Read the Docs build information Build id: 1564818 Project: institute-for-disease-modeling-phylomodels Version: latest Commit: c6545bd2acb0495299d7743e7ad3277f001646d0 Date: 2023-06-27T19:11:23.075248Z State: finished Success: True [rtd-command-info] start-time: 2023-06-27T19:11:32.480503Z, end-time: 2023-06-27T19:11:39.128666Z, duration: 6, 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: 2023-06-27T19:11:39.605266Z, end-time: 2023-06-27T19:11:39.696264Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: false # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip - pdf # Optionally set the version of Python and requirements required to build your docs python: version: 3.8 install: - requirements: requirements.txt - method: setuptools path: . - requirements: docs/requirements.txt system_packages: true # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank search: ranking: index.html: 3 modules.html: 2 [rtd-command-info] start-time: 2023-06-27T19:11:41.927038Z, end-time: 2023-06-27T19:11:50.123993Z, duration: 8, exit-code: 0 python3.8 -mvirtualenv --system-site-packages $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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. 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/tmp/pip-ephem-wheel-cache-y0djzc7f/wheels/29/8b/34/0bfba46dfc73a9065eed53bca787117321a9fec0d98cb8c7d2 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinxcontrib-jquery, recommonmark, sphinx-rtd-theme Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.7.0 mock-1.0.1 packaging-23.1 pillow-9.5.0 pytz-2023.3 readthedocs-sphinx-ext-2.2.1 recommonmark-0.5.0 requests-2.31.0 setuptools-58.2.0 snowballstemmer-2.2.0 sphinx-6.2.1 sphinx-rtd-theme-1.2.2 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-2.0.3 zipp-3.15.0 [rtd-command-info] start-time: 2023-06-27T19:12:08.524036Z, end-time: 2023-06-27T19:13:47.672728Z, duration: 99, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: numpy in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.24.3) Collecting scipy (from -r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/69/f0/fb07a9548e48b687b8bf2fa81d71aba9cfc548d365046ca1c791e24db99d/scipy-1.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB) 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Building wheel for pyDOE (setup.py): started Building wheel for pyDOE (setup.py): finished with status 'done' Created wheel for pyDOE: filename=pyDOE-0.3.8-py3-none-any.whl size=18184 sha256=d6690a3bb0ab668aad1626e4edbff8ec8982b122efecf6af3ce6911f130b204b Stored in directory: /tmp/pip-ephem-wheel-cache-k39h84mz/wheels/80/02/2f/addb15cd7424cf5ca7222decbe8898cfcb69111600ed0d260b Successfully built ete3 pyDOE Installing collected packages: webencodings, wcwidth, Wand, tbb, PyQt5-Qt5, py-cpuinfo, pure-eval, ptyprocess, pickleshare, msgpack, ipython-genutils, intel-openmp, fastjsonschema, executing, ete3, backcall, xlrd, widgetsnbextension, websocket-client, webcolors, uri-template, typing-extensions, traitlets, tornado, tinycss2, threadpoolctl, soupsieve, sniffio, Send2Trash, scipy, rfc3986-validator, rfc3339-validator, qtpy, pyzmq, pyyaml, python-json-logger, pyrsistent, PyQt5-sip, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pkgutil-resolve-name, pexpect, patsy, parso, pandocfilters, overrides, numexpr, ngesh, networkx, nest-asyncio, mkl, mistune, lxml, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, joblib, fqdn, exceptiongroup, et-xmlfile, defusedxml, decorator, debugpy, cython, blosc2, bleach, backports.zoneinfo, attrs, asttokens, unittest-xml-reporting, tzlocal, terminado, tables, stack-data, scikit-learn, PyQt5, pyDOE, openpyxl, matplotlib-inline, jupyter-core, jsonschema, jedi, comm, cffi, beautifulsoup4, arrow, anyio, statsmodels, seaborn, nbformat, jupyter-server-terminals, jupyter-client, isoduration, ipython, argon2-cffi-bindings, nbclient, ipykernel, argon2-cffi, qtconsole, nbconvert, jupyter-events, jupyter-console, ipywidgets, jupyter-server, notebook-shim, nbclassic, notebook, jupyter Successfully installed PyQt5-5.15.9 PyQt5-Qt5-5.15.2 PyQt5-sip-12.12.1 Send2Trash-1.8.2 Wand-0.6.11 anyio-3.7.0 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 arrow-1.2.3 asttokens-2.2.1 attrs-23.1.0 backcall-0.2.0 backports.zoneinfo-0.2.1 beautifulsoup4-4.12.2 bleach-6.0.0 blosc2-2.0.0 cffi-1.15.1 comm-0.1.3 cython-0.29.35 debugpy-1.6.7 decorator-5.1.1 defusedxml-0.7.1 et-xmlfile-1.1.0 ete3-3.1.3 exceptiongroup-1.1.1 executing-1.2.0 fastjsonschema-2.17.1 fqdn-1.5.1 intel-openmp-2023.1.0 ipykernel-6.23.3 ipython-8.12.2 ipython-genutils-0.2.0 ipywidgets-8.0.6 isoduration-20.11.0 jedi-0.18.2 joblib-1.2.0 jsonpointer-2.4 jsonschema-4.17.3 jupyter-1.0.0 jupyter-client-8.3.0 jupyter-console-6.6.3 jupyter-core-5.3.1 jupyter-events-0.6.3 jupyter-server-2.7.0 jupyter-server-terminals-0.4.4 jupyterlab-pygments-0.2.2 jupyterlab-widgets-3.0.7 lxml-4.9.2 matplotlib-inline-0.1.6 mistune-3.0.1 mkl-2023.1.0 msgpack-1.0.5 nbclassic-1.0.0 nbclient-0.8.0 nbconvert-7.6.0 nbformat-5.9.0 nest-asyncio-1.5.6 networkx-3.1 ngesh-1.2.1 notebook-6.5.4 notebook-shim-0.2.3 numexpr-2.8.4 openpyxl-3.1.2 overrides-7.3.1 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.3 pexpect-4.8.0 pickleshare-0.7.5 pkgutil-resolve-name-1.3.10 platformdirs-3.8.0 prometheus-client-0.17.0 prompt-toolkit-3.0.38 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 py-cpuinfo-9.0.0 pyDOE-0.3.8 pycparser-2.21 pyrsistent-0.19.3 python-json-logger-2.0.7 pyyaml-6.0 pyzmq-25.1.0 qtconsole-5.4.3 qtpy-2.3.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 scikit-learn-1.2.2 scipy-1.10.1 seaborn-0.12.2 sniffio-1.3.0 soupsieve-2.4.1 stack-data-0.6.2 statsmodels-0.14.0 tables-3.8.0 tbb-2021.9.0 terminado-0.17.1 threadpoolctl-3.1.0 tinycss2-1.2.1 tornado-6.3.2 traitlets-5.9.0 typing-extensions-4.6.3 tzlocal-5.0.1 unittest-xml-reporting-3.2.0 uri-template-1.3.0 wcwidth-0.2.6 webcolors-1.13 webencodings-0.5.1 websocket-client-1.6.1 widgetsnbextension-4.0.7 xlrd-2.0.1 [rtd-command-info] start-time: 2023-06-27T19:13:48.321011Z, end-time: 2023-06-27T19:13:55.226375Z, 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/sampling copying phylomodels/sampling/sample_treeIndependent.py -> build/lib/phylomodels/sampling copying phylomodels/sampling/__init__.py -> build/lib/phylomodels/sampling 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/examples copying phylomodels/examples/__init__.py -> build/lib/phylomodels/examples creating build/lib/phylomodels/models copying phylomodels/models/seir_taoLeap_getIncidenceSampled.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/distributions_gaussian.py -> build/lib/phylomodels/models copying phylomodels/models/test_distributions_gaussian.py -> build/lib/phylomodels/models copying phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models 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/calibration copying phylomodels/calibration/cal_parameterSweep.