Read the Docs build information
Build id: 256417
Project: life-epigenetics-methylcheck
Version: latest
Commit: 768860994101839c812a979bdb4f7fe9b6b03284
Date: 2019-11-05T16:24:19.917066Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-11-05T16:31:59.944968Z, end-time: 2019-11-05T16:32:06.971343Z, duration: 7, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylcheck.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-11-05T16:32:07.752509Z, end-time: 2019-11-05T16:32:08.933703Z, 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 7688609 fixed bug (#24)

[rtd-command-info] start-time: 2019-11-05T16:32:09.013063Z, end-time: 2019-11-05T16:32:09.033860Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-11-05T16:32:10.156869Z, end-time: 2019-11-05T16:32:14.087779Z, duration: 3, 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-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: 2019-11-05T16:32:14.191752Z, end-time: 2019-11-05T16:32:17.100538Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip pip
Collecting pip
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Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-19.3.1

[rtd-command-info] start-time: 2019-11-05T16:32:17.197523Z, end-time: 2019-11-05T16:32:31.048785Z, duration: 13, exit-code: 0
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Building wheels for collected packages: mock, future
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Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pyparsing, packaging, snowballstemmer, chardet, idna, urllib3, certifi, requests, imagesize, MarkupSafe, Jinja2, sphinxcontrib-websupport, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 40.6.3
    Uninstalling setuptools-40.6.3:
      Successfully uninstalled setuptools-40.6.3
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-0.18.2 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.2 pillow-5.4.1 pyparsing-2.4.3 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: 2019-11-05T16:32:31.141515Z, end-time: 2019-11-05T16:33:08.082252Z, duration: 36, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/.cache/pip -r requirements.txt
Collecting numpy
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Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 10)) (1.8.5)
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Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 2)) (2019.3)
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Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from matplotlib->-r requirements.txt (line 4)) (2.4.3)
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Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from python-coveralls->-r requirements.txt (line 9)) (1.12.0)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (2.3.1)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (0.14)
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Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (2.10.3)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from sphinx>=1.4->-r requirements.txt (line 10)) (0.7.12)
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Collecting pbr
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Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (2.8)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (2019.9.11)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from requests->python-coveralls->-r requirements.txt (line 9)) (1.25.6)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.4->-r requirements.txt (line 10)) (1.1.1)
Collecting ipython-genutils
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Collecting pyzmq>=13
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Collecting pickleshare
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Building wheels for collected packages: m2r, PyYAML, tornado, backcall, pandocfilters, pyrsistent
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Successfully built m2r PyYAML tornado backcall pandocfilters pyrsistent
Installing collected packages: numpy, python-dateutil, pandas, scipy, cycler, kiwisolver, matplotlib, seaborn, more-itertools, atomicwrites, wcwidth, zipp, importlib-metadata, pluggy, py, attrs, pytest, coverage, PyYAML, python-coveralls, pbr, sphinxcontrib-apidoc, mistune, m2r, tqdm, tornado, ipython-genutils, decorator, traitlets, jupyter-core, pyzmq, jupyter-client, parso, jedi, ptyprocess, pexpect, backcall, pickleshare, prompt-toolkit, ipython, ipykernel, pyrsistent, jsonschema, nbformat, webencodings, bleach, testpath, entrypoints, pandocfilters, defusedxml, nbconvert, nbsphinx
Successfully installed PyYAML-5.1.2 atomicwrites-1.3.0 attrs-19.3.0 backcall-0.1.0 bleach-3.1.0 coverage-4.5.4 cycler-0.10.0 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-0.23 ipykernel-5.1.3 ipython-7.9.0 ipython-genutils-0.2.0 jedi-0.15.1 jsonschema-3.1.1 jupyter-client-5.3.4 jupyter-core-4.6.1 kiwisolver-1.1.0 m2r-0.2.1 matplotlib-3.1.1 mistune-0.8.4 more-itertools-7.2.0 nbconvert-5.6.1 nbformat-4.4.0 nbsphinx-0.4.3 numpy-1.17.3 pandas-0.25.3 pandocfilters-1.4.2 parso-0.5.1 pbr-5.4.3 pexpect-4.7.0 pickleshare-0.7.5 pluggy-0.13.0 prompt-toolkit-2.0.10 ptyprocess-0.6.0 py-1.8.0 pyrsistent-0.15.5 pytest-5.2.2 python-coveralls-2.9.3 python-dateutil-2.8.1 pyzmq-18.1.0 scipy-1.3.1 seaborn-0.9.0 sphinxcontrib-apidoc-0.3.0 testpath-0.4.4 tornado-6.0.3 tqdm-4.37.0 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1 zipp-0.6.0

