Read the Docs build information Build id: 3532143 Project: institute-for-disease-modeling-phylomodels Version: 72 Commit: 20946eaf05e6f70704f9f15651d0b30bb28c2afb Date: 2025-11-18T17:39:44.031698Z State: finished Success: True [rtd-command-info] start-time: 2025-11-18T17:39:44.931327Z, end-time: 2025-11-18T17:39:46.733186Z, duration: 1, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/phyloModels.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2025-11-18T17:39:46.840220Z, end-time: 2025-11-18T17:39:50.181849Z, duration: 3, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/72/head:external-72 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/phyloModels * [new ref] refs/pull/72/head -> external-72 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. * [new tag] 0.5.1 -> 0.5.1 [rtd-command-info] start-time: 2025-11-18T17:39:51.232649Z, end-time: 2025-11-18T17:39:51.337420Z, duration: 0, exit-code: 0 git checkout --force 20946eaf05e6f70704f9f15651d0b30bb28c2afb Note: switching to '20946eaf05e6f70704f9f15651d0b30bb28c2afb'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 20946ea Merge branch 'master' into gfnc [rtd-command-info] start-time: 2025-11-18T17:39:51.422180Z, end-time: 2025-11-18T17:39:51.463826Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: false # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip # Optionally set the version of Python and requirements required to build your docs python: install: - requirements: requirements.txt - method: setuptools path: . - requirements: docs/requirements.txt # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank search: ranking: index.html: 3 modules.html: 2 [rtd-command-info] start-time: 2025-11-18T17:39:56.703734Z, end-time: 2025-11-18T17:39:56.768105Z, duration: 0, exit-code: 0 asdf global python 3.9.22 [rtd-command-info] start-time: 2025-11-18T17:39:57.216257Z, end-time: 2025-11-18T17:39:58.464322Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.22.final.0-64 in 942ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-11-18T17:39:58.548842Z, end-time: 2025-11-18T17:40:06.937882Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages (23.1) Collecting pip Downloading pip-25.3-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 42.6 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages (67.6.1) Collecting setuptools Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 251.1 MB/s eta 0:00:00 Installing collected packages: setuptools, pip 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sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 tomli-2.3.0 urllib3-2.5.0 zipp-3.23.0 [rtd-command-info] start-time: 2025-11-18T17:40:12.420243Z, end-time: 2025-11-18T17:41:08.850226Z, duration: 56, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting numpy (from -r requirements.txt (line 1)) Downloading numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) Collecting scipy (from -r requirements.txt (line 2)) Downloading scipy-1.13.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) Collecting pandas (from -r requirements.txt (line 3)) Downloading pandas-2.3.3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB) Collecting matplotlib (from -r requirements.txt (line 4)) Downloading matplotlib-3.9.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 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psutil-7.1.3-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl.metadata (23 kB) Collecting statsmodels (from -r requirements.txt (line 14)) Downloading statsmodels-0.14.5-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (9.5 kB) Collecting tornado (from -r requirements.txt (line 15)) Downloading tornado-6.5.2-cp39-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.8 kB) Collecting xlrd (from -r requirements.txt (line 16)) Downloading xlrd-2.0.2-py2.py3-none-any.whl.metadata (3.5 kB) Collecting ete3 (from -r requirements.txt (line 17)) Downloading ete3-3.1.3.tar.gz (4.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 195.7 MB/s 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata 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stack_data-0.6.3-py3-none-any.whl (24 kB) Downloading asttokens-3.0.1-py3-none-any.whl (27 kB) Downloading executing-2.2.1-py2.py3-none-any.whl (28 kB) Downloading pure_eval-0.2.3-py3-none-any.whl (11 kB) Downloading uri_template-1.3.0-py3-none-any.whl (11 kB) Downloading wcwidth-0.2.14-py2.py3-none-any.whl (37 kB) Building wheels for collected packages: ete3, pyDOE Building wheel for ete3 (pyproject.toml): started Building wheel for ete3 (pyproject.toml): finished with status 'done' Created wheel for ete3: filename=ete3-3.1.3-py3-none-any.whl size=2273900 sha256=8fef5fd4ab6626c7909da40ca1e10cb435fdf1600067b5797570146393338534 Stored in directory: /tmp/pip-ephem-wheel-cache-fdr_1ddk/wheels/ad/2e/cc/edcca721b423e1604c84f480a1e8e0547a223bfc068d373259 Building wheel for pyDOE (pyproject.toml): started Building wheel for pyDOE (pyproject.toml): finished with status 'done' Created wheel for pyDOE: filename=pydoe-0.3.8-py3-none-any.whl size=18224 sha256=f6e2570bd4947b1af3d67a42de1ecda086d5656e37e89f84ff8dbcad23235e12 Stored in directory: /tmp/pip-ephem-wheel-cache-fdr_1ddk/wheels/3c/ca/0d/63b767ad585fbcb3ea222541572dcb78859d0383510672b105 Successfully built ete3 pyDOE Installing collected packages: webencodings, Wand, tcmlib, pytz, PyQt5-Qt5, py-cpuinfo, pure-eval, ptyprocess, onemkl-license, fastjsonschema, ete3, xlrd, widgetsnbextension, websocket-client, webcolors, wcwidth, uri-template, umf, tzlocal, tzdata, typing-extensions, traitlets, tornado, tinycss2, threadpoolctl, tbb, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, PyQt5-sip, pyparsing, pycparser, psutil, prometheus-client, platformdirs, pillow, pexpect, parso, pandocfilters, overrides, numpy, networkx, nest-asyncio, ndindex, msgpack, lxml, lark, kiwisolver, jupyterlab_widgets, jupyterlab-pygments, jsonpointer, json5, joblib, importlib-resources, h11, fqdn, fonttools, executing, et-xmlfile, defusedxml, decorator, debugpy, cycler, comm, bleach, attrs, asttokens, unittest-xml-reporting, terminado, stack-data, scipy, rfc3987-syntax, rfc3339-validator, referencing, python-json-logger, python-dateutil, PyQt5, prompt-toolkit, patsy, openpyxl, numexpr, ngesh, mistune, matplotlib-inline, jupyter-core, jedi, intel-cmplr-lib-ur, httpcore, exceptiongroup, contourpy, cffi, blosc2, beautifulsoup4, async-lru, tables, scikit-learn, pyDOE, pandas, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, ipython, intel-openmp, arrow, argon2-cffi-bindings, anyio, statsmodels, seaborn, mkl, jsonschema, isoduration, ipywidgets, ipykernel, httpx, argon2-cffi, nbformat, jupyter-console, nbclient, jupyter-events, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter Successfully installed PyQt5-5.15.11 PyQt5-Qt5-5.15.18 PyQt5-sip-12.17.1 Wand-0.6.13 anyio-4.11.0 argon2-cffi-25.1.0 argon2-cffi-bindings-25.1.0 arrow-1.4.0 asttokens-3.0.1 async-lru-2.0.5 attrs-25.4.0 beautifulsoup4-4.14.2 bleach-6.2.0 blosc2-2.5.1 cffi-2.0.0 comm-0.2.3 contourpy-1.3.0 cycler-0.12.1 debugpy-1.8.17 decorator-5.2.1 defusedxml-0.7.1 et-xmlfile-2.0.0 ete3-3.1.3 exceptiongroup-1.3.0 executing-2.2.1 fastjsonschema-2.21.2 fonttools-4.60.1 fqdn-1.5.1 h11-0.16.0 httpcore-1.0.9 httpx-0.28.1 importlib-resources-6.5.2 intel-cmplr-lib-ur-2025.3.1 intel-openmp-2025.3.1 ipykernel-6.31.0 ipython-8.18.1 ipywidgets-8.1.8 isoduration-20.11.0 jedi-0.19.2 joblib-1.5.2 json5-0.12.1 jsonpointer-3.0.0 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 jupyter-1.1.1 jupyter-client-8.6.3 jupyter-console-6.6.3 jupyter-core-5.8.1 jupyter-events-0.12.0 jupyter-lsp-2.3.0 jupyter-server-2.17.0 jupyter-server-terminals-0.5.3 jupyterlab-4.4.10 jupyterlab-pygments-0.3.0 jupyterlab-server-2.28.0 jupyterlab_widgets-3.0.16 kiwisolver-1.4.7 lark-1.3.1 lxml-6.0.2 matplotlib-3.9.4 matplotlib-inline-0.2.1 mistune-3.1.4 mkl-2025.3.0 msgpack-1.1.2 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 ndindex-1.10.0 nest-asyncio-1.6.0 networkx-3.2.1 ngesh-1.2.1 notebook-7.4.7 notebook-shim-0.2.4 numexpr-2.10.2 numpy-2.0.2 onemkl-license-2025.3.0 openpyxl-3.1.5 overrides-7.7.0 pandas-2.3.3 pandocfilters-1.5.1 parso-0.8.5 patsy-1.0.2 pexpect-4.9.0 pillow-11.3.0 platformdirs-4.4.0 prometheus-client-0.23.1 prompt-toolkit-3.0.52 psutil-7.1.3 ptyprocess-0.7.0 pure-eval-0.2.3 py-cpuinfo-9.0.0 pyDOE-0.3.8 pycparser-2.23 pyparsing-3.2.5 python-dateutil-2.9.0.post0 python-json-logger-4.0.0 pytz-2025.2 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.36.2 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rfc3987-syntax-1.1.0 rpds-py-0.27.1 scikit-learn-1.6.1 scipy-1.13.1 seaborn-0.13.2 send2trash-1.8.3 six-1.17.0 sniffio-1.3.1 soupsieve-2.8 stack-data-0.6.3 statsmodels-0.14.5 tables-3.9.2 tbb-2022.3.0 tcmlib-1.4.1 terminado-0.18.1 threadpoolctl-3.6.0 tinycss2-1.4.0 tornado-6.5.2 traitlets-5.14.3 typing-extensions-4.15.0 tzdata-2025.2 tzlocal-5.3.1 umf-1.0.2 unittest-xml-reporting-3.2.0 uri-template-1.3.0 wcwidth-0.2.14 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.9.0 widgetsnbextension-4.0.15 xlrd-2.0.2 [rtd-command-info] start-time: 2025-11-18T17:41:08.940285Z, end-time: 2025-11-18T17:41:09.518084Z, duration: 0, exit-code: 0 python ./setup.py install --force running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py creating build/lib/phylomodels copying phylomodels/__init__.py -> build/lib/phylomodels creating build/lib/phylomodels/sampling copying phylomodels/sampling/sample_treeIndependent.py -> build/lib/phylomodels/sampling copying phylomodels/sampling/__init__.py -> build/lib/phylomodels/sampling creating build/lib/phylomodels/utilities copying phylomodels/utilities/__init__.py -> build/lib/phylomodels/utilities creating build/lib/phylomodels/models copying phylomodels/models/test_sir_taoLeap_getIncidence.py -> build/lib/phylomodels/models copying phylomodels/models/seir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models copying phylomodels/models/distributions_gaussian.py -> build/lib/phylomodels/models copying phylomodels/models/sir_taoLeap_getIncidenceSampled.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/__init__.py -> build/lib/phylomodels/models 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/network copying phylomodels/network/__init__.py -> build/lib/phylomodels/network copying phylomodels/network/phyloTree.py -> build/lib/phylomodels/network creating build/lib/phylomodels/examples copying phylomodels/examples/__init__.py -> build/lib/phylomodels/examples creating 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 copying phylomodels/features/testFeatures.py -> build/lib/phylomodels/features creating build/lib/phylomodels/calibration copying phylomodels/calibration/cal_parameterSweep.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_base.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/constants.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/__init__.py -> build/lib/phylomodels/calibration 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/lib/phylomodels/features/statistics copying phylomodels/features/statistics/var.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/fano.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/std.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/qcd.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/__init__.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/mean.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/rsd.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/skew.py -> build/lib/phylomodels/features/statistics creating build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum_log10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_gaussianFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum30.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum15.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_Linf.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_log10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum7.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_gaussianFit.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_derivative_cauchyFit.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_derivative2_cauchyFit.py -> build/lib/phylomodels/features/series creating build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_frac_basal.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_num.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_cherries.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_sackin.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_median.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_ratio_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mode.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_FurnasR.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_betweenness_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_LBI_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_B2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_max_adj_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_std.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_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_mean_path.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/calculate_external_branch_length_metrics.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_max.