Read the Docs build information
Build id: 238349
Project: life-epigenetics-methylprep
Version: latest
Commit: 37fb54abc7b93473ff46315cec031524be9f77b3
Date: 2019-09-03T19:02:49.083007Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-09-03T19:02:49.525130Z, end-time: 2019-09-03T19:02:53.120147Z, duration: 3, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylprep.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-09-03T19:02:54.138315Z, end-time: 2019-09-03T19:02:54.728340Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

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

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

  git checkout -b <new-branch-name>

HEAD is now at 37fb54a removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists (#19)

[rtd-command-info] start-time: 2019-09-03T19:02:54.809725Z, end-time: 2019-09-03T19:02:54.817755Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-09-03T19:02:55.767350Z, end-time: 2019-09-03T19:02:59.988065Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-09-03T19:03:00.105035Z, end-time: 2019-09-03T19:03:02.374760Z, duration: 2, 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
  Using cached https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl
Installing collected packages: pip
  Found existing installation: pip 19.1.1
    Uninstalling pip-19.1.1:
      Successfully uninstalled pip-19.1.1
Successfully installed pip-19.2.3

[rtd-command-info] start-time: 2019-09-03T19:03:02.462138Z, end-time: 2019-09-03T19:03:10.005137Z, duration: 7, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1
Collecting Pygments==2.3.1
  Using cached https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (41.0.1)
Collecting docutils==0.14
  Using cached https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl
Collecting mock==1.0.1
Collecting pillow==5.4.1
  Using cached https://files.pythonhosted.org/packages/ae/2a/0a0ab2833e5270664fb5fae590717f867ac6319b124160c09f1d3291de28/Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Using cached https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl
Collecting commonmark==0.8.1
  Using cached https://files.pythonhosted.org/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl
Collecting recommonmark==0.5.0
  Using cached https://files.pythonhosted.org/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl
Collecting sphinx<2
  Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl
Collecting sphinx-rtd-theme<0.5
  Using cached https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl
Collecting readthedocs-sphinx-ext<1.1
  Using cached https://files.pythonhosted.org/packages/51/43/a5a98d9aec325b2824bdf504fa446ae876d0909d03e28667018f9eb01bcd/readthedocs_sphinx_ext-1.0.0-py2.py3-none-any.whl
Collecting future (from commonmark==0.8.1)
Collecting Jinja2>=2.3 (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting snowballstemmer>=1.1 (from sphinx<2)
Collecting sphinxcontrib-websupport (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl
Collecting packaging (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/ec/22/630ac83e8f8a9566c4f88038447ed9e16e6f10582767a01f31c769d9a71e/packaging-19.1-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting imagesize (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<2)
  Using cached https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/98/7b/ff284bd8c80654e471b769062a9b43cc5d03e7a615048d96f4619df8d420/MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting attrs (from packaging->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests>=2.0.0->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/e6/60/247f23a7121ae632d62811ba7f273d0e58972d75e58a94d329d51550a47d/urllib3-1.25.3-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests>=2.0.0->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/69/1b/b853c7a9d4f6a6d00749e94eb6f3a041e342a885b87340b79c1ef73e3a78/certifi-2019.6.16-py2.py3-none-any.whl
Collecting pytz>=2015.7 (from babel!=2.0,>=1.3->sphinx<2)
  Using cached https://files.pythonhosted.org/packages/87/76/46d697698a143e05f77bec5a526bf4e56a0be61d63425b68f4ba553b51f2/pytz-2019.2-py2.py3-none-any.whl
Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, six, snowballstemmer, sphinxcontrib-websupport, attrs, pyparsing, packaging, urllib3, idna, chardet, certifi, requests, imagesize, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 attrs-19.1.0 babel-2.7.0 certifi-2019.6.16 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-19.1 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.2 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 six-1.12.0 snowballstemmer-1.9.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.3

