Read the Docs build information Build id: 2218920 Project: institute-for-disease-modeling-phylomodels Version: 70 Commit: e8c8ebc689c55726b7b6189505bd25d38dea3694 Date: 2024-05-15T19:47:25.359300Z State: finished Success: True [rtd-command-info] start-time: 2024-05-15T19:47:26.577549Z, end-time: 2024-05-15T19:47:28.152526Z, 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: 2024-05-15T19:47:28.228331Z, end-time: 2024-05-15T19:47:31.527789Z, duration: 3, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/70/head:external-70 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/phyloModels * [new ref] refs/pull/70/head -> external-70 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: 2024-05-15T19:47:31.647650Z, end-time: 2024-05-15T19:47:31.796358Z, duration: 0, exit-code: 0 git checkout --force e8c8ebc689c55726b7b6189505bd25d38dea3694 Note: switching to 'e8c8ebc689c55726b7b6189505bd25d38dea3694'. 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 e8c8ebc remove contents heading, not aligning [rtd-command-info] start-time: 2024-05-15T19:47:31.862837Z, end-time: 2024-05-15T19:47:31.919061Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-05-15T19:47:32.002461Z, end-time: 2024-05-15T19:47:32.057823Z, 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: 2024-05-15T19:47:37.879831Z, end-time: 2024-05-15T19:47:37.957770Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-05-15T19:47:38.382699Z, end-time: 2024-05-15T19:47:39.546361Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 872ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70, 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: 2024-05-15T19:47:39.607943Z, end-time: 2024-05-15T19:47:48.494478Z, 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/70/lib/python3.9/site-packages (23.1) Collecting pip Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 36.8 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages (67.6.1) Collecting setuptools Downloading 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started Building wheel for pyDOE (setup.py): finished with status 'done' Created wheel for pyDOE: filename=pyDOE-0.3.8-py3-none-any.whl size=18167 sha256=a4e63d4a88d000a4b113b777617d153e5880593fee4bccd5bb29d621f4cf997d Stored in directory: /tmp/pip-ephem-wheel-cache-z01u2eq4/wheels/3c/ca/0d/63b767ad585fbcb3ea222541572dcb78859d0383510672b105 Successfully built ete3 pyDOE Installing collected packages: webencodings, wcwidth, Wand, tbb, pytz, PyQt5-Qt5, py-cpuinfo, pure-eval, ptyprocess, intel-openmp, fastjsonschema, ete3, xlrd, widgetsnbextension, websocket-client, webcolors, uri-template, tzlocal, tzdata, typing-extensions, types-python-dateutil, traitlets, tornado, tinycss2, threadpoolctl, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, qtpy, pyzmq, pyyaml, python-json-logger, PyQt5-sip, pyparsing, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pillow, pexpect, parso, pandocfilters, overrides, numpy, networkx, nest-asyncio, ndindex, msgpack, mkl, mistune, lxml, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, joblib, importlib-resources, h11, fqdn, fonttools, executing, exceptiongroup, et-xmlfile, defusedxml, decorator, debugpy, cycler, attrs, unittest-xml-reporting, terminado, scipy, rfc3339-validator, referencing, python-dateutil, PyQt5, patsy, openpyxl, numexpr, ngesh, matplotlib-inline, jupyter-core, jedi, httpcore, contourpy, comm, cffi, blosc2, bleach, beautifulsoup4, async-lru, asttokens, anyio, tables, stack-data, scikit-learn, pyDOE, pandas, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, httpx, arrow, argon2-cffi-bindings, statsmodels, seaborn, jsonschema, isoduration, ipython, argon2-cffi, nbformat, ipywidgets, ipykernel, qtconsole, nbclient, jupyter-events, jupyter-console, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter Successfully installed PyQt5-5.15.10 PyQt5-Qt5-5.15.2 PyQt5-sip-12.13.0 Wand-0.6.13 anyio-4.3.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 blosc2-2.5.1 cffi-1.16.0 comm-0.2.2 contourpy-1.2.1 cycler-0.12.1 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 et-xmlfile-1.1.0 ete3-3.1.3 exceptiongroup-1.2.1 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.51.0 fqdn-1.5.1 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 importlib-resources-6.4.0 intel-openmp-2024.1.0 ipykernel-6.29.4 ipython-8.18.1 ipywidgets-8.1.2 isoduration-20.11.0 jedi-0.19.1 joblib-1.4.2 json5-0.9.25 jsonpointer-2.4 jsonschema-4.22.0 jsonschema-specifications-2023.12.1 jupyter-1.0.0 jupyter-client-8.6.1 jupyter-console-6.6.3 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.0 jupyter-server-terminals-0.5.3 jupyterlab-4.1.8 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.1 jupyterlab-widgets-3.0.10 kiwisolver-1.4.5 lxml-5.2.2 matplotlib-3.8.4 matplotlib-inline-0.1.7 mistune-3.0.2 mkl-2024.1.0 msgpack-1.0.8 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 ndindex-1.8 nest-asyncio-1.6.0 networkx-3.2.1 ngesh-1.2.1 notebook-7.1.3 notebook-shim-0.2.4 numexpr-2.10.0 numpy-1.26.4 openpyxl-3.1.2 overrides-7.7.0 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 patsy-0.5.6 pexpect-4.9.0 pillow-10.3.0 platformdirs-4.2.2 prometheus-client-0.20.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 py-cpuinfo-9.0.0 pyDOE-0.3.8 pycparser-2.22 pyparsing-3.1.2 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pytz-2024.1 pyyaml-6.0.1 pyzmq-26.0.3 qtconsole-5.5.2 qtpy-2.4.1 referencing-0.35.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.18.1 scikit-learn-1.4.2 scipy-1.13.0 seaborn-0.13.2 send2trash-1.8.3 six-1.16.0 sniffio-1.3.1 soupsieve-2.5 stack-data-0.6.3 statsmodels-0.14.2 tables-3.9.2 tbb-2021.12.0 terminado-0.18.1 threadpoolctl-3.5.0 tinycss2-1.3.0 tornado-6.4 traitlets-5.14.3 types-python-dateutil-2.9.0.20240316 typing-extensions-4.11.0 tzdata-2024.1 tzlocal-5.2 unittest-xml-reporting-3.2.0 uri-template-1.3.0 wcwidth-0.2.13 webcolors-1.13 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.10 xlrd-2.0.1 [rtd-command-info] start-time: 2024-05-15T19:48:58.533680Z, end-time: 2024-05-15T19:49:00.472539Z, duration: 1, exit-code: 0 python ./setup.py install --force running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() running bdist_egg running egg_info creating phyloModels.egg-info writing phyloModels.egg-info/PKG-INFO writing dependency_links to phyloModels.egg-info/dependency_links.txt writing requirements to phyloModels.egg-info/requires.txt writing top-level names to phyloModels.egg-info/top_level.txt writing manifest file 'phyloModels.egg-info/SOURCES.txt' reading manifest file 'phyloModels.egg-info/SOURCES.txt' writing manifest file 'phyloModels.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/phylomodels copying phylomodels/__init__.py -> build/lib/phylomodels creating build/lib/phylomodels/features copying phylomodels/features/features.py -> build/lib/phylomodels/features copying phylomodels/features/test.py -> build/lib/phylomodels/features copying phylomodels/features/inventory.py -> build/lib/phylomodels/features copying phylomodels/features/__init__.py -> build/lib/phylomodels/features copying phylomodels/features/testFeatures.py -> build/lib/phylomodels/features creating build/lib/phylomodels/utilities copying phylomodels/utilities/__init__.py -> build/lib/phylomodels/utilities 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/calibration copying phylomodels/calibration/constants.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_base.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/__init__.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/cal_parameterSweep.py -> build/lib/phylomodels/calibration copying phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/lib/phylomodels/calibration creating build/lib/phylomodels/examples copying phylomodels/examples/__init__.py -> build/lib/phylomodels/examples creating build/lib/phylomodels/network copying phylomodels/network/phyloTree.py -> build/lib/phylomodels/network copying phylomodels/network/__init__.py -> build/lib/phylomodels/network creating build/lib/phylomodels/visualization copying phylomodels/visualization/__init__.py -> build/lib/phylomodels/visualization copying phylomodels/visualization/parallelCoordinates.py -> build/lib/phylomodels/visualization creating build/lib/phylomodels/models copying phylomodels/models/seir_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/distributions_gaussian.py -> build/lib/phylomodels/models copying phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models copying phylomodels/models/__init__.py -> build/lib/phylomodels/models copying phylomodels/models/test_sir_taoLeap_getIncidence.py -> build/lib/phylomodels/models copying phylomodels/models/sir_taoLeap_getIncidenceSampled.py -> build/lib/phylomodels/models creating 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/mean.