Read the Docs build information
Build id: 898597
Project: institute-for-disease-modeling-phylomodels
Version: latest
Commit: 037437e91ebe05e9e423dd505c639d4ce32cbd4a
Date: 2022-03-28T22:47:47.903837Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-03-28T22:48:15.098423Z, end-time: 2022-03-28T22:48:17.958743Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/phyloModels.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-03-28T22:48:18.145024Z, end-time: 2022-03-28T22:48:18.320701Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 037437e Merge pull request #58 from JSchripsema-IDM/jinja2

[rtd-command-info] start-time: 2022-03-28T22:48:18.495416Z, end-time: 2022-03-28T22:48:18.559010Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-03-28T22:48:19.773939Z, end-time: 2022-03-28T22:48:26.779499Z, duration: 7, exit-code: 0
python3.8 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.8.6'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-03-28T22:48:26.955976Z, end-time: 2022-03-28T22:48:29.500360Z, duration: 2, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (22.0.4)
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[rtd-command-info] start-time: 2022-03-28T22:48:29.671985Z, end-time: 2022-03-28T22:49:03.197340Z, duration: 33, exit-code: 0
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Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed Jinja2-3.1.1 MarkupSafe-2.1.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.11.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 setuptools-58.2.0 snowballstemmer-2.2.0 sphinx-4.5.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-1.26.9 zipp-3.7.0

[rtd-command-info] start-time: 2022-03-28T22:49:03.361616Z, end-time: 2022-03-28T22:50:25.697112Z, duration: 82, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Building wheels for collected packages: ete3, pyDOE
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Installing collected packages: webencodings, wcwidth, Wand, tbb, Send2Trash, PyQt5-Qt5, pure-eval, ptyprocess, pickleshare, mistune, ipython-genutils, intel-openmp, executing, ete3, backcall, xlrd, tzdata, traitlets, tornado, threadpoolctl, testpath, soupsieve, scipy, pyzmq, pyrsistent, PyQt5-sip, pycparser, psutil, prompt-toolkit, prometheus-client, pillow, pexpect, patsy, parso, pandocfilters, ngesh, networkx, nest-asyncio, mkl, lxml, jupyterlab-widgets, jupyterlab-pygments, joblib, importlib-resources, et-xmlfile, entrypoints, defusedxml, decorator, debugpy, backports.zoneinfo, attrs, asttokens, unittest-xml-reporting, terminado, stack-data, scikit-learn, qtpy, pytz-deprecation-shim, PyQt5, pyDOE, openpyxl, numexpr, matplotlib-inline, jupyter-core, jsonschema, jedi, cffi, bleach, beautifulsoup4, tzlocal, tables, statsmodels, seaborn, nbformat, jupyter-client, ipython, argon2-cffi-bindings, nbclient, ipykernel, argon2-cffi, qtconsole, nbconvert, jupyter-console, notebook, widgetsnbextension, ipywidgets, jupyter
  Attempting uninstall: pillow
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    Uninstalling Pillow-5.4.1:
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Successfully installed PyQt5-5.15.6 PyQt5-Qt5-5.15.2 PyQt5-sip-12.9.1 Send2Trash-1.8.0 Wand-0.6.7 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 asttokens-2.0.5 attrs-21.4.0 backcall-0.2.0 backports.zoneinfo-0.2.1 beautifulsoup4-4.10.0 bleach-4.1.0 cffi-1.15.0 debugpy-1.6.0 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 et-xmlfile-1.1.0 ete3-3.1.2 executing-0.8.3 importlib-resources-5.6.0 intel-openmp-2022.0.2 ipykernel-6.10.0 ipython-8.2.0 ipython-genutils-0.2.0 ipywidgets-7.7.0 jedi-0.18.1 joblib-1.1.0 jsonschema-4.4.0 jupyter-1.0.0 jupyter-client-7.1.2 jupyter-console-6.4.3 jupyter-core-4.9.2 jupyterlab-pygments-0.1.2 jupyterlab-widgets-1.1.0 lxml-4.8.0 matplotlib-inline-0.1.3 mistune-0.8.4 mkl-2022.0.2 nbclient-0.5.13 nbconvert-6.4.5 nbformat-5.2.0 nest-asyncio-1.5.4 networkx-2.7.1 ngesh-1.1.1 notebook-6.4.10 numexpr-2.8.1 openpyxl-3.0.9 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.0.1 prometheus-client-0.13.1 prompt-toolkit-3.0.28 psutil-5.9.0 ptyprocess-0.7.0 pure-eval-0.2.2 pyDOE-0.3.8 pycparser-2.21 pyrsistent-0.18.1 pytz-deprecation-shim-0.1.0.post0 pyzmq-22.3.0 qtconsole-5.3.0 qtpy-2.0.1 scikit-learn-1.0.2 scipy-1.8.0 seaborn-0.11.2 soupsieve-2.3.1 stack-data-0.2.0 statsmodels-0.13.2 tables-3.7.0 tbb-2021.5.1 terminado-0.13.3 testpath-0.6.0 threadpoolctl-3.1.0 tornado-6.1 traitlets-5.1.1 tzdata-2022.1 tzlocal-4.1 unittest-xml-reporting-3.2.0 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.6.0 xlrd-2.0.1

