeding writing output... [ 45%] idmtools_calibra.interventions.support_scripts writing output... [ 46%] idmtools_calibra.interventions.triggered_campaign_delay_event writing output... [ 47%] idmtools_calibra.iteration_state writing output... [ 48%] idmtools_calibra.ll_calculators writing output... [ 49%] idmtools_calibra.output writing output... [ 50%] idmtools_calibra.output.output_parser writing output... [ 50%] idmtools_calibra.output.spatial_output writing output... [ 51%] idmtools_calibra.parameter_set writing output... [ 52%] idmtools_calibra.plotters writing output... [ 53%] idmtools_calibra.plotters.base_plotter writing output... [ 54%] idmtools_calibra.plotters.likelihood_plotter writing output... [ 55%] idmtools_calibra.plotters.optim_tool_pbnb_plotter writing output... [ 56%] idmtools_calibra.plotters.optim_tool_plotter writing output... [ 57%] idmtools_calibra.plotters.optim_tool_spsa_plotter writing output... [ 58%] idmtools_calibra.plotters.separatrix_bhm_plotter writing output... [ 58%] idmtools_calibra.plotters.site_data_plotter writing output... [ 59%] idmtools_calibra.prior writing output... [ 60%] idmtools_calibra.resample_manager writing output... [ 61%] idmtools_calibra.resamplers writing output... [ 62%] idmtools_calibra.resamplers.base_resampler writing output... [ 63%] idmtools_calibra.resamplers.calibration_point writing output... [ 64%] idmtools_calibra.resamplers.calibration_points writing output... [ 65%] idmtools_calibra.resamplers.cramer_rao_resampler writing output... [ 66%] idmtools_calibra.resamplers.random_perturbation_resampler writing output... [ 66%] idmtools_calibra.utilities writing output... [ 67%] idmtools_calibra.utilities.demographics writing output... [ 68%] idmtools_calibra.utilities.demographics.node writing output... [ 69%] idmtools_calibra.utilities.display writing output... [ 70%] idmtools_calibra.utilities.distro writing output... [ 71%] idmtools_calibra.utilities.emod_malaria_sim writing output... [ 72%] idmtools_calibra.utilities.encoding writing output... [ 73%] idmtools_calibra.utilities.generic writing output... [ 74%] idmtools_calibra.utilities.generic.climate writing output... [ 75%] idmtools_calibra.utilities.generic.demographics writing output... [ 75%] idmtools_calibra.utilities.generic.disease writing output... [ 76%] idmtools_calibra.utilities.generic.geography writing output... [ 77%] idmtools_calibra.utilities.generic.migration writing output... [ 78%] idmtools_calibra.utilities.generic.params writing output... [ 79%] idmtools_calibra.utilities.helper writing output... [ 80%] idmtools_calibra.utilities.mod_fn writing output... [ 81%] idmtools_calibra.utilities.parsers writing output... [ 82%] idmtools_calibra.utilities.parsers.JSON writing output... [ 83%] idmtools_calibra.utilities.parsers.bin2np writing output... [ 83%] idmtools_calibra.utilities.parsers.dict2pd writing output... [ 84%] idmtools_calibra.utilities.parsers.malaria_summary writing output... [ 85%] idmtools_calibra.utilities.parsers.np2json writing output... [ 86%] idmtools_calibra.utilities.parsers.np2pd writing output... [ 87%] idmtools_calibra.utilities.parsers.pd2csv writing output... [ 88%] idmtools_calibra.utilities.reports writing output... [ 89%] idmtools_calibra.utilities.reports.base_age_hist_report writing output... [ 90%] idmtools_calibra.utilities.reports.custom_report writing output... [ 91%] idmtools_calibra.utilities.reports.vector_report writing output... [ 91%] idmtools_calibra.utilities.vector writing output... [ 92%] idmtools_calibra.utilities.vector.larval_habitat writing output... [ 93%] idmtools_calibra.utilities.vector.params writing output... [ 94%] idmtools_calibra.utilities.vector.species writing output... [ 95%] idmtools_calibra.utilities.vector.study_sites writing output... [ 96%] idmtools_calibra.utils writing output... [ 97%] idmtools_calibra_index writing output... [ 98%] index writing output... [ 99%] installation writing output... [100%] overview generating indices... genindex py-modindexdone writing additional pages... search opensearchdone 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 _build/html. Updating searchtools for Read the Docs search... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idmtools-calibra/envs/latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) [rtd-command-info] start-time: 2021-04-28T17:17:48.710235Z, end-time: 2021-04-28T17:17:50.858668Z, duration: 2, exit-code: 0 python -m sphinx -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] idmtools_calibra_index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... installation overview idmtools_calibra_index idmtools_calibra idmtools_calibra.algorithms idmtools_calibra.algorithms.pbnb idmtools_calibra.algorithms.pbnb.c_sub_region idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting idmtools_calibra.algorithms.pbnb.optim_tool_pbnb idmtools_calibra.algorithms.fisher_inf_matrix idmtools_calibra.algorithms.generic_iterative_next_point idmtools_calibra.algorithms.gpc idmtools_calibra.algorithms.imis idmtools_calibra.algorithms.next_point_algorithm idmtools_calibra.algorithms.optim_tool idmtools_calibra.algorithms.optim_tools_pspo idmtools_calibra.algorithms.optim_tools_spsa idmtools_calibra.algorithms.separatrix_bhm idmtools_calibra.analyzers idmtools_calibra.analyzers.base_calibration_analyzer idmtools_calibra.analyzers.helpers idmtools_calibra.analyzers.malaria_summary idmtools_calibra.interventions idmtools_calibra.interventions.biting_risk idmtools_calibra.interventions.dengue_bednets_irs_vaccines idmtools_calibra.interventions.empty_campaign idmtools_calibra.interventions.habitat_scale idmtools_calibra.interventions.heg idmtools_calibra.interventions.incidence_counter idmtools_calibra.interventions.input_EIR idmtools_calibra.interventions.irs idmtools_calibra.interventions.itn idmtools_calibra.interventions.itn_age_season idmtools_calibra.interventions.ivermectin idmtools_calibra.interventions.migrate_to idmtools_calibra.interventions.mosquito_release idmtools_calibra.interventions.novel_vector_control idmtools_calibra.interventions.outbreakindividual idmtools_calibra.interventions.outbreakindividualdengue idmtools_calibra.interventions.property_change idmtools_calibra.interventions.seir_initial_seeding idmtools_calibra.interventions.seir_vitaldynamics idmtools_calibra.interventions.seirs idmtools_calibra.interventions.si_initial_seeding idmtools_calibra.interventions.sir_initial_seeding idmtools_calibra.interventions.sir_vaccinations_a_initial_seeding idmtools_calibra.interventions.sir_vaccinations_b_initial_seeding idmtools_calibra.interventions.sir_vaccinations_c_initial_seeding idmtools_calibra.interventions.sirs_initial_seeding idmtools_calibra.interventions.sis_initial_seeding idmtools_calibra.interventions.support_scripts idmtools_calibra.interventions.triggered_campaign_delay_event idmtools_calibra.output idmtools_calibra.output.output_parser idmtools_calibra.output.spatial_output idmtools_calibra.plotters idmtools_calibra.plotters.base_plotter idmtools_calibra.plotters.likelihood_plotter idmtools_calibra.plotters.optim_tool_pbnb_plotter idmtools_calibra.plotters.optim_tool_plotter idmtools_calibra.plotters.optim_tool_spsa_plotter idmtools_calibra.plotters.separatrix_bhm_plotter idmtools_calibra.plotters.site_data_plotter idmtools_calibra.resamplers idmtools_calibra.resamplers.base_resampler idmtools_calibra.resamplers.calibration_point idmtools_calibra.resamplers.calibration_points idmtools_calibra.resamplers.cramer_rao_resampler idmtools_calibra.resamplers.random_perturbation_resampler idmtools_calibra.utilities idmtools_calibra.utilities.demographics idmtools_calibra.utilities.demographics.node idmtools_calibra.utilities.generic idmtools_calibra.utilities.generic.climate idmtools_calibra.utilities.generic.demographics idmtools_calibra.utilities.generic.disease idmtools_calibra.utilities.generic.geography idmtools_calibra.utilities.generic.migration idmtools_calibra.utilities.generic.params idmtools_calibra.utilities.parsers idmtools_calibra.utilities.parsers.JSON idmtools_calibra.utilities.parsers.bin2np idmtools_calibra.utilities.parsers.dict2pd idmtools_calibra.utilities.parsers.malaria_summary idmtools_calibra.utilities.parsers.np2json idmtools_calibra.utilities.parsers.np2pd idmtools_calibra.utilities.parsers.pd2csv idmtools_calibra.utilities.reports idmtools_calibra.utilities.reports.base_age_hist_report idmtools_calibra.utilities.reports.custom_report idmtools_calibra.utilities.reports.vector_report idmtools_calibra.utilities.vector idmtools_calibra.utilities.vector.larval_habitat idmtools_calibra.utilities.vector.params idmtools_calibra.utilities.vector.species idmtools_calibra.utilities.vector.study_sites idmtools_calibra.utilities.display idmtools_calibra.utilities.distro idmtools_calibra.utilities.emod_malaria_sim idmtools_calibra.utilities.encoding idmtools_calibra.utilities.helper idmtools_calibra.utilities.mod_fn idmtools_calibra.calib_manager idmtools_calibra.calib_site idmtools_calibra.iteration_state idmtools_calibra.ll_calculators idmtools_calibra.parameter_set idmtools_calibra.prior idmtools_calibra.resample_manager idmtools_calibra.utils done writing... done writing additional files... opensearchdone copying static files... ... done copying 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The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-04-28T17:17:51.000286Z, end-time: 2021-04-28T17:17:53.164976Z, duration: 2, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] idmtools_calibra_index looking for now-outdated files... none found pickling environment... done checking consistency... done processing idmtools_calibra.tex... index installation overview idmtools_calibra_index idmtools_calibra idmtools_calibra.algorithms idmtools_calibra.algorithms.pbnb idmtools_calibra.algorithms.pbnb.c_sub_region idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting idmtools_calibra.algorithms.pbnb.optim_tool_pbnb idmtools_calibra.algorithms.fisher_inf_matrix