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/skew.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/var.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/__init__.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/qcd.py -> build/lib/phylomodels/features/statistics copying phylomodels/features/statistics/rsd.py -> build/lib/phylomodels/features/statistics creating build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_gaussianFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum2.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum30.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_diff_L1.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum10.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_log10.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_derivative2_gaussianFit.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_derivative2_laplaceFit.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_partialSum7.py -> build/lib/phylomodels/features/series copying phylomodels/features/series/series_sum_log10.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/BL_calculate_external_max.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/top_calculate_frac_ladder.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/group_calculate_mode.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_betweenness_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_skewness.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_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_min.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/LTT_calculate_mean_s_time.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_slope_1.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_FurnasR.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_diameter.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_fourprong.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_max.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_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_LBI_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/smallConfig_calculate_cherries.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_max_ladder.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_WD_ratio.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_frac_imbalance.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_num.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/calculate_external_branch_length_metrics.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/spectral_calculate_max_distLap_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/local_calculate_frac_basal.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/__init__.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_colless.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/tree_height_calculate_min.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_sackin.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_closeness_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_B2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_max_lineages.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_std.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_min.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/mean_NN_distance.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/netSci_calculate_mean_path.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_median.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_slope_2.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/top_calculate_max_dW.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/group_calculate_max.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_internal_median.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/LTT_calculate_mean_b_time.py -> build/lib/phylomodels/features/trees copying phylomodels/features/trees/BL_calculate_external_min.py -> build/lib/phylomodels/features/trees creating 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/unique_node_attr.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_adjacency_mat.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/check_values.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_eigenvalues_adj.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_LTT.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/__init__.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_node_properties.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_groups.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py -> build/lib/phylomodels/features/trees/helper copying phylomodels/features/trees/helper/process_optional_arguements.py -> build/lib/phylomodels/features/trees/helper creating build/lib/phylomodels/models/seir_taoLeap copying phylomodels/models/seir_taoLeap/__init__.py -> build/lib/phylomodels/models/seir_taoLeap copying phylomodels/models/seir_taoLeap/seirTaoLeap.py -> build/lib/phylomodels/models/seir_taoLeap creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/phylomodels creating build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/features.py -> build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/test.py -> build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/inventory.py -> build/bdist.linux-x86_64/egg/phylomodels/features creating build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/fano.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/skew.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/var.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/qcd.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/statistics/rsd.py -> build/bdist.linux-x86_64/egg/phylomodels/features/statistics copying build/lib/phylomodels/features/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features copying build/lib/phylomodels/features/testFeatures.py -> build/bdist.linux-x86_64/egg/phylomodels/features creating build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_gaussianFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_L2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_laplaceFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_sum.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum30.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_L1.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum10.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative_cauchyFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_log10.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_gaussianFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum15.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_diff_Linf.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_laplaceFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_partialSum7.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_sum_log10.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series copying build/lib/phylomodels/features/series/series_derivative2_cauchyFit.py -> build/bdist.linux-x86_64/egg/phylomodels/features/series creating build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_t_max_lineages.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_frac_ladder.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_kurtosis.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_mode.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_betweenness_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_skewness.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_adj_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_mean_s_time.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_pitchforks.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_1.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_double_cherries.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_FurnasR.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_diameter.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_fourprong.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_B1.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_ratio.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/local_calculate_LBI_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/smallConfig_calculate_cherries.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_max_ladder.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_WD_ratio.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_frac_imbalance.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_num.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/calculate_external_branch_length_metrics.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_min_lap_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/local_calculate_frac_basal.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_colless.