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/top_calculate_B1.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_t_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_sackin_var.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/BL_calculate_external_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_min_lap_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_max_ladder.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_fourprong.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_max_dW.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_WD_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/__init__.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/spectral_calculate_min_adj_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_colless.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_1.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_internal_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_closeness_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_diameter.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/mean_NN_distance.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> build/lib/phylomodels/features/trees creating 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_groups.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_LTT.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/get_eigenvalues_dist_lap.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/process_optional_arguements.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_node_properties.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/check_values.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/unique_node_attr.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/__init__.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/calculate_branch_length_metrics.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_adjacency_mat.py -> build/lib/phylomodels/features/trees/helper running install_lib creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/sampling copying build/lib/phylomodels/sampling/sample_treeIndependent.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/sampling copying build/lib/phylomodels/sampling/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/sampling creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/utilities copying build/lib/phylomodels/utilities/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/utilities creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/test_sir_taoLeap_getIncidence.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap/seirTaoLeap.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap_getIncidenceSampled.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/distributions_gaussian.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/sir_taoLeap_getIncidenceSampled.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/test_distributions_gaussian.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/sir_taoLeap_getIncidence.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models copying build/lib/phylomodels/models/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/visualization copying build/lib/phylomodels/visualization/parallelCoordinates.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/visualization copying build/lib/phylomodels/visualization/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/visualization creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/network copying build/lib/phylomodels/network/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/network copying build/lib/phylomodels/network/phyloTree.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/network creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/examples copying build/lib/phylomodels/examples/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/examples creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/var.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/fano.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/std.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/qcd.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/rsd.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/skew.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics copying build/lib/phylomodels/features/features.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features copying build/lib/phylomodels/features/test.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_sum_log10.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_gaussianFit.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum30.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_laplaceFit.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum2.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum15.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_Linf.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_L2.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_log10.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum7.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum10.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_gaussianFit.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_sum.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_cauchyFit.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_L1.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_laplaceFit.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_cauchyFit.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series copying build/lib/phylomodels/features/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/local_calculate_frac_basal.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_num.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_cherries.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_sackin.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_min.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_median.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_kurtosis.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_min.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_median.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_median.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_min.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_2.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_mode.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_FurnasR.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_betweenness_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_adj.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_groups.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_lap.