Read the Docs build information
Build id: 725727
Project: life-epigenetics-methylcheck
Version: latest
Commit: a534d67ae82a101ffba44fe0bb774b4d9eb1ab32
Date: 2021-09-20T20:04:34.144080Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-09-20T20:04:35.638327Z, end-time: 2021-09-20T20:05:07.914785Z, duration: 32, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylcheck.git .
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[rtd-command-info] start-time: 2021-09-20T20:05:08.045359Z, end-time: 2021-09-20T20:05:09.418297Z, duration: 1, 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 <new-branch-name>

HEAD is now at a534d67 Feature/v0.7.6 (#58)

[rtd-command-info] start-time: 2021-09-20T20:05:09.534983Z, end-time: 2021-09-20T20:05:09.620326Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-09-20T20:05:15.007172Z, end-time: 2021-09-20T20:05:19.172525Z, 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: 2021-09-20T20:05:19.281910Z, end-time: 2021-09-20T20:05:20.492490Z, 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 (21.2.4)
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[rtd-command-info] start-time: 2021-09-20T20:05:20.603360Z, end-time: 2021-09-20T20:05:29.676449Z, duration: 9, 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
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=5b1f8756c97d7b1cd04c27d9574c35e2d98b1c53ab4704cc03759362d77897d2
  Stored in directory: /tmp/pip-ephem-wheel-cache-1c39pzw5/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
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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 Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 charset-normalizer-2.0.6 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.2 imagesize-1.2.0 mock-1.0.1 packaging-21.0 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 setuptools-58.0.4 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 urllib3-1.26.6

[rtd-command-info] start-time: 2021-09-20T20:05:29.873994Z, end-time: 2021-09-20T20:05:44.942626Z, duration: 15, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Collecting pillow>=6.2.0
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Requirement already satisfied: requests>=2.0.0 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)) (2.26.0)
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: 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)) (1.2.0)
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Collecting attrs>=17.4.0
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Collecting pyrsistent>=0.14.0
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Collecting ptyprocess>=0.5
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Collecting wcwidth
  Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
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)) (2.0.6)
Requirement already satisfied: urllib3<1.27,>=1.21.1 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)) (1.26.6)
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Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 11)) (1.1.5)
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=d846730f4f61d053fb23cd24829074d98f14315cc7392f8495c8ae42603048b3
  Stored in directory: /tmp/pip-ephem-wheel-cache-7isjvhov/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f
Successfully built m2r
Installing collected packages: zipp, typing-extensions, traitlets, pyrsistent, 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-1.4.3 decorator-5.1.0 defusedxml-0.7.1 entrypoints-0.3 et-xmlfile-1.1.0 importlib-metadata-4.8.1 ipykernel-6.4.1 ipython-7.27.0 ipython-genutils-0.2.0 jedi-0.18.0 joblib-1.0.1 jsonschema-3.2.0 jupyter-client-7.0.3 jupyter-core-4.8.1 jupyterlab-pygments-0.1.2 m2r-0.2.1 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.5.4 nbconvert-6.1.0 nbformat-5.1.3 nbsphinx-0.8.7 nest-asyncio-1.5.1 openpyxl-3.0.8 pandas-1.2.5 pandocfilters-1.5.0 parso-0.8.2 pbr-5.6.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.3.2 prompt-toolkit-3.0.20 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-5.1.0 typing-extensions-3.10.0.2 wcwidth-0.2.5 webencodings-0.5.1 xlsxwriter-3.0.1 zipp-3.5.0

[rtd-command-info] start-time: 2021-09-20T20:05:45.973818Z, end-time: 2021-09-20T20:05:46.048544Z, 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 = '0.7.4'


# -- 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'
]

# 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', '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 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-mouse", "/en/feature-mouse/"),
    ],
    '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': 'a534d67a',
}