[rtd-command-info] start-time: 2022-03-28T22:50:25.937971Z, end-time: 2022-03-28T22:50:32.777652Z, duration: 6, exit-code: 0
python ./setup.py install --force
running install
running bdist_egg
running egg_info
creating phyloModels.egg-info
writing phyloModels.egg-info/PKG-INFO
writing dependency_links to phyloModels.egg-info/dependency_links.txt
writing requirements to phyloModels.egg-info/requires.txt
writing top-level names to phyloModels.egg-info/top_level.txt
writing manifest file 'phyloModels.egg-info/SOURCES.txt'
reading manifest file 'phyloModels.egg-info/SOURCES.txt'
writing manifest file 'phyloModels.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/phylomodels
copying phylomodels/__init__.py -> build/lib/phylomodels
creating build/lib/phylomodels/calibration
copying phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/lib/phylomodels/calibration
copying phylomodels/calibration/cal_parameterSweep.py -> build/lib/phylomodels/calibration
copying phylomodels/calibration/constants.py -> build/lib/phylomodels/calibration
copying phylomodels/calibration/init_historyMatching_base.py -> build/lib/phylomodels/calibration
copying phylomodels/calibration/__init__.py -> build/lib/phylomodels/calibration
creating build/lib/phylomodels/sampling
copying phylomodels/sampling/sample_treeIndependent.py -> build/lib/phylomodels/sampling
copying phylomodels/sampling/__init__.py -> build/lib/phylomodels/sampling
creating build/lib/phylomodels/network
copying phylomodels/network/phyloTree.py -> build/lib/phylomodels/network
copying phylomodels/network/__init__.py -> build/lib/phylomodels/network
creating build/lib/phylomodels/utilities
copying phylomodels/utilities/__init__.py -> build/lib/phylomodels/utilities
creating build/lib/phylomodels/features
copying phylomodels/features/testFeatures.py -> build/lib/phylomodels/features
copying phylomodels/features/features.py -> build/lib/phylomodels/features
copying phylomodels/features/test.py -> build/lib/phylomodels/features
copying phylomodels/features/__init__.py -> build/lib/phylomodels/features
copying phylomodels/features/inventory.py -> build/lib/phylomodels/features
creating build/lib/phylomodels/visualization
copying phylomodels/visualization/parallelCoordinates.py -> build/lib/phylomodels/visualization
copying phylomodels/visualization/__init__.py -> build/lib/phylomodels/visualization
creating build/lib/phylomodels/models
copying phylomodels/models/distributions_gaussian.py -> build/lib/phylomodels/models
copying phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models
copying phylomodels/models/test_distributions_gaussian.py -> build/lib/phylomodels/models
copying phylomodels/models/sir_taoLeap_getIncidence.py -> build/lib/phylomodels/models
copying phylomodels/models/test_sir_taoLeap_getIncidence.py -> build/lib/phylomodels/models
copying phylomodels/models/sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models
copying phylomodels/models/__init__.py -> build/lib/phylomodels/models
copying phylomodels/models/seir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models
creating build/lib/phylomodels/examples
copying phylomodels/examples/__init__.py -> build/lib/phylomodels/examples
creating build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/fano.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/skew.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/mean.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/qcd.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/rsd.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/__init__.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/var.py -> build/lib/phylomodels/features/statistics
copying phylomodels/features/statistics/std.py -> build/lib/phylomodels/features/statistics
creating build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_WD_ratio.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_ratio_min.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/local_calculate_frac_basal.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_max_adj_eigen.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_sackin_var.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_skewness.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_t_max_lineages.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/netSci_calculate_closeness_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_ratio_median.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_sackin.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_B1.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/smallConfig_calculate_cherries.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_max_lineages.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_median.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_slope_1.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_min.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/calculate_external_branch_length_metrics.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_external_min.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_external_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_frac_imbalance.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_FurnasR.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_slope_ratio.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/local_calculate_LBI_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_std.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/tree_height_calculate_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_ratio_std.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/netSci_calculate_mean_path.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_mean_b_time.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_max_dW.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_min_lap_eigen.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_mode.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/netSci_calculate_betweenness_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_kurtosis.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_external_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/tree_height_calculate_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_external_median.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/mean_NN_distance.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_internal_min.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_frac_ladder.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_colless.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_median.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_internal_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_ratio_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/spectral_calculate_min_adj_eigen.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_internal_max.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_external_std.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/smallConfig_calculate_fourprong.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_std.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_slope_2.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_internal_std.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/tree_height_calculate_min.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/LTT_calculate_mean_s_time.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/netSci_calculate_diameter.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_min.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/__init__.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/group_calculate_num.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_mean.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/BL_calculate_internal_median.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_max_ladder.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/top_calculate_B2.py -> build/lib/phylomodels/features/trees