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/__init__.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_base.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/constants.py -> build/lib/phylomodels/calibration 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/__init__.py -> build/lib/phylomodels/features copying phylomodels/features/test.py -> build/lib/phylomodels/features copying phylomodels/features/inventory.py -> build/lib/phylomodels/features copying phylomodels/features/features.py -> build/lib/phylomodels/features creating build/lib/phylomodels/models/seir_taoLeap copying phylomodels/models/seir_taoLeap/__init__.py -> build/lib/phylomodels/models/seir_taoLeap copying phylomodels/models/seir_taoLeap/seirTaoLeap.py -> build/lib/phylomodels/models/seir_taoLeap creating build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/std.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/fano.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/var.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/mean.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/skew.py -> build/lib/phylomodels/features/statistics creating build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum30.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_gaussianFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L1.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/__init__.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum_log10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum15.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_cauchyFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_gaussianFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_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.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum7.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_log10.py -> build/lib/phylomodels/features/series creating build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_cherries.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_kurtosis.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_colless.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_frac_imbalance.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_1.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_closeness_max.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/top_calculate_max_ladder.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_betweenness_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/group_calculate_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mode.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_LBI_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_internal_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mean.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_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_sackin.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_FurnasR.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_std.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/local_calculate_frac_basal.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_num.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/BL_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_B2.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/smallConfig_calculate_fourprong.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_mean_path.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_std.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/BL_calculate_internal_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/__init__.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_B1.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/tree_height_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_median.py -> 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_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_std.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_internal_max.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/top_calculate_sackin_var.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_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/LTT_calculate_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_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/LTT_calculate_t_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_skewness.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_std.py -> build/lib/phylomodels/features/trees creating 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_node_properties.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_eigenvalues_adj.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/process_optional_arguements.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/__init__.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/unique_node_attr.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/get_eigenvalues_dist_lap.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/check_values.py -> build/lib/phylomodels/features/trees/helper 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/sampling copying build/lib/phylomodels/sampling/sample_treeIndependent.py -> build/bdist.linux-x86_64/egg/phylomodels/sampling copying build/lib/phylomodels/sampling/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/sampling creating build/bdist.linux-x86_64/egg/phylomodels/visualization copying build/lib/phylomodels/visualization/parallelCoordinates.py -> build/bdist.linux-x86_64/egg/phylomodels/visualization copying build/lib/phylomodels/visualization/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/visualization creating build/bdist.linux-x86_64/egg/phylomodels/examples copying build/lib/phylomodels/examples/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/examples creating build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/seir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/sir_taoLeap_getIncidence.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/test_sir_taoLeap_getIncidence.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/sir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/distributions_gaussian.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/test_distributions_gaussian.