[rtd-command-info] start-time: 2019-09-03T19:03:10.105770Z, end-time: 2019-09-03T19:03:29.087232Z, duration: 18, 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
Collecting numpy (from -r requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/25/eb/4ecf6b13897391cb07a4231e9d9c671b55dfbbf6f4a514a1a0c594f2d8d9/numpy-1.17.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting pandas (from -r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/7e/ab/ea76361f9d3e732e114adcd801d2820d5319c23d0ac5482fa3b412db217e/pandas-0.25.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting scipy (from -r requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/94/7f/b535ec711cbcc3246abea4385d17e1b325d4c3404dd86f15fc4f3dba1dbb/scipy-1.3.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting statsmodels (from -r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/01/cb/614f37ac4a9919eb0dbc0cd9eb939d1a33299f54f10e8a705dd9b08c2f3f/statsmodels-0.10.1-cp37-cp37m-manylinux1_x86_64.whl
Collecting pytest (from -r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/2f/19/d5f71752f71451ccc5ed5f6739e9da4a235f38783fdaf3629cae41b2ca7b/pytest-5.1.2-py3-none-any.whl
Collecting coverage (from -r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/82/8f/a2a687fa00059360858023c5cb74e94b8afaf318726e9a256934066a9d90/coverage-4.5.4-cp37-cp37m-manylinux1_x86_64.whl
Collecting coveralls-python (from -r requirements.txt (line 7))
Collecting sphinxcontrib-apidoc (from -r requirements.txt (line 8))
  Using cached https://files.pythonhosted.org/packages/60/8d/a426a9f7f9ffc8e02d377ca82e3f005817ccf0141b85dbb8653aad13901b/sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl
Collecting m2r (from -r requirements.txt (line 9))
Collecting nbsphinx (from -r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/78/0d/521a6bda0f7cf5b5129a543fd857238bf792d9b29f2d420d6e63490f9837/nbsphinx-0.4.2-py2.py3-none-any.whl
Collecting tqdm (from -r requirements.txt (line 11))
  Using cached https://files.pythonhosted.org/packages/dc/88/d3213e2f3492daf09d8b41631ad6899f56db17ce83ea9c8a579902bafe5e/tqdm-4.35.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.6.1 (from pandas->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pandas->-r requirements.txt (line 2)) (2019.2)
Collecting patsy>=0.4.0 (from statsmodels->-r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pytest->-r requirements.txt (line 5)) (19.1)
Collecting py>=1.5.0 (from pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Collecting importlib-metadata>=0.12; python_version < "3.8" (from pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/89/77/8bae90e4534a8fee1e0c3ee4890e2c7d215dccd7386cf2ec7555e529d6bb/importlib_metadata-0.20-py2.py3-none-any.whl
Requirement already satisfied: attrs>=17.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pytest->-r requirements.txt (line 5)) (19.1.0)
Collecting wcwidth (from pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/45/dc/3241eef99eb45f1def35cf93af35d1cf9ef4c0991792583b8f33ea41b092/more_itertools-7.2.0-py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/52/90/6155aa926f43f2b2a22b01be7241be3bfd1ceaf7d0b3267213e8127d41f4/atomicwrites-1.3.0-py2.py3-none-any.whl
Collecting pluggy<1.0,>=0.12 (from pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/06/ee/de89e0582276e3551df3110088bf20844de2b0e7df2748406876cc78e021/pluggy-0.12.0-py2.py3-none-any.whl
Requirement already satisfied: Sphinx>=1.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.8.5)
Collecting pbr (from sphinxcontrib-apidoc->-r requirements.txt (line 8))
  Using cached https://files.pythonhosted.org/packages/f9/d8/bd657bfa0e89eb71ad5e977ed99a9bb2b44e5db68d9190970637c26501bb/pbr-5.4.2-py2.py3-none-any.whl
Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from m2r->-r requirements.txt (line 9)) (0.14)
Collecting mistune (from m2r->-r requirements.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Collecting nbformat (from nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl
Collecting traitlets (from nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/93/d6/abcb22de61d78e2fc3959c964628a5771e47e7cc60d53e9342e21ed6cc9a/traitlets-4.3.2-py2.py3-none-any.whl
Collecting nbconvert!=5.4 (from nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/f9/df/4505c0a7fea624cac461d0f41051f33456ae656753f65cee8c2f43121cb2/nbconvert-5.6.0-py2.py3-none-any.whl
Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from nbsphinx->-r requirements.txt (line 10)) (2.10.1)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from python-dateutil>=2.6.1->pandas->-r requirements.txt (line 2)) (1.12.0)
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)
Collecting zipp>=0.5 (from importlib-metadata>=0.12; python_version < "3.8"->pytest->-r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.9.0)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.22.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.7.0)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.1.2)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.1.0)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.3.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (41.0.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (0.7.12)
Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/54/48/f5f11003ceddcd4ad292d4d9b5677588e9169eef41f88e38b2888e7ec6c4/jsonschema-3.0.2-py2.py3-none-any.whl
Collecting ipython-genutils (from nbformat->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting jupyter-core (from nbformat->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/e6/25/6ffb0f6e57fa6ef5d2f814377133b361b42a6dd39105f4885a4f1666c2c3/jupyter_core-4.5.0-py2.py3-none-any.whl
Collecting decorator (from traitlets->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting testpath (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/be/a4/162f9ebb6489421fe46dcca2ae420369edfee4b563c668d93cb4605d12ba/testpath-0.4.2-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2 (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting bleach (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl
Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
Collecting defusedxml (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from jinja2->nbsphinx->-r requirements.txt (line 10)) (1.1.1)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2019.6.16)
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-methylprep/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.25.3)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.8)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (3.0.4)
Collecting pyrsistent>=0.14.0 (from jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx->-r requirements.txt (line 10))
Collecting webencodings (from bleach->nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10))
  Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Installing collected packages: numpy, python-dateutil, pandas, scipy, patsy, statsmodels, py, more-itertools, zipp, importlib-metadata, wcwidth, atomicwrites, pluggy, pytest, coverage, coveralls-python, pbr, sphinxcontrib-apidoc, mistune, m2r, pyrsistent, jsonschema, decorator, ipython-genutils, traitlets, jupyter-core, nbformat, testpath, entrypoints, webencodings, bleach, pandocfilters, defusedxml, nbconvert, nbsphinx, tqdm
Successfully installed atomicwrites-1.3.0 bleach-3.1.0 coverage-4.5.4 coveralls-python-0.0.1 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-0.20 ipython-genutils-0.2.0 jsonschema-3.0.2 jupyter-core-4.5.0 m2r-0.2.1 mistune-0.8.4 more-itertools-7.2.0 nbconvert-5.6.0 nbformat-4.4.0 nbsphinx-0.4.2 numpy-1.17.1 pandas-0.25.1 pandocfilters-1.4.2 patsy-0.5.1 pbr-5.4.2 pluggy-0.12.0 py-1.8.0 pyrsistent-0.15.4 pytest-5.1.2 python-dateutil-2.8.0 scipy-1.3.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.10.1 testpath-0.4.2 tqdm-4.35.0 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 zipp-0.6.0