copying phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> build/lib/phylomodels/features/trees
creating build/lib/phylomodels/features/series
copying phylomodels/features/series/series_partialSum15.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_diff.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_diff_L2.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_partialSum30.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative2_gaussianFit.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_partialSum2.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative2_cauchyFit.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_diff_Linf.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_partialSum10.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative2.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative2_laplaceFit.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative_gaussianFit.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_partialSum7.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_sum.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/__init__.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_sum_log10.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_log10.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_diff_L1.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative_laplaceFit.py -> build/lib/phylomodels/features/series
copying phylomodels/features/series/series_derivative_cauchyFit.py -> build/lib/phylomodels/features/series
creating build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/process_optional_arguements.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/unique_node_attr.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_node_properties.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/check_values.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_groups.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_LTT.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_eigenvalues_lap.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/calculate_branch_length_metrics.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_adjacency_mat.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_eigenvalues_adj.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/get_distance_mat.py -> build/lib/phylomodels/features/trees/helper
copying phylomodels/features/trees/helper/__init__.py -> build/lib/phylomodels/features/trees/helper
creating build/lib/phylomodels/models/seir_taoLeap
copying phylomodels/models/seir_taoLeap/seirTaoLeap.py -> build/lib/phylomodels/models/seir_taoLeap
copying phylomodels/models/seir_taoLeap/__init__.py -> build/lib/phylomodels/models/seir_taoLeap
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/phylomodels
creating build/bdist.linux-x86_64/egg/phylomodels/calibration
copying build/lib/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration
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creating build/bdist.linux-x86_64/egg/phylomodels/network
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creating build/bdist.linux-x86_64/egg/phylomodels/utilities
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creating build/bdist.linux-x86_64/egg/phylomodels/features
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creating build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper
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Processing dependencies for phyloModels==0.5
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Downloading https://files.pythonhosted.org/packages/d4/bf/d884da8e2f7096d201c891d515eb6813a8e85df5eb6f5e12e867bf1d831c/PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl#sha256=ac1eb5a114b6e7788e8be378be41c5e54b17d5158994504e85e43b5fca006a39
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Installing PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/PyQt5-5.11.3-py3.8-linux-x86_64.egg
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Downloading https://files.pythonhosted.org/packages/27/04/3348131511d6bf95b3d121a1d5543132cd663a4452c7ad7869428c4fbfa6/sip-6.5.1-cp36-abi3-manylinux2014_x86_64.whl#sha256=13b09357615c2d8bcb23bf21c1637941ac8ff5f28b346c1ccad7efafa57673e9
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Installing sip-sdist script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing sip-wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/sip-6.5.1-py3.8-linux-x86_64.egg
Searching for PyQt5_sip<4.20,>=4.19.11
Reading https://pypi.org/simple/PyQt5_sip/
Downloading https://files.pythonhosted.org/packages/c2/70/eb9d398ecbcab83e9a968fa63336a16b21034bbd4e318128fe11e08bffab/PyQt5_sip-4.19.19-cp38-cp38-manylinux1_x86_64.whl#sha256=304acf771b6033cb4bafc415939d227c91265d30664ed643b298d7e95f509f81
Best match: PyQt5-sip 4.19.19
Processing PyQt5_sip-4.19.19-cp38-cp38-manylinux1_x86_64.whl
Installing PyQt5_sip-4.19.19-cp38-cp38-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Adding PyQt5-sip 4.19.19 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/PyQt5_sip-4.19.19-py3.8-linux-x86_64.egg
Searching for toml
Reading https://pypi.org/simple/toml/
Downloading https://files.pythonhosted.org/packages/44/6f/7120676b6d73228c96e17f1f794d8ab046fc910d781c8d151120c3f1569e/toml-0.10.2-py2.py3-none-any.whl#sha256=806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b
Best match: toml 0.10.2
Processing toml-0.10.2-py2.py3-none-any.whl
Installing toml-0.10.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Adding toml 0.10.2 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/toml-0.10.2-py3.8.egg
Searching for xlrd==2.0.1
Best match: xlrd 2.0.1
Adding xlrd 2.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for openpyxl==3.0.9
Best match: openpyxl 3.0.9
Adding openpyxl 3.0.9 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for unittest-xml-reporting==3.2.0
Best match: unittest-xml-reporting 3.2.0
Adding unittest-xml-reporting 3.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for psutil==5.9.0
Best match: psutil 5.9.0
Adding psutil 5.9.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jupyter-client==7.1.2
Best match: jupyter-client 7.1.2
Adding jupyter-client 7.1.2 to easy-install.pth file
Installing jupyter-kernel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-kernelspec script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-run script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jupyter-console==6.4.3
Best match: jupyter-console 6.4.3
Adding jupyter-console 6.4.3 to easy-install.pth file
Installing jupyter-console script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jupyter-core==4.9.2
Best match: jupyter-core 4.9.2
Adding jupyter-core 4.9.2 to easy-install.pth file
Installing jupyter script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-migrate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-troubleshoot script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jupyter==1.0.0
Best match: jupyter 1.0.0
Adding jupyter 1.0.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for scikit-learn==1.0.2
Best match: scikit-learn 1.0.2
Adding scikit-learn 1.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for mkl==2022.0.2
Best match: mkl 2022.0.2
Adding mkl 2022.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for seaborn==0.11.2
Best match: seaborn 0.11.2
Adding seaborn 0.11.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for matplotlib==3.3.2
Best match: matplotlib 3.3.2
Adding matplotlib 3.3.2 to easy-install.pth file