# 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/725727/'

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: 2021-09-20T20:05:46.166678Z, end-time: 2021-09-20T20:06:01.887700Z, duration: 15, exit-code: 0
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.
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: 11 added, 0 changed, 0 removed
reading sources... [  9%] README
reading sources... [ 18%] docs/filtering-probes
reading sources... [ 27%] docs/loading-data
reading sources... [ 36%] docs/mds-example
reading sources... [ 45%] docs/quality-control-example
reading sources... [ 54%] docs/release-history
reading sources... [ 63%] docs/research_notebooks/postprocessQC_example
reading sources... [ 72%] docs/research_notebooks/pval
reading sources... [ 81%] docs/research_notebooks/rawQC_example
reading sources... [ 90%] docs/source/modules
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/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)):
Matplotlib is building the font cache; this may take a moment.
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/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-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.load_both'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.combine_mds'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:6: WARNING: toctree references unknown document 'docs/source/_autosummary/methylcheck.assign'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:36: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:57: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:61: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title.

returns:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
WARNING: autodoc: failed to import module 'qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  9%] README
writing output... [ 18%] docs/filtering-probes
writing output... [ 27%] docs/loading-data
writing output... [ 36%] docs/mds-example
writing output... [ 45%] docs/quality-control-example
writing output... [ 54%] docs/release-history
writing output... [ 63%] docs/research_notebooks/postprocessQC_example
writing output... [ 72%] docs/research_notebooks/pval
writing output... [ 81%] docs/research_notebooks/rawQC_example
writing output... [ 90%] docs/source/modules
writing output... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_M_vs_U'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_controls'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.plot_beta_by_type'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.list_problem_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.exclude_sex_control_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.drop_nan_probes'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.sample_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_density_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.mean_beta_compare'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.beta_mds_plot'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.combine_mds'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cumulative_sum_beta_distribution'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.predict'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.get_sex'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst:41:<autosummary>:: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.assign'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.cli'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_pipeline'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.run_qc'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.read_geo'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.load_both'
b'<partial node>':: WARNING: toctree contains reference to nonexisting document 'docs/source/_autosummary/methylcheck.qc_signal_intensity'
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[rtd-command-info] start-time: 2021-09-20T20:06:02.029583Z, end-time: 2021-09-20T20:06:05.655218Z, duration: 3, exit-code: 0
python -m sphinx -T -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:36: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:57: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:61: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title.

returns:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
WARNING: autodoc: failed to import module 'qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
looking for now-outdated files... none found
pickling environment... done
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done
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docs/release-history 
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[rtd-command-info] start-time: 2021-09-20T20:06:05.834513Z, end-time: 2021-09-20T20:06:12.110971Z, duration: 6, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
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.
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: [] 0 added, 1 changed, 0 removed
reading sources... [100%] docs/source/modules

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   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:36: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:57: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:61: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title.

returns:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
WARNING: autodoc: failed to import module 'qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/pval.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/research_notebooks/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
processing methylcheck.tex...index docs/loading-data docs/filtering-probes docs/quality-control-example docs/mds-example docs/source/modules docs/source/_autosummary/methylcheck.cli /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  if toctrees[0].get('maxdepth') > 0:
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.cli'
docs/source/_autosummary/methylcheck.run_pipeline /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_pipeline'
docs/source/_autosummary/methylcheck.run_qc /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.run_qc'
docs/source/_autosummary/methylcheck.read_geo /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.read_geo'
docs/source/_autosummary/methylcheck.load /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/source/modules.rst: WARNING: toctree contains ref to nonexisting file 'docs/source/_autosummary/methylcheck.load'
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The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
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[rtd-command-info] start-time: 2021-09-20T20:06:16.260060Z, end-time: 2021-09-20T20:06:16.339850Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2021-09-20T20:06:16.475610Z, end-time: 2021-09-20T20:06:26.400472Z, duration: 9, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode
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LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi
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Overfull \hbox (975.67087pt too wide) in paragraph at lines 2--241
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[1] [2 <./methylcheck_overview.png>]
Chapter 1.
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Chapter 2.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6]
Chapter 3.
[7] [8]
Chapter 4.

