Read the Docs build information Build id: 786937 Project: institute-for-disease-modeling-phylomodels Version: latest Commit: 1707a58706f9688a31e8f142114a5e4effc666d3 Date: 2021-12-01T00:05:51.820865Z State: finished Success: True [rtd-command-info] start-time: 2021-12-01T00:05:53.315561Z, end-time: 2021-12-01T00:05:56.426452Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/phyloModels.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2021-12-01T00:05:56.559752Z, end-time: 2021-12-01T00:05:56.732574Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 1707a58 Merge pull request #38 from InstituteforDiseaseModeling/JSchripsema-IDM-patch-1 [rtd-command-info] start-time: 2021-12-01T00:05:56.837238Z, end-time: 2021-12-01T00:05:56.909332Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-12-01T00:05:57.964235Z, end-time: 2021-12-01T00:06:03.469524Z, duration: 5, exit-code: 0 python3.8 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-12-01T00:06:03.589610Z, end-time: 2021-12-01T00:06:05.520092Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (21.3.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (59.4.0) [rtd-command-info] start-time: 2021-12-01T00:06:05.625885Z, end-time: 2021-12-01T00:06:41.586485Z, duration: 35, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2 Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting mock==1.0.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/15/45/30273ee91feb60dabb8fbb2da7868520525f02cf910279b3047182feed80/mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3c/7e/443be24431324bd34d22dd9d11cc845d995bcd3b500676bcf23142756975/Pillow-5.4.1.tar.gz (16.0 MB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading 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/tmp/pip-ephem-wheel-cache-ekhwnyd4/wheels/19/18/22/b49394d6f0922527d787e31a3efc2bcd6d996cac657e52d502 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=6b8a4fb38cc6c0cfab0e05150692f922298f863b2a8eead902b3cb33aaf4e674 Stored in directory: /tmp/pip-ephem-wheel-cache-ekhwnyd4/wheels/0f/0a/c6/50e5007158dc6781dbe311e0bd363f1ff0714248b456b6f77c Successfully built mock pillow future Installing collected packages: urllib3, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.8 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.6 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 setuptools-59.4.0 snowballstemmer-2.2.0 sphinx-4.3.1 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-1.26.7 [rtd-command-info] start-time: 2021-12-01T00:06:41.715703Z, end-time: 2021-12-01T00:08:12.183884Z, duration: 90, 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)) (1.19.2) Collecting scipy Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f8/3d/26a75c8045181c2fab9c76936ca84318a6674707e33e42c727c1d84f1df4/scipy-1.7.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 MB) Requirement already satisfied: pandas in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.1.3) Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (3.3.2) Collecting seaborn Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/5b/0479d7d845b5ba410ca702ffcd7f2cd95a14a4dfff1fde2637802b258b9b/seaborn-0.11.2-py3-none-any.whl (292 kB) Collecting mkl Downloading 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https://packages.idmod.org/api/pypi/pypi-production/packages/packages/bd/df/d4a4974a3e3957fd1c1fa3082366d7fff6e428ddb55f074bf64876f8e8ad/zipp-3.6.0-py3-none-any.whl (5.3 kB) Building wheels for collected packages: ete3, pyDOE Building wheel for ete3 (setup.py): started Building wheel for ete3 (setup.py): finished with status 'done' Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2273013 sha256=ced122749c53a1107afae4b2498affccb0c7639cb78542d6e07894928474eb25 Stored in directory: /tmp/pip-ephem-wheel-cache-vkq48jc1/wheels/02/a7/41/29eb8b327ac7326f1610806e86133e427d4f086e3332fb4ab0 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=6d040eaf7622a51514ff4abd6de24a70315aa594ea3fdc85255047608e99d03e Stored in directory: /tmp/pip-ephem-wheel-cache-vkq48jc1/wheels/80/02/2f/addb15cd7424cf5ca7222decbe8898cfcb69111600ed0d260b Successfully built ete3 pyDOE Installing collected packages: zipp, traitlets, pyrsistent, importlib-resources, attrs, wcwidth, tornado, pyzmq, ptyprocess, parso, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, pycparser, prompt-toolkit, pickleshare, pexpect, nbformat, matplotlib-inline, jupyter-client, jedi, decorator, backcall, testpath, pandocfilters, nbclient, mistune, jupyterlab-pygments, ipython, defusedxml, debugpy, cffi, bleach, terminado, Send2Trash, prometheus-client, nbconvert, ipykernel, argon2-cffi, notebook, widgetsnbextension, tzdata, qtpy, pillow, jupyterlab-widgets, backports.zoneinfo, threadpoolctl, tbb, scipy, qtconsole, pytz-deprecation-shim, PyQt5-sip, PyQt5-Qt5, patsy, numexpr, jupyter-console, joblib, ipywidgets, intel-openmp, ete3, et-xmlfile, xlrd, Wand, unittest-xml-reporting, tzlocal, tables, statsmodels, seaborn, scikit-learn, PyQt5, pyDOE, psutil, openpyxl, ngesh, networkx, mkl, jupyter Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed PyQt5-5.15.6 PyQt5-Qt5-5.15.2 PyQt5-sip-12.9.0 Send2Trash-1.8.0 Wand-0.6.7 argon2-cffi-21.1.0 attrs-21.2.0 backcall-0.2.0 backports.zoneinfo-0.2.1 bleach-4.1.0 cffi-1.15.0 debugpy-1.5.1 decorator-5.1.0 defusedxml-0.7.1 entrypoints-0.3 et-xmlfile-1.1.0 ete3-3.1.2 importlib-resources-5.4.0 intel-openmp-2021.4.0 ipykernel-6.5.1 ipython-7.30.0 ipython-genutils-0.2.0 ipywidgets-7.6.5 jedi-0.18.1 joblib-1.1.0 jsonschema-4.2.1 jupyter-1.0.0 jupyter-client-7.1.0 jupyter-console-6.4.0 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 jupyterlab-widgets-1.0.2 matplotlib-inline-0.1.3 mistune-0.8.4 mkl-2021.4.0 nbclient-0.5.9 nbconvert-6.3.0 nbformat-5.1.3 nest-asyncio-1.5.1 networkx-2.6.3 ngesh-1.1.1 notebook-6.4.6 numexpr-2.7.3 openpyxl-3.0.9 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.4.0 prometheus-client-0.12.0 prompt-toolkit-3.0.23 psutil-5.8.0 ptyprocess-0.7.0 pyDOE-0.3.8 pycparser-2.21 pyrsistent-0.18.0 pytz-deprecation-shim-0.1.0.post0 pyzmq-22.3.0 qtconsole-5.2.1 qtpy-1.11.2 scikit-learn-1.0.1 scipy-1.7.3 seaborn-0.11.2 statsmodels-0.13.1 tables-3.6.1 tbb-2021.4.0 terminado-0.12.1 testpath-0.5.0 threadpoolctl-3.0.0 tornado-6.1 traitlets-5.1.1 tzdata-2021.5 tzlocal-4.1 unittest-xml-reporting-3.0.4 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.5.2 xlrd-2.0.1 zipp-3.6.0 [rtd-command-info] start-time: 2021-12-01T00:08:12.333563Z, end-time: 2021-12-01T00:08:27.263104Z, duration: 14, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating phyloModels.egg-info writing phyloModels.egg-info/PKG-INFO writing dependency_links to phyloModels.egg-info/dependency_links.txt writing requirements to phyloModels.egg-info/requires.txt writing top-level names to phyloModels.egg-info/top_level.txt writing manifest file 'phyloModels.egg-info/SOURCES.txt' reading manifest file 'phyloModels.egg-info/SOURCES.txt' writing manifest file 'phyloModels.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/phylomodels copying phylomodels/__init__.py -> build/lib/phylomodels creating build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/cal_parameterSweep.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/constants.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_base.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/__init__.py -> build/lib/phylomodels/calibration creating build/lib/phylomodels/sampling copying phylomodels/sampling/observationModel.py -> build/lib/phylomodels/sampling copying phylomodels/sampling/__init__.py -> build/lib/phylomodels/sampling creating build/lib/phylomodels/network copying phylomodels/network/phyloTree.py -> build/lib/phylomodels/network copying phylomodels/network/__init__.py -> build/lib/phylomodels/network creating build/lib/phylomodels/utilities copying phylomodels/utilities/__init__.py -> build/lib/phylomodels/utilities creating build/lib/phylomodels/features copying phylomodels/features/testFeatures.py -> build/lib/phylomodels/features copying phylomodels/features/features.py -> build/lib/phylomodels/features copying phylomodels/features/test.py -> build/lib/phylomodels/features copying phylomodels/features/__init__.py -> build/lib/phylomodels/features copying phylomodels/features/inventory.py -> build/lib/phylomodels/features creating build/lib/phylomodels/visualization copying phylomodels/visualization/parallelCoordinates.py -> build/lib/phylomodels/visualization copying phylomodels/visualization/__init__.py -> build/lib/phylomodels/visualization creating build/lib/phylomodels/models copying phylomodels/models/distributions_gaussian.py -> build/lib/phylomodels/models copying phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models copying phylomodels/models/test_distributions_gaussian.py -> build/lib/phylomodels/models copying phylomodels/models/sir_taoLeap_getIncidence.py -> build/lib/phylomodels/models copying phylomodels/models/test_sir_taoLeap_getIncidence.py -> build/lib/phylomodels/models copying phylomodels/models/sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models copying phylomodels/models/__init__.py -> build/lib/phylomodels/models copying phylomodels/models/seir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models creating build/lib/phylomodels/examples copying phylomodels/examples/__init__.py -> build/lib/phylomodels/examples creating build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/fano.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/skew.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/mean.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/qcd.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/rsd.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/__init__.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/var.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/std.py -> build/lib/phylomodels/features/statistics creating build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_WD_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_frac_basal.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_max_adj_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_sackin_var.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_skewness.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_t_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_closeness_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_sackin.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_B1.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_cherries.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_1.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_frac_imbalance.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_FurnasR.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_LBI_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_mean_path.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_mean_b_time.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_max_dW.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_min_lap_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mode.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_betweenness_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_kurtosis.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/mean_NN_distance.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_frac_ladder.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_colless.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_min_adj_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_fourprong.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_mean_s_time.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_diameter.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/__init__.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_num.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_max_ladder.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_B2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> build/lib/phylomodels/features/trees creating build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum15.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum30.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_gaussianFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_cauchyFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_Linf.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_gaussianFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum7.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/__init__.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum_log10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_log10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L1.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_cauchyFit.py -> build/lib/phylomodels/features/series creating build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/process_optional_arguements.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/unique_node_attr.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_groups.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_LTT.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_eigenvalues_lap.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_adjacency_mat.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_eigenvalues_adj.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_distance_mat.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/__init__.py -> build/lib/phylomodels/features/trees/helper creating build/lib/phylomodels/models/seir_taoLeap copying phylomodels/models/seir_taoLeap/seirTaoLeap.py -> build/lib/phylomodels/models/seir_taoLeap copying phylomodels/models/seir_taoLeap/__init__.py -> build/lib/phylomodels/models/seir_taoLeap creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/phylomodels creating build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/cal_parameterSweep.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/constants.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/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration creating build/bdist.linux-x86_64/egg/phylomodels/sampling copying build/lib/phylomodels/sampling/observationModel.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/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 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 creating 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/skew.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/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/var.py -> 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/features.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/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_ratio_min.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/local_calculate_frac_basal.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/spectral_calculate_max_adj_eigen.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_skewness.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/netSci_calculate_closeness_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/top_calculate_sackin.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/smallConfig_calculate_cherries.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/BL_calculate_median.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/LTT_calculate_slope_1.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/group_calculate_mean.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/BL_calculate_external_mean.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/top_calculate_FurnasR.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/local_calculate_LBI_mean.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/tree_height_calculate_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_ratio_std.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/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/spectral_calculate_min_lap_eigen.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/netSci_calculate_betweenness_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/group_calculate_max.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/BL_calculate_external_max.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/BL_calculate_max.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/BL_calculate_internal_min.py -> 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/top_calculate_frac_ladder.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/top_calculate_colless.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/BL_calculate_internal_mean.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/spectral_calculate_min_adj_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees 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/BL_calculate_external_std.