idmtools_calibra.algorithms.generic_iterative_next_point idmtools_calibra.algorithms.gpc idmtools_calibra.algorithms.imis idmtools_calibra.algorithms.next_point_algorithm idmtools_calibra.algorithms.optim_tool idmtools_calibra.algorithms.optim_tools_pspo idmtools_calibra.algorithms.optim_tools_spsa idmtools_calibra.algorithms.separatrix_bhm idmtools_calibra.analyzers idmtools_calibra.analyzers.base_calibration_analyzer idmtools_calibra.analyzers.helpers idmtools_calibra.analyzers.malaria_summary idmtools_calibra.interventions idmtools_calibra.interventions.biting_risk idmtools_calibra.interventions.dengue_bednets_irs_vaccines idmtools_calibra.interventions.empty_campaign idmtools_calibra.interventions.habitat_scale idmtools_calibra.interventions.heg idmtools_calibra.interventions.incidence_counter idmtools_calibra.interventions.input_EIR idmtools_calibra.interventions.irs idmtools_calibra.interventions.itn idmtools_calibra.interventions.itn_age_season idmtools_calibra.interventions.ivermectin idmtools_calibra.interventions.migrate_to idmtools_calibra.interventions.mosquito_release idmtools_calibra.interventions.novel_vector_control idmtools_calibra.interventions.outbreakindividual idmtools_calibra.interventions.outbreakindividualdengue idmtools_calibra.interventions.property_change idmtools_calibra.interventions.seir_initial_seeding idmtools_calibra.interventions.seir_vitaldynamics idmtools_calibra.interventions.seirs idmtools_calibra.interventions.si_initial_seeding idmtools_calibra.interventions.sir_initial_seeding idmtools_calibra.interventions.sir_vaccinations_a_initial_seeding idmtools_calibra.interventions.sir_vaccinations_b_initial_seeding idmtools_calibra.interventions.sir_vaccinations_c_initial_seeding idmtools_calibra.interventions.sirs_initial_seeding idmtools_calibra.interventions.sis_initial_seeding idmtools_calibra.interventions.support_scripts idmtools_calibra.interventions.triggered_campaign_delay_event idmtools_calibra.output idmtools_calibra.output.output_parser idmtools_calibra.output.spatial_output idmtools_calibra.plotters idmtools_calibra.plotters.base_plotter idmtools_calibra.plotters.likelihood_plotter idmtools_calibra.plotters.optim_tool_pbnb_plotter idmtools_calibra.plotters.optim_tool_plotter idmtools_calibra.plotters.optim_tool_spsa_plotter idmtools_calibra.plotters.separatrix_bhm_plotter idmtools_calibra.plotters.site_data_plotter idmtools_calibra.resamplers idmtools_calibra.resamplers.base_resampler idmtools_calibra.resamplers.calibration_point idmtools_calibra.resamplers.calibration_points idmtools_calibra.resamplers.cramer_rao_resampler idmtools_calibra.resamplers.random_perturbation_resampler idmtools_calibra.utilities idmtools_calibra.utilities.demographics idmtools_calibra.utilities.demographics.node idmtools_calibra.utilities.generic idmtools_calibra.utilities.generic.climate idmtools_calibra.utilities.generic.demographics idmtools_calibra.utilities.generic.disease idmtools_calibra.utilities.generic.geography idmtools_calibra.utilities.generic.migration idmtools_calibra.utilities.generic.params idmtools_calibra.utilities.parsers idmtools_calibra.utilities.parsers.JSON idmtools_calibra.utilities.parsers.bin2np idmtools_calibra.utilities.parsers.dict2pd idmtools_calibra.utilities.parsers.malaria_summary idmtools_calibra.utilities.parsers.np2json idmtools_calibra.utilities.parsers.np2pd idmtools_calibra.utilities.parsers.pd2csv idmtools_calibra.utilities.reports idmtools_calibra.utilities.reports.base_age_hist_report idmtools_calibra.utilities.reports.custom_report idmtools_calibra.utilities.reports.vector_report idmtools_calibra.utilities.vector idmtools_calibra.utilities.vector.larval_habitat idmtools_calibra.utilities.vector.params idmtools_calibra.utilities.vector.species idmtools_calibra.utilities.vector.study_sites idmtools_calibra.utilities.display idmtools_calibra.utilities.distro idmtools_calibra.utilities.emod_malaria_sim idmtools_calibra.utilities.encoding idmtools_calibra.utilities.helper idmtools_calibra.utilities.mod_fn idmtools_calibra.calib_manager idmtools_calibra.calib_site idmtools_calibra.iteration_state idmtools_calibra.ll_calculators idmtools_calibra.parameter_set idmtools_calibra.prior idmtools_calibra.resample_manager idmtools_calibra.utils resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. 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-idmtools-calibra/checkouts/latest/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-04-28T17:17:53.377252Z, end-time: 2021-04-28T17:17:53.444609Z, 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'} . 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Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.385 Having the estimated optimal point (θ *), the next step is generating ... ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.390 ...p is the number of parameters (size of θ ). The number of cross\sph... ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.391 ...of the model at the given final point (θ *). 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Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.4093 \end{sphinxtheindex} ! Missing $ inserted. $ l.4093 \end{sphinxtheindex} ! Missing } inserted. } l.4093 \end{sphinxtheindex} [40] No file institute-for-disease-modeling-idmtools-calibra.ind. (./institute-for-disease-modeling-idmtools-calibra.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-idmtools-c alibra.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb> Output written on institute-for-disease-modeling-idmtools-calibra.pdf (44 pages , 259604 bytes). Transcript written on institute-for-disease-modeling-idmtools-calibra.log. Latexmk: Index file 'institute-for-disease-modeling-idmtools-calibra.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-idmtools-calibra.ind' from line 'No file institute-for-disease-modeling-idmtools-calibra.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-idmtools-calibra.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-idmtools-calibra.pdf' Latexmk: List of undefined refs and citations: Reference `idmtools_calibra.algorithms.fisher_inf_matrix:module-idmtools_calibra.algorithms.fisher_inf_matrix' on page 39 undefined on input line 3987 Reference `idmtools_calibra.algorithms.generic_iterative_next_point:module-idmtools_calibra.algorithms.generic_iterative_next_point' on page 39 undefined on input line 3988 Reference `idmtools_calibra.algorithms.gpc:module-idmtools_calibra.algorithms.gpc' on page 39 undefined on input line 3989 Reference `idmtools_calibra.algorithms.imis:module-idmtools_calibra.algorithms.imis' on page 39 undefined on input line 3990 Reference `idmtools_calibra.algorithms.next_point_algorithm:module-idmtools_calibra.algorithms.next_point_algorithm' on page 39 undefined on input line 3991 Reference `idmtools_calibra.algorithms.optim_tool:module-idmtools_calibra.algorithms.optim_tool' on page 39 undefined on input line 3992 Reference `idmtools_calibra.algorithms.optim_tools_pspo:module-idmtools_calibra.algorithms.optim_tools_pspo' on page 39 undefined on input line 3993 Reference `idmtools_calibra.algorithms.optim_tools_spsa:module-idmtools_calibra.algorithms.optim_tools_spsa' on page 39 undefined on input line 3994 Reference `idmtools_calibra.algorithms.pbnb.c_sub_region:module-idmtools_calibra.algorithms.pbnb.c_sub_region' on page 39 undefined on input line 3996 Reference `idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions:module-idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions' on page 39 undefined on input line 3997 Reference `idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting:module-idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting' on page 39 undefined on input line 3998 Reference `idmtools_calibra.algorithms.pbnb.optim_tool_pbnb:module-idmtools_calibra.algorithms.pbnb.optim_tool_pbnb' on page 39 undefined on input line 3999 Reference `idmtools_calibra.algorithms.pbnb:module-idmtools_calibra.algorithms.pbnb' on page 39 undefined on input line 3995 Reference `idmtools_calibra.algorithms.separatrix_bhm:module-idmtools_calibra.algorithms.separatrix_bhm' on page 39 undefined on input line 4000 Reference `idmtools_calibra.algorithms:module-idmtools_calibra.algorithms' on page 39 undefined on input line 3986 Reference `idmtools_calibra.analyzers.base_calibration_analyzer:module-idmtools_calibra.analyzers.base_calibration_analyzer' on page 39 undefined on input line 4002 Reference `idmtools_calibra.analyzers.helpers:module-idmtools_calibra.analyzers.helpers' on page 39 undefined on input line 4003 Reference `idmtools_calibra.analyzers.malaria_summary:module-idmtools_calibra.analyzers.malaria_summary' on page 39 undefined on input line 4004 Reference `idmtools_calibra.analyzers:module-idmtools_calibra.analyzers' on page 39 undefined on input line 4001 Reference `idmtools_calibra.calib_manager:module-idmtools_calibra.calib_manager' on page 39 undefined on input line 4005 Reference `idmtools_calibra.calib_site:module-idmtools_calibra.calib_site' on page 39 undefined on input line 4006 Reference `idmtools_calibra.interventions.biting_risk:module-idmtools_calibra.interventions.biting_risk' on page 39 undefined on input line 4008 Reference `idmtools_calibra.interventions.dengue_bednets_irs_vaccines:module-idmtools_calibra.interventions.dengue_bednets_irs_vaccines' on page 39 undefined on input line 4009 Reference `idmtools_calibra.interventions.empty_campaign:module-idmtools_calibra.interventions.empty_campaign' on page 39 undefined on input line 4010 Reference `idmtools_calibra.interventions.habitat_scale:module-idmtools_calibra.interventions.habitat_scale' on page 39 undefined on input line 4011 Reference `idmtools_calibra.interventions.heg:module-idmtools_calibra.interventions.heg' on page 39 undefined on input line 4012 Reference `idmtools_calibra.interventions.incidence_counter:module-idmtools_calibra.interventions.incidence_counter' on page 39 undefined on input line 4013 Reference `idmtools_calibra.interventions.input_EIR:module-idmtools_calibra.interventions.input_EIR' on page 39 undefined on input line 4014 Reference `idmtools_calibra.interventions.irs:module-idmtools_calibra.interventions.irs' on page 39 undefined on input line 4015 Reference `idmtools_calibra.interventions.itn:module-idmtools_calibra.interventions.itn' on page 39 undefined on input line 4016 Reference `idmtools_calibra.interventions.itn_age_season:module-idmtools_calibra.interventions.itn_age_season' on page 39 undefined on input line 4017 Reference `idmtools_calibra.interventions.ivermectin:module-idmtools_calibra.interventions.ivermectin' on page 39 undefined on input line 4018 Reference 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Missing $ inserted. $ l.377 \paragraph{Submodules} ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.377 \paragraph{Submodules} ! Missing $ inserted. $ l.377 \paragraph{Submodules} ! Missing } inserted. } l.377 \paragraph{Submodules} [9] Underfull \hbox (badness 10000) in paragraph at lines 384--384 []\T1/ptm/m/it/10 center\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xmin\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 xmax\T1/ptm/m/n/10 , \T1/ptm/m/it/10 m=10\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 n=5\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 ple_size=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 res-o-lu- Overfull \hbox (3.07457pt too wide) in paragraph at lines 384--384 \T1/ptm/m/it/10 tion_raw=None\T1/pcr/m/n/10 ) ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.385 Having the estimated optimal point (θ *), the next step is generating ... ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.390 ...p is the number of parameters (size of θ ). The number of cross\sph... ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.391 ...of the model at the given final point (θ *). 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Missing $ inserted. $ l.1523 S eparatrix using Bayesian History Matching ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.1523 S eparatrix using Bayesian History Matching ! Missing $ inserted. $ l.1523 S eparatrix using Bayesian History Matching ! Missing } inserted. } l.1523 S eparatrix using Bayesian History Matching [17] ! Missing $ inserted. $ l.1619 ...ion{idmtools\_calibra.analyzers package} ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.1619 ...ion{idmtools\_calibra.analyzers package} ! Missing $ inserted. $ l.1619 ...ion{idmtools\_calibra.analyzers package} ! 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[42] Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\T1/pcr/m/n/10 create_iteration_state() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 161--163 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 163--165 []\T1/pcr/m/n/10 cSubRegion \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in idm- Underfull \hbox (badness 10000) in paragraph at lines 163--165 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.c_sub_region\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 168--170 []\T1/pcr/m/n/10 default_experiment_builder_function() Overfull \hbox (4.57077pt too wide) in paragraph at lines 168--170 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 define_kernel() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 170--172 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tools_calibra.algorithms.fisher_inf_matrix\T1/ptm/m/n/10 ), Overfull \hbox (74.26904pt too wide) in paragraph at lines 185--187 []\T1/pcr/m/n/10 DYNAMIC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.resa mplers.calibration_point.CalibrationPoint Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (134.17853pt too wide) in paragraph at lines 190--192 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 192--194 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 192--194 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 194--196 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (80.17957pt too wide) in paragraph at lines 194--196 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 196--198 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 196--198 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tool.OptimTool Underfull \hbox (badness 10000) in paragraph at lines 198--200 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (52.1302pt too wide) in paragraph at lines 198--200 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO Underfull \hbox (badness 10000) in paragraph at lines 200--202 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (48.80013pt too wide) in paragraph at lines 200--202 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA Underfull \hbox (badness 10000) in paragraph at lines 202--204 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (69.9406pt too wide) in paragraph at lines 202--204 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB Underfull \hbox (badness 10000) in paragraph at lines 204--206 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (41.0602pt too wide) in paragraph at lines 204--206 \T1/ptm/m/it/10 tools_calibra.algorithms.separatrix_bhm.SeparatrixBHM Underfull \hbox (badness 10000) in paragraph at lines 206--208 []\T1/pcr/m/n/10 ento_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 208--210 []\T1/pcr/m/n/10 ento_spatial_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 210--212 []\T1/pcr/m/n/10 ep_predict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 210--212 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 212--214 []\T1/pcr/m/n/10 euclidean_distance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e idm- Underfull \hbox (badness 10000) in paragraph at lines 216--217 []\T1/pcr/m/n/10 evaluate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.a lgorithms.gpc.GPC Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 expectation_propagation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 217--219 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 222--224 []\T1/pcr/m/n/10 finalize_calibration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 222--224 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 224--226 []\T1/pcr/m/n/10 find_posterior_mode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 224--226 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC method\T1/ptm/m/n/10 ), Overfull \hbox (21.43024pt too wide) in paragraph at lines 226--228 []\T1/pcr/m/n/10 finished() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.i teration_state.IterationState Underfull \hbox (badness 10000) in paragraph at lines 228--230 []\T1/pcr/m/n/10 from_bytes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (10.28046pt too wide) in paragraph at lines 228--230 \T1/ptm/m/it/10 tools_calibra.output.spatial_output.SpatialOutput Underfull \hbox (badness 10000) in paragraph at lines 230--232 []\T1/pcr/m/n/10 from_calibration_parameter() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i dm- Overfull \hbox (72.98964pt too wide) in paragraph at lines 230--232 \T1/ptm/m/it/10 tools_calibra.resamplers.calibration_point.CalibrationParameter Underfull \hbox (badness 10000) in paragraph at lines 232--234 []\T1/pcr/m/n/10 from_config() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 232--234 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC class Overfull \hbox (26.20059pt too wide) in paragraph at lines 236--238 []\T1/pcr/m/n/10 from_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra. parameter_set.ParameterSet Overfull \hbox (119.21948pt too wide) in paragraph at lines 238--240 []\T1/pcr/m/n/10 from_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra. resamplers.calibration_point.CalibrationParameter Overfull \hbox (98.26964pt too wide) in paragraph at lines 240--242 []\T1/pcr/m/n/10 from_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra. resamplers.calibration_point.CalibrationPoint Overfull \hbox (27.43024pt too wide) in paragraph at lines 242--244 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra. iteration_state.IterationState Underfull \hbox (badness 10000) in paragraph at lines 244--246 []\T1/pcr/m/n/10 from_range() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 244--246 \T1/ptm/m/it/10 tools_calibra.prior.SampleFunctionContainer Underfull \hbox (badness 10000) in paragraph at lines 246--248 []\T1/pcr/m/n/10 from_tuple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 246--248 \T1/ptm/m/it/10 tools_calibra.prior.SampleFunctionContainer ! Missing $ inserted. $ l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... ! Missing $ inserted. $ l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... ! Missing } inserted. } l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... [43] Underfull \hbox (badness 10000) in paragraph at lines 248--250 []\T1/pcr/m/n/10 fun_ci_builder() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule id m- Overfull \hbox (54.59044pt too wide) in paragraph at lines 248--250 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 250--252 []\T1/pcr/m/n/10 fun_elite_indicator() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 250--252 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 252--254 []\T1/pcr/m/n/10 fun_generate_samples_from_df() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (69.9406pt too wide) in paragraph at lines 252--254 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB Overfull \hbox (54.59044pt too wide) in paragraph at lines 254--256 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Overfull \hbox (54.59044pt too wide) in paragraph at lines 256--258 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 258--260 []\T1/pcr/m/n/10 fun_order_region() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 258--260 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 260--262 []\T1/pcr/m/n/10 fun_order_subregion() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 260--262 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 262--264 []\T1/pcr/m/n/10 fun_plot2D() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull 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tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 270--272 []\T1/pcr/m/n/10 fun_quantile_update() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 270--272 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 272--274 []\T1/pcr/m/n/10 fun_reg_branching() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 272--274 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 8113) in paragraph at lines 274--276 []\T1/pcr/m/n/10 fun_replication_update() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 274--276 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 276--278 []\T1/pcr/m/n/10 fun_results_organizer_deterministic() Underfull \hbox (badness 10000) in paragraph at lines 276--278 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 276--278 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 278--280 []\T1/pcr/m/n/10 fun_results_organizer_noise() Underfull \hbox (badness 10000) in paragraph at lines 278--280 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 278--280 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Overfull \hbox (28.1225pt too wide) in paragraph at lines 280--282 []\T1/pcr/m/n/10 fun_sample_points_generator_deterministic() Underfull \hbox (badness 10000) in paragraph at lines 280--282 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 280--282 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 282--284 []\T1/pcr/m/n/10 fun_sample_points_generator_noise() Underfull \hbox (badness 10000) in paragraph at lines 282--284 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 282--284 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 284--286 []\T1/pcr/m/n/10 fun_worst_indicator() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 284--286 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 func_wrapper() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- 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\T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Overfull \hbox (172.3389pt too wide) in paragraph at lines 301--303 \T1/ptm/m/it/10 tools_calibra.resamplers.random_perturbation_resampler.RandomPe rturbationResampler Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/pcr/m/n/10 generate_samples_from_df() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm - Overfull \hbox (80.17957pt too wide) in paragraph at lines 303--305 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/pcr/m/n/10 generate_variables_from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 305--307 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 GenericIterativeNextPoint \T1/ptm/m/n/10 (\T1/ptm/m/it/10 clas s in idm- Overfull \hbox (32.7498pt too wide) in paragraph at lines 307--309 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 309--311 []\T1/pcr/m/n/10 get_analyzer_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (31.2794pt too wide) in paragraph at lines 309--311 \T1/ptm/m/it/10 tools_calibra.plotters.site_data_plotter.SiteDataPlotter Underfull \hbox (badness 10000) in paragraph at lines 311--313 []\T1/pcr/m/n/10 get_analyzers() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 311--313 \T1/ptm/m/it/10 tools_calibra.calib_site.CalibSite method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 313--315 []\T1/pcr/m/n/10 get_attribute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (52.0398pt too wide) in paragraph at lines 313--315 \T1/ptm/m/it/10 tools_calibra.resamplers.calibration_point.CalibrationPoint Underfull \hbox (badness 10000) in paragraph at lines 315--316 []\T1/pcr/m/n/10 get_bins() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.p rior.SampleRange Underfull \hbox (badness 10000) in paragraph at lines 316--318 []\T1/pcr/m/n/10 get_bins_for_summary_grouping() Underfull \hbox (badness 10000) in paragraph at lines 316--318 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 316--318 \T1/ptm/m/it/10 tools_calibra.analyzers.malaria_summary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 318--320 []\T1/pcr/m/n/10 get_calibrated_points() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (19.18066pt too wide) in paragraph at lines 318--320 \T1/ptm/m/it/10 tools_calibra.resample_manager.ResampleManager Underfull \hbox (badness 10000) in paragraph at lines 320--322 []\T1/pcr/m/n/10 get_even_spaced_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 320--322 \T1/ptm/m/it/10 tools_calibra.prior.SampleFunctionContainer ! Missing $ inserted. $ l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... ! Missing $ inserted. $ l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... ! Missing } inserted. } l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... [44] Underfull \hbox (badness 10000) in paragraph at lines 322--324 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (134.17853pt too wide) in paragraph at lines 322--324 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 324--326 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 324--326 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 326--328 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (80.17957pt too wide) in paragraph at lines 326--328 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 328--330 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 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\T1/pcr/m/n/10 idmtools_calibra.interventions.mosquito_release\T1/ptm/m/n/1 0 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 745--746 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.novel_vector_control\T1/ptm/m /n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 746--747 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.outbreakindividual\T1/ptm/m/n /10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 747--748 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.outbreakindividualdengue\T1/p tm/m/n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 748--749 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.property_change\T1/ptm/m/n/10 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 749--750 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.seir_initial_seeding\T1/ptm/m /n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 750--751 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.seir_vitaldynamics\T1/ptm/m/n /10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 751--752 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.seirs\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 752--753 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.si_initial_seeding\T1/ptm/m/n /10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 753--754 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_initial_seeding\T1/ptm/m/ n/10 , Overfull \hbox (182.6225pt too wide) in paragraph at lines 754--756 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_vaccinations_a_initial_se eding\T1/ptm/m/n/10 , Overfull \hbox (182.6225pt too wide) in paragraph at lines 756--758 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_vaccinations_b_initial_se eding\T1/ptm/m/n/10 , Overfull \hbox (182.6225pt too wide) in paragraph at lines 758--760 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_vaccinations_c_initial_se eding\T1/ptm/m/n/10 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 760--761 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sirs_initial_seeding\T1/ptm/m /n/10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 761--762 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sis_initial_seeding\T1/ptm/m/ n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 762--763 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.support_scripts\T1/ptm/m/n/10 , Overfull \hbox (158.6225pt too wide) in paragraph at lines 763--765 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.triggered_campaign_delay_even t\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 768--769 []| \T1/pcr/m/n/10 idmtools_calibra.output.output_parser\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 769--770 []| \T1/pcr/m/n/10 idmtools_calibra.output.spatial_output\T1/ptm/m/n/10 , ! Missing $ inserted. $ l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... ! Missing $ inserted. $ l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... ! Missing } inserted. } l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... [49] Overfull \hbox (20.6225pt too wide) in paragraph at lines 772--773 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.base_plotter\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 773--774 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.likelihood_plotter\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 774--775 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.optim_tool_pbnb_plotter\T1/ptm/m/n /10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 775--776 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.optim_tool_plotter\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 776--777 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.optim_tool_spsa_plotter\T1/ptm/m/n /10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 777--778 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.separatrix_bhm_plotter\T1/ptm/m/n/ 10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 778--779 []| \T1/pcr/m/n/10 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lines 789--790 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.demographics\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 790--791 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.demographics.node\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 791--792 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.display\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 792--793 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.distro\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 793--794 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.emod_malaria_sim\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 794--795 