[rtd-command-info] start-time: 2019-09-03T19:03:29.677876Z, end-time: 2019-09-03T19:03:29.992083Z, 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/"),
    ("epub", "//readthedocs.com/projects/life-epigenetics-methylprep/downloads/epub/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': '37fb54ab',
}




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: 2019-09-03T19:03:30.080550Z, end-time: 2019-09-03T19:03:33.649509Z, duration: 3, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 13 source files that are out of date
updating environment: 13 added, 0 changed, 0 removed
reading sources... [  7%] README
reading sources... [ 15%] docs/README
reading sources... [ 23%] docs/cli
reading sources... [ 30%] docs/installation
reading sources... [ 38%] docs/methylprep_tutorial
reading sources... [ 46%] docs/package
reading sources... [ 53%] docs/source/methpype
reading sources... [ 61%] docs/source/methpype.arrays
reading sources... [ 69%] docs/source/methpype.preprocess
reading sources... [ 76%] docs/source/methpype.samples
reading sources... [ 84%] docs/source/methpype.utils
reading sources... [ 92%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:190: WARNING: Title level inconsistent:

``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:220: WARNING: Title level inconsistent:

``get_manifest``
~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:254: WARNING: Title level inconsistent:

``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methqc".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:362: WARNING: Title level inconsistent:

Filtering by Probes
~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:433: WARNING: Title level inconsistent:

Visual Filtering Functions
~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:2: WARNING: Title underline too short.

methylprep package
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.utils'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short.

methylprep.cli module
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short.

methylprep.cli module
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:2: WARNING: Title underline too short.

methylprep.arrays package
=======================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short.

methylprep.arrays.arrays module
-----------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short.