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/group_calculate_std.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/BL_calculate_internal_std.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/LTT_calculate_mean_s_time.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 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/__init__.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/BL_calculate_mean.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/process_optional_arguements.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_dist_lap.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_LTT.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_adjacency_mat.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_distance_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/BL_calculate_internal_median.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/top_calculate_B2.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 creating 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.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_diff_L2.py -> 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_gaussianFit.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_partialSum2.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_diff_Linf.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_derivative2.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_derivative_gaussianFit.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_sum.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_sum_log10.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/series/series_diff_L1.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_derivative_cauchyFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/inventory.py -> build/bdist.linux-x86_64/egg/phylomodels/features 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/models creating 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 copying build/lib/phylomodels/models/seir_taoLeap/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/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 copying build/lib/phylomodels/models/test_distributions_gaussian.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/seir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models creating build/bdist.linux-x86_64/egg/phylomodels/examples copying build/lib/phylomodels/examples/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/examples copying build/lib/phylomodels/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels 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/cal_parameterSweep.py to cal_parameterSweep.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/calibration/init_historyMatching_base.py to init_historyMatching_base.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/sampling/observationModel.py to observationModel.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/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/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/statistics/fano.py to fano.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/statistics/mean.py to mean.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/var.py to var.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/features.py to features.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/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_ratio_min.py to BL_calculate_ratio_min.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/local_calculate_frac_basal.py to local_calculate_frac_basal.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/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/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_skewness.py to spectral_calculate_skewness.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/netSci_calculate_closeness_max.py to netSci_calculate_closeness_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/top_calculate_sackin.py to top_calculate_sackin.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/smallConfig_calculate_cherries.py to smallConfig_calculate_cherries.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/BL_calculate_median.py to BL_calculate_median.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/LTT_calculate_slope_1.py to LTT_calculate_slope_1.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/group_calculate_mean.py to group_calculate_mean.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/BL_calculate_external_mean.py to BL_calculate_external_mean.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/top_calculate_FurnasR.py to top_calculate_FurnasR.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/local_calculate_LBI_mean.py to local_calculate_LBI_mean.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/tree_height_calculate_mean.py to tree_height_calculate_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_ratio_std.py to BL_calculate_ratio_std.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/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/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/group_calculate_mode.py to group_calculate_mode.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/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/group_calculate_max.py to group_calculate_max.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/BL_calculate_external_max.py to BL_calculate_external_max.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/BL_calculate_max.py to BL_calculate_max.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/BL_calculate_internal_min.py to BL_calculate_internal_min.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/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_ratio_mean.py to BL_calculate_ratio_mean.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/group_calculate_median.py to group_calculate_median.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_max.py to BL_calculate_ratio_max.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_internal_max.py to BL_calculate_internal_max.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/smallConfig_calculate_fourprong.py to smallConfig_calculate_fourprong.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/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/BL_calculate_internal_std.py to BL_calculate_internal_std.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/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/netSci_calculate_diameter.py to netSci_calculate_diameter.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/__init__.py to __init__.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/BL_calculate_mean.py to BL_calculate_mean.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/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_dist_lap.py to get_eigenvalues_dist_lap.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_LTT.py to get_LTT.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_adjacency_mat.py to get_adjacency_mat.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_distance_mat.py to get_distance_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/BL_calculate_internal_median.py to BL_calculate_internal_median.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/top_calculate_B2.py to top_calculate_B2.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/series/series_partialSum15.py to series_partialSum15.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_diff.py to series_diff.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/series_partialSum30.py to series_partialSum30.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_derivative.py to series_derivative.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_derivative2_cauchyFit.py to series_derivative2_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_partialSum10.py to series_partialSum10.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_derivative2_laplaceFit.py to series_derivative2_laplaceFit.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_partialSum7.py to series_partialSum7.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/__init__.py to __init__.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_log10.py to series_log10.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_derivative_laplaceFit.py to series_derivative_laplaceFit.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/__init__.py to __init__.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/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/models/seir_taoLeap/seirTaoLeap.py to seirTaoLeap.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/distributions_gaussian.py to 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/test_distributions_gaussian.py to test_distributions_gaussian.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/seir_taoLeap_getIncidenceSampled.py to seir_taoLeap_getIncidenceSampled.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/__init__.py to __init__.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 lxml Reading https://pypi.org/simple/lxml/ Downloading https://files.pythonhosted.org/packages/65/2f/e50ce8cfcbb8396aa6f473f9e7b816ad25638cca344ee10851c45c1520c2/lxml-4.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl#sha256=cf201bf5594d1aab139fe53e3fca457e4f8204a5bbd65d48ab3b82a16f517868 Best match: lxml 4.6.4 Processing lxml-4.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl Installing lxml-4.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Adding lxml 4.6.4 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/lxml-4.6.4-py3.8-linux-x86_64.egg 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/a2/80/340ed190dfd6fbc388d4bd3a9a145b85926f1f7ec8986368cfee7e5bf957/sip-6.4.0-cp36-abi3-manylinux2014_x86_64.whl#sha256=87539b534d730aaabde7396bd2edb7c5b86093ca2500eeaa617d588150b7fda9 Best match: sip 6.4.0 Processing sip-6.4.0-cp36-abi3-manylinux2014_x86_64.whl Installing sip-6.4.0-cp36-abi3-manylinux2014_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 6.4.0 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-6.4.0-py3.8-linux-x86_64.egg Searching for PyQt5_sip<4.20,>=4.19.11 Reading https://pypi.org/simple/PyQt5_sip/ Downloading https://files.pythonhosted.org/packages/c2/70/eb9d398ecbcab83e9a968fa63336a16b21034bbd4e318128fe11e08bffab/PyQt5_sip-4.19.19-cp38-cp38-manylinux1_x86_64.whl#sha256=304acf771b6033cb4bafc415939d227c91265d30664ed643b298d7e95f509f81 Best match: PyQt5-sip 4.19.19 Processing PyQt5_sip-4.19.19-cp38-cp38-manylinux1_x86_64.whl Installing PyQt5_sip-4.19.19-cp38-cp38-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Adding PyQt5-sip 4.19.19 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/PyQt5_sip-4.19.19-py3.8-linux-x86_64.egg Searching for toml Reading https://pypi.org/simple/toml/ Downloading https://files.pythonhosted.org/packages/44/6f/7120676b6d73228c96e17f1f794d8ab046fc910d781c8d151120c3f1569e/toml-0.10.2-py2.py3-none-any.whl#sha256=806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b Best match: toml 0.10.2 Processing toml-0.10.2-py2.py3-none-any.whl Installing toml-0.10.2-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Adding toml 0.10.2 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/toml-0.10.2-py3.8.egg Searching for xlrd==2.0.1 Best match: xlrd 2.0.1 Adding xlrd 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for openpyxl==3.0.9 Best match: openpyxl 3.0.9 Adding openpyxl 3.0.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for unittest-xml-reporting==3.0.4 Best match: unittest-xml-reporting 3.0.4 Adding unittest-xml-reporting 3.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for psutil==5.8.0 Best match: psutil 5.8.0 Adding psutil 5.8.0 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 jupyter-client==7.1.0 Best match: jupyter-client 7.1.0 Adding jupyter-client 7.1.0 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==6.4.0 Best match: jupyter-console 6.4.0 Adding jupyter-console 6.4.0 to easy-install.pth file Installing jupyter-console script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for jupyter-core==4.9.1 Best match: jupyter-core 4.9.1 Adding jupyter-core 4.9.1 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==1.0.1 Best match: scikit-learn 1.0.1 Adding scikit-learn 1.0.1 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 mkl==2021.4.0 Best match: mkl 2021.4.0 Adding mkl 2021.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for seaborn==0.11.2 Best match: seaborn 0.11.2 Adding seaborn 0.11.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for matplotlib==3.3.2 Best match: matplotlib 3.3.2 Adding matplotlib 3.3.2 to easy-install.pth file Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for pandas==1.1.3 Best match: pandas 1.1.3 pandas 1.1.3 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for networkx==2.6.3 Best match: networkx 2.6.3 Adding networkx 2.6.3 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 ete3==3.1.2 Best match: ete3 3.1.2 Adding ete3 3.1.2 to easy-install.pth file Installing ete3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for six==1.15.0 Best match: six 1.15.0 six 1.15.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for scipy==1.7.3 Best match: scipy 1.7.3 Adding scipy 1.7.3 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 numpy==1.19.2 Best match: numpy 1.19.2 numpy 1.19.2 is already the active version in easy-install.pth Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing f2py3.8 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for et-xmlfile==1.1.0 Best match: et-xmlfile 1.1.0 Adding et-xmlfile 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for pyzmq==22.3.0 Best match: pyzmq 22.3.0 Adding pyzmq 22.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for tornado==6.1 Best match: tornado 6.1 Adding tornado 6.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for entrypoints==0.3 Best match: entrypoints 0.3 Adding entrypoints 0.3 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 nest-asyncio==1.5.1 Best match: nest-asyncio 1.5.1 Adding nest-asyncio 1.5.1 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 traitlets==5.1.1 Best match: traitlets 5.1.1 Adding traitlets 5.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for Pygments==2.10.0 Best match: Pygments 2.10.0 Adding Pygments 2.10.0 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 ipython==7.30.0 Best match: ipython 7.30.0 Adding ipython 7.30.0 to easy-install.pth file Installing iptest script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing iptest3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin 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 prompt-toolkit==3.0.23 Best match: prompt-toolkit 3.0.23 Adding prompt-toolkit 3.0.23 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 ipykernel==6.5.1 Best match: ipykernel 6.5.1 Adding ipykernel 6.5.1 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 notebook==6.4.6 Best match: notebook 6.4.6 Adding notebook 6.4.6 to easy-install.pth file Installing jupyter-bundlerextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing jupyter-nbextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing jupyter-notebook script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Installing jupyter-serverextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for qtconsole==5.2.1 Best match: qtconsole 5.2.1 Adding qtconsole 5.2.1 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 nbconvert==6.3.0 Best match: nbconvert 6.3.0 Adding nbconvert 6.3.0 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 ipywidgets==7.6.5 Best match: ipywidgets 7.6.5 Adding ipywidgets 7.6.5 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 threadpoolctl==3.0.0 Best match: threadpoolctl 3.0.0 Adding threadpoolctl 3.0.0 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 joblib==1.1.0 Best match: joblib 1.1.0 Adding joblib 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for intel-openmp==2021.4.0 Best match: intel-openmp 2021.4.0 Adding intel-openmp 2021.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for tbb==2021.4.0 Best match: tbb 2021.4.0 Adding tbb 2021.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for Pillow==8.4.0 Best match: Pillow 8.4.0 Adding Pillow 8.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for certifi==2021.10.8 Best match: certifi 2021.10.8 Adding certifi 2021.10.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for kiwisolver==1.2.0 Best match: kiwisolver 1.2.0 kiwisolver 1.2.