Read the Docs build information Build id: 278205 Project: life-epigenetics-methylprep Version: latest Commit: e132dac8fb1871c23764363f728bde6b3cf80763 Date: 2020-01-20T20:35:34.799131Z State: finished Success: True [rtd-command-info] start-time: 2020-01-20T20:35:35.359342Z, end-time: 2020-01-20T20:35:35.370226Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/LifeEGX/methylprep.git [rtd-command-info] start-time: 2020-01-20T20:35:35.472338Z, end-time: 2020-01-20T20:35:35.986535Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/LifeEGX/methylprep d3d6360..e132dac master -> origin/master [rtd-command-info] start-time: 2020-01-20T20:35:36.220981Z, end-time: 2020-01-20T20:35:36.231796Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was d3d6360 Feature/composite (#39) HEAD is now at e132dac Feature/composite (#40) [rtd-command-info] start-time: 2020-01-20T20:35:36.312533Z, end-time: 2020-01-20T20:35:36.324134Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-01-20T20:35:37.247155Z, end-time: 2020-01-20T20:35:41.356419Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-01-20T20:35:41.456190Z, end-time: 2020-01-20T20:35:43.832029Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip pip Collecting pip Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2020-01-20T20:35:43.917608Z, end-time: 2020-01-20T20:35:54.143701Z, duration: 10, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 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Downloading https://files.pythonhosted.org/packages/8a/b5/73b740dc7182b4f458de18ab54adaf5698ace3a723569c5e2a748130a314/readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl Collecting future Downloading https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (829kB) Collecting sphinxcontrib-websupport Downloading https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl Collecting packaging Downloading https://files.pythonhosted.org/packages/d8/5b/3098db49a61ccc8583ffead6aedc226f08ff56dc03106b6ec54451e27a30/packaging-20.0-py2.py3-none-any.whl Collecting six>=1.5 Downloading https://files.pythonhosted.org/packages/65/eb/1f97cb97bfc2390a276969c6fae16075da282f5058082d4cb10c6c5c1dba/six-1.14.0-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 Downloading https://files.pythonhosted.org/packages/15/a1/522dccd23e5d2e47aed4b6a16795b8213e3272c7506e625f2425ad025a19/Babel-2.8.0-py2.py3-none-any.whl (8.6MB) Collecting imagesize Downloading https://files.pythonhosted.org/packages/31/b2/b5522a0c8d11e4aff83f8342f3f0dea68c2fb25aa44403e420587f0ce204/imagesize-1.2.0-py2.py3-none-any.whl Collecting snowballstemmer>=1.1 Downloading https://files.pythonhosted.org/packages/7d/4b/cdf1113a0e88b641893b814e9c36f69a6fda28cd88b62c7f0d858cde3166/snowballstemmer-2.0.0-py2.py3-none-any.whl (97kB) Collecting requests>=2.0.0 Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB) Collecting Jinja2>=2.3 Downloading https://files.pythonhosted.org/packages/65/e0/eb35e762802015cab1ccee04e8a277b03f1d8e53da3ec3106882ec42558b/Jinja2-2.10.3-py2.py3-none-any.whl (125kB) Collecting pyparsing>=2.0.2 Downloading 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https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting MarkupSafe>=0.23 Downloading https://files.pythonhosted.org/packages/98/7b/ff284bd8c80654e471b769062a9b43cc5d03e7a615048d96f4619df8d420/MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl 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-cp37-none-any.whl size=23754 sha256=f090fa07d595023a118bf748495cf83ef79265a8a653e838403eb14773f718e3 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: 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https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB) 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>=0.4.0 Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl (231kB) Collecting pluggy<1.0,>=0.12 Downloading https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl Collecting py>=1.5.0 Downloading https://files.pythonhosted.org/packages/99/8d/21e1767c009211a62a8e3067280bfce76e89c9f876180308515942304d2d/py-1.8.1-py2.py3-none-any.whl (83kB) Requirement already satisfied: packaging in 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https://files.pythonhosted.org/packages/3d/d9/ea9816aea31beeadccd03f1f8b625ecf8f645bd66744484d162d84803ce5/PyYAML-5.3.tar.gz (268kB) 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) 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: 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 https://files.pythonhosted.org/packages/7a/db/a968fd7beb9fe06901c1841cb25c9ccb666ca1b9a19b114d1bbedf1126fc/pbr-5.4.4-py2.py3-none-any.whl (110kB) Collecting mistune 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https://files.pythonhosted.org/packages/5d/69/87745d03d1964649ef734238b32bf08eb843a6594cb03e8bc77edc8f33e9/nbformat-5.0.3-py3-none-any.whl (169kB) Collecting beautifulsoup4 Downloading https://files.pythonhosted.org/packages/cb/a1/c698cf319e9cfed6b17376281bd0efc6bfc8465698f54170ef60a485ab5d/beautifulsoup4-4.8.2-py3-none-any.whl (106kB) 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) Collecting zipp>=0.5 Downloading https://files.pythonhosted.org/packages/45/d8/f1e05f399573d2b4723dae1c1f1487dd2e7871c79ed32da741f49faaa226/zipp-2.0.0-py3-none-any.whl 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 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https://files.pythonhosted.org/packages/90/aa/cdcf7ef88cc0f831b6f14c8c57318824c9de9913fe8de38e46a98c069a35/pyrsistent-0.15.7.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=e02946cc85bc4057f8307001fa7106e335878969eefabaeb49c2a53cdd1f6637 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: filename=bs4-0.0.1-cp37-none-any.whl size=1272 sha256=027a71960337809418424925ebf9f387cc8e14093297243ab3c2fafa25878b62 Stored in directory: 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pyrsistent, jsonschema, nbformat, defusedxml, pandocfilters, entrypoints, testpath, 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-1.4.0 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-core-4.6.1 lxml-4.4.2 m2r-0.2.1 mistune-0.8.4 more-itertools-8.1.0 nbconvert-5.6.1 nbformat-5.0.3 nbsphinx-0.5.0 numpy-1.18.1 pandas-0.25.3 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-5.3.4 python-coveralls-2.9.3 python-dateutil-2.8.1 scipy-1.4.1 soupsieve-1.9.5 sphinxcontrib-apidoc-0.3.0 statsmodels-0.10.2 testpath-0.4.4 tqdm-4.41.1 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 zipp-2.0.0 [rtd-command-info] start-time: 2020-01-20T20:36:19.918968Z, end-time: 2020-01-20T20:36:20.134654Z, 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', 'proxied_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': 'e132dac8', } 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: 2020-01-20T20:36:20.218951Z, end-time: 2020-01-20T20:36:24.822629Z, 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... 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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' /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' /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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