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Overfull \vbox (13.12581pt too high) detected at line 824
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[]\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port
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Chapter 5.
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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
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Writing index file life-epigenetics-methylcheck.idx
(./life-epigenetics-methylcheck.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
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*geometry* driver: auto-detecting
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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./life-epigenetics-methylcheck.out) (./life-epigenetics-methylcheck.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
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(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] (./life-epigenetics-methylcheck.toc
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1]) [2]

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

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                                                  ^^M

Package hyperref Warning: Suppressing empty link on input line 2.


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LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epi
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[1] [2 <./methylcheck_overview.png>]
Chapter 1.
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Chapter 3.
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[10]

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See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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[13]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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Overfull \vbox (13.12581pt too high) detected at line 824
[14]

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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[15] [16]
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[17 <./docs_loading-data_15_1.png>] [18 <./docs_loading-data_17_0.png>]
[19]

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[20]
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[23]
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[26]
Underfull \hbox (badness 10000) in paragraph at lines 1589--1590
[]\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that
 will be saved in the

Underfull \hbox (badness 10000) in paragraph at lines 1589--1590
\T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look
 sim-i-lar to this:

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[]
[27 <./bead_array_report.png>]
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[40 <./docs_quality-control-example_9_19.png>]

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! Package inputenc Error: Unicode char █ (U+2588)
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[]\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port
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[]
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Chapter 5.
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[85]) (./life-epigenetics-methylcheck.aux)

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(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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[12]

! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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! Package inputenc Error: Unicode char █ (U+2588)
(inputenc)                not set up for use with LaTeX.

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[13]

! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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Overfull \vbox (13.12581pt too high) detected at line 824
[14]

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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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[15] [16]
Underfull \vbox (badness 10000) detected at line 1015
[17 <./docs_loading-data_15_1.png>] [18 <./docs_loading-data_17_0.png>]
[19]

! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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! Package inputenc Error: Unicode char █ (U+2588)
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[20]
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Underfull \vbox (badness 10000) detected at line 1407
[23]
Underfull \vbox (badness 10000) detected at line 1426
[24 <./docs_filtering-probes_16_1.png>] [25 <./docs_filtering-probes_17_0.png>]


! Package inputenc Error: Unicode char █ (U+2588)
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[26]
Underfull \hbox (badness 10000) in paragraph at lines 1589--1590
[]\T1/ptm/m/n/10 The color-coded re-sults are con-tained in an ex-cel file that
 will be saved in the

Underfull \hbox (badness 10000) in paragraph at lines 1589--1590
\T1/ptm/m/n/10 same di-rec-tory that was spec-i-fied as an in-put. It will look
 sim-i-lar to this:

Overfull \hbox (283.13986pt too wide) in paragraph at lines 1589--1590
[]
[27 <./bead_array_report.png>]
Underfull \vbox (badness 10000) detected at line 1637
[28 <./docs_quality-control-example_9_0.png>]
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[29 <./docs_quality-control-example_9_1.png>]
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[30 <./docs_quality-control-example_9_3.png>]
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[31 <./docs_quality-control-example_9_4.png>]
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[32 <./docs_quality-control-example_9_5.png>]
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[39 <./docs_quality-control-example_9_16.png>]
Underfull \vbox (badness 10000) detected at line 1888
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[]\T1/ptm/m/n/10 If you want a quick one-line ver-sion with no fur-ther re-port
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Chapter 5.
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[85]) (./life-epigenetics-methylcheck.aux) )
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Output written on life-epigenetics-methylcheck.pdf (89 pages, 2176883 bytes).
Transcript written on life-epigenetics-methylcheck.log.
Latexmk: Index file 'life-epigenetics-methylcheck.idx' was written
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line
  'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23'
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line
  'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.'
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line
  'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 23'
Latexmk: Missing input file: '{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.pngheight=50">`' from line
  'LaTeX Warning: File `{/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_build/doctrees/images/47bf9ad002e200c607c859701ca44dd9574bfece/python3.6}.png"height="50">`' not found on input line 238.'
Latexmk: Log file says output to 'life-epigenetics-methylcheck.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Errors, in force_mode: so I tried finishing targets

[rtd-command-info] start-time: 2021-09-20T20:06:26.561131Z, end-time: 2021-09-20T20:06:26.643570Z, duration: 0, exit-code: 0
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[rtd-command-info] start-time: 2021-09-20T20:06:26.752310Z, end-time: 2021-09-20T20:06:39.153107Z, duration: 12, exit-code: 0
python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
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   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:87: WARNING: Unknown directive type "todo".