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for pandas==1.1.3
Best match: pandas 1.1.3
pandas 1.1.3 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for networkx==2.7.1
Best match: networkx 2.7.1
Adding networkx 2.7.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for ete3==3.1.2
Best match: ete3 3.1.2
Adding ete3 3.1.2 to easy-install.pth file
Installing ete3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for six==1.15.0
Best match: six 1.15.0
six 1.15.0 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for lxml==4.8.0
Best match: lxml 4.8.0
Adding lxml 4.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for scipy==1.8.0
Best match: scipy 1.8.0
Adding scipy 1.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for numpy==1.19.2
Best match: numpy 1.19.2
numpy 1.19.2 is already the active version in easy-install.pth
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing f2py3.8 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for et-xmlfile==1.1.0
Best match: et-xmlfile 1.1.0
Adding et-xmlfile 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for nest-asyncio==1.5.4
Best match: nest-asyncio 1.5.4
Adding nest-asyncio 1.5.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for tornado==6.1
Best match: tornado 6.1
Adding tornado 6.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for traitlets==5.1.1
Best match: traitlets 5.1.1
Adding traitlets 5.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pyzmq==22.3.0
Best match: pyzmq 22.3.0
Adding pyzmq 22.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
python-dateutil 2.8.1 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for entrypoints==0.4
Best match: entrypoints 0.4
Adding entrypoints 0.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for ipython==8.2.0
Best match: ipython 8.2.0
Adding ipython 8.2.0 to easy-install.pth file
Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for Pygments==2.11.2
Best match: Pygments 2.11.2
Adding Pygments 2.11.2 to easy-install.pth file
Installing pygmentize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for ipykernel==6.10.0
Best match: ipykernel 6.10.0
Adding ipykernel 6.10.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for prompt-toolkit==3.0.28
Best match: prompt-toolkit 3.0.28
Adding prompt-toolkit 3.0.28 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for nbconvert==6.4.5
Best match: nbconvert 6.4.5
Adding nbconvert 6.4.5 to easy-install.pth file
Installing jupyter-dejavu script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-nbconvert script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for ipywidgets==7.7.0
Best match: ipywidgets 7.7.0
Adding ipywidgets 7.7.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for notebook==6.4.10
Best match: notebook 6.4.10
Adding notebook 6.4.10 to easy-install.pth file
Installing jupyter-bundlerextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-nbextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-notebook script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin
Installing jupyter-serverextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for qtconsole==5.3.0
Best match: qtconsole 5.3.0
Adding qtconsole 5.3.0 to easy-install.pth file
Installing jupyter-qtconsole script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for joblib==1.1.0
Best match: joblib 1.1.0
Adding joblib 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for threadpoolctl==3.1.0
Best match: threadpoolctl 3.1.0
Adding threadpoolctl 3.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for intel-openmp==2022.0.2
Best match: intel-openmp 2022.0.2
Adding intel-openmp 2022.0.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for tbb==2021.5.1
Best match: tbb 2021.5.1
Adding tbb 2021.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for cycler==0.10.0
Best match: cycler 0.10.0
cycler 0.10.0 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for kiwisolver==1.2.0
Best match: kiwisolver 1.2.0
kiwisolver 1.2.0 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages
Searching for certifi==2021.10.8
Best match: certifi 2021.10.8
Adding certifi 2021.10.8 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pyparsing==3.0.7
Best match: pyparsing 3.0.7
Adding pyparsing 3.0.7 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for Pillow==9.0.1
Best match: Pillow 9.0.1
Adding Pillow 9.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pytz==2022.1
Best match: pytz 2022.1
Adding pytz 2022.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for setuptools==58.2.0
Best match: setuptools 58.2.0
Adding setuptools 58.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for packaging==21.3
Best match: packaging 21.3
Adding packaging 21.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for matplotlib-inline==0.1.3
Best match: matplotlib-inline 0.1.3
Adding matplotlib-inline 0.1.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for decorator==5.1.1
Best match: decorator 5.1.1
Adding decorator 5.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pexpect==4.8.0
Best match: pexpect 4.8.0
Adding pexpect 4.8.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for stack-data==0.2.0
Best match: stack-data 0.2.0
Adding stack-data 0.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jedi==0.18.1
Best match: jedi 0.18.1
Adding jedi 0.18.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for backcall==0.2.0
Best match: backcall 0.2.0
Adding backcall 0.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pickleshare==0.7.5
Best match: pickleshare 0.7.5
Adding pickleshare 0.7.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for debugpy==1.6.0
Best match: debugpy 1.6.0
Adding debugpy 1.6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for wcwidth==0.2.5
Best match: wcwidth 0.2.5
Adding wcwidth 0.2.5 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for Jinja2==3.1.1
Best match: Jinja2 3.1.1
Adding Jinja2 3.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for defusedxml==0.7.1
Best match: defusedxml 0.7.1
Adding defusedxml 0.7.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for bleach==4.1.0
Best match: bleach 4.1.0
Adding bleach 4.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pandocfilters==1.5.0
Best match: pandocfilters 1.5.0
Adding pandocfilters 1.5.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jupyterlab-pygments==0.1.2
Best match: jupyterlab-pygments 0.1.2
Adding jupyterlab-pygments 0.1.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for MarkupSafe==2.1.1
Best match: MarkupSafe 2.1.1
Adding MarkupSafe 2.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for nbclient==0.5.13
Best match: nbclient 0.5.13
Adding nbclient 0.5.13 to easy-install.pth file
Installing jupyter-execute script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for beautifulsoup4==4.10.0
Best match: beautifulsoup4 4.10.0
Adding beautifulsoup4 4.10.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for mistune==0.8.4
Best match: mistune 0.8.4
Adding mistune 0.8.4 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for testpath==0.6.0
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Adding testpath 0.6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for nbformat==5.2.0
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Adding nbformat 5.2.0 to easy-install.pth file
Installing jupyter-trust script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for jupyterlab-widgets==1.1.0
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Adding jupyterlab-widgets 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Adding widgetsnbextension 3.6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Adding ipython-genutils 0.2.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Adding terminado 0.13.3 to easy-install.pth file