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for pyparsing==3.0.6 Best match: pyparsing 3.0.6 Adding pyparsing 3.0.6 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 cycler==0.10.0 Best match: cycler 0.10.0 cycler 0.10.0 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages Searching for pytz==2021.3 Best match: pytz 2021.3 Adding pytz 2021.3 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 setuptools==59.4.0 Best match: setuptools 59.4.0 Adding setuptools 59.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for packaging==21.3 Best match: packaging 21.3 Adding packaging 21.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for decorator==5.1.0 Best match: decorator 5.1.0 Adding decorator 5.1.0 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 matplotlib-inline==0.1.3 Best match: matplotlib-inline 0.1.3 Adding matplotlib-inline 0.1.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for jedi==0.18.1 Best match: jedi 0.18.1 Adding jedi 0.18.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for backcall==0.2.0 Best match: backcall 0.2.0 Adding backcall 0.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for pickleshare==0.7.5 Best match: pickleshare 0.7.5 Adding pickleshare 0.7.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for 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 wcwidth==0.2.5 Best match: wcwidth 0.2.5 Adding wcwidth 0.2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for debugpy==1.5.1 Best match: debugpy 1.5.1 Adding debugpy 1.5.1 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 terminado==0.12.1 Best match: terminado 0.12.1 Adding terminado 0.12.1 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==21.1.0 Best match: argon2-cffi 21.1.0 Adding argon2-cffi 21.1.0 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 Jinja2==3.0.3 Best match: Jinja2 3.0.3 Adding Jinja2 3.0.3 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 prometheus-client==0.12.0 Best match: prometheus-client 0.12.0 Adding prometheus-client 0.12.0 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==1.8.0 Best match: Send2Trash 1.8.0 Adding Send2Trash 1.8.0 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 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 nbformat==5.1.3 Best match: nbformat 5.1.3 Adding nbformat 5.1.3 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 QtPy==1.11.2 Best match: QtPy 1.11.2 Adding QtPy 1.11.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for jupyterlab-pygments==0.1.2 Best match: jupyterlab-pygments 0.1.2 Adding jupyterlab-pygments 0.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for 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 mistune==0.8.4 Best match: mistune 0.8.4 Adding mistune 0.8.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for testpath==0.5.0 Best match: testpath 0.5.0 Adding testpath 0.5.0 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 nbclient==0.5.9 Best match: nbclient 0.5.9 Adding nbclient 0.5.9 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 bleach==4.1.0 Best match: bleach 4.1.0 Adding bleach 4.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for 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 widgetsnbextension==3.5.2 Best match: widgetsnbextension 3.5.2 Adding widgetsnbextension 3.5.2 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 jupyterlab-widgets==1.0.2 Best match: jupyterlab-widgets 1.0.2 Adding jupyterlab-widgets 1.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for 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 cffi==1.15.0 Best match: cffi 1.15.0 Adding cffi 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for MarkupSafe==2.0.1 Best match: MarkupSafe 2.0.1 Adding MarkupSafe 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 jsonschema==4.2.1 Best match: jsonschema 4.2.1 Adding jsonschema 4.2.1 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 pycparser==2.21 Best match: pycparser 2.21 Adding pycparser 2.21 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for attrs==21.2.0 Best match: attrs 21.2.0 Adding attrs 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 importlib-resources==5.4.0 Best match: importlib-resources 5.4.0 Adding importlib-resources 5.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Searching for pyrsistent==0.18.0 Best match: pyrsistent 0.18.0 Adding pyrsistent 0.18.0 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==3.6.0 Best match: zipp 3.6.0 Adding zipp 3.6.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages Finished processing dependencies for phyloModels==0.5 /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/setuptools/command/easy_install.py:156: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: is an invalid version and will not be supported in a future release warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 1.0-static is an invalid version and will not be supported in a future release warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: static is an invalid version and will not be supported in a future release warnings.warn( [rtd-command-info] start-time: 2021-12-01T00:08:27.377612Z, end-time: 2021-12-01T00:08:36.976305Z, duration: 9, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting sphinx~=3.5.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a3/e7/9af5e0766e801cf0ad64eedab70dcea17646c3a0d309980b25426ccc53ec/Sphinx-3.5.4-py3-none-any.whl (2.8 MB) Collecting plantweb~=1.2.1 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d6/6f/9ab1a1c3e33aaa0c0931983578c09336b092c75dce777ea666d3032f756e/plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinx-copybutton~=0.4.0 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/8b/7c9cf5956be80bfd826f2534e2b38ff2310f8c4274a77e4b3b2d846af552/sphinx_copybutton-0.4.0-py3-none-any.whl (12 kB) Collecting sphinx-rtd-theme~=0.5.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ac/24/2475e8f83519b54b2148d4a56eb1111f9cec630d088c3ffc214492c12107/sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/75/f2/6b7627dfe7b4e418e295e254bb15c3a6455f11f8c0ad0d43113f678049c3/sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinxext.remoteliteralinclude Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1b/25/0e9e17e0a13406592ebeabfae2622f44bd114706ca3801052c020b152cf5/sphinxext_remoteliteralinclude-0.3.0-py3-none-any.whl (6.3 kB) Collecting sphinxcontrib-programoutput~=0.17 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/30/ee/b7be4b3f45f4e36bfa6c444cd234098e0d09880379c67a43e6bb9ab99a86/sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting nbsphinx~=0.8.6 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/eb/4d/2c07c13682465e0d2159af292fa20cee26e6a6e322c02764e0ac5d74a824/nbsphinx-0.8.7-py3-none-any.whl (25 kB) Collecting jupyterlab~=3.1.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/32/e2/577343b7048c5ec6cf6d271dcbd36cb9d12eb0e7111c40e88c90ecd46379/jupyterlab-3.1.18-py3-none-any.whl (8.6 MB) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2.9.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2.2.0) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (1.1.5) Collecting docutils<0.17,>=0.12 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/44/8a15e45ffa96e6cf82956dd8d7af9e666357e16b0d93b253903475ee947f/docutils-0.16-py2.py3-none-any.whl (548 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2.10.0) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (1.0.3) Requirement already satisfied: sphinxcontrib-jsmath in 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2.26.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (59.4.0) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (1.0.2) Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (1.0.2) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (1.3.0) Requirement already satisfied: six in /home/docs/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 2)) (1.15.0) Collecting pockets>=0.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e9/2f/a4583c70fbd8cd04910e2884bcc2bdd670e884061f7b4d70bc13e632a993/pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: traitlets in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from nbsphinx~=0.8.6->-r docs/requirements.txt (line 8)) (5.1.1) Requirement already satisfied: nbconvert!=5.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from nbsphinx~=0.8.6->-r docs/requirements.txt (line 8)) (6.3.0) Requirement already satisfied: nbformat in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from nbsphinx~=0.8.6->-r docs/requirements.txt (line 8)) (5.1.3) Collecting nbclassic~=0.2 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5b/83/9858221f5318a872d92f9be0a516275e2700119d3702e0ec05a299ba75af/nbclassic-0.3.4-py3-none-any.whl (25 kB) Requirement already satisfied: tornado>=6.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from jupyterlab~=3.1.2->-r docs/requirements.txt (line 9)) (6.1) Collecting jupyterlab-server~=2.3 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6f/e1/27fc83c989e0c9a67d9bba3ecb71a4244d49ed20230a1177f387cfb3ca19/jupyterlab_server-2.8.2-py3-none-any.whl (58 kB) Collecting jupyter-server~=1.4 Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/07/48/c38b3ec0f60da2059554b21cd048914e9e88cb25ae19c183634945664038/jupyter_server-1.12.1-py3-none-any.whl (395 kB) Requirement already satisfied: jupyter-core in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from jupyterlab~=3.1.2->-r docs/requirements.txt (line 9)) (4.9.1) Requirement already satisfied: ipython in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from jupyterlab~=3.1.2->-r docs/requirements.txt (line 9)) (7.30.0) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from babel>=1.3->sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2021.3) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx~=3.5.4->-r docs/requirements.txt (line 1)) (2.0.1) Requirement already satisfied: terminado>=0.8.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from jupyter-server~=1.4->jupyterlab~=3.1.2->-r docs/requirements.txt (line 9)) (0.12.1) Requirement already satisfied: ipython-genutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/latest/lib/python3.8/site-packages (from jupyter-server~=1.4->jupyterlab~=3.1.2->-r 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docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 4.3.1 Uninstalling Sphinx-4.3.1: Successfully uninstalled Sphinx-4.3.1 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 1.0.0 Uninstalling sphinx-rtd-theme-1.0.0: Successfully uninstalled sphinx-rtd-theme-1.0.0 Successfully installed anyio-3.4.0 docutils-0.16 json5-0.9.6 jupyter-server-1.12.1 jupyterlab-3.1.18 jupyterlab-server-2.8.2 nbclassic-0.3.4 nbsphinx-0.8.7 plantweb-1.2.1 pockets-0.9.1 sniffio-1.2.0 sphinx-3.5.4 sphinx-copybutton-0.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.3.0 websocket-client-1.2.1 [rtd-command-info] start-time: 2021-12-01T00:08:37.847648Z, end-time: 2021-12-01T00:08:37.916270Z, 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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/phylomodels/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/phylomodels/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-phylomodels', 'name': u'phyloModels', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/phylomodels/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'phyloModels', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '1707a587', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-phylomodels/builds/786937/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-12-01T00:08:38.027350Z, end-time: 2021-12-01T00:08:55.054463Z, duration: 17, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v3.5.4 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 147 source files that are out of date updating environment: [new config] 147 added, 0 changed, 0 removed reading sources... 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[ 32%] phylomodels.features.testFeatures *** Test data: *** 0 1 2 3 4 0 0.653590 0.115007 0.950283 0.482191 0.872475 1 0.212333 0.040710 0.397194 0.233132 0.841741 0 1 2 3 4 0 0.207082 0.74247 0.392154 0.182257 0.743539 ****************** reading sources... [ 33%] phylomodels.features.trees reading sources... [ 34%] phylomodels.features.trees.BL_calculate_external_max reading sources... [ 34%] phylomodels.features.trees.BL_calculate_external_mean reading sources... [ 35%] phylomodels.features.trees.BL_calculate_external_median reading sources... [ 36%] phylomodels.features.trees.BL_calculate_external_min reading sources... [ 36%] phylomodels.features.trees.BL_calculate_external_std reading sources... [ 37%] phylomodels.features.trees.BL_calculate_internal_max reading sources... [ 38%] phylomodels.features.trees.BL_calculate_internal_mean reading sources... [ 38%] phylomodels.features.trees.BL_calculate_internal_median reading sources... 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WARNING: autodoc: failed to import module 'test_distributions_gaussian' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'test_sir_taoLeap_getIncidence' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'test_sir_taoLeap_getIncidenceSampled' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'observationModel' from module 'phylomodels.sampling'; the following exception was raised: No module named 'yaml' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... 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[100%] phylomodels.visualization.parallelCoordinates 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, 5 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-12-01T00:08:55.251865Z, end-time: 2021-12-01T00:08:58.641309Z, duration: 3, exit-code: 0 python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v3.5.4 loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 6 changed, 0 removed reading sources... [ 16%] modules reading sources... [ 33%] phylomodels.features.testFeatures *** Test data: *** 0 1 2 3 4 0 0.653590 0.115007 0.950283 0.482191 0.872475 1 0.212333 0.040710 0.397194 0.233132 0.841741 0 1 2 3 4 0 0.207082 0.74247 0.392154 0.182257 0.743539 ****************** reading sources... [ 50%] phylomodels.models.test_distributions_gaussian reading sources... [ 66%] phylomodels.models.test_sir_taoLeap_getIncidence reading sources... [ 83%] phylomodels.models.test_sir_taoLeap_getIncidenceSampled reading sources... [100%] phylomodels.sampling.observationModel WARNING: autodoc: failed to import module 'testFeatures' from module 'phylomodels.features'; the module executes module level statement and it might call sys.exit(). WARNING: autodoc: failed to import module 'test_distributions_gaussian' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'test_sir_taoLeap_getIncidence' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'test_sir_taoLeap_getIncidenceSampled' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'observationModel' from module 'phylomodels.sampling'; the following exception was raised: No module named 'yaml' looking for now-outdated files... 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.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.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.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.observationModel 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, 5 warnings. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-12-01T00:08:58.786771Z, end-time: 2021-12-01T00:09:01.933018Z, duration: 3, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.5.4 loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 6 changed, 0 removed reading sources... [ 16%] modules reading sources... [ 33%] phylomodels.features.testFeatures *** Test data: *** 0 1 2 3 4 0 0.653590 0.115007 0.950283 0.482191 0.872475 1 0.212333 0.040710 0.397194 0.233132 0.841741 0 1 2 3 4 0 0.207082 0.74247 0.392154 0.182257 0.743539 ****************** reading sources... [ 50%] phylomodels.models.test_distributions_gaussian reading sources... [ 66%] phylomodels.models.test_sir_taoLeap_getIncidence reading sources... [ 83%] phylomodels.models.test_sir_taoLeap_getIncidenceSampled reading sources... [100%] phylomodels.sampling.observationModel WARNING: autodoc: failed to import module 'testFeatures' from module 'phylomodels.features'; the module executes module level statement and it might call sys.exit(). WARNING: autodoc: failed to import module 'test_distributions_gaussian' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'test_sir_taoLeap_getIncidence' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'test_sir_taoLeap_getIncidenceSampled' from module 'phylomodels.models'; the following exception was raised: Cannot load backend 'TKAgg' which requires the 'tk' interactive framework, as 'headless' is currently running WARNING: autodoc: failed to import module 'observationModel' from module 'phylomodels.sampling'; the following exception was raised: No module named 'yaml' 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.