Read the Docs build information Build id: 772055 Project: life-epigenetics-methylcheck Version: latest Commit: 055cef14faa07d03ccfb3b712f89002ca616a953 Date: 2021-11-12T20:53:04.471300Z State: finished Success: False [rtd-command-info] start-time: 2021-11-12T20:53:06.291416Z, end-time: 2021-11-12T20:53:35.437326Z, duration: 29, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git . Cloning into '.'... 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[rtd-command-info] start-time: 2021-11-12T20:53:35.578130Z, end-time: 2021-11-12T20:53:36.205723Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 055cef1 Feature/v0.7.7 - unlocked pandas version to support 1.3+ (#60) [rtd-command-info] start-time: 2021-11-12T20:53:36.327453Z, end-time: 2021-11-12T20:53:36.402117Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-11-12T20:53:41.324986Z, end-time: 2021-11-12T20:53:45.761418Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-11-12T20:53:45.874658Z, end-time: 2021-11-12T20:53:47.064893Z, duration: 1, 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/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (21.3.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (58.5.3) [rtd-command-info] start-time: 2021-11-12T20:53:47.187589Z, end-time: 2021-11-12T20:53:56.036875Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting docutils>=0.11 Downloading docutils-0.18-py2.py3-none-any.whl (569 kB) Collecting packaging Downloading packaging-21.2-py3-none-any.whl (40 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting setuptools Downloading setuptools-58.5.3-py3-none-any.whl (946 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.7-py3-none-any.whl (38 kB) Collecting pyparsing<3,>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=a78e7c263f88d2229efb89ace5543bb40dd5e54b1815065579fddeae4360a8b3 Stored in directory: /tmp/pip-ephem-wheel-cache-jghlllb4/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=19575fd0aace112bf95017ad66c8e4984328e8ffaddb7b2bdf3cb47a677a97e7 Stored in directory: /tmp/pip-ephem-wheel-cache-jghlllb4/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.7 commonmark-0.8.1 docutils-0.18 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.2 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 setuptools-58.5.3 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7 [rtd-command-info] start-time: 2021-11-12T20:53:56.157677Z, end-time: 2021-11-12T20:54:11.061087Z, duration: 14, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: numpy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Collecting pandas>=1.3.0 Downloading pandas-1.3.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) Requirement already satisfied: scipy in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.5.3) Requirement already satisfied: matplotlib in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (3.3.2) Collecting seaborn Downloading seaborn-0.11.2-py3-none-any.whl (292 kB) Collecting tqdm Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting nbsphinx Downloading nbsphinx-0.8.7-py3-none-any.whl (25 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 11)) (1.8.5) Collecting ipykernel Downloading ipykernel-6.5.0-py3-none-any.whl (125 kB) Collecting joblib Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB) Collecting xlsxwriter Downloading XlsxWriter-3.0.2-py3-none-any.whl (149 kB) Collecting openpyxl Downloading openpyxl-3.0.9-py2.py3-none-any.whl (242 kB) Requirement already satisfied: python-dateutil>=2.7.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from pandas>=1.3.0->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pandas>=1.3.0->-r requirements.txt (line 2)) (2021.3) Requirement already satisfied: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (2021.10.8) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (1.2.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (2.4.7) Requirement already satisfied: cycler>=0.10 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (0.10.0) Collecting pillow>=6.2.0 Downloading Pillow-8.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) Collecting pbr Downloading pbr-5.7.0-py2.py3-none-any.whl (112 kB) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from m2r->-r requirements.txt (line 9)) (0.18) Collecting traitlets Downloading traitlets-5.1.1-py3-none-any.whl (102 kB) Collecting nbconvert!=5.4 Downloading nbconvert-6.3.0-py3-none-any.whl (556 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from nbsphinx->-r requirements.txt (line 10)) (3.0.3) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.16.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (0.7.12) Requirement already satisfied: packaging in 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(from sphinx->-r requirements.txt (line 11)) (58.5.3) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.3.0) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (2.9.1) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx->-r requirements.txt (line 11)) (1.2.4) Collecting debugpy<2.0,>=1.0.0 Downloading debugpy-1.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.9 MB) Collecting importlib-metadata<5 Downloading importlib_metadata-4.8.2-py3-none-any.whl (17 kB) Collecting 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pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.8-py3-none-any.whl (70 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-4.2.1-py3-none-any.whl (69 kB) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (3.3) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 11)) (2.0.7) Requirement already 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wcwidth-0.2.5-py2.py3-none-any.whl (30 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: m2r Building wheel for m2r (setup.py): started Building wheel for m2r (setup.py): finished with status 'done' Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10475 sha256=ca93607bf60289186788e6e5665d061c8b8132a125d915c1a637074a7190061f Stored in directory: /tmp/pip-ephem-wheel-cache-8f1ddmhy/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Successfully built m2r Installing collected packages: zipp, typing-extensions, traitlets, pyrsistent, importlib-resources, importlib-metadata, attrs, tornado, pyzmq, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, wcwidth, ptyprocess, parso, nbformat, jupyter-client, testpath, prompt-toolkit, pillow, pickleshare, pexpect, pandocfilters, nbclient, mistune, matplotlib-inline, jupyterlab-pygments, jedi, defusedxml, decorator, bleach, backcall, pbr, pandas, nbconvert, ipython, et-xmlfile, debugpy, argcomplete, xlsxwriter, tqdm, sphinxcontrib-apidoc, seaborn, openpyxl, nbsphinx, m2r, joblib, ipykernel Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: pandas Found existing installation: pandas 1.1.3 Not uninstalling pandas at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest Can't uninstall 'pandas'. No files were found to uninstall. Successfully installed argcomplete-1.12.3 attrs-21.2.0 backcall-0.2.0 bleach-4.1.0 debugpy-1.5.1 decorator-5.1.0 defusedxml-0.7.1 entrypoints-0.3 et-xmlfile-1.1.0 importlib-metadata-4.8.2 importlib-resources-5.4.0 ipykernel-6.5.0 ipython-7.29.0 ipython-genutils-0.2.0 jedi-0.18.0 joblib-1.1.0 jsonschema-4.2.1 jupyter-client-7.0.6 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.5.8 nbconvert-6.3.0 nbformat-5.1.3 nbsphinx-0.8.7 nest-asyncio-1.5.1 openpyxl-3.0.9 pandas-1.3.4 pandocfilters-1.5.0 parso-0.8.2 pbr-5.7.