Read the Docs build information Build id: 631300 Project: life-epigenetics-methylprep Version: latest Commit: b1be71b748f7c8361623bf37b486cc7b7b3ce4bc Date: 2021-05-12T02:48:52.537953Z State: finished Success: False [rtd-command-info] start-time: 2021-05-12T02:48:54.025455Z, end-time: 2021-05-12T02:49:02.295816Z, duration: 8, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylprep.git . Cloning into '.'... 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[rtd-command-info] start-time: 2021-05-12T02:49:02.440742Z, end-time: 2021-05-12T02:49:03.013808Z, 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 b1be71b Feature/v1.4.4 (#83) [rtd-command-info] start-time: 2021-05-12T02:49:03.139473Z, end-time: 2021-05-12T02:49:03.207235Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-05-12T02:49:05.713969Z, end-time: 2021-05-12T02:49:09.826346Z, 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-methylprep/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-05-12T02:49:09.952781Z, end-time: 2021-05-12T02:49:11.080701Z, 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-methylprep/envs/latest/lib/python3.7/site-packages (21.1.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (56.2.0) [rtd-command-info] start-time: 2021-05-12T02:49:11.187339Z, end-time: 2021-05-12T02:49:20.093648Z, 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) 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) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting requests>=2.0.0 Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting setuptools Downloading setuptools-56.2.0-py3-none-any.whl (785 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.0-py3-none-any.whl (133 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0.0rc2 Downloading MarkupSafe-2.0.0-cp37-cp37m-manylinux2010_x86_64.whl (31 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.4-py2.py3-none-any.whl (153 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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=23755 sha256=2b6c7108745f15a04214bf9ad9bbc87836cf87eeeffee5e9d6ebef9b46b04bf7 Stored in directory: /tmp/pip-ephem-wheel-cache-xxdoht8b/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=491059 sha256=a8a4fce9204fbec4ab09c3ff269d0d1f58e1cdf97f63e5fc55f795dcb32e7cde Stored in directory: /tmp/pip-ephem-wheel-cache-xxdoht8b/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, 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 Jinja2-3.0.0 MarkupSafe-2.0.0 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 setuptools-56.2.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4 [rtd-command-info] start-time: 2021-05-12T02:49:20.199168Z, end-time: 2021-05-12T02:49:34.493579Z, duration: 14, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: numpy>=1.18.5 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Requirement already satisfied: pandas>=1.0 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (1.1.3) Requirement already satisfied: scipy>=1.2.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.5.3) Collecting statsmodels Downloading statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) Collecting pytest Downloading pytest-6.2.4-py3-none-any.whl (280 kB) Collecting coverage Downloading coverage-5.5-cp37-cp37m-manylinux2010_x86_64.whl (242 kB) Collecting python-coveralls Downloading python_coveralls-2.9.3-py2.py3-none-any.whl (9.9 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) Collecting nbsphinx Downloading nbsphinx-0.8.4-py3-none-any.whl (24 kB) Collecting tqdm Downloading tqdm-4.60.0-py2.py3-none-any.whl (75 kB) Collecting bs4 Downloading bs4-0.0.1.tar.gz (1.1 kB) Collecting lxml Downloading lxml-4.6.3-cp37-cp37m-manylinux2014_x86_64.whl (6.3 MB) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 14)) (2.25.1) Requirement already satisfied: python-dateutil>=2.7.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from pandas>=1.0->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pandas>=1.0->-r requirements.txt (line 2)) (2021.1) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas>=1.0->-r requirements.txt (line 2)) (1.16.0) Collecting patsy>=0.5 Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting attrs>=19.2.0 Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting pluggy<1.0.0a1,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting py>=1.8.2 Downloading py-1.10.0-py2.py3-none-any.whl (97 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pytest->-r requirements.txt (line 5)) (20.9) Collecting importlib-metadata>=0.12 Downloading importlib_metadata-4.0.1-py3-none-any.whl (16 kB) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting zipp>=0.5 Downloading zipp-3.4.1-py3-none-any.whl (5.2 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-3.10.0.0-py3-none-any.whl (26 kB) Collecting PyYAML Downloading PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (636 kB) Collecting pbr Downloading pbr-5.6.0-py2.py3-none-any.whl (111 kB) Requirement already satisfied: Sphinx>=1.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.8.5) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (0.17.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (56.2.0) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.9.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.2.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.1.0) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.2.4) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (3.0.