Read the Docs build information
Build id: 429309
Project: life-epigenetics-methylprep
Version: latest
Commit: 89f412daf80101b1240bfe2caa657af3d078eb75
Date: 2020-09-22T21:32:50.912774Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-09-22T21:36:13.744906Z, end-time: 2020-09-22T21:36:24.653133Z, duration: 10, 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: 2020-09-22T21:36:25.401673Z, end-time: 2020-09-22T21:36:26.257100Z, 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 89f412d Revert "Allow processing IDAT files without decompression (#68)" (#70)

[rtd-command-info] start-time: 2020-09-22T21:36:27.323578Z, end-time: 2020-09-22T21:36:27.396745Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-09-22T21:36:33.159830Z, end-time: 2020-09-22T21:36:43.578494Z, duration: 10, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
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: 2020-09-22T21:36:43.968335Z, end-time: 2020-09-22T21:36:44.665443Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (20.2.3)

[rtd-command-info] start-time: 2020-09-22T21:36:44.808026Z, end-time: 2020-09-22T21:36:53.494899Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 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<1.1
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  Attempting uninstall: setuptools
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Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10

[rtd-command-info] start-time: 2020-09-22T21:36:53.614091Z, end-time: 2020-09-22T21:37:19.637458Z, duration: 26, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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  Building wheel for PyYAML (setup.py): finished with status 'done'
  Created wheel for PyYAML: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44619 sha256=acdef261628b3c037fe165ec701e48ec612bc7d05a4aeb334af92b8e6e76c75d
  Stored in directory: /tmp/pip-ephem-wheel-cache-cubiyvmj/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653
  Building wheel for pandocfilters (setup.py): started
  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7855 sha256=f276733c24f8790f7da3fc2a19532aa9030280fe5ccfdbd65b63698b27d4ca18
  Stored in directory: /tmp/pip-ephem-wheel-cache-cubiyvmj/wheels/63/99/01/9fe785b86d1e091a6b2a61e06ddb3d8eb1bc9acae5933d4740
  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115293 sha256=840f8a8fb6f55cc1bfb5779b71d7664b562d7acc0546b912f3eb330d0fbb9ff0
  Stored in directory: /tmp/pip-ephem-wheel-cache-cubiyvmj/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5
  Building wheel for tornado (setup.py): started
  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.4-cp37-cp37m-linux_x86_64.whl size=428567 sha256=53a2073b7c5cf17815c2aa8fd133b15aa0caef35f2462b742a6ace91637482c2
  Stored in directory: /tmp/pip-ephem-wheel-cache-cubiyvmj/wheels/7d/14/fa/d88fb5da77d813ea0ffca38a2ab2a052874e9e1142bad0b348
Successfully built m2r bs4 PyYAML pandocfilters pyrsistent tornado
Installing collected packages: numpy, python-dateutil, pandas, scipy, patsy, statsmodels, iniconfig, toml, py, zipp, importlib-metadata, pluggy, more-itertools, attrs, pytest, coverage, PyYAML, python-coveralls, pbr, sphinxcontrib-apidoc, mistune, m2r, pyrsistent, jsonschema, ipython-genutils, traitlets, jupyter-core, nbformat, pandocfilters, webencodings, bleach, defusedxml, jupyterlab-pygments, testpath, pyzmq, tornado, jupyter-client, nest-asyncio, async-generator, nbclient, entrypoints, nbconvert, nbsphinx, tqdm, soupsieve, beautifulsoup4, bs4, lxml
Successfully installed PyYAML-5.3.1 async-generator-1.10 attrs-20.2.0 beautifulsoup4-4.9.1 bleach-3.2.1 bs4-0.0.1 coverage-5.3 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-1.7.0 iniconfig-1.0.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.6.3 jupyterlab-pygments-0.1.1 lxml-4.5.2 m2r-0.2.1 mistune-0.8.4 more-itertools-8.5.0 nbclient-0.5.0 nbconvert-6.0.5 nbformat-5.0.7 nbsphinx-0.7.1 nest-asyncio-1.4.0 numpy-1.19.2 pandas-1.1.2 pandocfilters-1.4.2 patsy-0.5.1 pbr-5.5.0 pluggy-0.13.1 py-1.9.0 pyrsistent-0.17.3 pytest-6.0.2 python-coveralls-2.9.3 python-dateutil-2.8.1 pyzmq-19.0.2 scipy-1.5.2 soupsieve-2.0.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.12.0 testpath-0.4.4 toml-0.10.1 tornado-6.0.4 tqdm-4.49.0 traitlets-5.0.4 webencodings-0.5.1 zipp-3.2.0

[rtd-command-info] start-time: 2020-09-22T21:37:21.208644Z, end-time: 2020-09-22T21:37:21.286818Z, 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 = '2019, Life Epigenetics'
author = 'Life Epigenetics'

# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = '1.0'


# -- 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 = 'methylpredoc'


# -- 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, '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
#


import importlib
import sys
import os.path
from six import string_types

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/"),
    ],
    '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': '89f412da',
}




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")

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: 2020-09-22T21:37:21.662672Z, end-time: 2020-09-22T21:37:26.872392Z, duration: 5, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -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 [readthedocs]: targets for 12 source files that are out of date
updating environment: 12 added, 0 changed, 0 removed
reading sources... [  8%] README
reading sources... [ 16%] docs/README
reading sources... [ 25%] docs/cli
reading sources... [ 33%] docs/example_download
reading sources... [ 41%] docs/faq
reading sources... [ 50%] docs/how_to_add_new_array_type
reading sources... [ 58%] docs/installation
reading sources... [ 66%] docs/methylprep_tutorial
reading sources... [ 75%] docs/package
reading sources... [ 83%] docs/release-history
reading sources... [ 91%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:216: 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/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/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/processing/pipeline.py:docstring of methylprep.processing.SampleDataContainer:9: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.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/processing/__init__.py:docstring of methylprep.processing.read_geo:27: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/download/__init__.py:docstring of methylprep.download.pipeline_find_betas_any_source:34: WARNING: Bullet 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.read_geo:19: WARNING: Unknown target name: "matrix".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.read_geo:19: WARNING: Unknown target name: "matrix".
README.md:216: 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.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/cli.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree
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[rtd-command-info] start-time: 2020-09-22T21:37:27.499823Z, end-time: 2020-09-22T21:37:31.297883Z, duration: 3, exit-code: 0
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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
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     - ``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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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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
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``get_manifest``
~~~~~~~~~~~~~~~~~~~~
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``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
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README.md:216: 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.
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