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.4.0 prompt-toolkit-3.0.22 ptyprocess-0.7.0 pyrsistent-0.18.0 pyzmq-22.3.0 seaborn-0.11.2 sphinxcontrib-apidoc-0.3.0 testpath-0.5.0 tornado-6.1 tqdm-4.62.3 traitlets-5.1.1 typing-extensions-3.10.0.2 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-3.0.2 zipp-3.6.0 [rtd-command-info] start-time: 2021-11-12T20:54:11.976639Z, end-time: 2021-11-12T20:54:12.045549Z, duration: 0, exit-code: 0 cat conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- Path setup -------------------------------------------------------------- # 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 # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- project = 'methylcheck' copyright = '2021, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '0.7' # The full version, including alpha/beta/rc tags release = '0.7.7' # -- General configuration --------------------------------------------------- # If your documentation 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.autodoc', 'sphinxcontrib.apidoc', 'm2r', 'nbsphinx', 'sphinx.ext.autosummary' ] autosummary_generate = True # new in sphinx 3.1 2020 # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' #'alabaster' # 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 # documentation. # # html_theme_options = {} # 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 = ['_sphinx_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'methylcheckdoc' # -- 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, 'methylcheck.tex', 'methylcheck Documentation', 'FOXO Technologies, inc', 'manual'), ] # -- 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, 'methylcheck', 'methylcheck Documentation', [author], 1) ] # -- 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, 'methylcheck', 'methylcheck Documentation', author, 'methylcheck', 'Methylation array quality control and filtering.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- # numpydoc_show_class_members = False ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("feature-v0.7.9", "/en/feature-v0.7.9/"), ], 'downloads': [ ("pdf", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//life-epigenetics-methylcheck.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylcheck', 'name': u'methylcheck', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylcheck.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'FOXOBioScience', 'proxied_api_host': '/_', 'github_repo': 'methylcheck', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '055cef14', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/life-epigenetics-methylcheck/builds/772055/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-11-12T20:54:12.156581Z, end-time: 2021-11-12T20:54:33.839831Z, duration: 21, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.data_files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.predict.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.probes.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.reports.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.samples.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/modules.rst. [autosummary] generating autosummary for: README.md, docs/filtering-probes.ipynb, docs/loading-data.ipynb, docs/mds-example.ipynb, docs/quality-control-example.ipynb, docs/release-history.md, docs/research_notebooks/postprocessQC_example.ipynb, docs/research_notebooks/pval.ipynb, docs/research_notebooks/rawQC_example.ipynb, docs/source/modules.rst, index.rst Failed to import 'methylcheck.qc_report': no module named methylcheck.qc_report Failed to import 'methylcheck.p_value_probe_detection': no module named methylcheck.p_value_probe_detection Failed to import 'methylcheck.qc_report.ReportPDF': no module named methylcheck.qc_report.ReportPDF [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.assign.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.beta_density_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.beta_mds_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.cli.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.combine_mds.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.drop_nan_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.exclude_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.exclude_sex_control_probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.get_sex.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.plot_beta_by_type.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.plot_controls.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.predict.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.probes.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.qc_signal_intensity.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.read_geo.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.run_pipeline.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.run_qc.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.sample_plot.rst, /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/_autosummary/methylcheck.samples.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 11 source files that are out of date updating environment: 37 added, 0 changed, 0 removed reading sources... [ 2%] README reading sources... [ 5%] docs/filtering-probes reading sources... [ 8%] docs/loading-data reading sources... [ 10%] docs/mds-example reading sources... [ 13%] docs/quality-control-example reading sources... [ 16%] docs/release-history Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 304, in build_main app.build(args.force_all, filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 341, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 347, in build_update len(to_build)) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 360, in build updated_docnames = set(self.read()) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 468, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 490, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 534, in read_doc doctree = read_doc(self.app, self.env, self.env.doc2path(docname)) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/io.py", line 318, in read_doc pub.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/docutils/core.py", line 219, in publish self.apply_transforms() File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/docutils/core.py", line 200, in apply_transforms self.document.transformer.apply_transforms() File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/transforms/__init__.py", line 90, in apply_transforms Transformer.apply_transforms(self) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/docutils/transforms/__init__.py", line 171, in apply_transforms transform.apply(**kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/transforms/__init__.py", line 245, in apply apply_source_workaround(n) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py", line 94, in apply_source_workaround for classifier in reversed(node.parent.traverse(nodes.classifier)): TypeError: 'generator' object is not reversible Exception occurred: File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py", line 94, in apply_source_workaround for classifier in reversed(node.parent.traverse(nodes.classifier)): TypeError: 'generator' object is not reversible The full traceback has been saved in /tmp/sphinx-err-q7mo13w7.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. A bug report can be filed in the tracker at . Thanks!