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_LTT.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_distance_mat.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/process_optional_arguements.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_node_properties.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/check_values.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/unique_node_attr.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/calculate_branch_length_metrics.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_adjacency_mat.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/local_calculate_LBI_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_frac_imbalance.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_B2.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_adj_eigen.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_std.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_skewness.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_max_lineages.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_mean_path.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_min.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_std.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_min.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_median.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_eigen_gap.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/calculate_external_branch_length_metrics.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_mean_s_time.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_B1.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_ratio.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_t_max_lineages.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_sackin_var.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_mean_b_time.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_std.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_min_lap_eigen.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_max_ladder.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_fourprong.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_max_dW.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_WD_ratio.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_min_adj_eigen.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_colless.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_1.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_frac_ladder.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_min.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_std.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_median.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_closeness_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_diameter.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_std.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_mean.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/mean_NN_distance.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees copying build/lib/phylomodels/features/inventory.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features copying build/lib/phylomodels/features/testFeatures.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features copying build/lib/phylomodels/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration copying build/lib/phylomodels/calibration/cal_parameterSweep.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration copying build/lib/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration copying build/lib/phylomodels/calibration/init_historyMatching_base.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration copying build/lib/phylomodels/calibration/constants.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration copying build/lib/phylomodels/calibration/__init__.py -> /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/sampling/sample_treeIndependent.py to sample_treeIndependent.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/sampling/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/utilities/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/test_sir_taoLeap_getIncidence.py to test_sir_taoLeap_getIncidence.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/seir_taoLeap/seirTaoLeap.py to seirTaoLeap.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/seir_taoLeap/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/seir_taoLeap_getIncidenceSampled.py to seir_taoLeap_getIncidenceSampled.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/distributions_gaussian.py to distributions_gaussian.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/sir_taoLeap_getIncidenceSampled.py to sir_taoLeap_getIncidenceSampled.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py to test_sir_taoLeap_getIncidenceSampled.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/test_distributions_gaussian.py to test_distributions_gaussian.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/sir_taoLeap_getIncidence.py to sir_taoLeap_getIncidence.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/models/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/visualization/parallelCoordinates.py to parallelCoordinates.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/visualization/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/network/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/network/phyloTree.py to phyloTree.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/examples/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/var.py to var.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/fano.py to fano.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/std.py to std.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/qcd.py to qcd.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/mean.py to mean.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/rsd.py to rsd.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/statistics/skew.py to skew.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/features.py to features.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/test.py to test.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_sum_log10.py to series_sum_log10.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative_gaussianFit.py to series_derivative_gaussianFit.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_partialSum30.py to series_partialSum30.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative2_laplaceFit.py to series_derivative2_laplaceFit.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_partialSum2.py to series_partialSum2.