methylprep.arrays.arrays module
-----------------------------
WARNING: autodoc: failed to import module 'arrays.arrays' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short.

methylprep.arrays.controls module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short.

methylprep.arrays.controls module
-------------------------------
WARNING: autodoc: failed to import module 'arrays.controls' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short.

methylprep.arrays.manifest module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short.

methylprep.arrays.manifest module
-------------------------------
WARNING: autodoc: failed to import module 'arrays.manifest' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short.

methylprep.arrays.probes module
-----------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short.

methylprep.arrays.probes module
-----------------------------
WARNING: autodoc: failed to import module 'arrays.probes' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
WARNING: autodoc: failed to import module 'arrays' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:2: WARNING: Title underline too short.

methylprep.preprocess package
===========================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short.

methylprep.preprocess.idat module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short.

methylprep.preprocess.idat module
-------------------------------
WARNING: autodoc: failed to import module 'preprocess.idat' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short.

methylprep.preprocess.meth\_dataset module
----------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short.

methylprep.preprocess.meth\_dataset module
----------------------------------------
WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short.

methylprep.preprocess.noob module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short.

methylprep.preprocess.noob module
-------------------------------
WARNING: autodoc: failed to import module 'preprocess.noob' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short.

methylprep.preprocess.pipeline module
-----------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short.

methylprep.preprocess.pipeline module
-----------------------------------
WARNING: autodoc: failed to import module 'preprocess.pipeline' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short.

methylprep.preprocess.raw\_dataset module
---------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short.

methylprep.preprocess.raw\_dataset module
---------------------------------------
WARNING: autodoc: failed to import module 'preprocess.raw_dataset' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short.

methylprep.preprocess.utils module
--------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short.

methylprep.preprocess.utils module
--------------------------------
WARNING: autodoc: failed to import module 'preprocess.utils' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
WARNING: autodoc: failed to import module 'preprocess' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:2: WARNING: Title underline too short.

methylprep.samples package
========================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short.

methylprep.samples.sample module
------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short.

methylprep.samples.sample module
------------------------------
WARNING: autodoc: failed to import module 'samples.sample' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short.

methylprep.samples.sample\_sheet module
-------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short.

methylprep.samples.sample\_sheet module
-------------------------------------
WARNING: autodoc: failed to import module 'samples.sample_sheet' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.samples'
WARNING: autodoc: failed to import module 'samples' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:2: WARNING: Title underline too short.

methylprep.utils package
======================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short.

methylprep.utils.data module
--------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short.

methylprep.utils.data module
--------------------------
WARNING: autodoc: failed to import module 'data' from module 'methylprep.utils'; the following exception was raised:
No module named 'methylprep.utils.data'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short.

methylprep.utils.decorators module
--------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short.

methylprep.utils.decorators module
--------------------------------
WARNING: autodoc: failed to import module 'decorators' from module 'methylprep.utils'; the following exception was raised:
No module named 'methylprep.utils.decorators'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short.

methylprep.utils.files module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short.

methylprep.utils.files module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Title underline too short.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Unexpected section title.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Title underline too short.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Unexpected section title.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:2: WARNING: Title underline too short.

methylprep
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:4: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short.

Welcome to methylprep's documentation!
====================================
README.md:190: WARNING: Title level inconsistent:

``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
README.md:220: WARNING: Title level inconsistent:

``get_manifest``
~~~~~~~~~~~~~~~~~~~~
README.md:254: WARNING: Title level inconsistent:

``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  7%] README
writing output... [ 15%] docs/README
writing output... [ 23%] docs/cli
writing output... [ 30%] docs/installation
writing output... [ 38%] docs/methylprep_tutorial
writing output... [ 46%] docs/package
writing output... [ 53%] docs/source/methpype
writing output... [ 61%] docs/source/methpype.arrays
writing output... [ 69%] docs/source/methpype.preprocess
writing output... [ 76%] docs/source/methpype.samples
writing output... [ 84%] docs/source/methpype.utils
writing output... [ 92%] docs/source/modules
writing output... [100%] index

generating indices.../home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:278: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:422: WARNING: Could not lex literal_block as "python". Highlighting skipped.
 genindex py-modindex
writing additional pages... search
copying images... [  5%] docs/tutorial_figs/fig1.png
copying images... [ 11%] docs/tutorial_figs/fig2.png
copying images... [ 16%] docs/tutorial_figs/fig3.png
copying images... [ 22%] docs/tutorial_figs/fig4.png
copying images... [ 27%] docs/tutorial_figs/fig5.png
copying images... [ 33%] docs/tutorial_figs/fig6.png
copying images... [ 38%] docs/tutorial_figs/fig7.png
copying images... [ 44%] docs/tutorial_figs/fig8.png
copying images... [ 50%] docs/tutorial_figs/fig9.png
copying images... [ 55%] docs/tutorial_figs/fig10.png
copying images... [ 61%] docs/tutorial_figs/fig11.png
copying images... [ 66%] docs/tutorial_figs/fig12.png
copying images... [ 72%] docs/tutorial_figs/fig13.png
copying images... [ 77%] docs/tutorial_figs/fig14.png
copying images... [ 83%] docs/tutorial_figs/fig15.png
copying images... [ 88%] docs/tutorial_figs/fig16.png
copying images... [ 94%] docs/tutorial_figs/fig17.png
copying images... [100%] docs/tutorial_figs/fig18.png

copying static files... done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 86 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-09-03T19:03:33.787129Z, end-time: 2019-09-03T19:03:36.928633Z, duration: 3, 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-methylprep/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 13 added, 0 changed, 0 removed
reading sources... [  7%] README
reading sources... [ 15%] docs/README
reading sources... [ 23%] docs/cli
reading sources... [ 30%] docs/installation
reading sources... [ 38%] docs/methylprep_tutorial
reading sources... [ 46%] docs/package
reading sources... [ 53%] docs/source/methpype
reading sources... [ 61%] docs/source/methpype.arrays
reading sources... [ 69%] docs/source/methpype.preprocess
reading sources... [ 76%] docs/source/methpype.samples
reading sources... [ 84%] docs/source/methpype.utils
reading sources... [ 92%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:190: WARNING: Title level inconsistent:

``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:220: WARNING: Title level inconsistent:

``get_manifest``
~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:254: WARNING: Title level inconsistent:

``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methqc".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:362: WARNING: Title level inconsistent:

Filtering by Probes
~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:433: WARNING: Title level inconsistent:

Visual Filtering Functions
~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:2: WARNING: Title underline too short.

methylprep package
================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:7: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep.utils'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short.

methylprep.cli module
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst:18: WARNING: Title underline too short.

methylprep.cli module
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:2: WARNING: Title underline too short.

methylprep.arrays package
=======================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short.

methylprep.arrays.arrays module
-----------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:8: WARNING: Title underline too short.

methylprep.arrays.arrays module
-----------------------------
WARNING: autodoc: failed to import module 'arrays.arrays' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short.

methylprep.arrays.controls module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:16: WARNING: Title underline too short.

methylprep.arrays.controls module
-------------------------------
WARNING: autodoc: failed to import module 'arrays.controls' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short.

methylprep.arrays.manifest module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:24: WARNING: Title underline too short.

methylprep.arrays.manifest module
-------------------------------
WARNING: autodoc: failed to import module 'arrays.manifest' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short.

methylprep.arrays.probes module
-----------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst:32: WARNING: Title underline too short.

methylprep.arrays.probes module
-----------------------------
WARNING: autodoc: failed to import module 'arrays.probes' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
WARNING: autodoc: failed to import module 'arrays' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.arrays'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:2: WARNING: Title underline too short.

methylprep.preprocess package
===========================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short.

methylprep.preprocess.idat module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:8: WARNING: Title underline too short.

methylprep.preprocess.idat module
-------------------------------
WARNING: autodoc: failed to import module 'preprocess.idat' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short.

methylprep.preprocess.meth\_dataset module
----------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:16: WARNING: Title underline too short.

methylprep.preprocess.meth\_dataset module
----------------------------------------
WARNING: autodoc: failed to import module 'preprocess.meth_dataset' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short.

methylprep.preprocess.noob module
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:24: WARNING: Title underline too short.

methylprep.preprocess.noob module
-------------------------------
WARNING: autodoc: failed to import module 'preprocess.noob' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short.

methylprep.preprocess.pipeline module
-----------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:32: WARNING: Title underline too short.

methylprep.preprocess.pipeline module
-----------------------------------
WARNING: autodoc: failed to import module 'preprocess.pipeline' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short.

methylprep.preprocess.raw\_dataset module
---------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:40: WARNING: Title underline too short.

methylprep.preprocess.raw\_dataset module
---------------------------------------
WARNING: autodoc: failed to import module 'preprocess.raw_dataset' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short.

methylprep.preprocess.utils module
--------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst:48: WARNING: Title underline too short.

methylprep.preprocess.utils module
--------------------------------
WARNING: autodoc: failed to import module 'preprocess.utils' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
WARNING: autodoc: failed to import module 'preprocess' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.preprocess'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:2: WARNING: Title underline too short.

methylprep.samples package
========================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short.

methylprep.samples.sample module
------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:8: WARNING: Title underline too short.

methylprep.samples.sample module
------------------------------
WARNING: autodoc: failed to import module 'samples.sample' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short.

methylprep.samples.sample\_sheet module
-------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst:16: WARNING: Title underline too short.

methylprep.samples.sample\_sheet module
-------------------------------------
WARNING: autodoc: failed to import module 'samples.sample_sheet' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.samples'
WARNING: autodoc: failed to import module 'samples' from module 'methylprep'; the following exception was raised:
No module named 'methylprep.samples'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:2: WARNING: Title underline too short.

methylprep.utils package
======================
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short.

methylprep.utils.data module
--------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:8: WARNING: Title underline too short.

methylprep.utils.data module
--------------------------
WARNING: autodoc: failed to import module 'data' from module 'methylprep.utils'; the following exception was raised:
No module named 'methylprep.utils.data'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short.

methylprep.utils.decorators module
--------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:16: WARNING: Title underline too short.

methylprep.utils.decorators module
--------------------------------
WARNING: autodoc: failed to import module 'decorators' from module 'methylprep.utils'; the following exception was raised:
No module named 'methylprep.utils.decorators'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short.

methylprep.utils.files module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst:24: WARNING: Title underline too short.

methylprep.utils.files module
---------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Title underline too short.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/files.py:docstring of methylprep.utils.files.is_file_like:13: WARNING: Unexpected section title.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Title underline too short.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/utils/__init__.py:docstring of methylprep.utils.is_file_like:13: WARNING: Unexpected section title.

Examples:
--------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:2: WARNING: Title underline too short.

methylprep
========
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/modules.rst:4: WARNING: toctree contains reference to nonexisting document 'docs/source/methylprep'
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short.

Welcome to methylprep's documentation!
====================================
README.md:190: WARNING: Title level inconsistent:

``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
README.md:220: WARNING: Title level inconsistent:

``get_manifest``
~~~~~~~~~~~~~~~~~~~~
README.md:254: WARNING: Title level inconsistent:

``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.arrays.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.preprocess.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.samples.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.utils.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... docs/methylprep_tutorial docs/cli docs/source/modules 
writing... /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:278: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:422: WARNING: Could not lex literal_block as "python". Highlighting skipped.
done
writing additional files...
copying images... [  5%] docs/tutorial_figs/fig1.png
copying images... [ 11%] docs/tutorial_figs/fig2.png
copying images... [ 16%] docs/tutorial_figs/fig3.png
copying images... [ 22%] docs/tutorial_figs/fig4.png
copying images... [ 27%] docs/tutorial_figs/fig5.png
copying images... [ 33%] docs/tutorial_figs/fig6.png
copying images... [ 38%] docs/tutorial_figs/fig7.png
copying images... [ 44%] docs/tutorial_figs/fig8.png
copying images... [ 50%] docs/tutorial_figs/fig9.png
copying images... [ 55%] docs/tutorial_figs/fig10.png
copying images... [ 61%] docs/tutorial_figs/fig11.png
copying images... [ 66%] docs/tutorial_figs/fig12.png
copying images... [ 72%] docs/tutorial_figs/fig13.png
copying images... [ 77%] docs/tutorial_figs/fig14.png
copying images... [ 83%] docs/tutorial_figs/fig15.png
copying images... [ 88%] docs/tutorial_figs/fig16.png
copying images... [ 94%] docs/tutorial_figs/fig17.png
copying images... [100%] docs/tutorial_figs/fig18.png

copying static files... done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 86 warnings.

The HTML page is in _build/localmedia.