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Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for argon2-cffi==21.3.0
Best match: argon2-cffi 21.3.0
Adding argon2-cffi 21.3.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for ptyprocess==0.7.0
Best match: ptyprocess 0.7.0
Adding ptyprocess 0.7.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Best match: pure-eval 0.2.2
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Best match: webencodings 0.5.1
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Installing jsonschema script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for argon2-cffi-bindings==21.2.0
Best match: argon2-cffi-bindings 21.2.0
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Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
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Best match: pyrsistent 0.18.1
Adding pyrsistent 0.18.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for attrs==21.4.0
Best match: attrs 21.4.0
Adding attrs 21.4.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for importlib-resources==5.6.0
Best match: importlib-resources 5.6.0
Adding importlib-resources 5.6.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for cffi==1.15.0
Best match: cffi 1.15.0
Adding cffi 1.15.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for zipp==3.7.0
Best match: zipp 3.7.0
Adding zipp 3.7.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Searching for pycparser==2.21
Best match: pycparser 2.21
Adding pycparser 2.21 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages
Finished processing dependencies for phyloModels==0.5

[rtd-command-info] start-time: 2022-03-28T22:50:33.001573Z, end-time: 2022-03-28T22:50:43.148595Z, duration: 10, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting sphinx~=4.4.0
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Collecting docutils<0.18,>=0.14
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Collecting pockets>=0.3
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Installing collected packages: json5, websocket-client, sniffio, pockets, docutils, sphinxcontrib-napoleon, sphinx, plantweb, anyio, sphinxext.remoteliteralinclude, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, nbclassic, jupyterlab
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[rtd-command-info] start-time: 2022-03-28T22:50:44.586261Z, end-time: 2022-03-28T22:50:44.663846Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-
#
# Sphinx Demo docs build configuration file, created by
# sphinx-quickstart on Fri Aug 26 16:52:16 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# docs root, use os.path.abspath to make it absolute, like shown here.
#
import os
import subprocess
import sys
import sphinx_rtd_theme
import configparser
from datetime import datetime

if sys.platform in ["linux", "darwin"]:
    subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
else:
    subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))