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees creating build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_lap.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/unique_node_attr.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_distance_mat.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_adjacency_mat.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/check_values.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_adj.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/calculate_branch_length_metrics.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_LTT.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_node_properties.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_groups.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/helper/process_optional_arguements.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper copying build/lib/phylomodels/features/trees/top_calculate_sackin.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_closeness_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_B2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_max_lineages.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_std.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_min_adj_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/mean_NN_distance.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/netSci_calculate_mean_path.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_eigen_gap.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/tree_height_calculate_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_sackin_var.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_slope_2.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/top_calculate_max_dW.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_ratio_mean.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/group_calculate_max.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_internal_median.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/spectral_calculate_max_lap_eigen.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/LTT_calculate_mean_b_time.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees copying build/lib/phylomodels/features/trees/BL_calculate_external_min.py -> build/bdist.linux-x86_64/egg/phylomodels/features/trees creating build/bdist.linux-x86_64/egg/phylomodels/utilities copying build/lib/phylomodels/utilities/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/utilities creating build/bdist.linux-x86_64/egg/phylomodels/sampling copying build/lib/phylomodels/sampling/sample_treeIndependent.py -> build/bdist.linux-x86_64/egg/phylomodels/sampling copying build/lib/phylomodels/sampling/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/sampling creating build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/constants.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/init_historyMatching_base.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/cal_parameterSweep.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration copying build/lib/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py -> build/bdist.linux-x86_64/egg/phylomodels/calibration creating build/bdist.linux-x86_64/egg/phylomodels/examples copying build/lib/phylomodels/examples/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/examples creating build/bdist.linux-x86_64/egg/phylomodels/network copying build/lib/phylomodels/network/phyloTree.py -> build/bdist.linux-x86_64/egg/phylomodels/network copying build/lib/phylomodels/network/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/network copying build/lib/phylomodels/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels creating build/bdist.linux-x86_64/egg/phylomodels/visualization copying build/lib/phylomodels/visualization/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/visualization copying build/lib/phylomodels/visualization/parallelCoordinates.py -> build/bdist.linux-x86_64/egg/phylomodels/visualization creating build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/seir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/test_distributions_gaussian.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/sir_taoLeap_getIncidence.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/distributions_gaussian.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/models copying build/lib/phylomodels/models/test_sir_taoLeap_getIncidence.py -> build/bdist.linux-x86_64/egg/phylomodels/models creating build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap/__init__.py -> build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/seir_taoLeap/seirTaoLeap.py -> build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap copying build/lib/phylomodels/models/sir_taoLeap_getIncidenceSampled.py -> build/bdist.linux-x86_64/egg/phylomodels/models byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/features.py to features.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/test.py to test.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/inventory.py to inventory.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/fano.py to fano.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/std.py to std.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/mean.py to mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/skew.py to skew.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/var.py to var.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/qcd.py to qcd.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/statistics/rsd.py to rsd.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/testFeatures.py to testFeatures.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative_gaussianFit.py to series_derivative_gaussianFit.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff_L2.py to series_diff_L2.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative_laplaceFit.py to series_derivative_laplaceFit.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative.py to series_derivative.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff.py to series_diff.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_sum.py to series_sum.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2.py to series_derivative2.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum2.py to series_partialSum2.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum30.py to series_partialSum30.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff_L1.py to series_diff_L1.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum10.py to series_partialSum10.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative_cauchyFit.py to series_derivative_cauchyFit.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_log10.py to series_log10.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2_gaussianFit.py to series_derivative2_gaussianFit.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum15.py to series_partialSum15.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_diff_Linf.py to series_diff_Linf.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2_laplaceFit.py to series_derivative2_laplaceFit.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series.py to series.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_partialSum7.py to series_partialSum7.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_sum_log10.py to series_sum_log10.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/series/series_derivative2_cauchyFit.py to series_derivative2_cauchyFit.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_max.py to BL_calculate_external_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_t_max_lineages.py to LTT_calculate_t_max_lineages.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_frac_ladder.py to top_calculate_frac_ladder.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_median.py to BL_calculate_median.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_kurtosis.py to spectral_calculate_kurtosis.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_min.py to BL_calculate_ratio_min.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_mode.py to group_calculate_mode.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_betweenness_max.py to netSci_calculate_betweenness_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_skewness.py to spectral_calculate_skewness.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_median.py to BL_calculate_ratio_median.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_std.py to BL_calculate_external_std.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_min.py to BL_calculate_min.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_max_adj_eigen.py to spectral_calculate_max_adj_eigen.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_mean_s_time.py to LTT_calculate_mean_s_time.