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (0.7.12) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.9.0) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests->-r requirements.txt (line 14)) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests->-r requirements.txt (line 14)) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in 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sphinxcontrib-websupport->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.1.4) Building wheels for collected packages: m2r, pandocfilters, pyrsistent, bs4 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=10465 sha256=1a38b581cd00ac4b45bfa5d1064edc0f0d6a0fdd380b71e6ed299448d941dfa5 Stored in directory: /tmp/pip-ephem-wheel-cache-7yw_f2vq/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7992 sha256=04518ea710845359ec274922c83765eec363ba27d466e38a65d27c4ff03ddf1b Stored in directory: /tmp/pip-ephem-wheel-cache-7yw_f2vq/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115335 sha256=d09b59cbd2c7b6ebd0fd14e7a650be70f138485b4b74aeb9c6054db6949d8fc5 Stored in directory: /tmp/pip-ephem-wheel-cache-7yw_f2vq/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5 Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1273 sha256=ddf4d547ac2e38a7a1c6f2d6d30370fd1535ac495d18853ae7aad7e7c6603342 Stored in directory: /tmp/pip-ephem-wheel-cache-7yw_f2vq/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca Successfully built m2r pandocfilters pyrsistent bs4 Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, soupsieve, pandocfilters, nbclient, mistune, jupyterlab-pygments, entrypoints, defusedxml, bleach, toml, PyYAML, py, pluggy, pbr, patsy, nbconvert, iniconfig, coverage, beautifulsoup4, tqdm, statsmodels, sphinxcontrib-apidoc, python-coveralls, pytest, nbsphinx, m2r, lxml, bs4 Successfully installed PyYAML-5.4.1 async-generator-1.10 attrs-21.2.0 beautifulsoup4-4.9.3 bleach-3.3.0 bs4-0.0.1 coverage-5.5 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-4.0.1 iniconfig-1.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 lxml-4.6.3 m2r-0.2.1 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.3 nbsphinx-0.8.4 nest-asyncio-1.5.1 pandocfilters-1.4.3 patsy-0.5.1 pbr-5.6.0 pluggy-0.13.1 py-1.10.0 pyrsistent-0.17.3 pytest-6.2.4 python-coveralls-2.9.3 pyzmq-22.0.3 soupsieve-2.2.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.12.2 testpath-0.4.4 toml-0.10.2 tornado-6.1 tqdm-4.60.0 traitlets-5.0.5 typing-extensions-3.10.0.0 webencodings-0.5.1 zipp-3.4.1 [rtd-command-info] start-time: 2021-05-12T02:49:35.381368Z, end-time: 2021-05-12T02:49:35.451530Z, 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 = 'methylprep' copyright = '2021, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '1.4' # The full version, including alpha/beta/rc tags release = '1.4.2' # -- 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', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.githubpages', ] # 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' todo_include_todos = True # -- 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', 'nature' # 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 = 'methylpredoc' # -- Options for LaTeX output ------------------------------------------------ latex_engine = 'xelatex' #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, 'methylprep.tex', 'methylprep Documentation', 'Life Epigenetics', '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, 'methylprep', 'methylprep 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, 'methylprep', 'methylprep Documentation', author, 'methylprep', 'One line description of project.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- ########################################################################### # 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 should't rely on extra depencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("html", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylprep', 'name': u'methylprep', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylprep.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': 'methylprep', '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': 'b1be71b7', } # 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-methylprep/builds/631300/' 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: 2021-05-12T02:49:35.568052Z, end-time: 2021-05-12T02:49:36.923110Z, duration: 1, 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-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.download.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [html]: targets for 14 source files that are out of date updating environment: 14 added, 0 changed, 0 removed reading sources... [ 7%] README reading sources... [ 14%] docs/README reading sources... [ 21%] docs/cli reading sources... [ 28%] docs/debug_notebooks/float16_error /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: The iterable returned by Node.traverse() will become an iterator instead of a list in Docutils > 0.16. for classifier in reversed(node.parent.traverse(nodes.classifier)): /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:302: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 2 does not contain the same number of items as row 1 (3 vs 4). .. list-table:: :header-rows: 1 * - Argument - Type - Default - Description * - -h, --help - - show this help message and exit * - -d , --data_dir - ``str`` - [required path] - path to where the data series will be saved. Folder must exist already. * - -i ID, --id ID - ``str`` - [required ID] - The dataset's reference ID (Starts with ``GSE`` for GEO or ``E-MTAB-`` for ArrayExpress) * - -l LIST, --list LIST - ``multiple strings`` - optional - List of series IDs (can be either GEO or ArrayExpress), for partial downloading * - -o, --dict_only - ``True`` - pass flag only - If passed, will only create dictionaries and not process any samples * - -b BATCH_SIZE, --batch_size BATCH_SIZE - ``int`` - optional - Number of samples to process at a time, 100 by default. Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 1022, in parse rststring, resources = exporter.from_notebook_node(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 840, in from_notebook_node nb, resources, **kw) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 384, in from_notebook_node output = self.template.render(nb=nb_copy, resources=resources) File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/jinja2/environment.py", line 1289, in render self.environment.handle_exception() File "/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/jinja2/environment.py", line 924, in handle_exception raise rewrite_traceback_stack(source=source) File "