# Rename "phylomodels package" to "API reference"
filename = 'modules.rst' # This must match the Makefile
with open(filename) as f: # Read existing file
    lines = f.readlines()
lines[0] = "API reference\n" # Blast away the existing heading and replace with this
lines[1] = "=============\n" # Ensure the heading is the right length
with open(filename, "w") as f: # Write new file
    f.writelines(lines)

# -- General configuration ------------------------------------------------

# If your docs needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.mathjax',
    'sphinx.ext.githubpages',
    'sphinx.ext.autodoc',
    'sphinxcontrib.napoleon',
    'sphinx.ext.todo',
    'plantweb.directive',
    'sphinxcontrib.programoutput',
    'sphinx_copybutton',
    'sphinx.ext.intersphinx',
    'sphinxext.remoteliteralinclude',
    'sphinx.ext.viewcode'
]

plantuml = 'plantweb'

autodoc_default_options = {
    'member-order': 'bysource',
    'members': None,
    'exclude-members': '__all__'
}

autodoc_mock_imports = ['phylomodels.calibration.init_historyMatching',
                        'history_matching',
                        'features',
                        'phylomodels.models.sir_taoLeap']

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'phyloModels'
copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.'
author = u'Institute for Disease Modeling'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
#current_path = os.path.dirname(__file__)
#version_path = os.path.join(current_path, '..', '.bumpversion.cfg')
#config = configparser.ConfigParser()
#config.read(version_path)

#version = config['bumpversion']['current_version']
# The full version, including alpha/beta/rc tags.
# release = u'1.0'

# The language for content autogenerated by Sphinx. Refer to docs
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = 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.
# "<project> v<release> docs" by default.
#
# html_title = u'Sphinx Demo v1.0'

# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
html_logo = "images/IDM_white.png"

# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
html_favicon = "images/favicon.ico"

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']

html_context = {
    'css_files': [
        '_static/theme_overrides.css',
        '_static/copy_button.css'
        ]
}
html_js_files = ['show_block_by_os.js']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the docs.
#
# html_extra_path = []

# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
# html_last_updated_fmt = None

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#
# html_additional_pages = {}

# If false, no module index is generated.
#
# html_domain_indices = True

# If false, no index is generated.
#
# html_use_index = True

# If true, the index is split into individual pages for each letter.
#
# html_split_index = False

# If true, links to the reST sources are added to the pages.
#
html_show_sourcelink = False

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
html_show_sphinx = False

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> 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 = 'phylomodels'

# -- 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, 'phylomodels-docs.tex', u'phylomodels',
     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, 'phylomodels-docs', u'phylomodels',
     [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, 'phylomodels-docs', u'phylomodels',
     author, 'Institute for Disease Modeling', 'How to model phylogenetics with phyloModels.',
     'Miscellaneous'),
]

# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []

# If false, no module index is generated.
#
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
                       'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None),
                       'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None)
                       }




###########################################################################
#          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 shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    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/"),
    ("0.5.1", "/en/0.5.1/"),
    ],
    'downloads': [ 
    ("pdf", "//docs.idmod.org/_/downloads/phylomodels/en/latest/pdf/"),
    ("html", "//docs.idmod.org/_/downloads/phylomodels/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'institute-for-disease-modeling-phylomodels',
    'name': u'phyloModels',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://docs.idmod.org/projects/phylomodels/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': 'phyloModels',
    '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': '037437e9',
}

# 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-phylomodels/builds/898597/'

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: 2022-03-28T22:50:44.833311Z, end-time: 2022-03-28T22:50:55.727476Z, duration: 10, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.4.0
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.idmod.org/projects/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 151 source files that are out of date
updating environment: [new config] 151 added, 0 changed, 0 removed
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reading sources... [ 99%] test
reading sources... [100%] todo