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_mean.py to BL_calculate_internal_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_mean.py to BL_calculate_external_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_pitchforks.py to smallConfig_calculate_pitchforks.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_mean_imbalance_ratio.py to top_calculate_mean_imbalance_ratio.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_median.py to BL_calculate_external_median.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_slope_1.py to LTT_calculate_slope_1.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_std.py to BL_calculate_std.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_std.py to BL_calculate_internal_std.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_double_cherries.py to smallConfig_calculate_double_cherries.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_max.py to BL_calculate_ratio_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_FurnasR.py to top_calculate_FurnasR.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_diameter.py to netSci_calculate_diameter.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_min.py to BL_calculate_internal_min.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_fourprong.py to smallConfig_calculate_fourprong.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_max.py to BL_calculate_internal_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_max.py to BL_calculate_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_B1.py to top_calculate_B1.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_slope_ratio.py to LTT_calculate_slope_ratio.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_mean.py to BL_calculate_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/local_calculate_LBI_mean.py to local_calculate_LBI_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_std.py to group_calculate_std.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/smallConfig_calculate_cherries.py to smallConfig_calculate_cherries.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_mean.py to group_calculate_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_max_ladder.py to top_calculate_max_ladder.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_WD_ratio.py to top_calculate_WD_ratio.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_frac_imbalance.py to top_calculate_frac_imbalance.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_num.py to group_calculate_num.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_eigen_centrality_max.py to netSci_calculate_eigen_centrality_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/calculate_external_branch_length_metrics.py to calculate_external_branch_length_metrics.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_min_lap_eigen.py to spectral_calculate_min_lap_eigen.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_max_distLap_eigen.py to spectral_calculate_max_distLap_eigen.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/local_calculate_frac_basal.py to local_calculate_frac_basal.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_colless.py to top_calculate_colless.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/tree_height_calculate_mean.py to tree_height_calculate_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/tree_height_calculate_min.py to tree_height_calculate_min.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_eigenvalues_lap.py to get_eigenvalues_lap.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/unique_node_attr.py to unique_node_attr.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_distance_mat.py to get_distance_mat.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_adjacency_mat.py to get_adjacency_mat.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/check_values.py to check_values.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_eigenvalues_adj.py to get_eigenvalues_adj.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/calculate_branch_length_metrics.py to calculate_branch_length_metrics.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_LTT.py to get_LTT.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_node_properties.py to get_node_properties.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_groups.py to get_groups.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/get_eigenvalues_dist_lap.py to get_eigenvalues_dist_lap.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/helper/process_optional_arguements.py to process_optional_arguements.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_sackin.py to top_calculate_sackin.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_closeness_max.py to netSci_calculate_closeness_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_B2.py to top_calculate_B2.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_max_lineages.py to LTT_calculate_max_lineages.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_std.py to BL_calculate_ratio_std.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_min.py to group_calculate_min.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_min_adj_eigen.py to spectral_calculate_min_adj_eigen.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/mean_NN_distance.py to mean_NN_distance.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/netSci_calculate_mean_path.py to netSci_calculate_mean_path.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_eigen_gap.py to spectral_calculate_eigen_gap.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_median.py to group_calculate_median.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/tree_height_calculate_max.py to tree_height_calculate_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_sackin_var.py to top_calculate_sackin_var.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_slope_2.py to LTT_calculate_slope_2.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/top_calculate_max_dW.py to top_calculate_max_dW.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_ratio_mean.py to BL_calculate_ratio_mean.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/group_calculate_max.py to group_calculate_max.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_internal_median.py to BL_calculate_internal_median.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/spectral_calculate_max_lap_eigen.py to spectral_calculate_max_lap_eigen.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/LTT_calculate_mean_b_time.py to LTT_calculate_mean_b_time.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/features/trees/BL_calculate_external_min.py to BL_calculate_external_min.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/utilities/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/sampling/sample_treeIndependent.py to sample_treeIndependent.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/sampling/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/constants.py to constants.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/init_historyMatching_base.py to init_historyMatching_base.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/cal_parameterSweep.py to cal_parameterSweep.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/calibration/init_historyMatching_poissonGlmBasis.py to init_historyMatching_poissonGlmBasis.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/examples/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/network/phyloTree.py to phyloTree.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/network/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/visualization/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/visualization/parallelCoordinates.py to parallelCoordinates.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap_getIncidenceSampled.py to seir_taoLeap_getIncidenceSampled.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/test_distributions_gaussian.py to test_distributions_gaussian.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/sir_taoLeap_getIncidence.py to sir_taoLeap_getIncidence.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/distributions_gaussian.py to distributions_gaussian.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/test_sir_taoLeap_getIncidenceSampled.py to test_sir_taoLeap_getIncidenceSampled.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/test_sir_taoLeap_getIncidence.py to test_sir_taoLeap_getIncidence.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/seir_taoLeap/seirTaoLeap.py to seirTaoLeap.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/phylomodels/models/sir_taoLeap_getIncidenceSampled.py to sir_taoLeap_getIncidenceSampled.cpython-39.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying phyloModels.