Read the Docs build information
Build id: 248292
Project: life-epigenetics-methylprep
Version: latest
Commit: 8840d1acba4349a4a486382c10341522e1f9fce2
Date: 2019-10-08T15:54:24.131429Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-10-08T16:03:35.498956Z, end-time: 2019-10-08T16:03:40.541065Z, duration: 5, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylprep.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-10-08T16:03:40.824231Z, end-time: 2019-10-08T16:03:42.116293Z, 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 8840d1a v1.1.5 geo downloader fixes and documentation fixes (#29)

[rtd-command-info] start-time: 2019-10-08T16:03:42.206455Z, end-time: 2019-10-08T16:03:42.237686Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-10-08T16:03:43.667327Z, end-time: 2019-10-08T16:03:48.390557Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.7.1'
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: 2019-10-08T16:03:48.482010Z, end-time: 2019-10-08T16:03:51.838375Z, duration: 3, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl (1.4MB)
Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-19.2.3

[rtd-command-info] start-time: 2019-10-08T16:03:51.937228Z, end-time: 2019-10-08T16:04:04.227123Z, duration: 12, exit-code: 0
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Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, chardet, urllib3, idna, certifi, requests, sphinxcontrib-websupport, six, pytz, babel, MarkupSafe, Jinja2, imagesize, pyparsing, packaging, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 40.6.3
    Uninstalling setuptools-40.6.3:
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Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.7.0 certifi-2019.9.11 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.17.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.2 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.3 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 setuptools-41.0.1 six-1.12.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.6

[rtd-command-info] start-time: 2019-10-08T16:04:04.308423Z, end-time: 2019-10-08T16:04:35.110902Z, duration: 30, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip -r requirements.txt
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Collecting zipp>=0.5 (from importlib-metadata>=0.12; python_version < "3.8"->pytest->-r requirements.txt (line 5))
  Downloading https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from packaging->pytest->-r requirements.txt (line 5)) (2.4.2)
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Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
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  Downloading https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
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Installing collected packages: numpy, python-dateutil, pandas, scipy, patsy, statsmodels, py, wcwidth, attrs, more-itertools, zipp, importlib-metadata, atomicwrites, pluggy, pytest, coverage, coveralls-python, pbr, sphinxcontrib-apidoc, mistune, m2r, ipython-genutils, decorator, traitlets, jupyter-core, pyrsistent, jsonschema, nbformat, testpath, pandocfilters, defusedxml, entrypoints, webencodings, bleach, nbconvert, nbsphinx, tqdm, soupsieve, beautifulsoup4, bs4, lxml
Successfully installed atomicwrites-1.3.0 attrs-19.2.0 beautifulsoup4-4.8.1 bleach-3.1.0 bs4-0.0.1 coverage-4.5.4 coveralls-python-0.0.1 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-0.23 ipython-genutils-0.2.0 jsonschema-3.0.2 jupyter-core-4.6.0 lxml-4.4.1 m2r-0.2.1 mistune-0.8.4 more-itertools-7.2.0 nbconvert-5.6.0 nbformat-4.4.0 nbsphinx-0.4.3 numpy-1.17.2 pandas-0.25.1 pandocfilters-1.4.2 patsy-0.5.1 pbr-5.4.3 pluggy-0.13.0 py-1.8.0 pyrsistent-0.15.4 pytest-5.2.1 python-dateutil-2.8.0 scipy-1.3.1 soupsieve-1.9.4 sphinxcontrib-apidoc-0.3.0 statsmodels-0.10.1 testpath-0.4.2 tqdm-4.36.1 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1 zipp-0.6.0

[rtd-command-info] start-time: 2019-10-08T16:04:35.803145Z, end-time: 2019-10-08T16:04:36.153172Z, 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'
]

# 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://media.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://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("renamed", "/en/renamed/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/life-epigenetics-methylprep/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'life-epigenetics-methylprep',
    'name': u'methylprep',
    'rtd_language': u'en',
    'programming_language': u'words',
    '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': 'LifeEGX',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '8840d1ac',
}




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'