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative.py to series_derivative.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_diff.py to series_diff.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_partialSum15.py to series_partialSum15.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_diff_Linf.py to series_diff_Linf.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_diff_L2.py to series_diff_L2.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_log10.py to series_log10.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative2.py to series_derivative2.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_partialSum7.py to series_partialSum7.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_partialSum10.py to series_partialSum10.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series.py to series.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative2_gaussianFit.py to series_derivative2_gaussianFit.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_sum.py to series_sum.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative_cauchyFit.py to series_derivative_cauchyFit.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_diff_L1.py to series_diff_L1.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative_laplaceFit.py to series_derivative_laplaceFit.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/series/series_derivative2_cauchyFit.py to series_derivative2_cauchyFit.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/local_calculate_frac_basal.py to local_calculate_frac_basal.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/group_calculate_num.py to group_calculate_num.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/tree_height_calculate_mean.py to tree_height_calculate_mean.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/smallConfig_calculate_cherries.py to smallConfig_calculate_cherries.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/top_calculate_sackin.py to top_calculate_sackin.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/group_calculate_max.py to group_calculate_max.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/group_calculate_min.py to group_calculate_min.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_median.py to BL_calculate_median.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/spectral_calculate_kurtosis.py to spectral_calculate_kurtosis.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_ratio_min.py to BL_calculate_ratio_min.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_internal_median.py to BL_calculate_internal_median.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_ratio_median.py to BL_calculate_ratio_median.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_external_min.py to BL_calculate_external_min.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/LTT_calculate_slope_2.py to LTT_calculate_slope_2.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/group_calculate_mode.py to group_calculate_mode.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/top_calculate_FurnasR.py to top_calculate_FurnasR.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_max.py to BL_calculate_max.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_mean.py to BL_calculate_mean.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/netSci_calculate_betweenness_max.py to netSci_calculate_betweenness_max.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_eigenvalues_adj.py to get_eigenvalues_adj.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_groups.py to get_groups.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_eigenvalues_lap.py to get_eigenvalues_lap.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_LTT.py to get_LTT.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_distance_mat.py to get_distance_mat.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py to get_eigenvalues_dist_lap.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/process_optional_arguements.py to process_optional_arguements.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_node_properties.py to get_node_properties.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/check_values.py to check_values.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/unique_node_attr.py to unique_node_attr.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/calculate_branch_length_metrics.py to calculate_branch_length_metrics.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/helper/get_adjacency_mat.py to get_adjacency_mat.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/local_calculate_LBI_mean.py to local_calculate_LBI_mean.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/top_calculate_frac_imbalance.py to top_calculate_frac_imbalance.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/top_calculate_B2.py to top_calculate_B2.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/spectral_calculate_max_adj_eigen.py to spectral_calculate_max_adj_eigen.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_std.py to BL_calculate_std.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/spectral_calculate_skewness.py to spectral_calculate_skewness.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/LTT_calculate_max_lineages.py to LTT_calculate_max_lineages.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/smallConfig_calculate_double_cherries.py to smallConfig_calculate_double_cherries.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/netSci_calculate_mean_path.py to netSci_calculate_mean_path.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/tree_height_calculate_min.py to tree_height_calculate_min.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/smallConfig_calculate_pitchforks.py to smallConfig_calculate_pitchforks.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_internal_std.py to BL_calculate_internal_std.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_min.py to BL_calculate_min.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_external_median.py to BL_calculate_external_median.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/spectral_calculate_eigen_gap.py to spectral_calculate_eigen_gap.cpython-39.pyc byte-compiling 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/BL_calculate_external_mean.py to BL_calculate_external_mean.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py to netSci_calculate_eigen_centrality_max.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py to top_calculate_mean_imbalance_ratio.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/mean_NN_distance.py to mean_NN_distance.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/trees/spectral_calculate_max_lap_eigen.py to spectral_calculate_max_lap_eigen.