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating dist creating 'dist/phyloModels-0.5-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing phyloModels-0.5-py3.9.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages/phyloModels-0.5-py3.9.egg Extracting phyloModels-0.5-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Adding phyloModels 0.5 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages/phyloModels-0.5-py3.9.egg Processing dependencies for phyloModels==0.5 Searching for sip Reading https://pypi.org/simple/sip/ Downloading https://files.pythonhosted.org/packages/22/cb/3763a07a046884cdc14668758895cc6a8cd1b8d06281d5b6914b0e6948bc/sip-6.8.3-py3-none-any.whl#sha256=11c332566de0d752df92906101260e81401bf574417a6bc31fb99364ae6b652d Best match: sip 6.8.3 Processing sip-6.8.3-py3-none-any.whl Installing sip-6.8.3-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Adding sip 6.8.3 to easy-install.pth file detected new path './phyloModels-0.5-py3.9.egg' Installing sip-build script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing sip-distinfo script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing sip-install script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing sip-module script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing sip-sdist script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing sip-wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages/sip-6.8.3-py3.9.egg Searching for xlrd==2.0.1 Best match: xlrd 2.0.1 Adding xlrd 2.0.1 to easy-install.pth file detected new path './sip-6.8.3-py3.9.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for openpyxl==3.1.2 Best match: openpyxl 3.1.2 Adding openpyxl 3.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for unittest-xml-reporting==3.2.0 Best match: unittest-xml-reporting 3.2.0 Adding unittest-xml-reporting 3.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for psutil==5.9.8 Best match: psutil 5.9.8 Adding psutil 5.9.8 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-client==8.6.1 Best match: jupyter-client 8.6.1 Adding jupyter-client 8.6.1 to easy-install.pth file Installing jupyter-kernel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-kernelspec script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-run script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-console==6.6.3 Best match: jupyter-console 6.6.3 Adding jupyter-console 6.6.3 to easy-install.pth file Installing jupyter-console script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-core==5.7.2 Best match: jupyter-core 5.7.2 Adding jupyter-core 5.7.2 to easy-install.pth file Installing jupyter script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-migrate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-troubleshoot script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter==1.0.0 Best match: jupyter 1.0.0 Adding jupyter 1.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for scikit-learn==1.4.2 Best match: scikit-learn 1.4.2 Adding scikit-learn 1.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for mkl==2024.1.0 Best match: mkl 2024.1.0 Adding mkl 2024.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for seaborn==0.13.2 Best match: seaborn 0.13.2 Adding seaborn 0.13.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for matplotlib==3.8.4 Best match: matplotlib 3.8.4 Adding matplotlib 3.8.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pandas==2.2.2 Best match: pandas 2.2.2 Adding pandas 2.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for networkx==3.2.1 Best match: networkx 3.2.1 Adding networkx 3.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for ete3==3.1.3 Best match: ete3 3.1.3 Adding ete3 3.1.3 to easy-install.pth file Installing ete3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for lxml==5.2.2 Best match: lxml 5.2.2 Adding lxml 5.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for PyQt5==5.15.10 Best match: PyQt5 5.15.10 Adding PyQt5 5.15.10 to easy-install.pth file Installing pylupdate5 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing pyrcc5 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing pyuic5 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for scipy==1.13.0 Best match: scipy 1.13.0 Adding scipy 1.13.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for numpy==1.26.4 Best match: numpy 1.26.4 Adding numpy 1.26.4 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for et-xmlfile==1.1.0 Best match: et-xmlfile 1.1.0 Adding et-xmlfile 1.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for traitlets==5.14.3 Best match: traitlets 5.14.3 Adding traitlets 5.14.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for tornado==6.4 Best match: tornado 6.4 Adding tornado 6.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pyzmq==26.0.3 Best match: pyzmq 26.0.3 Adding pyzmq 26.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for python-dateutil==2.9.0.post0 Best match: python-dateutil 2.9.0.post0 Adding python-dateutil 2.9.0.post0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for importlib-metadata==7.1.0 Best match: importlib-metadata 7.1.0 Adding importlib-metadata 7.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pygments==2.18.0 Best match: pygments 2.18.0 Adding pygments 2.18.0 to easy-install.pth file Installing pygmentize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for prompt-toolkit==3.0.43 Best match: prompt-toolkit 3.0.43 Adding prompt-toolkit 3.0.43 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for ipython==8.18.1 Best match: ipython 8.18.1 Adding ipython 8.18.1 to easy-install.pth file Installing ipython script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing ipython3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for ipykernel==6.29.4 Best match: ipykernel 6.29.4 Adding ipykernel 6.29.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for platformdirs==4.2.2 Best match: platformdirs 4.2.2 Adding platformdirs 4.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for ipywidgets==8.1.2 Best match: ipywidgets 8.1.2 Adding ipywidgets 8.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for nbconvert==7.16.4 Best match: nbconvert 7.16.4 Adding nbconvert 7.16.4 to easy-install.pth file Installing jupyter-dejavu script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-nbconvert script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for qtconsole==5.5.2 Best match: qtconsole 5.5.2 Adding qtconsole 5.5.2 to easy-install.pth file Installing jupyter-qtconsole script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for notebook==7.1.3 Best match: notebook 7.1.3 Adding notebook 7.1.3 to easy-install.pth file Installing jupyter-notebook script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for threadpoolctl==3.5.0 Best match: threadpoolctl 3.5.0 Adding threadpoolctl 3.5.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for joblib==1.4.2 Best match: joblib 1.4.2 Adding joblib 1.4.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for tbb==2021.12.0 Best match: tbb 2021.12.0 Adding tbb 2021.12.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for intel-openmp==2024.1.0 Best match: intel-openmp 2024.1.0 Adding intel-openmp 2024.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for importlib-resources==6.4.0 Best match: importlib-resources 6.4.0 Adding importlib-resources 6.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pyparsing==3.1.2 Best match: pyparsing 3.1.2 Adding pyparsing 3.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pillow==10.3.0 Best match: pillow 10.3.0 Adding pillow 10.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for packaging==24.0 Best match: packaging 24.0 Adding packaging 24.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for kiwisolver==1.4.5 Best match: kiwisolver 1.4.5 Adding kiwisolver 1.4.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for fonttools==4.51.0 Best match: fonttools 4.51.0 Adding fonttools 4.51.0 to easy-install.pth file Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for cycler==0.12.1 Best match: cycler 0.12.1 Adding cycler 0.12.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for contourpy==1.2.1 Best match: contourpy 1.2.1 Adding contourpy 1.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for tzdata==2024.1 Best match: tzdata 2024.1 Adding tzdata 2024.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pytz==2024.1 Best match: pytz 2024.1 Adding pytz 2024.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for PyQt5-Qt5==5.15.2 Best match: PyQt5-Qt5 5.15.2 Adding PyQt5-Qt5 5.15.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for PyQt5-sip==12.13.0 Best match: PyQt5-sip 12.13.0 Adding PyQt5-sip 12.13.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for tomli==2.0.1 Best match: tomli 2.0.1 Adding tomli 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for setuptools==69.5.1 Best match: setuptools 69.5.1 Adding setuptools 69.