WARNING: autodoc: failed to import module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.cal_parameterSweep' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.constants' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.init_historyMatching_base' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.init_historyMatching_poissonGlmBasis' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'examples' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.features' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.inventory' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_cauchyFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_gaussianFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_laplaceFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_cauchyFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_gaussianFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_laplaceFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_L1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_L2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_Linf' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_log10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum15' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum30' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum7' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_sum' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_sum_log10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.fano' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.qcd' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.rsd' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.skew' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.var' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.test' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.testFeatures' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_max_lineages' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_b_time' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_s_time' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_t_max_lineages' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.calculate_external_branch_length_metrics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_mode' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_num' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.calculate_branch_length_metrics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.check_values' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_LTT' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_adjacency_mat' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_distance_mat' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_adj' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_dist_lap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_lap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_groups' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_node_properties' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.process_optional_arguements' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.unique_node_attr' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.local_calculate_LBI_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.local_calculate_frac_basal' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.mean_NN_distance' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_betweenness_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_closeness_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_diameter' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_eigen_centrality_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_mean_path' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_cherries' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_double_cherries' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_fourprong' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_pitchforks' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_eigen_gap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_kurtosis' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_adj_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_distLap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_lap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_adj_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_lap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_skewness' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_B1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_B2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_FurnasR' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_WD_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_colless' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_imbalance' from module 'phylomodels'; the following exception was raised:
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WARNING: autodoc: failed to import module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.cal_parameterSweep' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.constants' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.init_historyMatching_base' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.init_historyMatching_poissonGlmBasis' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'examples' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.features' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.inventory' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_cauchyFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_gaussianFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_laplaceFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_cauchyFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_gaussianFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_laplaceFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_L1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_L2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_Linf' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_log10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum15' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum30' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum7' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_sum' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_sum_log10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.fano' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.qcd' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.rsd' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.skew' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.var' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.test' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.testFeatures' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_max_lineages' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_b_time' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_s_time' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_t_max_lineages' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.calculate_external_branch_length_metrics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_mode' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_num' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.calculate_branch_length_metrics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.check_values' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_LTT' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_adjacency_mat' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_distance_mat' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_adj' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_dist_lap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_lap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_groups' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_node_properties' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.process_optional_arguements' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.unique_node_attr' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.local_calculate_LBI_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.local_calculate_frac_basal' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.mean_NN_distance' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_betweenness_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_closeness_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_diameter' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_eigen_centrality_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_mean_path' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_cherries' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_double_cherries' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_fourprong' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_pitchforks' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_eigen_gap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_kurtosis' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_adj_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_distLap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_lap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_adj_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_lap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_skewness' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_B1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_B2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_FurnasR' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_WD_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_colless' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_imbalance' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_ladder' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_max_dW' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_max_ladder' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_mean_imbalance_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_sackin' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_sackin_var' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.distributions_gaussian' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.seir_taoLeap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.seir_taoLeap.seirTaoLeap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.seir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.sir_taoLeap_getIncidence' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.sir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.test_distributions_gaussian' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.test_sir_taoLeap_getIncidence' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.test_sir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'network' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'network.phyloTree' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'sampling' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'sampling.sample_treeIndependent' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'utilities' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'visualization' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'visualization.parallelCoordinates' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
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assembling single document... models features calibration test examples modules phylomodels phylomodels.calibration phylomodels.calibration.cal_parameterSweep phylomodels.calibration.constants phylomodels.calibration.init_historyMatching_base phylomodels.calibration.init_historyMatching_poissonGlmBasis phylomodels.examples phylomodels.features phylomodels.features.series phylomodels.features.series.series phylomodels.features.series.series_derivative phylomodels.features.series.series_derivative2 phylomodels.features.series.series_derivative2_cauchyFit phylomodels.features.series.series_derivative2_gaussianFit phylomodels.features.series.series_derivative2_laplaceFit phylomodels.features.series.series_derivative_cauchyFit phylomodels.features.series.series_derivative_gaussianFit phylomodels.features.series.series_derivative_laplaceFit phylomodels.features.series.series_diff phylomodels.features.series.series_diff_L1 phylomodels.features.series.series_diff_L2 phylomodels.features.series.series_diff_Linf phylomodels.features.series.series_log10 phylomodels.features.series.series_partialSum10 phylomodels.features.series.series_partialSum15 phylomodels.features.series.series_partialSum2 phylomodels.features.series.series_partialSum30 phylomodels.features.series.series_partialSum7 phylomodels.features.series.series_sum phylomodels.features.series.series_sum_log10 phylomodels.features.statistics phylomodels.features.statistics.fano phylomodels.features.statistics.mean phylomodels.features.statistics.qcd phylomodels.features.statistics.rsd phylomodels.features.statistics.skew phylomodels.features.statistics.std phylomodels.features.statistics.var phylomodels.features.trees phylomodels.features.trees.helper phylomodels.features.trees.helper.calculate_branch_length_metrics phylomodels.features.trees.helper.check_values phylomodels.features.trees.helper.get_LTT phylomodels.features.trees.helper.get_adjacency_mat phylomodels.features.trees.helper.get_distance_mat phylomodels.features.trees.helper.get_eigenvalues_adj phylomodels.features.trees.helper.get_eigenvalues_dist_lap phylomodels.features.trees.helper.get_eigenvalues_lap phylomodels.features.trees.helper.get_groups phylomodels.features.trees.helper.get_node_properties phylomodels.features.trees.helper.process_optional_arguements phylomodels.features.trees.helper.unique_node_attr phylomodels.features.trees.BL_calculate_external_max phylomodels.features.trees.BL_calculate_external_mean phylomodels.features.trees.BL_calculate_external_median phylomodels.features.trees.BL_calculate_external_min phylomodels.features.trees.BL_calculate_external_std phylomodels.features.trees.BL_calculate_internal_max phylomodels.features.trees.BL_calculate_internal_mean phylomodels.features.trees.BL_calculate_internal_median phylomodels.features.trees.BL_calculate_internal_min phylomodels.features.trees.BL_calculate_internal_std phylomodels.features.trees.BL_calculate_max phylomodels.features.trees.BL_calculate_mean phylomodels.features.trees.BL_calculate_median phylomodels.features.trees.BL_calculate_min phylomodels.features.trees.BL_calculate_ratio_max phylomodels.features.trees.BL_calculate_ratio_mean phylomodels.features.trees.BL_calculate_ratio_median phylomodels.features.trees.BL_calculate_ratio_min phylomodels.features.trees.BL_calculate_ratio_std phylomodels.features.trees.BL_calculate_std phylomodels.features.trees.LTT_calculate_max_lineages phylomodels.features.trees.LTT_calculate_mean_b_time phylomodels.features.trees.LTT_calculate_mean_s_time phylomodels.features.trees.LTT_calculate_slope_1 phylomodels.features.trees.LTT_calculate_slope_2 phylomodels.features.trees.LTT_calculate_slope_ratio phylomodels.features.trees.LTT_calculate_t_max_lineages phylomodels.features.trees.calculate_external_branch_length_metrics phylomodels.features.trees.group_calculate_max phylomodels.features.trees.group_calculate_mean phylomodels.features.trees.group_calculate_median phylomodels.features.trees.group_calculate_min phylomodels.features.trees.group_calculate_mode phylomodels.features.trees.group_calculate_num phylomodels.features.trees.group_calculate_std phylomodels.features.trees.local_calculate_LBI_mean phylomodels.features.trees.local_calculate_frac_basal phylomodels.features.trees.mean_NN_distance phylomodels.features.trees.netSci_calculate_betweenness_max phylomodels.features.trees.netSci_calculate_closeness_max phylomodels.features.trees.netSci_calculate_diameter phylomodels.features.trees.netSci_calculate_eigen_centrality_max phylomodels.features.trees.netSci_calculate_mean_path phylomodels.features.trees.smallConfig_calculate_cherries phylomodels.features.trees.smallConfig_calculate_double_cherries phylomodels.features.trees.smallConfig_calculate_fourprong phylomodels.features.trees.smallConfig_calculate_pitchforks phylomodels.features.trees.spectral_calculate_eigen_gap phylomodels.features.trees.spectral_calculate_kurtosis phylomodels.features.trees.spectral_calculate_max_adj_eigen phylomodels.features.trees.spectral_calculate_max_distLap_eigen phylomodels.features.trees.spectral_calculate_max_lap_eigen phylomodels.features.trees.spectral_calculate_min_adj_eigen phylomodels.features.trees.spectral_calculate_min_lap_eigen phylomodels.features.trees.spectral_calculate_skewness phylomodels.features.trees.top_calculate_B1 phylomodels.features.trees.top_calculate_B2 phylomodels.features.trees.top_calculate_FurnasR phylomodels.features.trees.top_calculate_WD_ratio phylomodels.features.trees.top_calculate_colless phylomodels.features.trees.top_calculate_frac_imbalance phylomodels.features.trees.top_calculate_frac_ladder phylomodels.features.trees.top_calculate_max_dW phylomodels.features.trees.top_calculate_max_ladder phylomodels.features.trees.top_calculate_mean_imbalance_ratio phylomodels.features.trees.top_calculate_sackin phylomodels.features.trees.top_calculate_sackin_var phylomodels.features.trees.tree_height_calculate_max phylomodels.features.trees.tree_height_calculate_mean phylomodels.features.trees.tree_height_calculate_min phylomodels.features.features phylomodels.features.inventory phylomodels.features.test phylomodels.features.testFeatures phylomodels.models phylomodels.models.seir_taoLeap phylomodels.models.seir_taoLeap.seirTaoLeap phylomodels.models.distributions_gaussian phylomodels.models.seir_taoLeap_getIncidenceSampled phylomodels.models.sir_taoLeap_getIncidence phylomodels.models.sir_taoLeap_getIncidenceSampled phylomodels.models.test_distributions_gaussian phylomodels.models.test_sir_taoLeap_getIncidence phylomodels.models.test_sir_taoLeap_getIncidenceSampled phylomodels.network phylomodels.network.phyloTree phylomodels.sampling phylomodels.sampling.sample_treeIndependent phylomodels.utilities phylomodels.visualization 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build succeeded, 143 warnings.