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.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.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.observationModel phylomodels.utilities phylomodels.visualization phylomodels.visualization.parallelCoordinates todo resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded, 5 warnings. 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LaTeX Warning: Reference `phylomodels.network.phyloTree:module-phylomodels.netw ork.phyloTree' on page 51 undefined on input line 3987. LaTeX Warning: Reference `phylomodels.sampling:module-phylomodels.sampling' on page 51 undefined on input line 3988. LaTeX Warning: Reference `phylomodels.utilities:module-phylomodels.utilities' o n page 51 undefined on input line 3989. LaTeX Warning: Reference `phylomodels.visualization:module-phylomodels.visualiz ation' on page 51 undefined on input line 3990. LaTeX Warning: Reference `phylomodels.visualization.parallelCoordinates:module- phylomodels.visualization.parallelCoordinates' on page 51 undefined on input li ne 3991. Overfull \hbox (42.6225pt too wide) in paragraph at lines 3991--3992 []\T1/pcr/m/n/10 phylomodels.visualization.parallelCoordinates\T1/ptm/m/n/10 , [51] No file institute-for-disease-modeling-phylomodels.ind. (./institute-for-disease-modeling-phylomodels.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-phylomodel s.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on institute-for-disease-modeling-phylomodels.pdf (55 pages, 217 820 bytes). Transcript written on institute-for-disease-modeling-phylomodels.log. Latexmk: Index file 'institute-for-disease-modeling-phylomodels.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-phylomodels.ind' from line 'No file institute-for-disease-modeling-phylomodels.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-phylomodels.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-phylomodels.pdf' Latexmk: List of undefined refs and citations: Reference `phylomodels.calibration.cal_parameterSweep:module-phylomodels.calibration.cal_parameterSweep' on page 49 undefined on input line 3860 Reference `phylomodels.calibration.constants:module-phylomodels.calibration.constants' on page 49 undefined on input line 3861 Reference `phylomodels.calibration.init_historyMatching_base:module-phylomodels.calibration.init_historyMatching_base' on page 49 undefined on input line 3862 Reference `phylomodels.calibration.init_historyMatching_poissonGlmBasis:module-phylomodels.calibration.init_historyMatching_poissonGlmBasis' on page 49 undefined on input line 3863 Reference `phylomodels.calibration:module-phylomodels.calibration' on page 49 undefined on input line 3859 Reference `phylomodels.examples:module-phylomodels.examples' on page 49 undefined on input line 3864 Reference `phylomodels.features.features:module-phylomodels.features.features' on page 49 undefined on input line 3866 Reference `phylomodels.features.inventory:module-phylomodels.features.inventory' on page 49 undefined on input line 3867 Reference `phylomodels.features.series.series:module-phylomodels.features.series.series' on page 49 undefined on input line 3869 Reference `phylomodels.features.series.series_derivative2:module-phylomodels.features.series.series_derivative2' on page 49 undefined on input line 3871 Reference `phylomodels.features.series.series_derivative2_cauchyFit:module-phylomodels.features.series.series_derivative2_cauchyFit' on page 49 undefined on input line 3872 Reference `phylomodels.features.series.series_derivative2_gaussianFit:module-phylomodels.features.series.series_derivative2_gaussianFit' on page 49 undefined on input line 3873 Reference `phylomodels.features.series.series_derivative2_laplaceFit:module-phylomodels.features.series.series_derivative2_laplaceFit' on page 49 undefined on input line 3874 Reference `phylomodels.features.series.series_derivative:module-phylomodels.features.series.series_derivative' on page 49 undefined on input line 3870 Reference `phylomodels.features.series.series_derivative_cauchyFit:module-phylomodels.features.series.series_derivative_cauchyFit' on page 49 undefined on input line 3875 Reference `phylomodels.features.series.series_derivative_gaussianFit:module-phylomodels.features.series.series_derivative_gaussianFit' on page 49 undefined on input line 3876 Reference `phylomodels.features.series.series_derivative_laplaceFit:module-phylomodels.features.series.series_derivative_laplaceFit' on page 49 undefined on input line 3877 Reference `phylomodels.features.series.series_diff:module-phylomodels.features.series.series_diff' on page 49 undefined on input line 3878 Reference `phylomodels.features.series.series_diff_L1:module-phylomodels.features.series.series_diff_L1' on page 49 undefined on input line 3879 Reference `phylomodels.features.series.series_diff_L2:module-phylomodels.features.series.series_diff_L2' on page 49 undefined on input line 3880 Reference `phylomodels.features.series.series_diff_Linf:module-phylomodels.features.series.series_diff_Linf' on page 49 undefined on input line 3881 Reference `phylomodels.features.series.series_log10:module-phylomodels.features.series.series_log10' on page 49 undefined on input line 3882 Reference `phylomodels.features.series.series_partialSum10:module-phylomodels.features.series.series_partialSum10' on page 49 undefined on input line 3883 Reference `phylomodels.features.series.series_partialSum15:module-phylomodels.features.series.series_partialSum15' on page 49 undefined on input line 3884 Reference `phylomodels.features.series.series_partialSum2:module-phylomodels.features.series.series_partialSum2' on page 49 undefined on input line 3885 Reference `phylomodels.features.series.series_partialSum30:module-phylomodels.features.series.series_partialSum30' on page 49 undefined on input line 3886 Reference `phylomodels.features.series.series_partialSum7:module-phylomodels.features.series.series_partialSum7' on page 49 undefined on input line 3887 Reference `phylomodels.features.series.series_sum:module-phylomodels.features.series.series_sum' on page 49 undefined on input line 3888 Reference `phylomodels.features.series.series_sum_log10:module-phylomodels.features.series.series_sum_log10' on page 49 undefined on input line 3889 Reference `phylomodels.features.series:module-phylomodels.features.series' on page 49 undefined on input line 3868 Reference `phylomodels.features.statistics.fano:module-phylomodels.features.statistics.fano' on page 49 undefined on input line 3891 Reference `phylomodels.features.statistics.mean:module-phylomodels.features.statistics.mean' on page 49 undefined on input line 3892 Reference `phylomodels.features.statistics.qcd:module-phylomodels.features.statistics.qcd' on page 49 undefined on input line 3893 Reference `phylomodels.features.statistics.rsd:module-phylomodels.features.statistics.rsd' on page 49 undefined on input line 3894 Reference `phylomodels.features.statistics.skew:module-phylomodels.features.statistics.skew' on page 49 undefined on input line 3895 Reference `phylomodels.features.statistics.std:module-phylomodels.features.statistics.std' on page 49 undefined on input line 3896 Reference `phylomodels.features.statistics.var:module-phylomodels.features.statistics.var' on page 49 undefined on input line 3897 Reference `phylomodels.features.statistics:module-phylomodels.features.statistics' on page 49 undefined on input line 3890 Reference `phylomodels.features.test:module-phylomodels.features.test' on page 49 undefined on input line 3898 Reference `phylomodels.features.trees.BL_calculate_external_max:module-phylomodels.features.trees.BL_calculate_external_max' on page 49 undefined on input line 3900 Reference `phylomodels.features.trees.BL_calculate_external_mean:module-phylomodels.features.trees.BL_calculate_external_mean' on page 49 undefined on input line 3901 Reference `phylomodels.features.trees.BL_calculate_external_median:module-phylomodels.features.trees.BL_calculate_external_median' on page 49 undefined on input line 3902 Reference `phylomodels.features.trees.BL_calculate_external_min:module-phylomodels.features.trees.BL_calculate_external_min' on page 49 undefined on input line 3903 Reference `phylomodels.features.trees.BL_calculate_external_std:module-phylomodels.features.trees.BL_calculate_external_std' on page 49 undefined on input line 3904 Reference `phylomodels.features.trees.BL_calculate_internal_max:module-phylomodels.features.trees.BL_calculate_internal_max' on page 49 undefined on input line 3905 Reference `phylomodels.features.trees.BL_calculate_internal_mean:module-phylomodels.features.trees.BL_calculate_internal_mean' on page 49 undefined on input line 3906 Reference `phylomodels.features.trees.BL_calculate_internal_median:module-phylomodels.features.trees.BL_calculate_internal_median' on page 49 undefined on input line 3907 Reference `phylomodels.features.trees.BL_calculate_internal_min:module-phylomodels.features.trees.BL_calculate_internal_min' on page 50 undefined on input line 3908 Reference `phylomodels.features.trees.BL_calculate_internal_std:module-phylomodels.features.trees.BL_calculate_internal_std' on page 50 undefined on input line 3909 Reference `phylomodels.features.trees.BL_calculate_max:module-phylomodels.features.trees.BL_calculate_max' on page 50 undefined on input line 3910 Reference `phylomodels.features.trees.BL_calculate_mean:module-phylomodels.features.trees.BL_calculate_mean' on page 50 undefined on input line 3911 Reference `phylomodels.features.trees.BL_calculate_median:module-phylomodels.features.trees.BL_calculate_median' on page 50 undefined on input line 3912 Reference `phylomodels.features.trees.BL_calculate_min:module-phylomodels.features.trees.BL_calculate_min' on page 50 undefined on input line 3913 Reference `phylomodels.features.trees.BL_calculate_ratio_max:module-phylomodels.features.trees.BL_calculate_ratio_max' on page 50 undefined on input line 3914 Reference `phylomodels.features.trees.BL_calculate_ratio_mean:module-phylomodels.features.trees.BL_calculate_ratio_mean' on page 50 undefined on input line 3915 Reference `phylomodels.features.trees.BL_calculate_ratio_median:module-phylomodels.features.trees.BL_calculate_ratio_median' on page 50 undefined on input line 3916 Reference `phylomodels.features.trees.BL_calculate_ratio_min:module-phylomodels.features.trees.BL_calculate_ratio_min' on page 50 undefined on input line 3917 Reference `phylomodels.features.trees.BL_calculate_ratio_std:module-phylomodels.features.trees.BL_calculate_ratio_std' on page 50 undefined on input line 3918 Reference `phylomodels.features.trees.BL_calculate_std:module-phylomodels.features.trees.BL_calculate_std' on page 50 undefined on input line 3919 Reference `phylomodels.features.trees.LTT_calculate_max_lineages:module-phylomodels.features.trees.LTT_calculate_max_lineages' on page 50 undefined on input line 3939 Reference `phylomodels.features.trees.LTT_calculate_mean_b_time:module-phylomodels.features.trees.LTT_calculate_mean_b_time' on page 50 undefined on input line 3940 Reference `phylomodels.features.trees.LTT_calculate_mean_s_time:module-phylomodels.features.trees.LTT_calculate_mean_s_time' on page 50 undefined on input line 3941 Reference `phylomodels.features.trees.LTT_calculate_slope_1:module-phylomodels.features.trees.LTT_calculate_slope_1' on page 50 undefined on input line 3942 Reference `phylomodels.features.trees.LTT_calculate_slope_2:module-phylomodels.features.trees.LTT_calculate_slope_2' on page 50 undefined on input line 3943 Reference `phylomodels.features.trees.LTT_calculate_slope_ratio:module-phylomodels.features.trees.LTT_calculate_slope_ratio' on page 50 undefined on input line 3944 Reference `phylomodels.features.trees.LTT_calculate_t_max_lineages:module-phylomodels.features.trees.LTT_calculate_t_max_lineages' on page 50 undefined on input line 3945 Reference `phylomodels.features.trees.group_calculate_max:module-phylomodels.features.trees.group_calculate_max' on page 50 undefined on input line 3920 Reference `phylomodels.features.trees.group_calculate_mean:module-phylomodels.features.trees.group_calculate_mean' on page 50 undefined on input line 3921 Reference `phylomodels.features.trees.group_calculate_median:module-phylomodels.features.trees.group_calculate_median' on page 50 undefined on input line 3922 Reference `phylomodels.features.trees.group_calculate_min:module-phylomodels.features.trees.group_calculate_min' on page 50 undefined on input line 3923 Reference `phylomodels.features.trees.group_calculate_mode:module-phylomodels.features.trees.group_calculate_mode' on page 50 undefined on input line 3924 Reference `phylomodels.features.trees.group_calculate_num:module-phylomodels.features.trees.group_calculate_num' on page 50 undefined on input line 3925 Reference `phylomodels.features.trees.group_calculate_std:module-phylomodels.features.trees.group_calculate_std' on page 50 undefined on input line 3926 Reference `phylomodels.features.trees.helper.get_LTT:module-phylomodels.features.trees.helper.get_LTT' on page 50 undefined on input line 3934 Reference `phylomodels.features.trees.helper.get_adjacency_mat:module-phylomodels.features.trees.helper.get_adjacency_mat' on page 50 undefined on input line 3928 Reference `phylomodels.features.trees.helper.get_distance_mat:module-phylomodels.features.trees.helper.get_distance_mat' on page 50 undefined on input line 3929 Reference `phylomodels.features.trees.helper.get_eigenvalues_adj:module-phylomodels.features.trees.helper.get_eigenvalues_adj' on page 50 undefined on input line 3930 Reference `phylomodels.features.trees.helper.get_eigenvalues_dist_lap:module-phylomodels.features.trees.helper.get_eigenvalues_dist_lap' on page 50 undefined on input line 3931 Reference `phylomodels.features.trees.helper.get_eigenvalues_lap:module-phylomodels.features.trees.helper.get_eigenvalues_lap' on page 50 undefined on input line 3932 Reference `phylomodels.features.trees.helper.get_groups:module-phylomodels.features.trees.helper.get_groups' on page 50 undefined on input line 3933 Reference `phylomodels.features.trees.helper.process_optional_arguements:module-phylomodels.features.trees.helper.process_optional_arguements' on page 50 undefined on input line 3935 Reference `phylomodels.features.trees.helper.unique_node_attr:module-phylomodels.features.trees.helper.unique_node_attr' on page 50 undefined on input line 3936 Reference `phylomodels.features.trees.helper:module-phylomodels.features.trees.helper' on page 50 undefined on input line 3927 Reference `phylomodels.features.trees.local_calculate_LBI_mean:module-phylomodels.features.trees.local_calculate_LBI_mean' on page 50 undefined on input line 3938 Reference `phylomodels.features.trees.local_calculate_frac_basal:module-phylomodels.features.trees.local_calculate_frac_basal' on page 50 undefined on input line 3937 Reference `phylomodels.features.trees.mean_NN_distance:module-phylomodels.features.trees.mean_NN_distance' on page 50 undefined on input line 3946 Reference `phylomodels.features.trees.netSci_calculate_betweenness_max:module-phylomodels.features.trees.netSci_calculate_betweenness_max' on page 50 undefined on input line 3947 Reference `phylomodels.features.trees.netSci_calculate_closeness_max:module-phylomodels.features.trees.netSci_calculate_closeness_max' on page 50 undefined on input line 3948 Reference `phylomodels.features.trees.netSci_calculate_diameter:module-phylomodels.features.trees.netSci_calculate_diameter' on page 50 undefined on input line 3949 Reference `phylomodels.features.trees.netSci_calculate_eigen_centrality_max:module-phylomodels.features.trees.netSci_calculate_eigen_centrality_max' on page 50 undefined on input line 3950 Reference `phylomodels.features.trees.netSci_calculate_mean_path:module-phylomodels.features.trees.netSci_calculate_mean_path' on page 50 undefined on input line 3951 Reference `phylomodels.features.trees.smallConfig_calculate_cherries:module-phylomodels.features.trees.smallConfig_calculate_cherries' on page 50 undefined on input line 3952 Reference `phylomodels.features.trees.smallConfig_calculate_double_cherries:module-phylomodels.features.trees.smallConfig_calculate_double_cherries' on page 50 undefined on input line 3953 Reference `phylomodels.features.trees.smallConfig_calculate_fourprong:module-phylomodels.features.trees.smallConfig_calculate_fourprong' on page 50 undefined on input line 3954 Reference `phylomodels.features.trees.smallConfig_calculate_pitchforks:module-phylomodels.features.trees.smallConfig_calculate_pitchforks' on page 50 undefined