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for zipp==3.18.1 Best match: zipp 3.18.1 Adding zipp 3.18.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for wcwidth==0.2.13 Best match: wcwidth 0.2.13 Adding wcwidth 0.2.13 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pexpect==4.9.0 Best match: pexpect 4.9.0 Adding pexpect 4.9.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for exceptiongroup==1.2.1 Best match: exceptiongroup 1.2.1 Adding exceptiongroup 1.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for typing-extensions==4.11.0 Best match: typing-extensions 4.11.0 Adding typing-extensions 4.11.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for stack-data==0.6.3 Best match: stack-data 0.6.3 Adding stack-data 0.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for matplotlib-inline==0.1.7 Best match: matplotlib-inline 0.1.7 Adding matplotlib-inline 0.1.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jedi==0.19.1 Best match: jedi 0.19.1 Adding jedi 0.19.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for decorator==5.1.1 Best match: decorator 5.1.1 Adding decorator 5.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for nest-asyncio==1.6.0 Best match: nest-asyncio 1.6.0 Adding nest-asyncio 1.6.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for debugpy==1.8.1 Best match: debugpy 1.8.1 Adding debugpy 1.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for comm==0.2.2 Best match: comm 0.2.2 Adding comm 0.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyterlab-widgets==3.0.10 Best match: jupyterlab-widgets 3.0.10 Adding jupyterlab-widgets 3.0.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for widgetsnbextension==4.0.10 Best match: widgetsnbextension 4.0.10 Adding widgetsnbextension 4.0.10 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for tinycss2==1.3.0 Best match: tinycss2 1.3.0 Adding tinycss2 1.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pandocfilters==1.5.1 Best match: pandocfilters 1.5.1 Adding pandocfilters 1.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for nbformat==5.10.4 Best match: nbformat 5.10.4 Adding nbformat 5.10.4 to easy-install.pth file Installing jupyter-trust script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for nbclient==0.10.0 Best match: nbclient 0.10.0 Adding nbclient 0.10.0 to easy-install.pth file Installing jupyter-execute script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for mistune==3.0.2 Best match: mistune 3.0.2 Adding mistune 3.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for MarkupSafe==2.1.5 Best match: MarkupSafe 2.1.5 Adding MarkupSafe 2.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyterlab-pygments==0.3.0 Best match: jupyterlab-pygments 0.3.0 Adding jupyterlab-pygments 0.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jinja2==3.1.4 Best match: jinja2 3.1.4 Adding jinja2 3.1.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for defusedxml==0.7.1 Best match: defusedxml 0.7.1 Adding defusedxml 0.7.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for bleach==6.1.0 Best match: bleach 6.1.0 Adding bleach 6.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for beautifulsoup4==4.12.3 Best match: beautifulsoup4 4.12.3 Adding beautifulsoup4 4.12.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for QtPy==2.4.1 Best match: QtPy 2.4.1 Adding QtPy 2.4.1 to easy-install.pth file Installing qtpy script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for notebook-shim==0.2.4 Best match: notebook-shim 0.2.4 Adding notebook-shim 0.2.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyterlab==4.1.8 Best match: jupyterlab 4.1.8 Adding jupyterlab 4.1.8 to easy-install.pth file Installing jlpm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-lab script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-labextension script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Installing jupyter-labhub script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyterlab-server==2.27.1 Best match: jupyterlab-server 2.27.1 Adding jupyterlab-server 2.27.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-server==2.14.0 Best match: jupyter-server 2.14.0 Adding jupyter-server 2.14.0 to easy-install.pth file Installing jupyter-server script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for ptyprocess==0.7.0 Best match: ptyprocess 0.7.0 Adding ptyprocess 0.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pure-eval==0.2.2 Best match: pure-eval 0.2.2 Adding pure-eval 0.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for asttokens==2.4.1 Best match: asttokens 2.4.1 Adding asttokens 2.4.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for executing==2.0.1 Best match: executing 2.0.1 Adding executing 2.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for parso==0.8.4 Best match: parso 0.8.4 Adding parso 0.8.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for webencodings==0.5.1 Best match: webencodings 0.5.1 Adding webencodings 0.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jsonschema==4.22.0 Best match: jsonschema 4.22.0 Adding jsonschema 4.22.0 to easy-install.pth file Installing jsonschema script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for fastjsonschema==2.19.1 Best match: fastjsonschema 2.19.1 Adding fastjsonschema 2.19.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for soupsieve==2.5 Best match: soupsieve 2.5 Adding soupsieve 2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-lsp==2.2.5 Best match: jupyter-lsp 2.2.5 Adding jupyter-lsp 2.2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for httpx==0.27.0 Best match: httpx 0.27.0 Adding httpx 0.27.0 to easy-install.pth file Installing httpx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for async-lru==2.0.4 Best match: async-lru 2.0.4 Adding async-lru 2.0.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for requests==2.31.0 Best match: requests 2.31.0 Adding requests 2.31.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for json5==0.9.25 Best match: json5 0.9.25 Adding json5 0.9.25 to easy-install.pth file Installing pyjson5 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for Babel==2.15.0 Best match: Babel 2.15.0 Adding Babel 2.15.0 to easy-install.pth file Installing pybabel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for websocket-client==1.8.0 Best match: websocket-client 1.8.0 Adding websocket-client 1.8.0 to easy-install.pth file Installing wsdump script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for terminado==0.18.1 Best match: terminado 0.18.1 Adding terminado 0.18.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for Send2Trash==1.8.3 Best match: Send2Trash 1.8.3 Adding Send2Trash 1.8.3 to easy-install.pth file Installing send2trash script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for prometheus-client==0.20.0 Best match: prometheus-client 0.20.0 Adding prometheus-client 0.20.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for overrides==7.7.0 Best match: overrides 7.7.0 Adding overrides 7.7.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-server-terminals==0.5.3 Best match: jupyter-server-terminals 0.5.3 Adding jupyter-server-terminals 0.5.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jupyter-events==0.10.0 Best match: jupyter-events 0.10.0 Adding jupyter-events 0.10.0 to easy-install.pth file Installing jupyter-events script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for argon2-cffi==23.1.0 Best match: argon2-cffi 23.1.0 Adding argon2-cffi 23.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for anyio==4.3.0 Best match: anyio 4.3.0 Adding anyio 4.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for rpds-py==0.18.1 Best match: rpds-py 0.18.1 Adding rpds-py 0.18.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for referencing==0.35.1 Best match: referencing 0.35.1 Adding referencing 0.35.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jsonschema-specifications==2023.12.1 Best match: jsonschema-specifications 2023.12.1 Adding jsonschema-specifications 2023.12.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for attrs==23.2.0 Best match: attrs 23.2.0 Adding attrs 23.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for sniffio==1.3.1 Best match: sniffio 1.3.1 Adding sniffio 1.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for idna==3.7 Best match: idna 3.7 Adding idna 3.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for httpcore==1.0.5 Best match: httpcore 1.0.5 Adding httpcore 1.0.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for certifi==2024.2.2 Best match: certifi 2024.2.2 Adding certifi 2024.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for urllib3==2.2.1 Best match: urllib3 2.2.1 Adding urllib3 2.