Read the Docs build information
Build id: 671159
Project: life-epigenetics-methylprep
Version: latest
Commit: 34747bdfb9026259fb5a62be94f34b2082408dac
Date: 2021-07-06T22:52:22.566393Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-07-06T22:52:24.112806Z, end-time: 2021-07-06T22:52:44.612619Z, duration: 20, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylprep.git .
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[rtd-command-info] start-time: 2021-07-06T22:52:44.758820Z, end-time: 2021-07-06T22:52:45.560808Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 34747bd Update README.md

[rtd-command-info] start-time: 2021-07-06T22:52:45.669869Z, end-time: 2021-07-06T22:52:45.739185Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-07-06T22:52:45.845700Z, end-time: 2021-07-06T22:52:45.907082Z, duration: 0, exit-code: 0
git rev-parse HEAD
34747bdfb9026259fb5a62be94f34b2082408dac

[rtd-command-info] start-time: 2021-07-06T22:52:48.787673Z, end-time: 2021-07-06T22:52:53.798678Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-07-06T22:52:53.910870Z, end-time: 2021-07-06T22:52:55.033675Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
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[rtd-command-info] start-time: 2021-07-06T22:52:55.232729Z, end-time: 2021-07-06T22:53:04.109522Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2
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Building wheels for collected packages: mock, future
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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.
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[rtd-command-info] start-time: 2021-07-06T22:53:04.249910Z, end-time: 2021-07-06T22:53:15.559704Z, duration: 11, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.1.5)
Building wheels for collected packages: m2r, pandocfilters, bs4
  Building wheel for m2r (setup.py): started
  Building wheel for m2r (setup.py): finished with status 'done'
  Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10475 sha256=0722aff3fe16ac40919fa79bef5b88989d9e757edb397362921c1ed32d95d839
  Stored in directory: /tmp/pip-ephem-wheel-cache-cgi7oa3s/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f
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  Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=8006 sha256=d4e7198611d37d2aa5747b025e1b188117c845b049e01fc2900d79689b80f9fc
  Stored in directory: /tmp/pip-ephem-wheel-cache-cgi7oa3s/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000
  Building wheel for bs4 (setup.py): started
  Building wheel for bs4 (setup.py): finished with status 'done'
  Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1271 sha256=295b11c9e3ecfe3f2c2750113412da8029a1bec49549a078875d971bf4477a84
  Stored in directory: /tmp/pip-ephem-wheel-cache-cgi7oa3s/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca
Successfully built m2r pandocfilters bs4
Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, soupsieve, pandocfilters, nbclient, mistune, jupyterlab-pygments, entrypoints, defusedxml, bleach, toml, PyYAML, py, pluggy, pbr, patsy, nbconvert, iniconfig, coverage, beautifulsoup4, tqdm, statsmodels, sphinxcontrib-apidoc, python-coveralls, pytest, nbsphinx, m2r, lxml, bs4
Successfully installed PyYAML-5.4.1 async-generator-1.10 attrs-21.2.0 beautifulsoup4-4.9.3 bleach-3.3.0 bs4-0.0.1 coverage-5.5 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-4.6.1 iniconfig-1.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 lxml-4.6.3 m2r-0.2.1 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.1.0 nbformat-5.1.3 nbsphinx-0.8.6 nest-asyncio-1.5.1 pandocfilters-1.4.3 patsy-0.5.1 pbr-5.6.0 pluggy-0.13.1 py-1.10.0 pyrsistent-0.18.0 pytest-6.2.4 python-coveralls-2.9.3 pyzmq-22.1.0 soupsieve-2.2.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.12.2 testpath-0.5.0 toml-0.10.2 tornado-6.1 tqdm-4.61.2 traitlets-5.0.5 typing-extensions-3.10.0.0 webencodings-0.5.1 zipp-3.5.0

[rtd-command-info] start-time: 2021-07-06T22:53:16.344198Z, end-time: 2021-07-06T22:53:16.409855Z, duration: 0, exit-code: 0
git rev-parse HEAD
34747bdfb9026259fb5a62be94f34b2082408dac

[rtd-command-info] start-time: 2021-07-06T22:53:16.652831Z, end-time: 2021-07-06T22:53:16.717759Z, duration: 0, exit-code: 0
cat conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'methylprep'
copyright = '2021, FOXO Technologies, inc.'
author = 'FOXO Technologies, inc.'