The HTML page is in _build/localmedia.
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[rtd-command-info] start-time: 2022-03-28T22:51:01.718666Z, end-time: 2022-03-28T22:51:06.642528Z, duration: 4, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v4.4.0
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WARNING: autodoc: failed to import module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.cal_parameterSweep' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.constants' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.init_historyMatching_base' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'calibration.init_historyMatching_poissonGlmBasis' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'examples' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.features' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.inventory' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_cauchyFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_gaussianFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative2_laplaceFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_cauchyFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_gaussianFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_derivative_laplaceFit' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_L1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_L2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_diff_Linf' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_log10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum15' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum30' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_partialSum7' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_sum' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.series.series_sum_log10' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.fano' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.qcd' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.rsd' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.skew' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.statistics.var' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.test' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.testFeatures' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.BL_calculate_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_max_lineages' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_b_time' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_s_time' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_t_max_lineages' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.calculate_external_branch_length_metrics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_median' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_mode' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_num' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.group_calculate_std' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.calculate_branch_length_metrics' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.check_values' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_LTT' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_adjacency_mat' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_distance_mat' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_adj' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_dist_lap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_lap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_groups' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.get_node_properties' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.process_optional_arguements' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.helper.unique_node_attr' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.local_calculate_LBI_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.local_calculate_frac_basal' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.mean_NN_distance' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_betweenness_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_closeness_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_diameter' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_eigen_centrality_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_mean_path' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_cherries' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_double_cherries' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_fourprong' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_pitchforks' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_eigen_gap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_kurtosis' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_adj_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_distLap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_lap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_adj_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_lap_eigen' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_skewness' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_B1' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_B2' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_FurnasR' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_WD_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_colless' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_imbalance' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_ladder' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_max_dW' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_max_ladder' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_mean_imbalance_ratio' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_sackin' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.top_calculate_sackin_var' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_max' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_mean' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_min' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.distributions_gaussian' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.seir_taoLeap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.seir_taoLeap.seirTaoLeap' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.seir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.sir_taoLeap_getIncidence' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.sir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.test_distributions_gaussian' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.test_sir_taoLeap_getIncidence' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'models.test_sir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'network' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'network.phyloTree' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'sampling' from module 'phylomodels'; the following exception was raised:
cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg/phylomodels/__init__.py)
WARNING: autodoc: failed to import module 'sampling.sample_treeIndependent' from module 'phylomodels'; the following exception was raised:
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processing phylomodels-docs.tex... index models features calibration test examples modules phylomodels phylomodels.calibration phylomodels.calibration.cal_parameterSweep phylomodels.calibration.constants phylomodels.calibration.init_historyMatching_base phylomodels.calibration.init_historyMatching_poissonGlmBasis phylomodels.examples phylomodels.features phylomodels.features.series phylomodels.features.series.series phylomodels.features.series.series_derivative phylomodels.features.series.series_derivative2 phylomodels.features.series.series_derivative2_cauchyFit phylomodels.features.series.series_derivative2_gaussianFit phylomodels.features.series.series_derivative2_laplaceFit phylomodels.features.series.series_derivative_cauchyFit phylomodels.features.series.series_derivative_gaussianFit phylomodels.features.series.series_derivative_laplaceFit phylomodels.features.series.series_diff phylomodels.features.series.series_diff_L1 phylomodels.features.series.series_diff_L2 phylomodels.features.series.series_diff_Linf phylomodels.features.series.series_log10 phylomodels.features.series.series_partialSum10 phylomodels.features.series.series_partialSum15 phylomodels.features.series.series_partialSum2 phylomodels.features.series.series_partialSum30 phylomodels.features.series.series_partialSum7 phylomodels.features.series.series_sum phylomodels.features.series.series_sum_log10 phylomodels.features.statistics phylomodels.features.statistics.fano phylomodels.features.statistics.mean phylomodels.features.statistics.qcd phylomodels.features.statistics.rsd phylomodels.features.statistics.skew phylomodels.features.statistics.std phylomodels.features.statistics.var phylomodels.features.trees phylomodels.features.trees.helper phylomodels.features.trees.helper.calculate_branch_length_metrics phylomodels.features.trees.helper.check_values phylomodels.features.trees.helper.get_LTT phylomodels.features.trees.helper.get_adjacency_mat phylomodels.features.trees.helper.get_distance_mat phylomodels.features.trees.helper.get_eigenvalues_adj phylomodels.features.trees.helper.get_eigenvalues_dist_lap phylomodels.features.trees.helper.get_eigenvalues_lap phylomodels.features.trees.helper.get_groups phylomodels.features.trees.helper.get_node_properties phylomodels.features.trees.helper.process_optional_arguements phylomodels.features.trees.helper.unique_node_attr phylomodels.features.trees.BL_calculate_external_max phylomodels.features.trees.BL_calculate_external_mean phylomodels.features.trees.BL_calculate_external_median phylomodels.features.trees.BL_calculate_external_min phylomodels.features.trees.BL_calculate_external_std phylomodels.features.trees.BL_calculate_internal_max phylomodels.features.trees.BL_calculate_internal_mean phylomodels.features.trees.BL_calculate_internal_median phylomodels.features.trees.BL_calculate_internal_min phylomodels.features.trees.BL_calculate_internal_std phylomodels.features.trees.BL_calculate_max phylomodels.features.trees.BL_calculate_mean phylomodels.features.trees.BL_calculate_median phylomodels.features.trees.BL_calculate_min phylomodels.features.trees.BL_calculate_ratio_max phylomodels.features.trees.BL_calculate_ratio_mean phylomodels.features.trees.BL_calculate_ratio_median phylomodels.features.trees.BL_calculate_ratio_min phylomodels.features.trees.BL_calculate_ratio_std phylomodels.features.trees.BL_calculate_std phylomodels.features.trees.LTT_calculate_max_lineages phylomodels.features.trees.LTT_calculate_mean_b_time phylomodels.features.trees.LTT_calculate_mean_s_time phylomodels.features.trees.LTT_calculate_slope_1 phylomodels.features.trees.LTT_calculate_slope_2 phylomodels.features.trees.LTT_calculate_slope_ratio phylomodels.features.trees.LTT_calculate_t_max_lineages phylomodels.features.trees.calculate_external_branch_length_metrics phylomodels.features.trees.group_calculate_max phylomodels.features.trees.group_calculate_mean phylomodels.features.trees.group_calculate_median phylomodels.features.trees.group_calculate_min phylomodels.features.trees.group_calculate_mode phylomodels.features.trees.group_calculate_num phylomodels.features.trees.group_calculate_std phylomodels.features.trees.local_calculate_LBI_mean phylomodels.features.trees.local_calculate_frac_basal phylomodels.features.trees.mean_NN_distance phylomodels.features.trees.netSci_calculate_betweenness_max phylomodels.features.trees.netSci_calculate_closeness_max phylomodels.features.trees.netSci_calculate_diameter phylomodels.features.trees.netSci_calculate_eigen_centrality_max phylomodels.features.trees.netSci_calculate_mean_path phylomodels.features.trees.smallConfig_calculate_cherries phylomodels.features.trees.smallConfig_calculate_double_cherries phylomodels.features.trees.smallConfig_calculate_fourprong phylomodels.features.trees.smallConfig_calculate_pitchforks phylomodels.features.trees.spectral_calculate_eigen_gap phylomodels.features.trees.spectral_calculate_kurtosis phylomodels.features.trees.spectral_calculate_max_adj_eigen phylomodels.features.trees.spectral_calculate_max_distLap_eigen phylomodels.features.trees.spectral_calculate_max_lap_eigen phylomodels.features.trees.spectral_calculate_min_adj_eigen phylomodels.features.trees.spectral_calculate_min_lap_eigen phylomodels.features.trees.spectral_calculate_skewness phylomodels.features.trees.top_calculate_B1 phylomodels.features.trees.top_calculate_B2 phylomodels.features.trees.top_calculate_FurnasR phylomodels.features.trees.top_calculate_WD_ratio phylomodels.features.trees.top_calculate_colless phylomodels.features.trees.top_calculate_frac_imbalance phylomodels.features.trees.top_calculate_frac_ladder phylomodels.features.trees.top_calculate_max_dW phylomodels.features.trees.top_calculate_max_ladder phylomodels.features.trees.top_calculate_mean_imbalance_ratio phylomodels.features.trees.top_calculate_sackin phylomodels.features.trees.top_calculate_sackin_var phylomodels.features.trees.tree_height_calculate_max phylomodels.features.trees.tree_height_calculate_mean phylomodels.features.trees.tree_height_calculate_min phylomodels.features.features phylomodels.features.inventory phylomodels.features.test phylomodels.features.testFeatures phylomodels.models phylomodels.models.seir_taoLeap phylomodels.models.seir_taoLeap.seirTaoLeap phylomodels.models.distributions_gaussian phylomodels.models.seir_taoLeap_getIncidenceSampled phylomodels.models.sir_taoLeap_getIncidence phylomodels.models.sir_taoLeap_getIncidenceSampled phylomodels.models.test_distributions_gaussian phylomodels.models.test_sir_taoLeap_getIncidence phylomodels.models.test_sir_taoLeap_getIncidenceSampled phylomodels.network phylomodels.network.phyloTree phylomodels.sampling phylomodels.sampling.sample_treeIndependent phylomodels.utilities phylomodels.visualization 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[]\T1/qtm/m/n/10 Com-put-ing sum-mary statis-tics on phy-lo-ge-netic trees: phy
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ipynb 

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/examples/calibration_historyMatching_featureSelectionForSIR/calibration_histor
yMatching_featureSelectionForSIR.ipynb 
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