on input line 3955 Reference `phylomodels.features.trees.spectral_calculate_eigen_gap:module-phylomodels.features.trees.spectral_calculate_eigen_gap' on page 50 undefined on input line 3956 Reference `phylomodels.features.trees.spectral_calculate_kurtosis:module-phylomodels.features.trees.spectral_calculate_kurtosis' on page 50 undefined on input line 3957 Reference `phylomodels.features.trees.spectral_calculate_max_adj_eigen:module-phylomodels.features.trees.spectral_calculate_max_adj_eigen' on page 50 undefined on input line 3958 Reference `phylomodels.features.trees.spectral_calculate_max_distLap_eigen:module-phylomodels.features.trees.spectral_calculate_max_distLap_eigen' on page 50 undefined on input line 3959 Reference `phylomodels.features.trees.spectral_calculate_max_lap_eigen:module-phylomodels.features.trees.spectral_calculate_max_lap_eigen' on page 50 undefined on input line 3960 Reference `phylomodels.features.trees.spectral_calculate_min_adj_eigen:module-phylomodels.features.trees.spectral_calculate_min_adj_eigen' on page 50 undefined on input line 3961 Reference `phylomodels.features.trees.spectral_calculate_min_lap_eigen:module-phylomodels.features.trees.spectral_calculate_min_lap_eigen' on page 50 undefined on input line 3962 Reference `phylomodels.features.trees.spectral_calculate_skewness:module-phylomodels.features.trees.spectral_calculate_skewness' on page 51 undefined on input line 3963 Reference `phylomodels.features.trees.top_calculate_B1:module-phylomodels.features.trees.top_calculate_B1' on page 51 undefined on input line 3964 Reference `phylomodels.features.trees.top_calculate_B2:module-phylomodels.features.trees.top_calculate_B2' on page 51 undefined on input line 3965 Reference `phylomodels.features.trees.top_calculate_FurnasR:module-phylomodels.features.trees.top_calculate_FurnasR' on page 51 undefined on input line 3969 Reference `phylomodels.features.trees.top_calculate_WD_ratio:module-phylomodels.features.trees.top_calculate_WD_ratio' on page 51 undefined on input line 3975 Reference `phylomodels.features.trees.top_calculate_colless:module-phylomodels.features.trees.top_calculate_colless' on page 51 undefined on input line 3966 Reference `phylomodels.features.trees.top_calculate_frac_imbalance:module-phylomodels.features.trees.top_calculate_frac_imbalance' on page 51 undefined on input line 3967 Reference `phylomodels.features.trees.top_calculate_frac_ladder:module-phylomodels.features.trees.top_calculate_frac_ladder' on page 51 undefined on input line 3968 Reference `phylomodels.features.trees.top_calculate_max_dW:module-phylomodels.features.trees.top_calculate_max_dW' on page 51 undefined on input line 3970 Reference `phylomodels.features.trees.top_calculate_max_ladder:module-phylomodels.features.trees.top_calculate_max_ladder' on page 51 undefined on input line 3971 Reference `phylomodels.features.trees.top_calculate_mean_imbalance_ratio:module-phylomodels.features.trees.top_calculate_mean_imbalance_ratio' on page 51 undefined on input line 3972 Reference `phylomodels.features.trees.top_calculate_sackin:module-phylomodels.features.trees.top_calculate_sackin' on page 51 undefined on input line 3973 Reference 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\T1/ptm/m/it/10 c- Overfull \hbox (73.51491pt too wide) in paragraph at lines 3690--3690 \T1/ptm/m/it/10 Max\T1/ptm/m/n/10 , Overfull \hbox (68.24475pt too wide) in paragraph at lines 3690--3690 \T1/ptm/m/it/10 dst- Overfull \hbox (71.85486pt too wide) in paragraph at lines 3690--3690 \T1/ptm/m/it/10 Min\T1/ptm/m/n/10 , Overfull \hbox (68.24475pt too wide) in paragraph at lines 3690--3690 \T1/ptm/m/it/10 dst- Overfull \hbox (77.0448pt too wide) in paragraph at lines 3690--3690 \T1/ptm/m/it/10 Max\T1/pcr/m/n/10 ) [46] Overfull \hbox (42.18495pt too wide) in paragraph at lines 3696--3696 []\T1/ptm/m/it/10 x\T1/ptm/m/n/10 , Overfull \hbox (42.74501pt too wide) in paragraph at lines 3696--3696 \T1/ptm/m/it/10 n\T1/ptm/m/n/10 , Overfull \hbox (46.1548pt too wide) in paragraph at lines 3696--3696 \T1/ptm/m/it/10 sr- Overfull \hbox (58.2948pt too wide) in paragraph at lines 3696--3696 \T1/ptm/m/it/10 cMin\T1/ptm/m/n/10 , Overfull \hbox (46.1548pt too wide) in paragraph at lines 3696--3696 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phylomodels.features.trees.BL_calculate_internal_min\T1/ptm/m/ n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3909--3910 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_std\T1/ptm/m/ n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3910--3911 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_max\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3911--3912 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_mean\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3912--3913 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_median\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3913--3914 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_min\T1/ptm/m/n/10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3914--3915 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_ratio_max\T1/ptm/m/n/1 0 , Overfull \hbox (72.6225pt too 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phylomodels.features.trees.group_calculate_mean\T1/ptm/m/n/10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3922--3923 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_median\T1/ptm/m/n/1 0 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3923--3924 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_min\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3924--3925 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_mode\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3925--3926 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_num\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3926--3927 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_std\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3928--3929 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_adjacency_mat\T1/ptm/m/n /10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3929--3930 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_distance_mat\T1/ptm/m/n/ 10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3930--3931 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_eigenvalues_adj\T1/ptm/m /n/10 , Overfull \hbox (120.6225pt too wide) in paragraph at lines 3931--3932 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_eigenvalues_dist_lap\T1/ ptm/m/n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3932--3933 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_eigenvalues_lap\T1/ptm/m /n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3933--3934 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_groups\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 3934--3935 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_LTT\T1/ptm/m/n/10 , Overfull \hbox (138.6225pt too wide) in paragraph at lines 3935--3936 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.process_optional_arguements\ T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3936--3937 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.unique_node_attr\T1/ptm/m/n/ 10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3937--3938 []\T1/pcr/m/n/10 phylomodels.features.trees.local_calculate_frac_basal\T1/ptm/m /n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3938--3939 []\T1/pcr/m/n/10 phylomodels.features.trees.local_calculate_LBI_mean\T1/ptm/m/n /10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3939--3940 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_max_lineages\T1/ptm/m /n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3940--3941 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_mean_b_time\T1/ptm/m/ n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3941--3942 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_mean_s_time\T1/ptm/m/ n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3942--3943 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_slope_1\T1/ptm/m/n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3943--3944 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_slope_2\T1/ptm/m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3944--3945 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_slope_ratio\T1/ptm/m/ n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 3945--3946 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_t_max_lineages\T1/ptm /m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3946--3947 []\T1/pcr/m/n/10 phylomodels.features.trees.mean_NN_distance\T1/ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3947--3948 []\T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_betweenness_max\T1 /ptm/m/n/10 , Overfull \hbox (114.6225pt too wide) in paragraph at lines 3948--3949 []\T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_closeness_max\T1/p tm/m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3949--3950 []\T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_diameter\T1/ptm/m/ n/10 , Overfull \hbox (156.6225pt too wide) in paragraph at lines 3950--3951 []\T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_eigen_centrality_m ax\T1/ptm/m/n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3951--3952 []\T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_mean_path\T1/ptm/m /n/10 , Overfull \hbox (114.6225pt too wide) in paragraph at lines 3952--3953 []\T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_cherries\T1/p tm/m/n/10 , Overfull \hbox (156.6225pt too wide) in paragraph at lines 3953--3954 []\T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_double_cherri es\T1/ptm/m/n/10 , Overfull \hbox (120.6225pt too wide) in paragraph at lines 3954--3955 []\T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_fourprong\T1/ ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3955--3956 []\T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_pitchforks\T1 /ptm/m/n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 3956--3957 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_eigen_gap\T1/ptm /m/n/10 , Overfull \hbox (96.6225pt too wide) in paragraph at lines 3957--3958 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_kurtosis\T1/ptm/ m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3958--3959 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_adj_eigen\T1 /ptm/m/n/10 , Overfull \hbox (150.6225pt too wide) in paragraph at lines 3959--3960 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_distLap_eige n\T1/ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3960--3961 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_lap_eigen\T1 /ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3961--3962 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_adj_eigen\T1 /ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3962--3963 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_lap_eigen\T1 /ptm/m/n/10 , [50] Overfull \hbox (96.6225pt too wide) in paragraph at lines 3963--3964 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_skewness\T1/ptm/ m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3964--3965 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_B1\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3965--3966 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_B2\T1/ptm/m/n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3966--3967 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_colless\T1/ptm/m/n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 3967--3968 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_frac_imbalance\T1/ptm /m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3968--3969 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_frac_ladder\T1/ptm/m/ n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3969--3970 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_FurnasR\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3970--3971 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_max_dW\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3971--3972 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_max_ladder\T1/ptm/m/n /10 , Overfull \hbox (138.6225pt too wide) in paragraph at lines 3972--3973 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_mean_imbalance_ratio\ T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3973--3974 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_sackin\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3974--3975 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_sackin_var\T1/ptm/m/n /10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3975--3976 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_WD_ratio\T1/ptm/m/n/1 0 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3976--3977 []\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_max\T1/ptm/m/ n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3977--3978 []\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_mean\T1/ptm/m /n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3978--3979 []\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_min\T1/ptm/m/ n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 3980--3981 []\T1/pcr/m/n/10 phylomodels.models.distributions_gaussian\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3982--3983 []\T1/pcr/m/n/10 phylomodels.models.seir_taoLeap.seirTaoLeap\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3983--3984 []\T1/pcr/m/n/10 phylomodels.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m/n /10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3984--3985 []\T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidence\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3985--3986 []\T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidenceSampled\T1/ptm/m/n/ 10 , Overfull \hbox (42.6225pt too wide) in paragraph at lines 3991--3992 []\T1/pcr/m/n/10 phylomodels.visualization.parallelCoordinates\T1/ptm/m/n/10 , [51] (./institute-for-disease-modeling-phylomodels.ind [52] Overfull \hbox (32.14963pt too wide) in paragraph at lines 8--10 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Overfull \hbox (32.14963pt too wide) in paragraph at lines 10--12 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/pcr/m/n/10 attr_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 12--14 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 17--18 []\T1/pcr/m/n/10 buildTree() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo- mod- Underfull \hbox (badness 7576) in paragraph at lines 21--23 []\T1/pcr/m/n/10 cal_parameterSweep() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 calcBranchLength() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 compute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod-els.featu res.features.features Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 disableFeature() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/pcr/m/n/10 disableStatistic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 7576) in paragraph at lines 34--36 []\T1/pcr/m/n/10 distance_mat_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 34--36 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/pcr/m/n/10 distLap_eigenvalues_param() Underfull \hbox (badness 10000) in paragraph at lines 36--38 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 36--38 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 drawParallelCoordinatesPair() Underfull \hbox (badness 10000) in paragraph at lines 40--42 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 47--49 []\T1/pcr/m/n/10 enableFeature() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 49--51 []\T1/pcr/m/n/10 enableStatistic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 54--55 []\T1/pcr/m/n/10 fano() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 61--63 []\T1/pcr/m/n/10 get_adjacency_mat() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 61--63 \T1/ptm/m/it/10 els.features.trees.helper.get_adjacency_mat\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/pcr/m/n/10 get_distance_mat() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 63--65 \T1/ptm/m/it/10 els.features.trees.helper.get_distance_mat\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 65--67 \T1/ptm/m/it/10 els.features.trees.helper.get_eigenvalues_adj\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/pcr/m/n/10 get_eigenvalues_dist_lap() Underfull \hbox (badness 10000) in paragraph at lines 67--69 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (13.47978pt too wide) in paragraph at lines 67--69 \T1/ptm/m/it/10 els.features.trees.helper.get_eigenvalues_dist_lap\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 69--71 \T1/ptm/m/it/10 els.features.trees.helper.get_eigenvalues_lap\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 71--73 []\T1/pcr/m/n/10 get_groups() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Underfull \hbox (badness 10000) in paragraph at lines 73--75 []\T1/pcr/m/n/10 getArguments() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 7576) in paragraph at lines 75--77 []\T1/pcr/m/n/10 getDownsampledTree() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/pcr/m/n/10 getFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-l o-mod- Underfull \hbox (badness 10000) in paragraph at lines 77--79 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), [53] Underfull \hbox (badness 10000) in paragraph at lines 79--81 []\T1/pcr/m/n/10 getIncidence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Overfull \hbox (11.6203pt too wide) in paragraph at lines 79--81 \T1/ptm/m/it/10 els.models.seir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 81--83 []\T1/pcr/m/n/10 getInitialCandidatesFromFile() Underfull \hbox (badness 10000) in paragraph at lines 81--83 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 81--83 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 83--85 []\T1/pcr/m/n/10 getInitialCandidatesLHS() Underfull \hbox (badness 10000) in paragraph at lines 83--85 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 83--85 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 7576) in paragraph at lines 85--87 []\T1/pcr/m/n/10 getModelParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Overfull \hbox (3.87042pt too wide) in paragraph at lines 85--87 \T1/ptm/m/it/10 els.