# The short X.Y version
version = '1.4'
# The full version, including alpha/beta/rc tags
release = '1.4.2'


# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinxcontrib.apidoc',
    'm2r',
    'nbsphinx',
    'sphinx.ext.autosummary',
    'sphinx.ext.doctest',
    'sphinx.ext.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages',
]

# instead of CLI "sphinx-autodoc . _build/html" you write this
apidoc_module_dir = '.'
apidoc_output_dir = '_sphinx_build'
apidoc_excluded_paths = ['tests']
apidoc_separate_modules = False

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_sphinx_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
source_suffix = ['.rst', '.md']
# source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

todo_include_todos = True

# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme =  'sphinx_rtd_theme' #'alabaster', 'nature'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_sphinx_static']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'methylpredoc'


# -- Options for LaTeX output ------------------------------------------------

latex_engine = 'xelatex'
#latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
#}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'methylprep.tex', 'methylprep Documentation',
     'Life Epigenetics', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'methylprep', 'methylprep Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'methylprep', 'methylprep Documentation',
     author, 'methylprep', 'One line description of project.',
     'Miscellaneous'),
]


# -- Extension configuration -------------------------------------------------




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file should't rely on extra depencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("html", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ("epub", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'life-epigenetics-methylprep',
    'name': u'methylprep',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'FOXOBioScience',
    'proxied_api_host': '/_',
    'github_repo': 'methylprep',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '34747bdf',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/life-epigenetics-methylprep/builds/671159/'

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: 2021-07-06T22:53:16.831011Z, end-time: 2021-07-06T22:53:37.928168Z, duration: 21, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.download.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 14 source files that are out of date
updating environment: 14 added, 0 changed, 0 removed
reading sources... [  7%] README
reading sources... [ 14%] docs/README
reading sources... [ 21%] docs/cli
reading sources... [ 28%] docs/debug_notebooks/float16_error
reading sources... [ 35%] docs/debug_notebooks/improving idat.py
reading sources... [ 42%] docs/example_download
reading sources... [ 50%] docs/faq
reading sources... [ 57%] docs/how_to_add_new_array_type
reading sources... [ 64%] docs/installation
reading sources... [ 71%] docs/methylprep_tutorial
reading sources... [ 78%] docs/package
reading sources... [ 85%] docs/release-history
reading sources... [ 92%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:271: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:322: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 2 does not contain the same number of items as row 1 (3 vs 4).

.. list-table::
   :header-rows: 1

   * - Argument
     - Type
     - Default
     - Description
   * - -h, --help
     -
     - show this help message and exit
   * -   -d , --data_dir
     - ``str``
     - [required path]
     - path to where the data series will be saved. Folder must exist already.
   * -   -i ID, --id ID
     - ``str``
     - [required ID]
     - The dataset's reference ID (Starts with ``GSE`` for GEO or ``E-MTAB-`` for ArrayExpress)
   * -   -l LIST, --list LIST
     - ``multiple strings``
     - optional
     - List of series IDs (can be either GEO or ArrayExpress), for partial downloading
   * -   -o, --dict_only
     - ``True``
     - pass flag only
     - If passed, will only create dictionaries and not process any samples
   * -   -b BATCH_SIZE, --batch_size BATCH_SIZE
     - ``int``
     - optional
     - Number of samples to process at a time, 100 by default.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/debug_notebooks/float16_error.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/debug_notebooks/improving idat.py.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:203: WARNING: Title level inconsistent:

list of code edits by file in methylprep for mouse support
----------------------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:266: WARNING: Title level inconsistent:

testing
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:278: WARNING: Title level inconsistent:

other bugs discovered:
~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:285: WARNING: Title level inconsistent:

data flow through methylprep
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:124: WARNING: Unknown target name: "ctl".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylcheck".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:374: WARNING: Title level inconsistent:

Visual Filtering Functions
~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:161: WARNING: Title level inconsistent:

``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:191: WARNING: Title level inconsistent:

``get_manifest``
~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:225: WARNING: Title level inconsistent:

``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:27: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:92: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:105: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:106: WARNING: Block quote ends without a blank line; unexpected unindent.
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.. list-table::
   :header-rows: 1

   * - Argument
     - Type
     - Default
     - Description
   * - -h, --help
     -
     - show this help message and exit
   * -   -d , --data_dir
     - ``str``
     - [required path]
     - path to where the data series will be saved. Folder must exist already.
   * -   -i ID, --id ID
     - ``str``
     - [required ID]
     - The dataset's reference ID (Starts with ``GSE`` for GEO or ``E-MTAB-`` for ArrayExpress)
   * -   -l LIST, --list LIST
     - ``multiple strings``
     - optional
     - List of series IDs (can be either GEO or ArrayExpress), for partial downloading
   * -   -o, --dict_only
     - ``True``
     - pass flag only
     - If passed, will only create dictionaries and not process any samples
   * -   -b BATCH_SIZE, --batch_size BATCH_SIZE
     - ``int``
     - optional
     - Number of samples to process at a time, 100 by default.
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 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

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Chapter 1.
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Chapter 1.
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Chapter 1.
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