[rtd-command-info] start-time: 2019-11-05T16:33:08.180265Z, end-time: 2019-11-05T16:33:12.802586Z, duration: 4, exit-code: 0
python /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/setup.py install --force
running install
running bdist_egg
running egg_info
creating methylcheck.egg-info
writing methylcheck.egg-info/PKG-INFO
writing dependency_links to methylcheck.egg-info/dependency_links.txt
writing entry points to methylcheck.egg-info/entry_points.txt
writing requirements to methylcheck.egg-info/requires.txt
writing top-level names to methylcheck.egg-info/top_level.txt
writing manifest file 'methylcheck.egg-info/SOURCES.txt'
reading manifest file 'methylcheck.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README.rst'
writing manifest file 'methylcheck.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/methylcheck
copying methylcheck/__init__.py -> build/lib/methylcheck
copying methylcheck/cli.py -> build/lib/methylcheck
copying methylcheck/postprocessQC.py -> build/lib/methylcheck
copying methylcheck/__main__.py -> build/lib/methylcheck
copying methylcheck/QCreport.py -> build/lib/methylcheck
copying methylcheck/filters.py -> build/lib/methylcheck
copying methylcheck/rawQC.py -> build/lib/methylcheck
creating build/lib/methylcheck/data_files
copying methylcheck/data_files/450k_control.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/lib/methylcheck/data_files
copying methylcheck/data_files/450k_sex.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC+_control.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC+_sex.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC_control.npy -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC_polymorphic_crossRxtve_probes.csv.gz -> build/lib/methylcheck/data_files
copying methylcheck/data_files/EPIC_sex.npy -> build/lib/methylcheck/data_files
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/__init__.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/cli.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/postprocessQC.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/__main__.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/QCreport.py -> build/bdist.linux-x86_64/egg/methylcheck
copying build/lib/methylcheck/filters.py -> build/bdist.linux-x86_64/egg/methylcheck
creating build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/450k_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/EPIC_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/450k_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/EPIC+_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/EPIC+_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/450k_control.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/EPIC_sex.npy -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/data_files/EPIC_polymorphic_crossRxtve_probes.csv.gz -> build/bdist.linux-x86_64/egg/methylcheck/data_files
copying build/lib/methylcheck/rawQC.py -> build/bdist.linux-x86_64/egg/methylcheck
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/cli.py to cli.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/postprocessQC.py to postprocessQC.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/QCreport.py to QCreport.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/filters.py to filters.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylcheck/rawQC.py to rawQC.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying methylcheck.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylcheck.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylcheck.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylcheck.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylcheck.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylcheck.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/methylcheck-0.2.5-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing methylcheck-0.2.5-py3.7.egg
Copying methylcheck-0.2.5-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Adding methylcheck 0.2.5 to easy-install.pth file
Installing methylcheck-cli script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/methylcheck-0.2.5-py3.7.egg
Processing dependencies for methylcheck==0.2.5
Searching for scikit-learn
Reading https://pypi.org/simple/scikit-learn/
Downloading https://files.pythonhosted.org/packages/9f/c5/e5267eb84994e9a92a2c6a6ee768514f255d036f3c8378acfa694e9f2c99/scikit_learn-0.21.3-cp37-cp37m-manylinux1_x86_64.whl#sha256=8d319b71c449627d178f21c57614e21747e54bb3fc9602b6f42906c3931aa320
Best match: scikit-learn 0.21.3
Processing scikit_learn-0.21.3-cp37-cp37m-manylinux1_x86_64.whl
Installing scikit_learn-0.21.3-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.21.3-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt
Adding scikit-learn 0.21.3 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/scikit_learn-0.21.3-py3.7-linux-x86_64.egg
Searching for joblib>=0.11
Reading https://pypi.org/simple/joblib/
Downloading https://files.pythonhosted.org/packages/8f/42/155696f85f344c066e17af287359c9786b436b1bf86029bb3411283274f3/joblib-0.14.0-py2.py3-none-any.whl#sha256=006108c7576b3eb6c5b27761ddbf188eb6e6347696325ab2027ea1ee9a4b922d
Best match: joblib 0.14.0
Processing joblib-0.14.0-py2.py3-none-any.whl
Installing joblib-0.14.0-py2.py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Adding joblib 0.14.0 to easy-install.pth file