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models creating build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap/seirTaoLeap.py -> build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap creating build/bdist.linux-x86_64/egg/phylomodels/network copying build/lib/phylomodels/network/phyloTree.py -> build/bdist.linux-x86_64/egg/phylomodels/network copying build/lib/phylomodels/network/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/network copying build/lib/phylomodels/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels creating build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/cal_parameterSweep.py -> 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 copying build/lib/phylomodels/calibration/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/init_historyMatching_base.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/constants.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration creating build/bdist.linux-x86_64/egg/phylomodels/utilities copying build/lib/phylomodels/utilities/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/utilities creating build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/testFeatures.py -> build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/test.py -> build/bdist.linux-x86_64/egg/phylomodels/features creating build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/qcd.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/rsd.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/fano.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/var.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/skew.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics creating build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum30.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_laplaceFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_gaussianFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_L1.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_sum.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_L2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_laplaceFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_sum_log10.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum15.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum10.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_cauchyFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_gaussianFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_cauchyFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_Linf.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum7.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_log10.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/inventory.py -> build/bdist.linux-x86_64/egg/phylomodels/features creating build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_cherries.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_kurtosis.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_colless.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_ratio.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_frac_imbalance.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_1.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_closeness_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_mean_b_time.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_max_dW.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_max_ladder.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_betweenness_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_mode.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/local_calculate_LBI_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_frac_ladder.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_sackin.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_FurnasR.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_min_lap_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/local_calculate_frac_basal.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_num.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_mean_s_time.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_B2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_fourprong.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_mean_path.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_adj_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_B1.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_WD_ratio.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_diameter.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees creating build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/calculate_branch_length_metrics.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_node_properties.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_groups.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_adj.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_LTT.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/process_optional_arguements.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_adjacency_mat.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_distance_mat.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/unique_node_attr.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_lap.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/check_values.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/BL_calculate_internal_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/calculate_external_branch_length_metrics.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_sackin_var.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_min_adj_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/mean_NN_distance.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_max_lineages.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_t_max_lineages.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_skewness.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/features.py -> build/bdist.linux-x86_64/egg/phylomodels/features byte-compiling build/bdist.linux-x86_64/egg/phylomodels/sampling/sample_treeIndependent.py to sample_treeIndependent.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/sampling/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/visualization/parallelCoordinates.py to parallelCoordinates.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/visualization/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/examples/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap_getIncidenceSampled.py to seir_taoLeap_getIncidenceSampled.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/sir_taoLeap_getIncidence.py to sir_taoLeap_getIncidence.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/test_sir_taoLeap_getIncidence.py to test_sir_taoLeap_getIncidence.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/sir_taoLeap_getIncidenceSampled.py to sir_taoLeap_getIncidenceSampled.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/distributions_gaussian.py to distributions_gaussian.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/test_distributions_gaussian.py to test_distributions_gaussian.