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/inventory.py to inventory.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/features/testFeatures.py to testFeatures.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py to __init__.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration/cal_parameterSweep.py to cal_parameterSweep.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py to init_historyMatching_poissonGlmBasis.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration/init_historyMatching_base.py to init_historyMatching_base.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration/constants.py to constants.cpython-39.pyc byte-compiling /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/calibration/__init__.py to __init__.cpython-39.pyc running install_egg_info 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' Copying phyloModels.egg-info to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phyloModels-0.5-py3.9.egg-info running install_scripts [rtd-command-info] start-time: 2025-11-18T17:41:09.792852Z, end-time: 2025-11-18T17:41:17.138938Z, duration: 7, exit-code: 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pynacl, plantweb, markdown-it-py, deprecated, cryptography, sphinxcontrib-programoutput, pydata-sphinx-theme, mdit-py-plugins, pygithub, myst-parser, nbsphinx Attempting uninstall: docutils Found existing installation: docutils 0.21.2 Uninstalling docutils-0.21.2: Successfully uninstalled docutils-0.21.2 Attempting uninstall: sphinx Found existing installation: Sphinx 7.4.7 Uninstalling Sphinx-7.4.7: Successfully uninstalled Sphinx-7.4.7 Successfully installed accessible-pygments-0.0.5 cryptography-46.0.3 deprecated-1.3.1 docutils-0.19 markdown-it-py-3.0.0 mdit-py-plugins-0.4.2 mdurl-0.1.2 myst-parser-2.0.0 nbsphinx-0.9.7 plantweb-1.3.0 pockets-0.9.1 pydata-sphinx-theme-0.16.1 pygithub-1.59.1 pyjwt-2.10.1 pynacl-1.6.1 sphinx-6.2.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.18 sphinxext.remoteliteralinclude-0.6.0 wrapt-2.0.1 [rtd-command-info] start-time: 2025-11-18T17:41:17.285012Z, end-time: 2025-11-18T17:41:17.330616Z, 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.ext.intersphinx', 'sphinxext.remoteliteralinclude', 'sphinx.ext.viewcode', # link to view source code 'myst_parser' # source files written in MD or RST ] myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "linkify", "replacements", "smartquotes", "strikethrough", "substitution", "tasklist", ] 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', 'phylomodels.testFeatures'] 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'] # 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}, Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = 'en' # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'pydata_sphinx_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 = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "IDM docs", "url": "https://docs.idmod.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/institutefordiseasemodeling/phyloModels", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/idm-logo-transparent.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/phyloModels/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/phyloModels/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # 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_css_files = ['theme_overrides.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' # -- RTD Sphinx search for searching across the entire domain, default parent ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } # -- 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) } [rtd-command-info] start-time: 2025-11-18T17:41:17.417794Z, end-time: 2025-11-18T17:41:29.045032Z, duration: 11, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 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... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'dollarmath', 'amsmath', 'smartquotes', 'colon_fence', 'html_admonition', 'linkify', 'attrs_inline', 'replacements', 'fieldlist', 'html_image', 'substitution', 'tasklist', 'strikethrough', 'deflist'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 151 source files that are out of date updating environment: [new config] 151 added, 0 changed, 0 removed reading sources... 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[100%] todo WARNING: autodoc: failed to import module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'calibration' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'calibration.cal_parameterSweep' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'calibration.constants' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'calibration.init_historyMatching_base' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'calibration.init_historyMatching_poissonGlmBasis' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'examples' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.features' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.inventory' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative2' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative2_cauchyFit' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative2_gaussianFit' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative2_laplaceFit' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative_cauchyFit' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative_gaussianFit' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_derivative_laplaceFit' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_diff' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_diff_L1' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_diff_L2' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_diff_Linf' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_log10' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_partialSum10' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_partialSum15' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_partialSum2' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_partialSum30' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_partialSum7' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_sum' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.series.series_sum_log10' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.fano' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.qcd' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.rsd' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.skew' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.std' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