Read the Docs build information Build id: 288898 Project: life-epigenetics-methylprep Version: latest Commit: 6b6832079644878bf559d2b4351118e03f3b4bc7 Date: 2020-02-13T23:18:02.494745Z State: finished Success: True [rtd-command-info] start-time: 2020-02-13T23:18:04.876458Z, end-time: 2020-02-13T23:18:14.013594Z, duration: 9, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylprep.git . Cloning into '.'... 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[rtd-command-info] start-time: 2020-02-13T23:18:14.266537Z, end-time: 2020-02-13T23:18:15.756485Z, 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 HEAD is now at 6b68320 resolved merge conflict v.1.2.3 [rtd-command-info] start-time: 2020-02-13T23:18:15.816950Z, end-time: 2020-02-13T23:18:16.129261Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-02-13T23:18:19.011366Z, end-time: 2020-02-13T23:18:23.889897Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --no-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-02-13T23:18:23.953702Z, end-time: 2020-02-13T23:18:24.940059Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (20.0.2) [rtd-command-info] start-time: 2020-02-13T23:18:24.999824Z, end-time: 2020-02-13T23:18:36.649554Z, duration: 11, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl (14 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting requests>=2.0.0 Downloading requests-2.22.0-py2.py3-none-any.whl (57 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.0-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-20.1-py2.py3-none-any.whl (36 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting chardet<3.1.0,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB) Collecting certifi>=2017.4.17 Downloading certifi-2019.11.28-py2.py3-none-any.whl (156 kB) Collecting idna<2.9,>=2.5 Downloading idna-2.8-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.6-py2.py3-none-any.whl (67 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting pytz>=2015.7 Downloading pytz-2019.3-py2.py3-none-any.whl (509 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=f4e164f38bcbc8aee3be22b5b2df9d0d889a339642f4a987d87a27aeb56200ab Stored in directory: /tmp/pip-ephem-wheel-cache-ms9dadg7/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=46235de3a4dbcb20f704fa4efca1d9a5a5cea696d44cdf21318d64716a134846 Stored in directory: /tmp/pip-ephem-wheel-cache-ms9dadg7/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, imagesize, chardet, urllib3, certifi, idna, requests, sphinxcontrib-websupport, pyparsing, packaging, MarkupSafe, Jinja2, snowballstemmer, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 45.2.0 Uninstalling setuptools-45.2.0: Successfully uninstalled setuptools-45.2.0 Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.2.0 mock-1.0.1 packaging-20.1 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.0 urllib3-1.25.8 [rtd-command-info] start-time: 2020-02-13T23:18:36.712921Z, end-time: 2020-02-13T23:19:07.164680Z, duration: 30, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting numpy Downloading numpy-1.18.1-cp37-cp37m-manylinux1_x86_64.whl (20.1 MB) Collecting pandas Downloading pandas-1.0.1-cp37-cp37m-manylinux1_x86_64.whl (10.1 MB) Collecting scipy Downloading scipy-1.4.1-cp37-cp37m-manylinux1_x86_64.whl (26.1 MB) Collecting statsmodels Downloading statsmodels-0.11.0-cp37-cp37m-manylinux1_x86_64.whl (8.7 MB) Collecting pytest Downloading pytest-5.3.5-py3-none-any.whl (235 kB) Collecting coverage Downloading coverage-5.0.3-cp37-cp37m-manylinux1_x86_64.whl (227 kB) Collecting python-coveralls Downloading python_coveralls-2.9.3-py2.py3-none-any.whl (9.9 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Collecting nbsphinx Downloading nbsphinx-0.5.1-py2.py3-none-any.whl (21 kB) Collecting tqdm Downloading tqdm-4.42.1-py2.py3-none-any.whl (59 kB) Collecting bs4 Downloading bs4-0.0.1.tar.gz (1.1 kB) Collecting lxml Downloading lxml-4.5.0-cp37-cp37m-manylinux1_x86_64.whl (5.7 MB) Collecting python-dateutil>=2.6.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) 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)) (2019.3) Collecting patsy>=0.5 Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting py>=1.5.0 Downloading py-1.8.1-py2.py3-none-any.whl (83 kB) Collecting attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Collecting importlib-metadata>=0.12; python_version < "3.8" Downloading importlib_metadata-1.5.0-py2.py3-none-any.whl (30 kB) Collecting wcwidth Downloading wcwidth-0.1.8-py2.py3-none-any.whl (17 kB) 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)) (20.1) Collecting more-itertools>=4.0.0 Downloading more_itertools-8.2.0-py3-none-any.whl (43 kB) Collecting pluggy<1.0,>=0.12 Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from python-coveralls->-r requirements.txt (line 7)) (1.14.0) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from python-coveralls->-r requirements.txt (line 7)) (2.22.0) Collecting PyYAML Downloading PyYAML-5.3.tar.gz (268 kB) 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 Downloading pbr-5.4.4-py2.py3-none-any.whl (110 kB) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) 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) 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)) (2.11.1) Collecting nbformat Downloading nbformat-5.0.4-py3-none-any.whl (169 kB) Collecting traitlets Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB) Collecting nbconvert!