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py to test_sir_taoLeap_getIncidenceSampled.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap/seirTaoLeap.py to seirTaoLeap.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/network/phyloTree.py to phyloTree.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/network/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/cal_parameterSweep.py to cal_parameterSweep.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py to init_historyMatching_poissonGlmBasis.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/init_historyMatching_base.py to init_historyMatching_base.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/constants.py to constants.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/utilities/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/testFeatures.py to testFeatures.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/test.py to test.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/std.py to std.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/qcd.py to qcd.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/rsd.py to rsd.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/fano.py to fano.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/var.py to var.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/mean.py to mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/skew.py to skew.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum30.py to series_partialSum30.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2_laplaceFit.py to series_derivative2_laplaceFit.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff.py to series_diff.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative_gaussianFit.py to series_derivative_gaussianFit.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff_L1.py to series_diff_L1.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2.py to series_derivative2.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_sum.py to series_sum.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff_L2.py to series_diff_L2.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative_laplaceFit.py to series_derivative_laplaceFit.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_sum_log10.py to series_sum_log10.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum15.py to series_partialSum15.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum10.py to series_partialSum10.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative.py to series_derivative.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2_cauchyFit.py to series_derivative2_cauchyFit.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2_gaussianFit.py to series_derivative2_gaussianFit.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum2.py to series_partialSum2.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative_cauchyFit.py to series_derivative_cauchyFit.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff_Linf.py to series_diff_Linf.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series.py to series.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum7.py to series_partialSum7.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_log10.py to series_log10.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/inventory.py to inventory.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_pitchforks.py to smallConfig_calculate_pitchforks.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_cherries.py to smallConfig_calculate_cherries.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_min.py to BL_calculate_ratio_min.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_kurtosis.py to spectral_calculate_kurtosis.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_colless.py to top_calculate_colless.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_slope_ratio.py to LTT_calculate_slope_ratio.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_frac_imbalance.py to top_calculate_frac_imbalance.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_slope_1.py to LTT_calculate_slope_1.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_closeness_max.py to netSci_calculate_closeness_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_mean_b_time.py to LTT_calculate_mean_b_time.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_max_dW.py to top_calculate_max_dW.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_max_ladder.py to top_calculate_max_ladder.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_median.py to BL_calculate_internal_median.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_betweenness_max.py to netSci_calculate_betweenness_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_median.py to BL_calculate_ratio_median.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_median.py to group_calculate_median.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_mode.py to group_calculate_mode.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_std.py to BL_calculate_external_std.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/local_calculate_LBI_mean.py to local_calculate_LBI_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_double_cherries.py to smallConfig_calculate_double_cherries.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_min.py to BL_calculate_internal_min.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_mean.py to group_calculate_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_frac_ladder.py to top_calculate_frac_ladder.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_min.py to BL_calculate_min.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_sackin.py to top_calculate_sackin.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_min.py to BL_calculate_external_min.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_FurnasR.py to top_calculate_FurnasR.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_max.py to BL_calculate_external_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_max.py to group_calculate_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_mean.py to BL_calculate_external_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_std.py to BL_calculate_ratio_std.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_min_lap_eigen.py to spectral_calculate_min_lap_eigen.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/local_calculate_frac_basal.py to local_calculate_frac_basal.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_num.py to group_calculate_num.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_mean_s_time.py to LTT_calculate_mean_s_time.