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages/joblib-0.14.0-py3.7.egg
Searching for tqdm==4.37.0
Best match: tqdm 4.37.0
Adding tqdm 4.37.0 to easy-install.pth file
Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for matplotlib==3.1.1
Best match: matplotlib 3.1.1
Adding matplotlib 3.1.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for seaborn==0.9.0
Best match: seaborn 0.9.0
Adding seaborn 0.9.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for pandas==0.25.3
Best match: pandas 0.25.3
Adding pandas 0.25.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for numpy==1.17.3
Best match: numpy 1.17.3
Adding numpy 1.17.3 to easy-install.pth file
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.3.1
Best match: scipy 1.3.1
Adding scipy 1.3.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for kiwisolver==1.1.0
Best match: kiwisolver 1.1.0
Adding kiwisolver 1.1.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for pyparsing==2.4.3
Best match: pyparsing 2.4.3
Adding pyparsing 2.4.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for cycler==0.10.0
Best match: cycler 0.10.0
Adding cycler 0.10.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
Adding python-dateutil 2.8.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for pytz==2019.3
Best match: pytz 2019.3
Adding pytz 2019.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for setuptools==41.0.1
Best match: setuptools 41.0.1
Adding setuptools 41.0.1 to easy-install.pth file
Installing easy_install script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin
Installing easy_install-3.6 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Searching for six==1.12.0
Best match: six 1.12.0
Adding six 1.12.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for methylcheck==0.2.5

[rtd-command-info] start-time: 2019-11-05T16:33:13.510442Z, end-time: 2019-11-05T16:33:13.875348Z, 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 = '2019, Life Epigenetics'
author = 'Life Epigenetics'

# The short X.Y version
version = '0.2'
# The full version, including alpha/beta/rc tags
release = '0.2'


# -- 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'
]

# 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 = True

# 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',
     '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, '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
#


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/"),
    ],
    'downloads': [ 
    ("pdf", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/pdf/latest/"),
    ("html", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/htmlzip/latest/"),
    ("epub", "//readthedocs.com/projects/life-epigenetics-methylcheck/downloads/epub/latest/"),
    ],
    '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': 'LifeEGX',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '76886099',
}




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: 2019-11-05T16:33:13.999158Z, end-time: 2019-11-05T16:33:27.357839Z, duration: 13, 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-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.QCreport.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.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/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 10 source files that are out of date
updating environment: 10 added, 0 changed, 0 removed
reading sources... [ 10%] README
reading sources... [ 20%] docs/another-methylcheck-qc-example
reading sources... [ 30%] docs/demo-methylprep-to-methylcheck-example
reading sources... [ 40%] docs/demo_using_matched_meta_data
reading sources... [ 50%] docs/filtering_probes
reading sources... [ 60%] docs/methylprep_methylcheck_example
reading sources... [ 70%] docs/postprocessQC_example
reading sources... [ 80%] docs/rawQC_example
reading sources... [ 90%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
looking for now-outdated files... none found
pickling environment... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title.

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

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title.

combine (or segment) datasets how it works
------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title.

inputs
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title.

optional keyword arguments
--------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title.

analysis parameters
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short.

returns
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title.

returns
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
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/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
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dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 34 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-11-05T16:33:27.505626Z, end-time: 2019-11-05T16:33:33.992280Z, duration: 6, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
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.QCreport.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.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/modules.rst.
building [mo]: targets for 0 po files that are out of date
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updating environment: 10 added, 0 changed, 0 removed
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reading sources... [ 70%] docs/postprocessQC_example
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reading sources... [ 90%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title.