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 7576) in paragraph at lines 87--89 []\T1/pcr/m/n/10 getModelParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 87--89 \T1/ptm/m/it/10 els.models.sir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 89--91 []\T1/pcr/m/n/10 getNewickString() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 91--92 []\T1/pcr/m/n/10 getNewId() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-m od- Underfull \hbox (badness 10000) in paragraph at lines 92--93 []\T1/pcr/m/n/10 getPopSize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Underfull \hbox (badness 10000) in paragraph at lines 95--97 []\T1/pcr/m/n/10 getRightCoordinateValuesLinear() Underfull \hbox (badness 10000) in paragraph at lines 95--97 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/pcr/m/n/10 getRightCoordinateValuesLog() Underfull \hbox (badness 10000) in paragraph at lines 97--99 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 99--101 []\T1/pcr/m/n/10 getRightCoordinateValuesLogRevLogSrc() Underfull \hbox (badness 10000) in paragraph at lines 99--101 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 101--103 []\T1/pcr/m/n/10 getRightCoordinateValuesLogSrc() Underfull \hbox (badness 10000) in paragraph at lines 101--103 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 103--105 []\T1/pcr/m/n/10 getRightCoordinateValuesRevLogSrc() Underfull \hbox (badness 10000) in paragraph at lines 103--105 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 105--107 []\T1/pcr/m/n/10 groups_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy- lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 105--107 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 110--112 []\T1/pcr/m/n/10 init_historyMatching_base() Underfull \hbox (badness 10000) in paragraph at lines 110--112 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 110--112 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 112--114 []\T1/pcr/m/n/10 init_historyMatching_poissonGlmBasis() Underfull \hbox (badness 10000) in paragraph at lines 112--114 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (35.10982pt too wide) in paragraph at lines 112--114 \T1/ptm/m/it/10 els.calibration.init_historyMatching_poissonGlmBasis\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 114--116 []\T1/pcr/m/n/10 initializeOutputDirectory() Underfull \hbox (badness 10000) in paragraph at lines 114--116 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 114--116 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--120 []\T1/pcr/m/n/10 joinSubtrees() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy- lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 123--125 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 125--127 []\T1/pcr/m/n/10 listActiveFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mo d- Underfull \hbox (badness 10000) in paragraph at lines 127--129 []\T1/pcr/m/n/10 listActiveStats() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 129--131 []\T1/pcr/m/n/10 listFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/pcr/m/n/10 LTT_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo- mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 131--133 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/pcr/m/n/10 makeBifurcating() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 makeSamplesLeaves() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 142--143 []\T1/pcr/m/n/10 mean() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 143--145 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wide) in paragraph at lines 160--161 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative2\T1/ptm/m/n/10 , [54] Overfull \hbox (128.6225pt too wide) in paragraph at lines 161--162 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative2_cauchyFit\T1/ ptm/m/n/10 , Overfull \hbox (140.6225pt too wide) in paragraph at lines 162--164 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative2_gaussianFit\T 1/ptm/m/n/10 , Overfull \hbox (134.6225pt too wide) in paragraph at lines 164--165 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative2_laplaceFit\T1 /ptm/m/n/10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 165--166 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative_cauchyFit\T1/p tm/m/n/10 , Overfull \hbox (134.6225pt too wide) in paragraph at lines 166--167 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative_gaussianFit\T1 /ptm/m/n/10 , Overfull \hbox (128.6225pt too wide) in paragraph at lines 167--168 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phylomodels.features.trees.smallConfig_calculate_cherries\T1 /ptm/m/n/10 , Overfull \hbox (176.6225pt too wide) in paragraph at lines 248--250 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_double_cher ries\T1/ptm/m/n/10 , Overfull \hbox (140.6225pt too wide) in paragraph at lines 250--252 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_fourprong\T 1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 252--254 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_pitchforks\ T1/ptm/m/n/10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 254--255 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_eigen_gap\T1/p tm/m/n/10 , Overfull \hbox (116.6225pt too wide) in paragraph at lines 255--256 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_kurtosis\T1/pt m/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 256--258 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_adj_eigen\ T1/ptm/m/n/10 , Overfull \hbox (170.6225pt too wide) in paragraph at lines 258--260 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_distLap_ei gen\T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 260--262 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_lap_eigen\ T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 262--264 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_adj_eigen\ T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 264--266 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_lap_eigen\ T1/ptm/m/n/10 , Overfull \hbox (116.6225pt too wide) in paragraph at lines 266--267 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_skewness\T1/pt m/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 267--268 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_B1\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 268--269 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_B2\T1/ptm/m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 269--270 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_colless\T1/ptm/m/n/ 10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 270--271 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_frac_imbalance\T1/p tm/m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 271--272 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_frac_ladder\T1/ptm/ m/n/10 , Overfull \hbox (80.6225pt too wide) in paragraph at lines 272--273 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_FurnasR\T1/ptm/m/n/ 10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 273--274 []| \T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_max_dW\T1/ptm/m/n/1 0 , Overfull \hbox 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\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_mean\T1/ptm /m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 282--283 []| \T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_min\T1/ptm/ m/n/10 , Overfull \hbox (38.6225pt too wide) in paragraph at lines 284--285 []| \T1/pcr/m/n/10 phylomodels.models.distributions_gaussian\T1/ptm/m/n/10 , [56] Overfull \hbox (50.6225pt too wide) in paragraph at lines 286--287 []| \T1/pcr/m/n/10 phylomodels.models.seir_taoLeap.seirTaoLeap\T1/ptm/m/n/10 , Overfull \hbox (98.6225pt too wide) in paragraph at lines 287--288 []| \T1/pcr/m/n/10 phylomodels.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m /n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 288--289 []| \T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidence\T1/ptm/m/n/10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 289--290 []| \T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidenceSampled\T1/ptm/m/ n/10 , 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phylomodels.features.trees.tree_height_calculate_min Overfull \hbox (16.1225pt too wide) in paragraph at lines 545--546 []\T1/pcr/m/n/10 phylomodels.models.distributions_gaussian Overfull \hbox (28.1225pt too wide) in paragraph at lines 549--550 []\T1/pcr/m/n/10 phylomodels.models.seir_taoLeap.seirTaoLeap Overfull \hbox (76.1225pt too wide) in paragraph at lines 551--552 []\T1/pcr/m/n/10 phylomodels.models.seir_taoLeap_getIncidenceSampled Overfull \hbox (28.1225pt too wide) in paragraph at lines 553--554 []\T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidence Overfull \hbox (70.1225pt too wide) in paragraph at lines 555--556 []\T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidenceSampled Overfull \hbox (40.1225pt too wide) in paragraph at lines 567--568 []\T1/pcr/m/n/10 phylomodels.visualization.parallelCoordinates Overfull \hbox (52.29008pt too wide) in paragraph at lines 571--573 []\T1/pcr/m/n/10 plot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod-els.models.s eir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 573--575 []\T1/pcr/m/n/10 plotIncidence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Overfull \hbox (11.6203pt too wide) in paragraph at lines 573--575 \T1/ptm/m/it/10 els.models.seir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 575--577 []\T1/pcr/m/n/10 plotParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 575--577 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 577--579 []\T1/pcr/m/n/10 plotSimulations() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 577--579 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 583--585 []\T1/pcr/m/n/10 printArguments() 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in paragraph at lines 600--602 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), [59] Underfull \hbox (badness 10000) in paragraph at lines 606--608 []\T1/pcr/m/n/10 seir_taoLeap_getIncidenceSampled() Underfull \hbox (badness 10000) in paragraph at lines 606--608 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (3.87042pt too wide) in paragraph at lines 606--608 \T1/ptm/m/it/10 els.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/pcr/m/n/10 seirTaoLeap \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in phy-lo-mo d- Underfull \hbox (badness 10000) in paragraph at lines 610--612 []\T1/pcr/m/n/10 selectFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 610--612 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 612--614 []\T1/pcr/m/n/10 selectSampleNodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 614--615 []\T1/pcr/m/n/10 series() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod - Underfull \hbox (badness 10000) in paragraph at lines 615--617 []\T1/pcr/m/n/10 series_derivative() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 7576) in paragraph at lines 617--619 []\T1/pcr/m/n/10 series_derivative2() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 619--621 []\T1/pcr/m/n/10 series_derivative2_cauchyFit() Underfull \hbox (badness 10000) in paragraph at lines 619--621 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (7.6295pt too wide) in paragraph at lines 619--621 \T1/ptm/m/it/10 els.features.series.series_derivative2_cauchyFit\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 621--623 []\T1/pcr/m/n/10 series_derivative2_gaussianFit() Underfull \hbox (badness 10000) in paragraph at lines 621--623 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (15.01926pt too wide) in paragraph at lines 621--623 \T1/ptm/m/it/10 els.features.series.series_derivative2_gaussianFit\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 623--625 []\T1/pcr/m/n/10 series_derivative2_laplaceFit() Underfull \hbox (badness 10000) in paragraph at lines 623--625 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (8.89925pt too wide) in paragraph at lines 623--625 \T1/ptm/m/it/10 els.features.series.series_derivative2_laplaceFit\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 625--627 []\T1/pcr/m/n/10 series_derivative_cauchyFit() Underfull \hbox (badness 10000) in paragraph at lines 625--627 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (2.6295pt too wide) in paragraph at lines 625--627 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too wide) in paragraph at lines 3882--3883 []\T1/pcr/m/n/10 phylomodels.features.series.series_log10\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3883--3884 []\T1/pcr/m/n/10 phylomodels.features.series.series_partialSum10\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3884--3885 []\T1/pcr/m/n/10 phylomodels.features.series.series_partialSum15\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3885--3886 []\T1/pcr/m/n/10 phylomodels.features.series.series_partialSum2\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3886--3887 []\T1/pcr/m/n/10 phylomodels.features.series.series_partialSum30\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3887--3888 []\T1/pcr/m/n/10 phylomodels.features.series.series_partialSum7\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 3888--3889 []\T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_external_median\T1/ptm /m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3903--3904 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_external_min\T1/ptm/m/ n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3904--3905 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_external_std\T1/ptm/m/ n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3905--3906 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_max\T1/ptm/m/ n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3906--3907 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_mean\T1/ptm/m /n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 3907--3908 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_median\T1/ptm /m/n/10 , [49] Overfull \hbox (84.6225pt too wide) in paragraph at lines 3908--3909 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_min\T1/ptm/m/ n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3909--3910 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_std\T1/ptm/m/ n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3910--3911 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_max\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3911--3912 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_mean\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3912--3913 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_median\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3913--3914 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_min\T1/ptm/m/n/10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3914--3915 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_ratio_max\T1/ptm/m/n/1 0 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3915--3916 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_ratio_mean\T1/ptm/m/n/ 