[rtd-command-info] start-time: 2019-10-08T16:04:36.234123Z, end-time: 2019-10-08T16:04:40.703219Z, duration: 4, exit-code: 0
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Filtering by Probes
~~~~~~~~~~~~~~~~~~~
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Visual Filtering Functions
~~~~~~~~~~~~~~~~~~~~~~~~~~
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methylprep package
================
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methylprep.cli module
-------------------
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methylprep.cli module
-------------------
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methylprep.arrays package
=======================
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methylprep.arrays.arrays module
-----------------------------
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methylprep.arrays.arrays module
-----------------------------
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methylprep.arrays.controls module
-------------------------------
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methylprep.arrays.controls module
-------------------------------
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methylprep.arrays.manifest module
-------------------------------
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methylprep.arrays.manifest module
-------------------------------
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methylprep.arrays.probes module
-----------------------------
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methylprep.arrays.probes module
-----------------------------
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methylprep.preprocess package
===========================
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methylprep.preprocess.idat module
-------------------------------
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methylprep.preprocess.idat module
-------------------------------
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methylprep.preprocess.meth\_dataset module
----------------------------------------
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methylprep.preprocess.meth\_dataset module
----------------------------------------
WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised:
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methylprep.preprocess.noob module
-------------------------------
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methylprep.preprocess.noob module
-------------------------------
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methylprep.preprocess.pipeline module
-----------------------------------
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methylprep.preprocess.pipeline module
-----------------------------------
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methylprep.preprocess.raw\_dataset module
---------------------------------------
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methylprep.preprocess.raw\_dataset module
---------------------------------------
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methylprep.preprocess.utils module
--------------------------------
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methylprep.preprocess.utils module
--------------------------------
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methylprep.samples package
========================
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methylprep.samples.sample module
------------------------------
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methylprep.samples.sample module
------------------------------
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methylprep.samples.sample\_sheet module
-------------------------------------
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methylprep.samples.sample\_sheet module
-------------------------------------
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methylprep.utils package
======================
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methylprep.utils.data module
--------------------------
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methylprep.utils.data module
--------------------------
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methylprep.utils.decorators module
--------------------------------
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methylprep.utils.decorators module
--------------------------------
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methylprep.utils.files module
---------------------------
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methylprep.utils.files module
---------------------------
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Examples:
--------
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Examples:
--------
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Examples:
--------
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Examples:
--------
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Welcome to methylprep's documentation!
====================================
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Filtering by Probes
~~~~~~~~~~~~~~~~~~~
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Visual Filtering Functions
~~~~~~~~~~~~~~~~~~~~~~~~~~
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methylprep package
================
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methylprep.cli module
-------------------
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methylprep.cli module
-------------------
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methylprep.arrays package
=======================
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methylprep.arrays.arrays module
-----------------------------
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methylprep.arrays.arrays module
-----------------------------
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methylprep.arrays.controls module
-------------------------------
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methylprep.arrays.controls module
-------------------------------
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methylprep.arrays.manifest module
-------------------------------
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methylprep.arrays.manifest module
-------------------------------
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methylprep.arrays.probes module
-----------------------------
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methylprep.arrays.probes module
-----------------------------
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methylprep.preprocess package
===========================
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methylprep.preprocess.idat module
-------------------------------
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methylprep.preprocess.idat module
-------------------------------
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methylprep.preprocess.meth\_dataset module
----------------------------------------
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methylprep.preprocess.meth\_dataset module
----------------------------------------
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methylprep.preprocess.noob module
-------------------------------
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methylprep.preprocess.noob module
-------------------------------
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methylprep.preprocess.pipeline module
-----------------------------------
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methylprep.preprocess.pipeline module
-----------------------------------
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methylprep.preprocess.raw\_dataset module
---------------------------------------
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methylprep.preprocess.raw\_dataset module
---------------------------------------
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methylprep.preprocess.utils module
--------------------------------
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methylprep.preprocess.utils module
--------------------------------
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methylprep.samples package
========================
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methylprep.samples.sample module
------------------------------
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methylprep.samples.sample module
------------------------------
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methylprep.samples.sample\_sheet module
-------------------------------------
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methylprep.samples.sample\_sheet module
-------------------------------------
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methylprep.utils package
======================
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methylprep.utils.data module
--------------------------
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methylprep.utils.data module
--------------------------
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methylprep.utils.decorators module
--------------------------------
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methylprep.utils.decorators module
--------------------------------
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methylprep.utils.files module
---------------------------
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methylprep.utils.files module
---------------------------
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Examples:
--------
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Examples:
--------
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Examples:
--------
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Examples:
--------
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Welcome to methylprep's documentation!
====================================
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