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.encoding\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 795--796 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 796--797 []| 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810--811 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.np2pd\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 811--812 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.pd2csv\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 812--813 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports\T1/ptm/m/n/10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 813--814 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports.base_age_hist_report\T1/p tm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 814--815 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports.custom_report\T1/ptm/m/n/ 10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 815--816 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports.vector_report\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 816--817 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.vector\T1/ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in 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(badness 10000) in paragraph at lines 832--834 \T1/ptm/m/it/10 tools_calibra.algorithms.fisher_inf_matrix\T1/ptm/m/n/10 ), ! Missing $ inserted. $ l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... ! Missing $ inserted. $ l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... ! Missing } inserted. } l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... [50] Overfull \hbox (52.1225pt too wide) in paragraph at lines 836--838 []\T1/pcr/m/n/10 negative_log_marginal_likelihood_and_gradient() Underfull \hbox (badness 10000) in paragraph at lines 836--838 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.algorithms.gpc.GPC Underfull \hbox (badness 10000) in paragraph at lines 838--840 []\T1/pcr/m/n/10 next_point \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.u tils.StatusPoint Underfull \hbox (badness 10000) in paragraph at lines 840--842 []\T1/pcr/m/n/10 next_point_fn() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 840--842 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 842--844 []\T1/pcr/m/n/10 next_point_step() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 842--844 \T1/ptm/m/it/10 tools_calibra.iteration_state.IterationState Underfull \hbox (badness 10000) in paragraph at lines 844--846 []\T1/pcr/m/n/10 NextPointAlgorithm \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in id m- Overfull \hbox (3.95042pt too wide) in paragraph at lines 844--846 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm\T1/ptm/m/n/10 ), Overfull \hbox (62.26904pt too wide) in paragraph at lines 846--848 []\T1/pcr/m/n/10 NUMPY \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.resamp lers.calibration_point.CalibrationPoint Underfull \hbox (badness 10000) in paragraph at lines 851--853 []\T1/pcr/m/n/10 open_for_reading() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 851--853 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/pcr/m/n/10 optimize_hyperparameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm - 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Missing $ inserted. $ l.273 ...bnb.m\_intial\_paramters\_setting module} ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.273 ...bnb.m\_intial\_paramters\_setting module} ! Missing $ inserted. $ l.273 ...bnb.m\_intial\_paramters\_setting module} ! 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Missing $ inserted. $ l.377 \paragraph{Submodules} ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.377 \paragraph{Submodules} ! Missing $ inserted. $ l.377 \paragraph{Submodules} ! Missing } inserted. } l.377 \paragraph{Submodules} [9] Underfull \hbox (badness 10000) in paragraph at lines 384--384 []\T1/ptm/m/it/10 center\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xmin\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 xmax\T1/ptm/m/n/10 , \T1/ptm/m/it/10 m=10\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 n=5\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 ple_size=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 384--384 \T1/ptm/m/it/10 res-o-lu- Overfull \hbox (3.07457pt too wide) in paragraph at lines 384--384 \T1/ptm/m/it/10 tion_raw=None\T1/pcr/m/n/10 ) ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.385 Having the estimated optimal point (θ *), the next step is generating ... ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.390 ...p is the number of parameters (size of θ ). The number of cross\sph... ! Package inputenc Error: Unicode char θ (U+3B8) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.391 ...of the model at the given final point (θ *). 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Missing $ inserted. $ l.1523 S eparatrix using Bayesian History Matching ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.1523 S eparatrix using Bayesian History Matching ! Missing $ inserted. $ l.1523 S eparatrix using Bayesian History Matching ! Missing } inserted. } l.1523 S eparatrix using Bayesian History Matching [17] ! Missing $ inserted. $ l.1619 ...ion{idmtools\_calibra.analyzers package} ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.1619 ...ion{idmtools\_calibra.analyzers package} ! Missing $ inserted. $ l.1619 ...ion{idmtools\_calibra.analyzers package} ! 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[]\T1/pcr/m/n/10 commission_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 147--149 \T1/ptm/m/it/10 tools_calibra.iteration_state.IterationState Underfull \hbox (badness 10000) in paragraph at lines 149--151 []\T1/pcr/m/n/10 commission_step() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 149--151 \T1/ptm/m/it/10 tools_calibra.iteration_state.IterationState Underfull \hbox (badness 10000) in paragraph at lines 153--155 []\T1/pcr/m/n/10 convert_annualized() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e idm- Underfull \hbox (badness 10000) in paragraph at lines 155--157 []\T1/pcr/m/n/10 convert_to_counts() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/pcr/m/n/10 CramerRaoResampler \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in id m- Overfull \hbox (10.99026pt too wide) in paragraph at lines 157--159 \T1/ptm/m/it/10 tools_calibra.resamplers.cramer_rao_resampler\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/pcr/m/n/10 create_calibration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 159--161 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager ! Missing $ inserted. $ l.161 \item \spxentry{create\_iteration\_state()}\spxextra{idmtools\_calib... ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.161 \item \spxentry{create\_iteration\_state()}\spxextra{idmtools\_calib... ! Missing $ inserted. $ l.161 \item \spxentry{create\_iteration\_state()}\spxextra{idmtools\_calib... ! Missing } inserted. } l.161 \item \spxentry{create\_iteration\_state()}\spxextra{idmtools\_calib... [42] Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\T1/pcr/m/n/10 create_iteration_state() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 161--163 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 163--165 []\T1/pcr/m/n/10 cSubRegion \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in idm- Underfull \hbox (badness 10000) in paragraph at lines 163--165 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.c_sub_region\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 168--170 []\T1/pcr/m/n/10 default_experiment_builder_function() Overfull \hbox (4.57077pt too wide) in paragraph at lines 168--170 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 define_kernel() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 170--172 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tools_calibra.algorithms.fisher_inf_matrix\T1/ptm/m/n/10 ), Overfull \hbox (74.26904pt too wide) in paragraph at lines 185--187 []\T1/pcr/m/n/10 DYNAMIC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.resa mplers.calibration_point.CalibrationPoint Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (134.17853pt too wide) in paragraph at lines 190--192 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 192--194 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 192--194 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 194--196 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (80.17957pt too wide) in 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end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (69.9406pt too wide) in paragraph at lines 202--204 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB Underfull \hbox (badness 10000) in paragraph at lines 204--206 []\T1/pcr/m/n/10 end_condition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (41.0602pt too wide) in paragraph at lines 204--206 \T1/ptm/m/it/10 tools_calibra.algorithms.separatrix_bhm.SeparatrixBHM Underfull \hbox (badness 10000) in paragraph at lines 206--208 []\T1/pcr/m/n/10 ento_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 208--210 []\T1/pcr/m/n/10 ento_spatial_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 210--212 []\T1/pcr/m/n/10 ep_predict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 210--212 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 212--214 []\T1/pcr/m/n/10 euclidean_distance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e idm- Underfull \hbox (badness 10000) in paragraph at lines 216--217 []\T1/pcr/m/n/10 evaluate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.a lgorithms.gpc.GPC Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 expectation_propagation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 217--219 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 222--224 []\T1/pcr/m/n/10 finalize_calibration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 222--224 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 224--226 []\T1/pcr/m/n/10 find_posterior_mode() \T1/ptm/m/n/10 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Missing $ inserted. $ l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... ! Missing $ inserted. $ l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... ! Missing } inserted. } l.248 \item \spxentry{fun\_ci\_builder()} \spxextra{in module idmtools\_cal... 