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_mean.py to BL_calculate_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_B2.py to top_calculate_B2.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py to spectral_calculate_max_distLap_eigen.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_fourprong.py to smallConfig_calculate_fourprong.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_mean_path.py to netSci_calculate_mean_path.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_std.py to BL_calculate_internal_std.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_max_adj_eigen.py to spectral_calculate_max_adj_eigen.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_mean.py to BL_calculate_internal_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_mean.py to BL_calculate_ratio_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_B1.py to top_calculate_B1.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_max_lap_eigen.py to spectral_calculate_max_lap_eigen.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/tree_height_calculate_mean.py to tree_height_calculate_mean.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_median.py to BL_calculate_median.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_WD_ratio.py to top_calculate_WD_ratio.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_max.py to BL_calculate_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_std.py to BL_calculate_std.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_diameter.py to netSci_calculate_diameter.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/calculate_branch_length_metrics.py to calculate_branch_length_metrics.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_node_properties.py to get_node_properties.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_groups.py to get_groups.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_eigenvalues_adj.py to get_eigenvalues_adj.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_LTT.py to get_LTT.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/process_optional_arguements.py to process_optional_arguements.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_adjacency_mat.py to get_adjacency_mat.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_distance_mat.py to get_distance_mat.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/unique_node_attr.py to unique_node_attr.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_eigenvalues_lap.py to get_eigenvalues_lap.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py to get_eigenvalues_dist_lap.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/check_values.py to check_values.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_max.py to BL_calculate_internal_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/calculate_external_branch_length_metrics.py to calculate_external_branch_length_metrics.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_sackin_var.py to top_calculate_sackin_var.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_min_adj_eigen.py to spectral_calculate_min_adj_eigen.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_median.py to BL_calculate_external_median.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/mean_NN_distance.py to mean_NN_distance.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_max_lineages.py to LTT_calculate_max_lineages.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py to netSci_calculate_eigen_centrality_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_eigen_gap.py to spectral_calculate_eigen_gap.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_slope_2.py to LTT_calculate_slope_2.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/tree_height_calculate_max.py to tree_height_calculate_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py to top_calculate_mean_imbalance_ratio.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_t_max_lineages.py to LTT_calculate_t_max_lineages.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/tree_height_calculate_min.py to tree_height_calculate_min.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_skewness.py to spectral_calculate_skewness.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_min.py to group_calculate_min.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_max.py to BL_calculate_ratio_max.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_std.py to group_calculate_std.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/features.py to features.cpython-38.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating dist creating 'dist/phyloModels-0.5-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing phyloModels-0.5-py3.8.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/phyloModels-0.5-py3.8.egg Extracting phyloModels-0.5-py3.8.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Adding phyloModels 0.5 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/phyloModels-0.5-py3.8.egg Processing dependencies for phyloModels==0.5 Searching for PyQt5==5.11.3 Reading https://pypi.org/simple/PyQt5/ 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 Best match: PyQt5 5.11.3 Processing PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl 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 Adding PyQt5 5.11.3 to easy-install.pth file Installing pylupdate5 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing pyrcc5 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing pyuic5 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/PyQt5-5.11.3-py3.8-linux-x86_64.egg Searching for sip Reading https://pypi.org/simple/sip/ Downloading https://files.pythonhosted.org/packages/e6/51/c1eb77f706bc0d173f7dbfe697ff8ab8b4c511d3a71a1e84c6094c6becee/sip-6.7.9-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=a0adaaed74475fde5882d8db9e3a88a93697a77de3cd37c28b0eb0bb4b3eb8e8 Best match: sip 6.7.9 Processing sip-6.7.9-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.whl Installing sip-6.7.9-cp37-abi3-manylinux_2_5_x86_64.