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for charset-normalizer==3.3.2 Best match: charset-normalizer 3.3.2 Adding charset-normalizer 3.3.2 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for rfc3986-validator==0.1.1 Best match: rfc3986-validator 0.1.1 Adding rfc3986-validator 0.1.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for rfc3339-validator==0.1.4 Best match: rfc3339-validator 0.1.4 Adding rfc3339-validator 0.1.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for PyYAML==6.0.1 Best match: PyYAML 6.0.1 Adding PyYAML 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for python-json-logger==2.0.7 Best match: python-json-logger 2.0.7 Adding python-json-logger 2.0.7 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for argon2-cffi-bindings==21.2.0 Best match: argon2-cffi-bindings 21.2.0 Adding argon2-cffi-bindings 21.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for h11==0.14.0 Best match: h11 0.14.0 Adding h11 0.14.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for webcolors==1.13 Best match: webcolors 1.13 Adding webcolors 1.13 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for uri-template==1.3.0 Best match: uri-template 1.3.0 Adding uri-template 1.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for jsonpointer==2.4 Best match: jsonpointer 2.4 Adding jsonpointer 2.4 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for isoduration==20.11.0 Best match: isoduration 20.11.0 Adding isoduration 20.11.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for fqdn==1.5.1 Best match: fqdn 1.5.1 Adding fqdn 1.5.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for cffi==1.16.0 Best match: cffi 1.16.0 Adding cffi 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for arrow==1.3.0 Best match: arrow 1.3.0 Adding arrow 1.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for pycparser==2.22 Best match: pycparser 2.22 Adding pycparser 2.22 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Searching for types-python-dateutil==2.9.0.20240316 Best match: types-python-dateutil 2.9.0.20240316 Adding types-python-dateutil 2.9.0.20240316 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-phylomodels/envs/70/lib/python3.9/site-packages Finished processing dependencies for phyloModels==0.5 [rtd-command-info] start-time: 2024-05-15T19:49:00.619831Z, end-time: 2024-05-15T19:49:09.824574Z, duration: 9, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting sphinx~=6.2.1 (from -r docs/requirements.txt (line 1)) Downloading sphinx-6.2.1-py3-none-any.whl.metadata (6.2 kB) Collecting pydata-sphinx-theme (from -r docs/requirements.txt (line 2)) Downloading pydata_sphinx_theme-0.15.2-py3-none-any.whl.metadata (7.3 kB) Collecting sphinxcontrib-napoleon~=0.7 (from -r docs/requirements.txt (line 3)) Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl.metadata (6.2 kB) Collecting plantweb~=1.2.1 (from -r docs/requirements.txt (line 4)) Downloading plantweb-1.2.1-py3-none-any.whl.metadata (3.7 kB) Collecting sphinxcontrib-programoutput~=0.17 (from -r docs/requirements.txt (line 5)) Downloading sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl.metadata (7.2 kB) Collecting nbsphinx~=0.9.2 (from -r docs/requirements.txt (line 6)) Downloading 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docutils 0.21.2 Uninstalling docutils-0.21.2: Successfully uninstalled docutils-0.21.2 Attempting uninstall: sphinx Found existing installation: Sphinx 7.3.7 Uninstalling Sphinx-7.3.7: Successfully uninstalled Sphinx-7.3.7 Attempting uninstall: jupyterlab Found existing installation: jupyterlab 4.1.8 Uninstalling jupyterlab-4.1.8: Successfully uninstalled jupyterlab-4.1.8 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. notebook 7.1.3 requires jupyterlab<4.2,>=4.1.1, but you have jupyterlab 4.0.13 which is incompatible. Successfully installed accessible-pygments-0.0.5 cryptography-42.0.7 deprecated-1.2.14 docutils-0.19 jupyterlab-4.0.13 markdown-it-py-3.0.0 mdit-py-plugins-0.4.1 mdurl-0.1.2 myst-parser-2.0.0 nbsphinx-0.9.4 plantweb-1.2.1 pockets-0.9.1 pydata-sphinx-theme-0.15.2 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 readthedocs-sphinx-search-0.3.2 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0 wrapt-1.16.0 [rtd-command-info] start-time: 2024-05-15T19:49:10.443815Z, end-time: 2024-05-15T19:49:10.502027Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys #import sphinx_rtd_theme import configparser from datetime import datetime if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "phylomodels package" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx_copybutton', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude', 'sphinx.ext.viewcode', # link to view source code 'sphinx_search.extension', # search across multiple docsets in domain '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', '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}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = '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 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) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "70", 'version_slug': "70", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("0.5.1", "/en/0.5.1/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-phylomodels', 'name': u'phyloModels', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'phyloModels', 'github_version': 'e8c8ebc689c55726b7b6189505bd25d38dea3694', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'e8c8ebc689c55726b7b6189505bd25d38dea3694', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'e8c8ebc689c55726b7b6189505bd25d38dea3694', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'e8c8ebc6', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'external' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'https://github.com/InstituteforDiseaseModeling/phyloModels/pull/70' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-phylomodels/builds/2218920/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2024-05-15T19:49:10.570940Z, end-time: 2024-05-15T19:49:31.497851Z, duration: 20, 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={'attrs_inline', 'strikethrough', 'tasklist', 'linkify', 'smartquotes', 'dollarmath', 'replacements', 'deflist', 'fieldlist', 'colon_fence', 'html_admonition', 'amsmath', 'html_image', 'substitution'}, 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) The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492 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... [ 0%] calibration reading sources... [ 1%] examples reading sources... [ 1%] features reading sources... [ 2%] index reading sources... [ 3%] models reading sources... [ 3%] modules reading sources... [ 4%] phylomodels reading sources... [ 5%] phylomodels.calibration reading sources... [ 5%] phylomodels.calibration.cal_parameterSweep reading sources... [ 6%] phylomodels.calibration.constants reading sources... 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[100%] todo WARNING: A mocked object is detected: 'phylomodels' WARNING: A mocked object is detected: 'phylomodels.calibration' WARNING: A mocked object is detected: 'phylomodels.calibration.cal_parameterSweep' WARNING: A mocked object is detected: 'phylomodels.calibration.constants' WARNING: A mocked object is detected: 'phylomodels.calibration.init_historyMatching_base' WARNING: A mocked object is detected: 'phylomodels.calibration.init_historyMatching_poissonGlmBasis' WARNING: A mocked object is detected: 'phylomodels.examples' WARNING: A mocked object is detected: 'phylomodels.features' WARNING: A mocked object is detected: 'phylomodels.features.features' WARNING: A mocked object is detected: 'phylomodels.features.inventory' WARNING: A mocked object is detected: 'phylomodels.features.series' WARNING: A mocked object is detected: 'phylomodels.features.series.series' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative2' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative2_cauchyFit' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative2_gaussianFit' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative2_laplaceFit' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative_cauchyFit' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative_gaussianFit' WARNING: A mocked object is detected: 'phylomodels.features.series.series_derivative_laplaceFit' WARNING: A mocked object is detected: 'phylomodels.features.series.series_diff' WARNING: A mocked object is detected: 'phylomodels.features.series.series_diff_L1' WARNING: A mocked object is detected: 'phylomodels.features.series.series_diff_L2' WARNING: A mocked object is detected: 'phylomodels.features.series.series_diff_Linf' WARNING: A mocked object is detected: 