10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3916--3917 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_ratio_median\T1/ptm/m/ n/10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3917--3918 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_ratio_min\T1/ptm/m/n/1 0 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3918--3919 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_ratio_std\T1/ptm/m/n/1 0 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3919--3920 []\T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_std\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3920--3921 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_max\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3921--3922 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_mean\T1/ptm/m/n/10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3922--3923 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_median\T1/ptm/m/n/1 0 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3923--3924 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_min\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3924--3925 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_mode\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3925--3926 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_num\T1/ptm/m/n/10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 3926--3927 []\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_std\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3928--3929 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_adjacency_mat\T1/ptm/m/n /10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3929--3930 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_distance_mat\T1/ptm/m/n/ 10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3930--3931 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_eigenvalues_adj\T1/ptm/m /n/10 , Overfull \hbox (120.6225pt too wide) in paragraph at lines 3931--3932 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_eigenvalues_dist_lap\T1/ ptm/m/n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3932--3933 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_eigenvalues_lap\T1/ptm/m /n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 3933--3934 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_groups\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 3934--3935 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.get_LTT\T1/ptm/m/n/10 , Overfull \hbox (138.6225pt too wide) in paragraph at lines 3935--3936 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.process_optional_arguements\ T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3936--3937 []\T1/pcr/m/n/10 phylomodels.features.trees.helper.unique_node_attr\T1/ptm/m/n/ 10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3937--3938 []\T1/pcr/m/n/10 phylomodels.features.trees.local_calculate_frac_basal\T1/ptm/m /n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3938--3939 []\T1/pcr/m/n/10 phylomodels.features.trees.local_calculate_LBI_mean\T1/ptm/m/n /10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3939--3940 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_max_lineages\T1/ptm/m /n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3940--3941 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_mean_b_time\T1/ptm/m/ n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3941--3942 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_mean_s_time\T1/ptm/m/ n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3942--3943 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_slope_1\T1/ptm/m/n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3943--3944 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_slope_2\T1/ptm/m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3944--3945 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_slope_ratio\T1/ptm/m/ n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 3945--3946 []\T1/pcr/m/n/10 phylomodels.features.trees.LTT_calculate_t_max_lineages\T1/ptm /m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3946--3947 []\T1/pcr/m/n/10 phylomodels.features.trees.mean_NN_distance\T1/ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3947--3948 []\T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_betweenness_max\T1 /ptm/m/n/10 , 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in paragraph at lines 3960--3961 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_lap_eigen\T1 /ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3961--3962 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_adj_eigen\T1 /ptm/m/n/10 , Overfull \hbox (126.6225pt too wide) in paragraph at lines 3962--3963 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_lap_eigen\T1 /ptm/m/n/10 , [50] Overfull \hbox (96.6225pt too wide) in paragraph at lines 3963--3964 []\T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_skewness\T1/ptm/ m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3964--3965 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_B1\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3965--3966 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_B2\T1/ptm/m/n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3966--3967 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_colless\T1/ptm/m/n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 3967--3968 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_frac_imbalance\T1/ptm /m/n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3968--3969 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_frac_ladder\T1/ptm/m/ n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 3969--3970 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_FurnasR\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3970--3971 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_max_dW\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3971--3972 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_max_ladder\T1/ptm/m/n /10 , Overfull \hbox (138.6225pt too wide) in paragraph at lines 3972--3973 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_mean_imbalance_ratio\ T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 3973--3974 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_sackin\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3974--3975 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_sackin_var\T1/ptm/m/n /10 , Overfull \hbox (66.6225pt too wide) in paragraph at lines 3975--3976 []\T1/pcr/m/n/10 phylomodels.features.trees.top_calculate_WD_ratio\T1/ptm/m/n/1 0 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3976--3977 []\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_max\T1/ptm/m/ n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 3977--3978 []\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_mean\T1/ptm/m /n/10 , Overfull \hbox (84.6225pt too wide) in paragraph at lines 3978--3979 []\T1/pcr/m/n/10 phylomodels.features.trees.tree_height_calculate_min\T1/ptm/m/ n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 3980--3981 []\T1/pcr/m/n/10 phylomodels.models.distributions_gaussian\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3982--3983 []\T1/pcr/m/n/10 phylomodels.models.seir_taoLeap.seirTaoLeap\T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 3983--3984 []\T1/pcr/m/n/10 phylomodels.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m/n /10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 3984--3985 []\T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidence\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 3985--3986 []\T1/pcr/m/n/10 phylomodels.models.sir_taoLeap_getIncidenceSampled\T1/ptm/m/n/ 10 , Overfull \hbox (42.6225pt too wide) in paragraph at lines 3991--3992 []\T1/pcr/m/n/10 phylomodels.visualization.parallelCoordinates\T1/ptm/m/n/10 , [51] (./institute-for-disease-modeling-phylomodels.ind [52] Overfull \hbox (32.14963pt too wide) in paragraph at lines 8--10 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Overfull \hbox (32.14963pt too wide) in paragraph at lines 10--12 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/pcr/m/n/10 attr_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 12--14 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 17--18 []\T1/pcr/m/n/10 buildTree() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo- mod- Underfull \hbox (badness 7576) in paragraph at lines 21--23 []\T1/pcr/m/n/10 cal_parameterSweep() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 calcBranchLength() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 compute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod-els.featu res.features.features Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 disableFeature() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/pcr/m/n/10 disableStatistic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 7576) in paragraph at lines 34--36 []\T1/pcr/m/n/10 distance_mat_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 34--36 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/pcr/m/n/10 distLap_eigenvalues_param() Underfull \hbox (badness 10000) in paragraph at lines 36--38 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 36--38 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 drawParallelCoordinatesPair() Underfull \hbox (badness 10000) in paragraph at lines 40--42 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 47--49 []\T1/pcr/m/n/10 enableFeature() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 49--51 []\T1/pcr/m/n/10 enableStatistic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 54--55 []\T1/pcr/m/n/10 fano() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 61--63 []\T1/pcr/m/n/10 get_adjacency_mat() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 61--63 \T1/ptm/m/it/10 els.features.trees.helper.get_adjacency_mat\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/pcr/m/n/10 get_distance_mat() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 63--65 \T1/ptm/m/it/10 els.features.trees.helper.get_distance_mat\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 65--67 \T1/ptm/m/it/10 els.features.trees.helper.get_eigenvalues_adj\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 67--69 []\T1/pcr/m/n/10 get_eigenvalues_dist_lap() Underfull \hbox (badness 10000) in paragraph at lines 67--69 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (13.47978pt too wide) in paragraph at lines 67--69 \T1/ptm/m/it/10 els.features.trees.helper.get_eigenvalues_dist_lap\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 69--71 \T1/ptm/m/it/10 els.features.trees.helper.get_eigenvalues_lap\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 71--73 []\T1/pcr/m/n/10 get_groups() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Underfull \hbox (badness 10000) in paragraph at lines 73--75 []\T1/pcr/m/n/10 getArguments() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 7576) in paragraph at lines 75--77 []\T1/pcr/m/n/10 getDownsampledTree() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/pcr/m/n/10 getFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-l o-mod- Underfull \hbox (badness 10000) in paragraph at lines 77--79 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), [53] Underfull \hbox (badness 10000) in paragraph at lines 79--81 []\T1/pcr/m/n/10 getIncidence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Overfull \hbox (11.6203pt too wide) in paragraph at lines 79--81 \T1/ptm/m/it/10 els.models.seir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 81--83 []\T1/pcr/m/n/10 getInitialCandidatesFromFile() Underfull \hbox (badness 10000) in paragraph at lines 81--83 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 81--83 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 83--85 []\T1/pcr/m/n/10 getInitialCandidatesLHS() Underfull \hbox (badness 10000) in paragraph at lines 83--85 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 83--85 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 7576) in paragraph at lines 85--87 []\T1/pcr/m/n/10 getModelParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Overfull \hbox (3.87042pt too wide) in paragraph at lines 85--87 \T1/ptm/m/it/10 els.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 7576) in paragraph at lines 87--89 []\T1/pcr/m/n/10 getModelParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 87--89 \T1/ptm/m/it/10 els.models.sir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 89--91 []\T1/pcr/m/n/10 getNewickString() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 91--92 []\T1/pcr/m/n/10 getNewId() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-m od- Underfull \hbox (badness 10000) in paragraph at lines 92--93 []\T1/pcr/m/n/10 getPopSize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Underfull \hbox (badness 10000) in paragraph at lines 95--97 []\T1/pcr/m/n/10 getRightCoordinateValuesLinear() Underfull \hbox (badness 10000) in paragraph at lines 95--97 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/pcr/m/n/10 getRightCoordinateValuesLog() Underfull \hbox (badness 10000) in paragraph at lines 97--99 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 99--101 []\T1/pcr/m/n/10 getRightCoordinateValuesLogRevLogSrc() Underfull \hbox (badness 10000) in paragraph at lines 99--101 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 101--103 []\T1/pcr/m/n/10 getRightCoordinateValuesLogSrc() Underfull \hbox (badness 10000) in paragraph at lines 101--103 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 103--105 []\T1/pcr/m/n/10 getRightCoordinateValuesRevLogSrc() Underfull \hbox (badness 10000) in paragraph at lines 103--105 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 105--107 []\T1/pcr/m/n/10 groups_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy- lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 105--107 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 110--112 []\T1/pcr/m/n/10 init_historyMatching_base() Underfull \hbox (badness 10000) in paragraph at lines 110--112 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 110--112 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 112--114 []\T1/pcr/m/n/10 init_historyMatching_poissonGlmBasis() Underfull \hbox (badness 10000) in paragraph at lines 112--114 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (35.10982pt too wide) in paragraph at lines 112--114 \T1/ptm/m/it/10 els.calibration.init_historyMatching_poissonGlmBasis\T1/ptm/m/n /10 ), Underfull \hbox (badness 10000) in paragraph at lines 114--116 []\T1/pcr/m/n/10 initializeOutputDirectory() Underfull \hbox (badness 10000) in paragraph at lines 114--116 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 114--116 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--120 []\T1/pcr/m/n/10 joinSubtrees() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy- lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 123--125 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 125--127 []\T1/pcr/m/n/10 listActiveFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mo d- Underfull \hbox (badness 10000) in paragraph at lines 127--129 []\T1/pcr/m/n/10 listActiveStats() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 129--131 []\T1/pcr/m/n/10 listFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/pcr/m/n/10 LTT_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo- mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 131--133 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/pcr/m/n/10 makeBifurcating() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 makeSamplesLeaves() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 142--143 []\T1/pcr/m/n/10 mean() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 143--145 []\T1/pcr/m/n/10 mean_NN_distance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (44.6225pt too wide) in paragraph at lines 148--149 []| \T1/pcr/m/n/10 phylomodels.calibration.cal_parameterSweep\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 149--150 []| \T1/pcr/m/n/10 phylomodels.calibration.constants\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 150--151 []| \T1/pcr/m/n/10 phylomodels.calibration.init_historyMatching_base\T1/ptm/m/n /10 , Overfull \hbox (152.6225pt too wide) in paragraph at lines 151--153 []| \T1/pcr/m/n/10 phylomodels.calibration.init_historyMatching_poissonGlmBasis \T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 158--159 []| \T1/pcr/m/n/10 phylomodels.features.series.series\T1/ptm/m/n/10 , Overfull \hbox (62.6225pt too wide) in paragraph at lines 159--160 []| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative\T1/ptm/m/n/10 , Overfull \hbox (68.6225pt too 