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 sip 6.7.9 to easy-install.pth file Installing sip-build script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing sip-distinfo script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing sip-install script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing sip-module script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin 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-6.7.9-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 tomli Reading https://pypi.org/simple/tomli/ Downloading https://files.pythonhosted.org/packages/97/75/10a9ebee3fd790d20926a90a2547f0bf78f371b2f13aa822c759680ca7b9/tomli-2.0.1-py3-none-any.whl#sha256=939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc Best match: tomli 2.0.1 Processing tomli-2.0.1-py3-none-any.whl Installing tomli-2.0.1-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 tomli 2.0.1 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/tomli-2.0.1-py3.8.egg Searching for ply Reading https://pypi.org/simple/ply/ Downloading https://files.pythonhosted.org/packages/a3/58/35da89ee790598a0700ea49b2a66594140f44dec458c07e8e3d4979137fc/ply-3.11-py2.py3-none-any.whl#sha256=096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce Best match: ply 3.11 Processing ply-3.11-py2.py3-none-any.whl Installing ply-3.11-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 ply 3.11 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/ply-3.11-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==3.1.2 Best match: openpyxl 3.1.2 Adding openpyxl 3.1.2 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 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==5.9.5 Best match: psutil 5.9.5 Adding psutil 5.9.5 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 jupyter-client==8.3.0 Best match: jupyter-client 8.3.0 Adding jupyter-client 8.3.0 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==6.6.3 Best match: jupyter-console 6.6.3 Adding jupyter-console 6.6.3 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==5.3.1 Best match: jupyter-core 5.3.1 Adding jupyter-core 5.3.1 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==1.2.2 Best match: scikit-learn 1.2.2 Adding scikit-learn 1.2.2 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==2023.1.0 Best match: mkl 2023.1.0 Adding mkl 2023.1.0 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 seaborn==0.12.2 Best match: seaborn 0.12.2 Adding seaborn 0.12.2 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==3.7.1 Best match: matplotlib 3.7.1 Adding matplotlib 3.7.1 to easy-install.pth file Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for pandas==2.0.1 Best match: pandas 2.0.1 pandas 2.0.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for networkx==3.1 Best match: networkx 3.1 Adding networkx 3.1 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==3.1.3 Best match: ete3 3.1.3 Adding ete3 3.1.3 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==1.16.0 Best match: six 1.16.0 six 1.16.0 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==4.9.2 Best match: lxml 4.9.2 Adding lxml 4.9.2 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 scipy==1.10.1 Best match: scipy 1.10.1 Adding scipy 1.10.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for numpy==1.24.3 Best match: numpy 1.24.3 numpy 1.24.3 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 pyzmq==25.1.0 Best match: pyzmq 25.1.0 Adding pyzmq 25.1.0 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 importlib-metadata==6.7.0 Best match: importlib-metadata 6.7.0 Adding importlib-metadata 6.7.0 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 tornado==6.3.2 Best match: tornado 6.3.2 Adding tornado 6.3.2 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 python-dateutil==2.8.2 Best match: python-dateutil 2.8.2 python-dateutil 2.8.2 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for traitlets==5.9.0 Best match: traitlets 5.9.0 Adding traitlets 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 ipython==8.12.2 Best match: ipython 8.12.2 Adding ipython 8.12.2 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 ipykernel==6.23.3 Best match: ipykernel 6.23.3 Adding ipykernel 6.23.3 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 prompt-toolkit==3.0.38 Best match: prompt-toolkit 3.0.38 Adding prompt-toolkit 3.0.38 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 Pygments==2.15.1 Best match: Pygments 2.15.1 Adding Pygments 2.15.1 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 platformdirs==3.8.0 Best match: platformdirs 3.8.0 Adding platformdirs 3.8.0 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 qtconsole==5.4.3 Best match: qtconsole 5.4.3 Adding qtconsole 5.4.3 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 ipywidgets==8.0.6 Best match: ipywidgets 8.0.6 Adding ipywidgets 8.0.6 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==7.6.0 Best match: nbconvert 7.6.0 Adding nbconvert 7.6.0 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 notebook==6.5.4 Best match: notebook 6.5.4 Adding notebook 6.5.4 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 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 joblib==1.2.0 Best match: joblib 1.2.0 Adding joblib 1.2.0 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 tbb==2021.9.0 Best match: tbb 2021.9.0 Adding tbb 2021.9.0 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 intel-openmp==2023.1.0 Best match: intel-openmp 2023.1.0 Adding intel-openmp 2023.1.0 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 kiwisolver==1.4.4 Best match: kiwisolver 1.4.4 kiwisolver 1.4.4 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for Pillow==9.5.0 Best match: Pillow 9.5.0 Adding Pillow 9.5.0 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 cycler==0.11.0 Best match: cycler 0.11.0 cycler 0.11.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for importlib-resources==5.12.0 Best match: importlib-resources 5.12.0 importlib-resources 5.12.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for packaging==23.1 Best match: packaging 23.1 Adding packaging 23.1 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 fonttools==4.39.4 Best match: fonttools 4.39.4 fonttools 4.39.4 is already the active version in easy-install.pth Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing ttx 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 pyparsing==3.0.9 Best match: pyparsing 3.0.9 pyparsing 3.0.9 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for contourpy==1.0.7 Best match: contourpy 1.0.7 contourpy 1.0.7 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for pytz==2023.3 Best match: pytz 2023.3 Adding pytz 2023.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for tzdata==2023.3 Best match: tzdata 2023.3 tzdata 2023.