'phylomodels.features.series.series_log10' WARNING: A mocked object is detected: 'phylomodels.features.series.series_partialSum10' WARNING: A mocked object is detected: 'phylomodels.features.series.series_partialSum15' WARNING: A mocked object is detected: 'phylomodels.features.series.series_partialSum2' WARNING: A mocked object is detected: 'phylomodels.features.series.series_partialSum30' WARNING: A mocked object is detected: 'phylomodels.features.series.series_partialSum7' WARNING: A mocked object is detected: 'phylomodels.features.series.series_sum' WARNING: A mocked object is detected: 'phylomodels.features.series.series_sum_log10' WARNING: A mocked object is detected: 'phylomodels.features.statistics' WARNING: A mocked object is detected: 'phylomodels.features.statistics.fano' WARNING: A mocked object is detected: 'phylomodels.features.statistics.mean' WARNING: A mocked object is detected: 'phylomodels.features.statistics.qcd' WARNING: A mocked object is detected: 'phylomodels.features.statistics.rsd' WARNING: A mocked object is detected: 'phylomodels.features.statistics.skew' WARNING: A mocked object is detected: 'phylomodels.features.statistics.std' WARNING: A mocked object is detected: 'phylomodels.features.statistics.var' WARNING: A mocked object is detected: 'phylomodels.features.test' WARNING: A mocked object is detected: 'phylomodels.features.testFeatures' WARNING: A mocked object is detected: 'phylomodels.features.trees' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_external_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_external_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_external_median' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_external_min' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_external_std' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_internal_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_internal_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_internal_median' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_internal_min' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_internal_std' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_median' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_min' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_ratio_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_ratio_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_ratio_median' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_ratio_min' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_ratio_std' WARNING: A mocked object is detected: 'phylomodels.features.trees.BL_calculate_std' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_max_lineages' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_mean_b_time' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_mean_s_time' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_slope_1' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_slope_2' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_slope_ratio' WARNING: A mocked object is detected: 'phylomodels.features.trees.LTT_calculate_t_max_lineages' WARNING: A mocked object is detected: 'phylomodels.features.trees.calculate_external_branch_length_metrics' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_median' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_min' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_mode' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_num' WARNING: A mocked object is detected: 'phylomodels.features.trees.group_calculate_std' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.calculate_branch_length_metrics' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.check_values' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_LTT' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_adjacency_mat' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_distance_mat' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_eigenvalues_adj' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_eigenvalues_dist_lap' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_eigenvalues_lap' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_groups' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.get_node_properties' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.process_optional_arguements' WARNING: A mocked object is detected: 'phylomodels.features.trees.helper.unique_node_attr' WARNING: A mocked object is detected: 'phylomodels.features.trees.local_calculate_LBI_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.local_calculate_frac_basal' WARNING: A mocked object is detected: 'phylomodels.features.trees.mean_NN_distance' WARNING: A mocked object is detected: 'phylomodels.features.trees.netSci_calculate_betweenness_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.netSci_calculate_closeness_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.netSci_calculate_diameter' WARNING: A mocked object is detected: 'phylomodels.features.trees.netSci_calculate_eigen_centrality_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.netSci_calculate_mean_path' WARNING: A mocked object is detected: 'phylomodels.features.trees.smallConfig_calculate_cherries' WARNING: A mocked object is detected: 'phylomodels.features.trees.smallConfig_calculate_double_cherries' WARNING: A mocked object is detected: 'phylomodels.features.trees.smallConfig_calculate_fourprong' WARNING: A mocked object is detected: 'phylomodels.features.trees.smallConfig_calculate_pitchforks' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_eigen_gap' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_kurtosis' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_max_adj_eigen' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_max_distLap_eigen' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_max_lap_eigen' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_min_adj_eigen' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_min_lap_eigen' WARNING: A mocked object is detected: 'phylomodels.features.trees.spectral_calculate_skewness' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_B1' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_B2' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_FurnasR' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_WD_ratio' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_colless' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_frac_imbalance' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_frac_ladder' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_max_dW' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_max_ladder' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_mean_imbalance_ratio' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_sackin' WARNING: A mocked object is detected: 'phylomodels.features.trees.top_calculate_sackin_var' WARNING: A mocked object is detected: 'phylomodels.features.trees.tree_height_calculate_max' WARNING: A mocked object is detected: 'phylomodels.features.trees.tree_height_calculate_mean' WARNING: A mocked object is detected: 'phylomodels.features.trees.tree_height_calculate_min' WARNING: A mocked object is detected: 'phylomodels.models' WARNING: A mocked object is detected: 'phylomodels.models.distributions_gaussian' WARNING: A mocked object is detected: 'phylomodels.models.seir_taoLeap' WARNING: A mocked object is detected: 'phylomodels.models.seir_taoLeap.seirTaoLeap' WARNING: A mocked object is detected: 'phylomodels.models.seir_taoLeap_getIncidenceSampled' WARNING: A mocked object is detected: 'phylomodels.models.sir_taoLeap_getIncidence' WARNING: A mocked object is detected: 'phylomodels.models.sir_taoLeap_getIncidenceSampled' WARNING: A mocked object is detected: 'phylomodels.models.test_distributions_gaussian' WARNING: A mocked object is detected: 'phylomodels.models.test_sir_taoLeap_getIncidence' WARNING: A mocked object is detected: 'phylomodels.models.test_sir_taoLeap_getIncidenceSampled' WARNING: A mocked object is detected: 'phylomodels.network' WARNING: A mocked object is detected: 'phylomodels.network.phyloTree' WARNING: A mocked object is detected: 'phylomodels.sampling' WARNING: A mocked object is detected: 'phylomodels.sampling.sample_treeIndependent' WARNING: A mocked object is detected: 'phylomodels.utilities' WARNING: A mocked object is detected: 'phylomodels.visualization' WARNING: A mocked object is detected: 'phylomodels.visualization.parallelCoordinates' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... 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[100%] todo generating indices... genindex py-modindex 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 Updating searchtools for Read the Docs search... build succeeded, 143 warnings. The HTML pages are in ../_readthedocs/html.