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[]| \T1/pcr/m/n/10 phylomodels.features.series.series_derivative_laplaceFit\T1/ ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 168--169 []| \T1/pcr/m/n/10 phylomodels.features.series.series_diff\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 169--170 []| \T1/pcr/m/n/10 phylomodels.features.series.series_diff_L1\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 170--171 []| \T1/pcr/m/n/10 phylomodels.features.series.series_diff_L2\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 171--172 []| \T1/pcr/m/n/10 phylomodels.features.series.series_diff_Linf\T1/ptm/m/n/10 , Overfull \hbox (32.6225pt too wide) in paragraph at lines 172--173 []| \T1/pcr/m/n/10 phylomodels.features.series.series_log10\T1/ptm/m/n/10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 173--174 []| \T1/pcr/m/n/10 phylomodels.features.series.series_partialSum10\T1/ptm/m/n/1 0 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 174--175 []| \T1/pcr/m/n/10 phylomodels.features.series.series_partialSum15\T1/ptm/m/n/1 0 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 175--176 []| \T1/pcr/m/n/10 phylomodels.features.series.series_partialSum2\T1/ptm/m/n/10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 176--177 []| \T1/pcr/m/n/10 phylomodels.features.series.series_partialSum30\T1/ptm/m/n/1 0 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 177--178 []| \T1/pcr/m/n/10 phylomodels.features.series.series_partialSum7\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 178--179 []| \T1/pcr/m/n/10 phylomodels.features.series.series_sum\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 179--180 []| \T1/pcr/m/n/10 phylomodels.features.series.series_sum_log10\T1/ptm/m/n/10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 181--182 []| \T1/pcr/m/n/10 phylomodels.features.statistics.fano\T1/ptm/m/n/10 , 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[]| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_median\T1/p tm/m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 198--199 []| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_min\T1/ptm/ m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 199--200 []| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_internal_std\T1/ptm/ m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 200--201 []| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_max\T1/ptm/m/n/10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 201--202 []| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_mean\T1/ptm/m/n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 202--203 []| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_median\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 203--204 []| \T1/pcr/m/n/10 phylomodels.features.trees.BL_calculate_min\T1/ptm/m/n/10 , 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\T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_max\T1/ptm/m/n/10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 211--212 []| \T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_mean\T1/ptm/m/n/1 0 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 212--213 []| \T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_median\T1/ptm/m/n /10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 213--214 []| \T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_min\T1/ptm/m/n/10 , Overfull \hbox (74.6225pt too wide) in paragraph at lines 214--215 []| \T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_mode\T1/ptm/m/n/1 0 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 215--216 []| \T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_num\T1/ptm/m/n/10 , Overfull \hbox (68.6225pt too wide) in paragraph at lines 216--217 []| \T1/pcr/m/n/10 phylomodels.features.trees.group_calculate_std\T1/ptm/m/n/10 , [55] Underfull \hbox 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238--239 []| \T1/pcr/m/n/10 phylomodels.features.trees.mean_NN_distance\T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 239--241 []| \T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_betweenness_max\ T1/ptm/m/n/10 , Overfull \hbox (134.6225pt too wide) in paragraph at lines 241--243 []| \T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_closeness_max\T1 /ptm/m/n/10 , Overfull \hbox (104.6225pt too wide) in paragraph at lines 243--244 []| \T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_diameter\T1/ptm/ m/n/10 , Overfull \hbox (176.6225pt too wide) in paragraph at lines 244--246 []| \T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_eigen_centrality _max\T1/ptm/m/n/10 , Overfull \hbox (110.6225pt too wide) in paragraph at lines 246--247 []| \T1/pcr/m/n/10 phylomodels.features.trees.netSci_calculate_mean_path\T1/ptm /m/n/10 , Overfull \hbox (134.6225pt too wide) in paragraph at lines 247--248 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_cherries\T1 /ptm/m/n/10 , Overfull \hbox (176.6225pt too wide) in paragraph at lines 248--250 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_double_cher ries\T1/ptm/m/n/10 , Overfull \hbox (140.6225pt too wide) in paragraph at lines 250--252 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_fourprong\T 1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 252--254 []| \T1/pcr/m/n/10 phylomodels.features.trees.smallConfig_calculate_pitchforks\ T1/ptm/m/n/10 , Overfull \hbox (122.6225pt too wide) in paragraph at lines 254--255 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_eigen_gap\T1/p tm/m/n/10 , Overfull \hbox (116.6225pt too wide) in paragraph at lines 255--256 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_kurtosis\T1/pt m/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 256--258 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_adj_eigen\ T1/ptm/m/n/10 , Overfull \hbox (170.6225pt too wide) in paragraph at lines 258--260 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_distLap_ei gen\T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 260--262 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_max_lap_eigen\ T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 262--264 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_adj_eigen\ T1/ptm/m/n/10 , Overfull \hbox (146.6225pt too wide) in paragraph at lines 264--266 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_min_lap_eigen\ T1/ptm/m/n/10 , Overfull \hbox (116.6225pt too wide) in paragraph at lines 266--267 []| \T1/pcr/m/n/10 phylomodels.features.trees.spectral_calculate_skewness\T1/pt m/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 267--268 []| \T1/pcr/m/n/10 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eir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 573--575 []\T1/pcr/m/n/10 plotIncidence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Overfull \hbox (11.6203pt too wide) in paragraph at lines 573--575 \T1/ptm/m/it/10 els.models.seir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 575--577 []\T1/pcr/m/n/10 plotParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 575--577 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 577--579 []\T1/pcr/m/n/10 plotSimulations() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 577--579 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 583--585 []\T1/pcr/m/n/10 printArguments() 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in paragraph at lines 600--602 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), [59] Underfull \hbox (badness 10000) in paragraph at lines 606--608 []\T1/pcr/m/n/10 seir_taoLeap_getIncidenceSampled() Underfull \hbox (badness 10000) in paragraph at lines 606--608 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (3.87042pt too wide) in paragraph at lines 606--608 \T1/ptm/m/it/10 els.models.seir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/pcr/m/n/10 seirTaoLeap \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in phy-lo-mo d- Underfull \hbox (badness 10000) in paragraph at lines 610--612 []\T1/pcr/m/n/10 selectFeatures() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 610--612 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 612--614 []\T1/pcr/m/n/10 selectSampleNodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 614--615 []\T1/pcr/m/n/10 series() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod - Underfull \hbox (badness 10000) in paragraph at lines 615--617 []\T1/pcr/m/n/10 series_derivative() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 7576) in paragraph at lines 617--619 []\T1/pcr/m/n/10 series_derivative2() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 619--621 []\T1/pcr/m/n/10 series_derivative2_cauchyFit() Underfull \hbox (badness 10000) in paragraph at lines 619--621 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (7.6295pt too wide) in paragraph at lines 619--621 \T1/ptm/m/it/10 els.features.series.series_derivative2_cauchyFit\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 621--623 []\T1/pcr/m/n/10 series_derivative2_gaussianFit() Underfull \hbox (badness 10000) in paragraph at lines 621--623 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (15.01926pt too wide) in paragraph at lines 621--623 \T1/ptm/m/it/10 els.features.series.series_derivative2_gaussianFit\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 623--625 []\T1/pcr/m/n/10 series_derivative2_laplaceFit() Underfull \hbox (badness 10000) in paragraph at lines 623--625 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (8.89925pt too wide) in paragraph at lines 623--625 \T1/ptm/m/it/10 els.features.series.series_derivative2_laplaceFit\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 625--627 []\T1/pcr/m/n/10 series_derivative_cauchyFit() Underfull \hbox (badness 10000) in paragraph at lines 625--627 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (2.6295pt too wide) in paragraph at lines 625--627 \T1/ptm/m/it/10 els.features.series.series_derivative_cauchyFit\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 627--629 []\T1/pcr/m/n/10 series_derivative_gaussianFit() Underfull \hbox (badness 10000) in paragraph at lines 627--629 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (10.01926pt too wide) in paragraph at lines 627--629 \T1/ptm/m/it/10 els.features.series.series_derivative_gaussianFit\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 629--631 []\T1/pcr/m/n/10 series_derivative_laplaceFit() Underfull \hbox (badness 10000) in paragraph at lines 629--631 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Overfull \hbox (3.89925pt too wide) in paragraph at lines 629--631 \T1/ptm/m/it/10 els.features.series.series_derivative_laplaceFit\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 631--633 []\T1/pcr/m/n/10 series_diff() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-l o-mod- Underfull 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series_sum() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Underfull \hbox (badness 10000) in paragraph at lines 653--655 []\T1/pcr/m/n/10 series_sum_log10() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 657--659 []\T1/pcr/m/n/10 setHistoryMatchingParameters() Underfull \hbox (badness 10000) in paragraph at lines 657--659 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 657--659 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 659--660 []\T1/pcr/m/n/10 setUp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod-els.feature s.test.FeaturesTests Underfull \hbox (badness 10000) in paragraph at lines 660--662 []\T1/pcr/m/n/10 simulate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Overfull \hbox (11.6203pt too wide) in paragraph at lines 660--662 \T1/ptm/m/it/10 els.models.seir_taoLeap.seirTaoLeap.seirTaoLeap Underfull \hbox (badness 10000) in paragraph at lines 664--666 []\T1/pcr/m/n/10 sir_taoLeap_getIncidenceSampled() Underfull \hbox (badness 10000) in paragraph at lines 664--666 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 664--666 \T1/ptm/m/it/10 els.models.sir_taoLeap_getIncidenceSampled\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 666--667 []\T1/pcr/m/n/10 skew() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 671--673 []\T1/pcr/m/n/10 tau_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo- mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 671--673 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 7012) in paragraph at lines 673--675 []\T1/pcr/m/n/10 tearDown() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod-els.feat ures.test.FeaturesTests Underfull \hbox (badness 10000) in paragraph at lines 675--677 []\T1/pcr/m/n/10 test_array() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 677--679 []\T1/pcr/m/n/10 test_create_feature() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-m od- Underfull \hbox (badness 10000) in paragraph at lines 679--681 []\T1/pcr/m/n/10 test_empty_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo- mod- Underfull \hbox (badness 10000) in paragraph at lines 681--683 []\T1/pcr/m/n/10 test_x_inf() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- [60] Underfull \hbox (badness 10000) in paragraph at lines 683--685 []\T1/pcr/m/n/10 test_x_nan() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 685--687 []\T1/pcr/m/n/10 test_xref_inf() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 687--689 []\T1/pcr/m/n/10 test_xref_nan() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 689--691 []\T1/pcr/m/n/10 threshold_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 689--691 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 691--693 []\T1/pcr/m/n/10 topology_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 691--693 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 693--695 []\T1/pcr/m/n/10 transform_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 693--695 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 697--699 []\T1/pcr/m/n/10 tree_param() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo -mod- Overfull \hbox (32.14963pt too wide) in paragraph at lines 697--699 \T1/ptm/m/it/10 els.features.trees.helper.process_optional_arguements\T1/ptm/m/ n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 699--701 []\T1/pcr/m/n/10 tree_to_newick() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 701--703 []\T1/pcr/m/n/10 trimParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 701--703 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 706--708 []\T1/pcr/m/n/10 unique_node_attr() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 706--708 \T1/ptm/m/it/10 els.features.trees.helper.unique_node_attr\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 708--710 []\T1/pcr/m/n/10 updateHistory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy -lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 708--710 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 713--715 []\T1/pcr/m/n/10 validateHistoryMatchingOutput() Underfull \hbox (badness 10000) in paragraph at lines 713--715 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 713--715 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 715--717 []\T1/pcr/m/n/10 validateHistoryMatchingParameters() Underfull \hbox (badness 10000) in paragraph at lines 715--717 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 715--717 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 717--719 []\T1/pcr/m/n/10 validateInputs() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule ph y-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 717--719 \T1/ptm/m/it/10 els.calibration.init_historyMatching_base\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 723--725 []\T1/pcr/m/n/10 writeNewickString() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule phy-lo-mod- Underfull \hbox (badness 10000) in paragraph at lines 725--727 []\T1/pcr/m/n/10 writeTreeToFile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule p hy-lo-mod- [61]) (./institute-for-disease-modeling-phylomodels.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb> Output written on institute-for-disease-modeling-phylomodels.pdf (65 pages, 252 294 bytes). Transcript written on institute-for-disease-modeling-phylomodels.log. Latexmk: Index file 'institute-for-disease-modeling-phylomodels.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-phylomodels.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-phylomodels.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 [rtd-command-info] start-time: 2021-12-01T00:09:04.756782Z, end-time: 2021-12-01T00:09:04.837214Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/checkouts/latest/docs/_build/latex/institute-for-disease-modeling-phylomodels.pdf /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/artifacts/latest/sphinx_pdf/institute-for-disease-modeling-phylomodels.pdf