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tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Overfull \hbox (54.59044pt too wide) in paragraph at lines 256--258 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 258--260 []\T1/pcr/m/n/10 fun_order_region() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 258--260 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 260--262 []\T1/pcr/m/n/10 fun_order_subregion() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 260--262 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 262--264 []\T1/pcr/m/n/10 fun_plot2D() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull 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tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 270--272 []\T1/pcr/m/n/10 fun_quantile_update() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 270--272 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 272--274 []\T1/pcr/m/n/10 fun_reg_branching() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 272--274 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 8113) in paragraph at lines 274--276 []\T1/pcr/m/n/10 fun_replication_update() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 274--276 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 276--278 []\T1/pcr/m/n/10 fun_results_organizer_deterministic() Underfull \hbox (badness 10000) in paragraph at lines 276--278 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 276--278 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 278--280 []\T1/pcr/m/n/10 fun_results_organizer_noise() Underfull \hbox (badness 10000) in paragraph at lines 278--280 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 278--280 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Overfull \hbox (28.1225pt too wide) in paragraph at lines 280--282 []\T1/pcr/m/n/10 fun_sample_points_generator_deterministic() Underfull \hbox (badness 10000) in paragraph at lines 280--282 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 280--282 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 282--284 []\T1/pcr/m/n/10 fun_sample_points_generator_noise() Underfull \hbox (badness 10000) in paragraph at lines 282--284 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 282--284 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 284--286 []\T1/pcr/m/n/10 fun_worst_indicator() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le idm- Overfull \hbox (54.59044pt too wide) in paragraph at lines 284--286 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.fun_pbnb_support_functions\T1/ptm /m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 func_wrapper() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 286--288 \T1/ptm/m/it/10 tools_calibra.algorithms.gpc.GPC static Overfull \hbox (6.2203pt too wide) in paragraph at lines 288--290 []\T1/pcr/m/n/10 functions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra. prior.MultiVariatePrior Underfull \hbox (badness 10000) in paragraph at lines 293--295 []\T1/pcr/m/n/10 gamma_poisson() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm - Underfull \hbox (badness 10000) in paragraph at lines 295--297 []\T1/pcr/m/n/10 gamma_poisson_pandas() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule idm- Underfull \hbox (badness 10000) in paragraph at lines 297--299 []\T1/pcr/m/n/10 garki_ento_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule i dm- Underfull \hbox (badness 10000) in paragraph at lines 299--301 []\T1/pcr/m/n/10 garki_multi_year_ento_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 301--303 []\T1/pcr/m/n/10 generate_perturbed_points() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Overfull \hbox (172.3389pt too wide) in paragraph at lines 301--303 \T1/ptm/m/it/10 tools_calibra.resamplers.random_perturbation_resampler.RandomPe rturbationResampler Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/pcr/m/n/10 generate_samples_from_df() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm - Overfull \hbox (80.17957pt too wide) in paragraph at lines 303--305 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/pcr/m/n/10 generate_variables_from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 305--307 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 GenericIterativeNextPoint \T1/ptm/m/n/10 (\T1/ptm/m/it/10 clas s in idm- Overfull \hbox (32.7498pt too wide) in paragraph at lines 307--309 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 309--311 []\T1/pcr/m/n/10 get_analyzer_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (31.2794pt too wide) in paragraph at lines 309--311 \T1/ptm/m/it/10 tools_calibra.plotters.site_data_plotter.SiteDataPlotter Underfull \hbox (badness 10000) in paragraph at lines 311--313 []\T1/pcr/m/n/10 get_analyzers() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 311--313 \T1/ptm/m/it/10 tools_calibra.calib_site.CalibSite method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 313--315 []\T1/pcr/m/n/10 get_attribute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (52.0398pt too wide) in paragraph at lines 313--315 \T1/ptm/m/it/10 tools_calibra.resamplers.calibration_point.CalibrationPoint Underfull \hbox (badness 10000) in paragraph at lines 315--316 []\T1/pcr/m/n/10 get_bins() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.p rior.SampleRange Underfull \hbox (badness 10000) in paragraph at lines 316--318 []\T1/pcr/m/n/10 get_bins_for_summary_grouping() Underfull \hbox (badness 10000) in paragraph at lines 316--318 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 316--318 \T1/ptm/m/it/10 tools_calibra.analyzers.malaria_summary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 318--320 []\T1/pcr/m/n/10 get_calibrated_points() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (19.18066pt too wide) in paragraph at lines 318--320 \T1/ptm/m/it/10 tools_calibra.resample_manager.ResampleManager Underfull \hbox (badness 10000) in paragraph at lines 320--322 []\T1/pcr/m/n/10 get_even_spaced_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 320--322 \T1/ptm/m/it/10 tools_calibra.prior.SampleFunctionContainer ! Missing $ inserted. $ l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... ! Missing $ inserted. $ l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... ! Missing } inserted. } l.322 \item \spxentry{get\_final\_samples()}\spxextra{idmtools\_calibra.al... [44] Underfull \hbox (badness 10000) in paragraph at lines 322--324 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (134.17853pt too wide) in paragraph at lines 322--324 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 324--326 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 324--326 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 326--328 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (80.17957pt too wide) in paragraph at lines 326--328 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 328--330 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 328--330 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tool.OptimTool Underfull \hbox (badness 10000) in paragraph at lines 330--332 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (52.1302pt too wide) in paragraph at lines 330--332 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO Underfull \hbox (badness 10000) in paragraph at lines 332--334 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (48.80013pt too wide) in paragraph at lines 332--334 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (69.9406pt too wide) in paragraph at lines 334--336 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB Underfull \hbox (badness 10000) in paragraph at lines 336--338 []\T1/pcr/m/n/10 get_final_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (41.0602pt too wide) in paragraph at lines 336--338 \T1/ptm/m/it/10 tools_calibra.algorithms.separatrix_bhm.SeparatrixBHM Underfull \hbox (badness 10000) in paragraph at lines 338--340 []\T1/pcr/m/n/10 get_grouping_for_summary_channel() Underfull \hbox (badness 10000) in paragraph at lines 338--340 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 338--340 \T1/ptm/m/it/10 tools_calibra.analyzers.malaria_summary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/pcr/m/n/10 get_iteration_directory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 340--342 \T1/ptm/m/it/10 tools_calibra.plotters.base_plotter.BasePlotter Underfull \hbox (badness 10000) in paragraph at lines 342--344 []\T1/pcr/m/n/10 get_last_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 342--344 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 344--346 []\T1/pcr/m/n/10 get_next_samples_for_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/ 10 idm- Underfull \hbox (badness 10000) in paragraph at lines 344--346 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 346--348 []\T1/pcr/m/n/10 get_param_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (134.17853pt too wide) in paragraph at lines 346--348 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\T1/pcr/m/n/10 get_param_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 348--350 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 350--352 []\T1/pcr/m/n/10 get_param_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (80.17957pt too wide) in paragraph at lines 350--352 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 352--354 []\T1/pcr/m/n/10 get_param_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 352--354 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tool.OptimTool Underfull \hbox (badness 10000) in paragraph at lines 354--356 []\T1/pcr/m/n/10 get_param_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (52.1302pt too wide) in paragraph at lines 354--356 