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for 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 zipp==3.15.0 Best match: zipp 3.15.0 Adding zipp 3.15.0 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 matplotlib-inline==0.1.6 Best match: matplotlib-inline 0.1.6 Adding matplotlib-inline 0.1.6 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 stack-data==0.6.2 Best match: stack-data 0.6.2 Adding stack-data 0.6.2 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 typing-extensions==4.6.3 Best match: typing-extensions 4.6.3 Adding typing-extensions 4.6.3 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 jedi==0.18.2 Best match: jedi 0.18.2 Adding jedi 0.18.2 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 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 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 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 nest-asyncio==1.5.6 Best match: nest-asyncio 1.5.6 Adding nest-asyncio 1.5.6 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 comm==0.1.3 Best match: comm 0.1.3 Adding comm 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 debugpy==1.6.7 Best match: debugpy 1.6.7 Adding debugpy 1.6.7 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 wcwidth==0.2.6 Best match: wcwidth 0.2.6 Adding wcwidth 0.2.6 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-genutils==0.2.0 Best match: ipython-genutils 0.2.0 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 Searching for QtPy==2.3.1 Best match: QtPy 2.3.1 Adding QtPy 2.3.1 to easy-install.pth file Installing qtpy 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 widgetsnbextension==4.0.7 Best match: widgetsnbextension 4.0.7 Adding widgetsnbextension 4.0.7 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 jupyterlab-widgets==3.0.7 Best match: jupyterlab-widgets 3.0.7 Adding jupyterlab-widgets 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 nbformat==5.9.0 Best match: nbformat 5.9.0 Adding nbformat 5.9.0 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 Jinja2==3.1.2 Best match: Jinja2 3.1.2 Adding Jinja2 3.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for bleach==6.0.0 Best match: bleach 6.0.0 Adding bleach 6.0.0 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 nbclient==0.8.0 Best match: nbclient 0.8.0 Adding nbclient 0.8.0 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 MarkupSafe==2.1.3 Best match: MarkupSafe 2.1.3 Adding MarkupSafe 2.1.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for jupyterlab-pygments==0.2.2 Best match: jupyterlab-pygments 0.2.2 Adding jupyterlab-pygments 0.2.2 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 mistune==3.0.1 Best match: mistune 3.0.1 Adding mistune 3.0.1 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 tinycss2==1.2.1 Best match: tinycss2 1.2.1 Adding tinycss2 1.2.1 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 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 beautifulsoup4==4.12.2 Best match: beautifulsoup4 4.12.2 Adding beautifulsoup4 4.12.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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 terminado==0.17.1 Best match: terminado 0.17.1 Adding terminado 0.17.1 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 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 Searching for nbclassic==1.0.0 Best match: nbclassic 1.0.0 Adding nbclassic 1.0.0 to easy-install.pth file Installing jupyter-nbclassic script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing jupyter-nbclassic-bundlerextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing jupyter-nbclassic-extension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing jupyter-nbclassic-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 prometheus-client==0.17.0 Best match: prometheus-client 0.17.0 Adding prometheus-client 0.17.0 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 Send2Trash==1.8.2 Best match: Send2Trash 1.8.2 Adding Send2Trash 1.8.2 to easy-install.pth file Installing send2trash 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 pure-eval==0.2.2 Best match: pure-eval 0.2.2 Adding pure-eval 0.2.2 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 executing==1.2.0 Best match: executing 1.2.0 Adding executing 1.2.0 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 asttokens==2.2.1 Best match: asttokens 2.2.1 Adding asttokens 2.2.1 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 parso==0.8.3 Best match: parso 0.8.3 Adding parso 0.8.3 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 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 Searching for fastjsonschema==2.17.1 Best match: fastjsonschema 2.17.1 Adding fastjsonschema 2.17.1 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 jsonschema==4.17.3 Best match: jsonschema 4.17.3 Adding jsonschema 4.17.3 to easy-install.pth file 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 webencodings==0.5.1 Best match: webencodings 0.5.1 Adding webencodings 0.5.1 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 soupsieve==2.4.1 Best match: soupsieve 2.4.1 Adding soupsieve 2.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for argon2-cffi-bindings==21.2.0 Best match: argon2-cffi-bindings 21.2.0 Adding argon2-cffi-bindings 21.2.0 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 notebook-shim==0.2.3 Best match: notebook-shim 0.2.3 Adding notebook-shim 0.2.3 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 jupyter-server==2.7.0 Best match: jupyter-server 2.7.0 Adding jupyter-server 2.7.0 to easy-install.pth file Installing jupyter-server 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 attrs==23.1.0 Best match: attrs 23.1.0 Adding attrs 23.1.0 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 pyrsistent==0.19.3 Best match: pyrsistent 0.19.3 Adding pyrsistent 0.19.3 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 pkgutil-resolve-name==1.3.10 Best match: pkgutil-resolve-name 1.3.10 Adding pkgutil-resolve-name 1.3.10 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==1.15.1 Best match: cffi 1.15.1 Adding cffi 1.15.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for anyio==3.7.0 Best match: anyio 3.7.0 Adding anyio 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 jupyter-events==0.6.3 Best match: jupyter-events 0.6.3 Adding jupyter-events 0.6.3 to easy-install.pth file Installing jupyter-events 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-server-terminals==0.4.4 Best match: jupyter-server-terminals 0.4.4 Adding jupyter-server-terminals 0.4.4 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 overrides==7.3.1 Best match: overrides 7.3.1 Adding overrides 7.3.1 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 websocket-client==1.6.1 Best match: websocket-client 1.6.1 Adding websocket-client 1.6.1 to easy-install.pth file Installing wsdump script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Using 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jsonpointer 2.4 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 webcolors==1.13 Best match: webcolors 1.13 Adding webcolors 1.13 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 arrow==1.2.3 Best match: arrow 1.2.3 Adding arrow 1.2.3 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 Finished processing dependencies for phyloModels==0.5 [rtd-command-info] start-time: 2023-06-27T19:13:55.669243Z, end-time: 2023-06-27T19:14:07.692504Z, duration: 12, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from argon2-cffi-bindings->argon2-cffi->jupyter-server~=1.4->jupyterlab~=3.1.2->-r docs/requirements.txt (line 9)) (1.15.1) Requirement already satisfied: pycparser in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->jupyter-server~=1.4->jupyterlab~=3.1.2->-r docs/requirements.txt (line 9)) (2.21) Installing collected packages: json5, sphinxext.remoteliteralinclude, pockets, docutils, sphinxcontrib-napoleon, sphinx, plantweb, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, nbsphinx, jupyter-server, jupyterlab-server, nbclassic, jupyterlab Attempting uninstall: docutils Found existing installation: docutils 0.18.1 Uninstalling docutils-0.18.1: Successfully uninstalled docutils-0.18.1 Attempting 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2023-06-27T19:14:14.578748Z, end-time: 2023-06-27T19:14:14.668072Z, 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. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css', '_static/copy_button.css' ] } html_js_files = ['show_block_by_os.js'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = '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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("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': '', 'analytics_code': 'G-SVDSQH04EM', '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': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': 'c6545bd2', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-phylomodels/builds/1564818/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-06-27T19:14:15.110361Z, end-time: 2023-06-27T19:14:28.341299Z, duration: 13, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/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 reading sources... 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[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'; 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[100%] todo generating indices... genindex done writing additional pages... search opensearch done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 143 warnings. The HTML pages are in ../_readthedocs/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-06-27T19:14:28.741436Z, end-time: 2023-06-27T19:14:35.540156Z, duration: 6, exit-code: 0 python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/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 [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 151 added, 0 changed, 0 removed reading sources... [ 0%] calibration reading sources... [ 1%] examples reading sources... [ 1%] features reading sources... [ 2%] index reading sources... [ 3%] models reading sources... 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[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: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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) looking for now-outdated files... 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 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import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-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) none found pickling environment... done checking consistency... done preparing documents... done 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 phylomodels.visualization.parallelCoordinates todo done writing... done writing additional files... opensearchdone copying static files... done copying extra files... done dumping object inventory... done build succeeded, 143 warnings. The HTML page is in ../_readthedocs/htmlzip. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-06-27T19:14:36.845527Z, end-time: 2023-06-27T19:14:43.405232Z, duration: 6, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/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 [latex]: all documents updating environment: [new config] 151 added, 0 changed, 0 removed reading sources... [ 0%] calibration reading sources... [ 1%] examples reading sources... [ 1%] features reading sources... [ 2%] index reading sources... 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(/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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) 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(/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-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) looking for now-outdated files... none found pickling environment... done checking consistency... done 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 phylomodels.visualization.parallelCoordinates todo resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded, 143 warnings. The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/checkouts/latest/_readthedocs/pdf/_static/searchtools.js [rtd-command-info] start-time: 2023-06-27T19:14:44.077854Z, end-time: 2023-06-27T19:14:44.156987Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2023-06-27T19:14:44.580526Z, end-time: 2023-06-27T19:14:46.748247Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-phylomodels -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-phylomodels" "phylomodels-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./phylomodels-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Nothing written in institute-for-disease-modeling-phylomodels.ind. Transcript written in institute-for-disease-modeling-phylomodels.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-phylomodels.aux' 'institute-for-disease-modeling-phylomodels.ind' ------------ Run number 2 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-phylomodels" "phylomodels-docs.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./phylomodels-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[3] [4] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [9] [10] Chapter 5. [11] [12] Chapter 6. Overfull \hbox (131.74986pt too wide) in paragraph at lines 307--309 []\T1/qtm/m/n/10 Com-put-ing sum-mary statis-tics on phy-lo-ge-netic trees: phy -lo-mod-els/examples/features_computeTreeFeatures/features_computeTreeFeatures. ipynb Overfull \hbox (273.4299pt too wide) in paragraph at lines 311--313 []\T1/qtm/m/n/10 Model cal-i-bra-tion us-ing His-tory Match-ing: phy-lo-mod-els /examples/calibration_historyMatching_featureSelectionForSIR/calibration_histor yMatching_featureSelectionForSIR.ipynb [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] (./institute-for-disease-modeling-phylomodels.ind) [31] (./institute-for-disease-modeling-phylomodels.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on institute-for-disease-modeling-phylomodels.pdf (35 pages, 203 142 bytes). 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