Read the Docs build information Build id: 256478 Project: life-epigenetics-methylprep Version: latest Commit: 59d86919079673ed96df6ccbbcc9c1e2dfcdadf6 Date: 2019-11-05T18:18:31.643798Z State: finished Success: True [rtd-command-info] start-time: 2019-11-05T18:29:02.448782Z, end-time: 2019-11-05T18:29:06.968783Z, duration: 4, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/LifeEGX/methylprep.git . Cloning into '.'... [rtd-command-info] start-time: 2019-11-05T18:29:07.494234Z, end-time: 2019-11-05T18:29:08.819231Z, 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 59d8691 Minor bug fixes, and coveralls stopped working (#35) [rtd-command-info] start-time: 2019-11-05T18:29:08.904909Z, end-time: 2019-11-05T18:29:08.922688Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-11-05T18:29:10.825485Z, end-time: 2019-11-05T18:29:14.208698Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.1' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-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. 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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)) (1.1.0) 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) Collecting ipython-genutils Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl Collecting decorator Downloading 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https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl Collecting pyrsistent>=0.14.0 Downloading https://files.pythonhosted.org/packages/30/86/53a88c0a57698fa228db29a4000c28f4124823010388cb7042fe6e2be8dd/pyrsistent-0.15.5.tar.gz (107kB) 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-cp37-none-any.whl size=10465 sha256=1a3ec26a5214f6398f9496398c26925dea092798a01815169252d13683dbd23f Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip/wheels/47/f8/dc/80f56bc4abf785834d422c2f5c864a14bf34576612aeb03492 Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: 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sha256=3c36865f97bfc53db5ee031fc735958b59b4bd59b1d4a8d8c115e2e781b9dfd0 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip/wheels/39/01/56/f1b08a6275acc59e846fa4c1e1b65dbc1919f20157d9e66c20 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.15.5-cp37-cp37m-linux_x86_64.whl size=115954 sha256=2fcd4d412843dad41cb603fe40fcf60d07055165d1bc3c62fe65c47e6fb78ba1 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip/wheels/c4/5a/b2/d22f93864c638398dad50541af906e9838bb22044d2cc3ad3a Successfully built m2r bs4 PyYAML pandocfilters pyrsistent Installing collected packages: numpy, python-dateutil, pandas, scipy, patsy, statsmodels, more-itertools, zipp, importlib-metadata, pluggy, atomicwrites, py, wcwidth, attrs, pytest, coverage, PyYAML, python-coveralls, pbr, sphinxcontrib-apidoc, mistune, m2r, ipython-genutils, decorator, traitlets, testpath, defusedxml, webencodings, bleach, jupyter-core, entrypoints, pandocfilters, pyrsistent, jsonschema, nbformat, nbconvert, nbsphinx, tqdm, soupsieve, beautifulsoup4, bs4, lxml Successfully installed PyYAML-5.1.2 atomicwrites-1.3.0 attrs-19.3.0 beautifulsoup4-4.8.1 bleach-3.1.0 bs4-0.0.1 coverage-4.5.4 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-0.23 ipython-genutils-0.2.0 jsonschema-3.1.1 jupyter-core-4.6.1 lxml-4.4.1 m2r-0.2.1 mistune-0.8.4 more-itertools-7.2.0 nbconvert-5.6.1 nbformat-4.4.0 nbsphinx-0.4.3 numpy-1.17.3 pandas-0.25.3 pandocfilters-1.4.2 patsy-0.5.1 pbr-5.4.3 pluggy-0.13.0 py-1.8.0 pyrsistent-0.15.5 pytest-5.2.2 python-coveralls-2.9.3 python-dateutil-2.8.1 scipy-1.3.1 soupsieve-1.9.5 sphinxcontrib-apidoc-0.3.0 statsmodels-0.10.1 testpath-0.4.4 tqdm-4.37.0 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1 zipp-0.6.0 [rtd-command-info] start-time: 2019-11-05T18:30:05.747280Z, end-time: 2019-11-05T18:30:06.073208Z, 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", "//readthedocs.com/projects/life-epigenetics-methylprep/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylprep', 'name': u'methylprep', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'LifeEGX', 'github_repo': 'methylprep', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '59d86919', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-11-05T18:30:06.172634Z, end-time: 2019-11-05T18:30:10.379475Z, 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 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... 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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: "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/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/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: "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/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/index.rst:7: WARNING: Title underline too short. 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