.statistics.var' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.test' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.testFeatures' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_median' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_min' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_external_std' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_median' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_min' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_internal_std' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_median' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_min' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_median' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_min' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_ratio_std' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.BL_calculate_std' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_max_lineages' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_b_time' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_mean_s_time' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_1' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_2' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_slope_ratio' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.LTT_calculate_t_max_lineages' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.calculate_external_branch_length_metrics' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_median' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_min' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_mode' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_num' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.group_calculate_std' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.calculate_branch_length_metrics' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.check_values' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_LTT' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_adjacency_mat' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_distance_mat' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_adj' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_dist_lap' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_eigenvalues_lap' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_groups' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.get_node_properties' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.process_optional_arguements' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.helper.unique_node_attr' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.local_calculate_LBI_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.local_calculate_frac_basal' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.mean_NN_distance' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_betweenness_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_closeness_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_diameter' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_eigen_centrality_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.netSci_calculate_mean_path' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_cherries' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_double_cherries' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_fourprong' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.smallConfig_calculate_pitchforks' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_eigen_gap' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_kurtosis' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_adj_eigen' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_distLap_eigen' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_max_lap_eigen' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_adj_eigen' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_min_lap_eigen' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.spectral_calculate_skewness' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_B1' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_B2' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_FurnasR' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_WD_ratio' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_colless' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_imbalance' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_frac_ladder' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_max_dW' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_max_ladder' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_mean_imbalance_ratio' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_sackin' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.top_calculate_sackin_var' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_max' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_mean' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'features.trees.tree_height_calculate_min' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.distributions_gaussian' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.seir_taoLeap' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.seir_taoLeap.seirTaoLeap' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.seir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.sir_taoLeap_getIncidence' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.sir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.test_distributions_gaussian' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.test_sir_taoLeap_getIncidence' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'models.test_sir_taoLeap_getIncidenceSampled' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'network' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'network.phyloTree' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'sampling' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'sampling.sample_treeIndependent' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'utilities' from module 'phylomodels'; the following exception was raised: cannot import name 'trees' from partially initialized module 'phylomodels' (most likely due to a circular import) (/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/72/lib/python3.9/site-packages/phylomodels/__init__.py) WARNING: autodoc: failed to import module 'visualization' from module 'phylomodels'; 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[100%] todo generating indices... genindex done highlighting module code... writing additional pages... search opensearch done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 143 warnings. The HTML pages are in ../_readthedocs/html.