.. todo::
    - BUG: custom fields cannot auto detect the -pval- column and this isn't supplied in kwargs
    - DONE: meth_df deal with batches of files
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:4: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.container_to_pkl:17: WARNING: Unexpected section title.

example:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:27: WARNING: Unexpected indentation.
WARNING: autodoc: failed to import module 'qc_report' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:11: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_sex_control_probes:26: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.exclude_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:8: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:13: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.problem_probe_reasons:28: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:22: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:50: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/probes/__init__.py:docstring of methylcheck.probes.list_problem_probes:47: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_density_plot:37: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.sample_plot:1: WARNING: Inline literal start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:4: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:36: WARNING: Unexpected section title.

Options
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:47: WARNING: Unexpected section title.

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:52: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:57: WARNING: Unexpected section title.

notes
-----
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.beta_mds_plot:61: WARNING: Unknown directive type "todo".

.. todo::

    - Reads the manifest file for the array, or at least a list of probe names to exclude/include.
    - manifest_file = pd.read_csv('/Users/nrigby/GitHub/stp-prelim-analysis/working_data/CombinedManifestEPIC.manifest.CoreColumns.csv')[['IlmnID', 'CHR']]
    - probe_names_no_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x not in ['X', 'Y', np.nan]), 'IlmnID'].values
    - probe_names_sex_probes = manifest_file.loc[manifest_file['CHR'].apply(lambda x: x in ['X', 'Y']), 'IlmnID'].values
    df_no_sex_probes = df[probe_names_no_sex_probes]
    df_no_sex_probes.head()
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.mean_beta_compare:3: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:3: WARNING: Unexpected section title or transition.

--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:5: WARNING: Unexpected section title.

how it works:
--------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:18: WARNING: Unexpected section title or transition.

-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:20: WARNING: Unexpected section title.

inputs:
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:25: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:28: WARNING: Unexpected section title.

optional keyword arguments:
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:40: WARNING: Unexpected section title.

analysis parameters:
--------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:47: WARNING: Unexpected section title.

returns:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/samples/__init__.py:docstring of methylcheck.samples.combine_mds:51: WARNING: Unknown directive type "todo".

.. todo::
    - TODO: one dataframe of the retained samples, cutoff box is avg of datasets
    - TODO: each dataset's results as a transformed file
    - default: list of samples retained or excluded
    - option: a list of pyplot subplot objects
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:4: WARNING: Unexpected section title.

input (one of these):
=====================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:23: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:24: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:27: WARNING: Unexpected section title.

optional params:
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.qc_signal_intensity:40: WARNING: Unexpected section title.

returns:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:4: WARNING: Unexpected section title.

input (choose one of these):
============================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:34: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_M_vs_U:36: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:5: WARNING: Unexpected section title.

input:
======
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:11: WARNING: Unexpected section title.

options:
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/qc_plot.py:docstring of methylcheck.qc_plot.plot_controls:14: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/predict/__init__.py:docstring of methylcheck.predict.get_sex:4: WARNING: Unexpected section title.

inputs:
=======
WARNING: autodoc: failed to import module 'p_value_probe_detection' from module 'methylcheck'; the following exception was raised:
No module named 'statsmodels'
WARNING: autodoc: failed to import module 'qc_report.ReportPDF' from module 'methylcheck'; the following exception was raised:
No module named 'methylcheck.qc_report'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load:44: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/load_processed.py:docstring of methylcheck.load_processed.load_both:15: WARNING: Unknown target name: "gse150999".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/read_geo_processed.py:docstring of methylcheck.read_geo_processed.read_geo:19: WARNING: Unknown target name: "matrix".
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