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO Underfull \hbox (badness 10000) in paragraph at lines 356--358 []\T1/pcr/m/n/10 get_param_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox 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lines 364--366 []\T1/pcr/m/n/10 get_parameter_sets_with_likelihoods() Overfull \hbox (4.57077pt too wide) in paragraph at lines 364--366 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 366--368 []\T1/pcr/m/n/10 get_parameter_sets_with_likelihoods() Underfull \hbox (badness 10000) in paragraph at lines 366--368 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.iteration_state.IterationStat e Underfull \hbox (badness 10000) in paragraph at lines 368--370 []\T1/pcr/m/n/10 get_plot_directory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 368--370 \T1/ptm/m/it/10 tools_calibra.plotters.base_plotter.BasePlotter Overfull \hbox (22.14032pt too wide) in paragraph at lines 370--372 []\T1/pcr/m/n/10 get_r() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.algo rithms.optim_tool.OptimTool Underfull \hbox (badness 10000) in paragraph at lines 372--374 []\T1/pcr/m/n/10 get_reference_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 372--374 \T1/ptm/m/it/10 tools_calibra.calib_site.CalibSite method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 374--376 []\T1/pcr/m/n/10 get_results_to_cache() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (134.17853pt too wide) in paragraph at lines 374--376 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 376--378 []\T1/pcr/m/n/10 get_results_to_cache() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (80.17957pt too wide) in paragraph at lines 376--378 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 378--380 []\T1/pcr/m/n/10 get_results_to_cache() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Overfull \hbox (69.9406pt too wide) in paragraph at lines 378--380 \T1/ptm/m/it/10 tools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB Underfull \hbox (badness 10000) in paragraph at lines 380--382 []\T1/pcr/m/n/10 get_risk_by_distance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule idm- Underfull \hbox (badness 10000) in paragraph at lines 382--384 []\T1/pcr/m/n/10 get_sample_function() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 382--384 \T1/ptm/m/it/10 tools_calibra.prior.SampleRange method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/pcr/m/n/10 get_samples_for_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Overfull \hbox (134.17853pt too wide) in paragraph at lines 384--386 \T1/ptm/m/it/10 tools_calibra.algorithms.generic_iterative_next_point.GenericIt erativeNextPoint Underfull \hbox (badness 10000) in paragraph at lines 386--388 []\T1/pcr/m/n/10 get_samples_for_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Underfull \hbox (badness 10000) in paragraph at lines 386--388 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 388--390 []\T1/pcr/m/n/10 get_samples_for_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Overfull \hbox (80.17957pt too wide) in paragraph at lines 388--390 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm.NextPointAlgorith m Underfull \hbox (badness 10000) in paragraph at lines 390--392 []\T1/pcr/m/n/10 get_samples_for_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Underfull \hbox (badness 10000) in paragraph at lines 390--392 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tool.OptimTool Underfull \hbox (badness 10000) in paragraph at lines 392--394 []\T1/pcr/m/n/10 get_samples_for_iteration() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 id m- Overfull \hbox (52.1302pt too wide) in paragraph at lines 392--394 \T1/ptm/m/it/10 tools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO ! Missing $ inserted. $ l.394 \item \spxentry{get\_samples\_for\_iteration()}\spxextra{idmtools\_c... ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.394 \item \spxentry{get\_samples\_for\_iteration()}\spxextra{idmtools\_c... ! Missing $ inserted. $ l.394 \item \spxentry{get\_samples\_for\_iteration()}\spxextra{idmtools\_c... ! Missing } inserted. } l.394 \item \spxentry{get\_samples\_for\_iteration()}\spxextra{idmtools\_c... 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Missing } inserted. } l.704 \item \spxentry{module} [48] Overfull \hbox (62.6225pt too wide) in paragraph at lines 707--708 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.fisher_inf_matrix\T1/ptm/m/n/10 , Overfull \hbox (128.6225pt too wide) in paragraph at lines 708--710 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.generic_iterative_next_point\T1/ ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 712--713 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.next_point_algorithm\T1/ptm/m/n/ 10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 713--714 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.optim_tool\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 714--715 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.optim_tools_pspo\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 715--716 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.optim_tools_spsa\T1/ptm/m/n/10 , Overfull \hbox (62.6225pt too wide) in paragraph at lines 717--718 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.pbnb.c_sub_region\T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 718--720 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions\ T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 720--722 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting\ T1/ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 722--723 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.pbnb.optim_tool_pbnb\T1/ptm/m/n/ 10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 723--724 []| \T1/pcr/m/n/10 idmtools_calibra.algorithms.separatrix_bhm\T1/ptm/m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 725--726 []| \T1/pcr/m/n/10 idmtools_calibra.analyzers.base_calibration_analyzer\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 726--727 []| \T1/pcr/m/n/10 idmtools_calibra.analyzers.helpers\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 727--728 []| \T1/pcr/m/n/10 idmtools_calibra.analyzers.malaria_summary\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 731--732 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.biting_risk\T1/ptm/m/n/10 , Overfull \hbox (140.6225pt too wide) in paragraph at lines 732--734 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.dengue_bednets_irs_vaccines\T 1/ptm/m/n/10 , Overfull \hbox (62.6225pt too wide) in paragraph at lines 734--735 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.empty_campaign\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 735--736 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.habitat_scale\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 736--737 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.heg\T1/ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 737--738 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.incidence_counter\T1/ptm/m/n/ 10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 738--739 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.input_EIR\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 739--740 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.irs\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 740--741 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.itn\T1/ptm/m/n/10 , Overfull \hbox (62.6225pt too wide) in paragraph at lines 741--742 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.itn_age_season\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 742--743 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.ivermectin\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 743--744 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.migrate_to\T1/ptm/m/n/10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 744--745 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.mosquito_release\T1/ptm/m/n/1 0 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 745--746 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.novel_vector_control\T1/ptm/m /n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 746--747 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.outbreakindividual\T1/ptm/m/n /10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 747--748 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.outbreakindividualdengue\T1/p tm/m/n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 748--749 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.property_change\T1/ptm/m/n/10 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 749--750 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.seir_initial_seeding\T1/ptm/m /n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 750--751 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.seir_vitaldynamics\T1/ptm/m/n /10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 751--752 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.seirs\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 752--753 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.si_initial_seeding\T1/ptm/m/n /10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 753--754 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_initial_seeding\T1/ptm/m/ n/10 , Overfull \hbox (182.6225pt too wide) in paragraph at lines 754--756 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_vaccinations_a_initial_se eding\T1/ptm/m/n/10 , Overfull \hbox (182.6225pt too wide) in paragraph at lines 756--758 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_vaccinations_b_initial_se eding\T1/ptm/m/n/10 , Overfull \hbox (182.6225pt too wide) in paragraph at lines 758--760 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sir_vaccinations_c_initial_se eding\T1/ptm/m/n/10 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 760--761 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sirs_initial_seeding\T1/ptm/m /n/10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 