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

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title.

combine (or segment) datasets how it works
------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title.

inputs
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title.

optional keyword arguments
--------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title.

analysis parameters
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short.

returns
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title.

returns
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:39: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
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/postprocessQC_example.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... docs/demo-methylprep-to-methylcheck-example docs/filtering_probes docs/methylprep_methylcheck_example docs/another-methylcheck-qc-example docs/demo_using_matched_meta_data docs/source/methylcheck 
writing... done
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done
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copying extra files... done
dumping object inventory... done
build succeeded, 34 warnings.

The HTML page is in _build/localmedia.

[rtd-command-info] start-time: 2019-11-05T16:33:34.145242Z, end-time: 2019-11-05T16:33:45.212433Z, duration: 11, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
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.QCreport.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.cli.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.filters.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.postprocessQC.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/_sphinx_build/methylcheck.rawQC.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/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 10 added, 0 changed, 0 removed
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reading sources... [ 20%] docs/another-methylcheck-qc-example
reading sources... [ 30%] docs/demo-methylprep-to-methylcheck-example
reading sources... [ 40%] docs/demo_using_matched_meta_data
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reading sources... [ 60%] docs/methylprep_methylcheck_example
reading sources... [ 70%] docs/postprocessQC_example
reading sources... [ 80%] docs/rawQC_example
reading sources... [ 90%] docs/source/methylcheck
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/filtering_probes.ipynb:100: WARNING: Title level inconsistent:

Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/methylprep_methylcheck_example.ipynb:370: WARNING: Title level inconsistent:

(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_probes:11: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:4: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:7: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:10: WARNING: Unexpected section title.

Optional Arguments
------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.exclude_sex_control_probes:25: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:16: WARNING: Unexpected section title.

Parameters
----------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:26: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:34: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:43: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:47: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/filters.py:docstring of methylcheck.filters.list_problem_probes:57: WARNING: Unexpected section title.

Returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_density_plot:8: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:10: WARNING: Unexpected section title.

Arguments
---------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:29: WARNING: Unexpected section title.

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

returns
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.beta_mds_plot:41: WARNING: Unexpected section title.

requires
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:2: WARNING: Unexpected section title.

combine (or segment) datasets how it works
------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:15: WARNING: Unexpected section title.

inputs
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:16: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:18: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:21: WARNING: Unexpected section title.

optional keyword arguments
--------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:32: WARNING: Unexpected section title.

analysis parameters
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:34: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Title underline too short.

returns
------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.combine_mds:37: WARNING: Unexpected section title.

returns
------
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/methylcheck/postprocessQC.py:docstring of methylcheck.postprocessQC.mean_beta_plot:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
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/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/docs/rawQC_example.ipynb: WARNING: document isn't included in any toctree
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build succeeded, 39 warnings.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).

[rtd-command-info] start-time: 2019-11-05T16:33:52.891027Z, end-time: 2019-11-05T16:33:53.242032Z, 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: 2019-11-05T16:33:53.339759Z, end-time: 2019-11-05T16:33:59.967030Z, duration: 6, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=life-epigenetics-methylcheck -interaction=nonstopmode
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, <GEN1> chunk 1.
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Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
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Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
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Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylcheck"  "methylcheck.tex"'
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Chapter 5.
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[1] [2]

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[1] [2]
Chapter 1.
[3] [4]
Chapter 2.
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Chapter 3.
[7] [8]
Chapter 4.
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Chapter 5.
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[1] [2]
Chapter 1.
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Chapter 3.
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Filter either by the publication source, or by the type of effect (e.g. Polymorphism)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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(These return a filtered data set)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Parameters
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Optional Arguments
------------------
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Returns
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Parameters
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Returns
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Arguments
---------
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Options
--------
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returns
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requires
--------
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combine (or segment) datasets how it works
------------------------------------------
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inputs
------
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optional keyword arguments
--------------------------
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analysis parameters
-------------------
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returns
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returns
------
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build succeeded, 34 warnings.

The ePub file is in _build/epub.

[rtd-command-info] start-time: 2019-11-05T16:34:18.491944Z, end-time: 2019-11-05T16:34:18.834275Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/checkouts/latest/./_build/epub/methylcheck.epub /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylcheck/artifacts/latest/sphinx_epub/life-epigenetics-methylcheck.epub