=5.4 Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB) Collecting beautifulsoup4 Downloading beautifulsoup4-4.8.2-py3-none-any.whl (106 kB) Collecting zipp>=0.5 Downloading zipp-2.2.0-py36-none-any.whl (4.6 kB) 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)) (2.4.6) 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->python-coveralls->-r requirements.txt (line 7)) (1.25.8) 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->python-coveralls->-r requirements.txt (line 7)) (2.8) 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->python-coveralls->-r requirements.txt (line 7)) (2019.11.28) 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->python-coveralls->-r requirements.txt (line 7)) (3.0.4) 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: 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: 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)) (2.0.0) 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)) (1.2.0) 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)) (1.2.0) 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)) (2.8.0) 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) 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) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting jupyter-core Downloading jupyter_core-4.6.2-py2.py3-none-any.whl (83 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting decorator Downloading decorator-4.4.1-py2.py3-none-any.whl (9.2 kB) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting bleach Downloading bleach-3.1.0-py2.py3-none-any.whl (157 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.2.tar.gz (14 kB) Collecting soupsieve>=1.2 Downloading soupsieve-1.9.5-py2.py3-none-any.whl (33 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.15.7.tar.gz (107 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: m2r, bs4, PyYAML, pandocfilters, pyrsistent Building wheel for m2r (setup.py): started Building wheel for m2r (setup.py): finished with status 'done' Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10466 sha256=c421989b1d3059563b41ee5a7ad7b59598cb40ab60f057153f41a143102ae349 Stored in directory: /tmp/pip-ephem-wheel-cache-a0ixadjr/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1272 sha256=9e5853b113c710f26c8d92e2b1f14d7794ebd7ffbb3febb1b89937de5268abfb Stored in directory: /tmp/pip-ephem-wheel-cache-a0ixadjr/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca Building wheel for PyYAML (setup.py): started Building wheel for PyYAML (setup.py): finished with status 'done' Created wheel for PyYAML: filename=PyYAML-5.3-cp37-cp37m-linux_x86_64.whl size=44228 sha256=95518c0d15c2fcdc51a2128996dc55569070c87b14cbc50fb0289f3b8b1c5d0e Stored in directory: /tmp/pip-ephem-wheel-cache-a0ixadjr/wheels/8a/55/a4/c0a81d27c33462cfdcb904db018f5550197e88b2b6b85beed2 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=4ec1d44fe9adfa416b341653720e126510d09dea4049b46b087b4de303cd6c3d Stored in directory: /tmp/pip-ephem-wheel-cache-a0ixadjr/wheels/63/99/01/9fe785b86d1e091a6b2a61e06ddb3d8eb1bc9acae5933d4740 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.15.7-cp37-cp37m-linux_x86_64.whl size=115961 sha256=993dd664c1acf5e1973ac52cae78357346192a9beeac8e1526bcb54f0ee591f1 Stored in directory: /tmp/pip-ephem-wheel-cache-a0ixadjr/wheels/57/74/e3/61db397ec89f304e49711ec9f68490f15814b80c1c0ee9b8c0 Successfully built m2r bs4 PyYAML pandocfilters pyrsistent Installing collected packages: numpy, python-dateutil, pandas, scipy, patsy, statsmodels, py, attrs, zipp, importlib-metadata, wcwidth, more-itertools, pluggy, pytest, coverage, PyYAML, python-coveralls, pbr, sphinxcontrib-apidoc, mistune, m2r, pyrsistent, jsonschema, decorator, ipython-genutils, traitlets, jupyter-core, nbformat, testpath, defusedxml, entrypoints, webencodings, bleach, pandocfilters, nbconvert, nbsphinx, tqdm, soupsieve, beautifulsoup4, bs4, lxml Successfully installed PyYAML-5.3 attrs-19.3.0 beautifulsoup4-4.8.2 bleach-3.1.0 bs4-0.0.1 coverage-5.0.3 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-1.5.0 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-core-4.6.2 lxml-4.5.0 m2r-0.2.1 mistune-0.8.4 more-itertools-8.2.0 nbconvert-5.6.1 nbformat-5.0.4 nbsphinx-0.5.1 numpy-1.18.1 pandas-1.0.1 pandocfilters-1.4.2 patsy-0.5.1 pbr-5.4.4 pluggy-0.13.1 py-1.8.1 pyrsistent-0.15.7 pytest-5.3.5 python-coveralls-2.9.3 python-dateutil-2.8.1 scipy-1.4.1 soupsieve-1.9.5 sphinxcontrib-apidoc-0.3.0 statsmodels-0.11.0 testpath-0.4.4 tqdm-4.42.1 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 zipp-2.2.0 [rtd-command-info] start-time: 2020-02-13T23:19:07.852362Z, end-time: 2020-02-13T23:19:08.161600Z, 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/"), ], 'downloads': [ ("html", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylprep', 'name': u'methylprep', 'rtd_language': u'en', 'programming_language': u'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', 'proxied_api_host': '/_', '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': '6b683207', } 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: 2020-02-13T23:19:08.231038Z, end-time: 2020-02-13T23:19:13.221312Z, duration: 4, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.download.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst. building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 15 source files that are out of date updating environment: 15 added, 0 changed, 0 removed reading sources... [ 6%] README reading sources... [ 13%] docs/README reading sources... [ 20%] docs/cli reading sources... [ 26%] docs/example_download reading sources... [ 33%] docs/faq reading sources... [ 40%] docs/installation reading sources... [ 46%] docs/methylprep_tutorial reading sources... [ 53%] docs/package reading sources... [ 60%] docs/source/methpype reading sources... [ 66%] docs/source/methpype.arrays reading sources... [ 73%] docs/source/methpype.preprocess reading sources... [ 80%] docs/source/methpype.samples reading sources... [ 86%] docs/source/methpype.utils reading sources... [ 93%] docs/source/modules reading sources... [100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylcheck". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/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 ------------------- WARNING: missing attribute mentioned in :members: or __all__: module methylprep, attribute build_composite_dataset /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load:17: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load_both:15: WARNING: Unknown target name: "gse150999". /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 ------------------------------- looking for now-outdated files... none found pickling environment... /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: -------- WARNING: missing attribute mentioned in :members: or __all__: module methylprep, attribute build_composite_dataset /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.get_manifest:1: WARNING: duplicate object description of methylprep.get_manifest, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.get_raw_datasets:1: WARNING: duplicate object description of methylprep.get_raw_datasets, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:1: WARNING: duplicate object description of methylprep.run_pipeline, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.get_sample_sheet:1: WARNING: duplicate object description of methylprep.get_sample_sheet, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.consolidate_values_for_sheet:1: WARNING: duplicate object description of methylprep.consolidate_values_for_sheet, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_series:1: WARNING: duplicate object description of methylprep.run_series, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_series_list:1: WARNING: duplicate object description of methylprep.run_series_list, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.convert_miniml:1: WARNING: duplicate object description of methylprep.convert_miniml, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load:1: WARNING: duplicate object description of methylprep.load, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load_both:1: WARNING: duplicate object description of methylprep.load_both, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:1: WARNING: duplicate object description of methylprep.read_geo, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load:17: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short. 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[100%] index /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylcheck". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/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 ------------------- WARNING: missing attribute mentioned in :members: or __all__: module methylprep, attribute build_composite_dataset /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load:17: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load_both:15: WARNING: Unknown target name: "gse150999". /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' looking for now-outdated files... none found pickling environment... /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: -------- WARNING: missing attribute mentioned in :members: or __all__: module methylprep, attribute build_composite_dataset /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.get_manifest:1: WARNING: duplicate object description of methylprep.get_manifest, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.get_raw_datasets:1: WARNING: duplicate object description of methylprep.get_raw_datasets, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:1: WARNING: duplicate object description of methylprep.run_pipeline, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.get_sample_sheet:1: WARNING: duplicate object description of methylprep.get_sample_sheet, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.consolidate_values_for_sheet:1: WARNING: duplicate object description of methylprep.consolidate_values_for_sheet, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_series:1: WARNING: duplicate object description of methylprep.run_series, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_series_list:1: WARNING: duplicate object description of methylprep.run_series_list, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.convert_miniml:1: WARNING: duplicate object description of methylprep.convert_miniml, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load:1: WARNING: duplicate object description of methylprep.load, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load_both:1: WARNING: duplicate object description of methylprep.load_both, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:1: WARNING: duplicate object description of methylprep.read_geo, other instance in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/source/methpype.rst, use :noindex: for one of them /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load:17: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.load_both:15: WARNING: Unknown target name: "gse150999". /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/index.rst:7: WARNING: Title underline too short. 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