761--762 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.sis_initial_seeding\T1/ptm/m/ n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 762--763 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.support_scripts\T1/ptm/m/n/10 , Overfull \hbox (158.6225pt too wide) in paragraph at lines 763--765 []| \T1/pcr/m/n/10 idmtools_calibra.interventions.triggered_campaign_delay_even t\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 768--769 []| \T1/pcr/m/n/10 idmtools_calibra.output.output_parser\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 769--770 []| \T1/pcr/m/n/10 idmtools_calibra.output.spatial_output\T1/ptm/m/n/10 , ! Missing $ inserted. $ l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... ! Extra }, or forgotten $. \f@nch@orh ...tle \sphinxheadercomma \py@release } \strut l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... ! Missing $ inserted. $ l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... ! Missing } inserted. } l.772 \subitem \spxentry{idmtools\_calibra.plotters.base\_plotter}, \hyp... [49] Overfull \hbox (20.6225pt too wide) in paragraph at lines 772--773 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.base_plotter\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 773--774 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.likelihood_plotter\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 774--775 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.optim_tool_pbnb_plotter\T1/ptm/m/n /10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 775--776 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.optim_tool_plotter\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 776--777 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.optim_tool_spsa_plotter\T1/ptm/m/n /10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 777--778 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.separatrix_bhm_plotter\T1/ptm/m/n/ 10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 778--779 []| \T1/pcr/m/n/10 idmtools_calibra.plotters.site_data_plotter\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 780--781 []| \T1/pcr/m/n/10 idmtools_calibra.resample_manager\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 782--783 []| \T1/pcr/m/n/10 idmtools_calibra.resamplers.base_resampler\T1/ptm/m/n/10 , Overfull \hbox (62.6225pt too wide) in paragraph at lines 783--784 []| \T1/pcr/m/n/10 idmtools_calibra.resamplers.calibration_point\T1/ptm/m/n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 784--785 []| \T1/pcr/m/n/10 idmtools_calibra.resamplers.calibration_points\T1/ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 785--786 []| \T1/pcr/m/n/10 idmtools_calibra.resamplers.cramer_rao_resampler\T1/ptm/m/n/ 10 , Overfull \hbox (134.6225pt too wide) in paragraph at lines 786--788 []| \T1/pcr/m/n/10 idmtools_calibra.resamplers.random_perturbation_resampler\T1 /ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 789--790 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.demographics\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 790--791 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.demographics.node\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 791--792 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.display\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 792--793 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.distro\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 793--794 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.emod_malaria_sim\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 794--795 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.encoding\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 795--796 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 796--797 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic.climate\T1/ptm/m/n/10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 797--798 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic.demographics\T1/ptm/m/n/1 0 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 798--799 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic.disease\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 799--800 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic.geography\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 800--801 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic.migration\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 801--802 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.generic.params\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 802--803 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.helper\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 803--804 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.mod_fn\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 804--805 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 805--806 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.bin2np\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 806--807 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.dict2pd\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 807--808 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.JSON\T1/ptm/m/n/10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 808--809 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.malaria_summary\T1/ptm/m/ n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 809--810 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.np2json\T1/ptm/m/n/10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 810--811 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.np2pd\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 811--812 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.parsers.pd2csv\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 812--813 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports\T1/ptm/m/n/10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 813--814 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports.base_age_hist_report\T1/p tm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 814--815 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports.custom_report\T1/ptm/m/n/ 10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 815--816 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.reports.vector_report\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 816--817 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.vector\T1/ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 817--818 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.vector.larval_habitat\T1/ptm/m/n/ 10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 818--819 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.vector.params\T1/ptm/m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 819--820 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.vector.species\T1/ptm/m/n/10 , Overfull \hbox (62.6225pt too wide) in paragraph at lines 820--821 []| \T1/pcr/m/n/10 idmtools_calibra.utilities.vector.study_sites\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 822--824 []\T1/pcr/m/n/10 multi_year_ento_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule idm- Underfull \hbox (badness 10000) in paragraph at lines 826--827 []\T1/pcr/m/n/10 MultiVariatePrior \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in idm - Underfull \hbox (badness 10000) in paragraph at lines 832--834 []\T1/pcr/m/n/10 near_pd() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule idm- Underfull \hbox (badness 10000) in paragraph at lines 832--834 \T1/ptm/m/it/10 tools_calibra.algorithms.fisher_inf_matrix\T1/ptm/m/n/10 ), ! Missing $ inserted. $ l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... ! Extra }, or forgotten $. \f@nch@elh ...tle \sphinxheadercomma \py@release } \strut l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... ! Missing $ inserted. $ l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... ! Missing } inserted. } l.836 \item \spxentry{negative\_log\_marginal\_likelihood\_and\_gradient()... [50] Overfull \hbox (52.1225pt too wide) in paragraph at lines 836--838 []\T1/pcr/m/n/10 negative_log_marginal_likelihood_and_gradient() Underfull \hbox (badness 10000) in paragraph at lines 836--838 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.algorithms.gpc.GPC Underfull \hbox (badness 10000) in paragraph at lines 838--840 []\T1/pcr/m/n/10 next_point \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.u tils.StatusPoint Underfull \hbox (badness 10000) in paragraph at lines 840--842 []\T1/pcr/m/n/10 next_point_fn() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 840--842 \T1/ptm/m/it/10 tools_calibra.algorithms.imis.IMIS method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 842--844 []\T1/pcr/m/n/10 next_point_step() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 842--844 \T1/ptm/m/it/10 tools_calibra.iteration_state.IterationState Underfull \hbox (badness 10000) in paragraph at lines 844--846 []\T1/pcr/m/n/10 NextPointAlgorithm \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in id m- Overfull \hbox (3.95042pt too wide) in paragraph at lines 844--846 \T1/ptm/m/it/10 tools_calibra.algorithms.next_point_algorithm\T1/ptm/m/n/10 ), Overfull \hbox (62.26904pt too wide) in paragraph at lines 846--848 []\T1/pcr/m/n/10 NUMPY \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm-tools_calibra.resamp lers.calibration_point.CalibrationPoint Underfull \hbox (badness 10000) in paragraph at lines 851--853 []\T1/pcr/m/n/10 open_for_reading() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm- Underfull \hbox (badness 10000) in paragraph at lines 851--853 \T1/ptm/m/it/10 tools_calibra.calib_manager.CalibManager Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/pcr/m/n/10 optimize_hyperparameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 idm - 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tools_calibra.resample_manager.ResampleManager ! 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