Read the Docs build information
Build id: 1091164
Project: cyverse-foss
Version: latest
Commit: 035156a213d61a24fb9ddf6988254773a1fbbb44
Date: 2022-09-10T14:36:47.423441Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-09-10T14:36:53.205901Z, end-time: 2022-09-10T14:37:03.318571Z, duration: 10, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/foss.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-09-10T14:37:03.530229Z, end-time: 2022-09-10T14:37:04.117598Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 switching back to a branch.

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 035156a Merge pull request #55 from CyVerse-learning-materials/mkdocs

[rtd-command-info] start-time: 2022-09-10T14:37:04.320881Z, end-time: 2022-09-10T14:37:04.381326Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-09-10T14:37:09.378132Z, end-time: 2022-09-10T14:37:26.842290Z, duration: 17, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-09-10T14:37:27.117239Z, end-time: 2022-09-10T14:37:29.048536Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/latest/lib/python3.7/site-packages (22.2.2)
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.3.0
    Uninstalling setuptools-65.3.0:
      Successfully uninstalled setuptools-65.3.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-09-10T14:37:29.268201Z, end-time: 2022-09-10T14:37:36.066120Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0
Collecting pillow
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  Preparing metadata (setup.py): started
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Building wheels for collected packages: mock
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=7a1a60281cc2c2f7a27a138724fcf31588cb2b984da9e12e344c267b242c1f3c
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Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15.1 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.3 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 pytz-2022.2.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.12

[rtd-command-info] start-time: 2022-09-10T14:37:36.270350Z, end-time: 2022-09-10T14:38:22.014672Z, duration: 45, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Successfully built livereload mkdocs-jupyter docopt path-and-address
Installing collected packages: webencodings, wcwidth, ptyprocess, pickleshare, path-and-address, mistune, fastjsonschema, docopt, distlib, cached-property, brotli, backcall, zopfli, zipp, Werkzeug, watchdog, typing-extensions, traitlets, tornado, tomli, toml, tinycss2, soupsieve, smmap, rfc3986, pyzmq, PyYAML, python-dateutil, pyrsistent, Pyphen, pygments, pyflakes, pydyf, pycparser, pycodestyle, py, psutil, prompt-toolkit, platformdirs, pkgutil-resolve-name, pkginfo, pexpect, parso, pandocfilters, nest-asyncio, more-itertools, mkdocs-material-extensions, mergedeep, mdurl, mccabe, jupyterlab-pygments, jeepney, itsdangerous, html5lib, fonttools, filelock, entrypoints, defusedxml, decorator, debugpy, coverage, bump2version, bleach, attrs, astunparse, rich, requests-toolbelt, readme-renderer, pyyaml-env-tag, pytkdocs, matplotlib-inline, markdown-it-py, livereload, jupyter-core, jedi, jaraco.classes, importlib-resources, importlib-metadata, gitdb, ghp-import, cssselect2, cffi, beautifulsoup4, weasyprint, virtualenv, pluggy, mdit-py-plugins, Markdown, jupyter-client, jsonschema, ipython, GitPython, flake8, cryptography, click, tox, SecretStorage, pymdown-extensions, nbformat, mkdocs, markdown-callouts, ipykernel, Flask, nbclient, mkdocs-pdf-export-plugin, mkdocs-material, mkdocs-git-revision-date-plugin, mkdocs-autorefs, keyring, jupytext, grip, twine, nbconvert, mkdocstrings, mkdocstrings-python-legacy, mkdocstrings-crystal, mkdocs-jupyter
  Attempting uninstall: pygments
    Found existing installation: Pygments 2.13.0
    Uninstalling Pygments-2.13.0:
      Successfully uninstalled Pygments-2.13.0
Successfully installed Flask-2.2.2 GitPython-3.1.27 Markdown-3.3.4 PyYAML-6.0 Pyphen-0.13.0 SecretStorage-3.3.3 Werkzeug-2.2.2 astunparse-1.6.3 attrs-22.1.0 backcall-0.2.0 beautifulsoup4-4.11.1 bleach-5.0.1 brotli-1.0.9 bump2version-1.0.1 cached-property-1.5.2 cffi-1.15.1 click-8.1.3 coverage-6.4.4 cryptography-38.0.1 cssselect2-0.6.0 debugpy-1.6.3 decorator-5.1.1 defusedxml-0.7.1 distlib-0.3.6 docopt-0.6.2 entrypoints-0.4 fastjsonschema-2.16.1 filelock-3.8.0 flake8-5.0.4 fonttools-4.37.1 ghp-import-2.1.0 gitdb-4.0.9 grip-4.6.1 html5lib-1.1 importlib-metadata-4.2.0 importlib-resources-5.9.0 ipykernel-6.15.2 ipython-7.34.0 itsdangerous-2.1.2 jaraco.classes-3.2.2 jedi-0.18.1 jeepney-0.8.0 jsonschema-4.16.0 jupyter-client-7.3.5 jupyter-core-4.11.1 jupyterlab-pygments-0.2.2 jupytext-1.14.1 keyring-23.9.1 livereload-2.6.3 markdown-callouts-0.2.0 markdown-it-py-2.1.0 matplotlib-inline-0.1.6 mccabe-0.7.0 mdit-py-plugins-0.3.0 mdurl-0.1.2 mergedeep-1.3.4 mistune-0.8.4 mkdocs-1.2.4 mkdocs-autorefs-0.4.1 mkdocs-git-revision-date-plugin-0.3.2 mkdocs-jupyter-0.20.1 mkdocs-material-8.2.7 mkdocs-material-extensions-1.0.3 mkdocs-pdf-export-plugin-0.5.10 mkdocstrings-0.19.0 mkdocstrings-crystal-0.3.5 mkdocstrings-python-legacy-0.2.3 more-itertools-8.14.0 nbclient-0.6.8 nbconvert-6.5.0 nbformat-5.4.0 nest-asyncio-1.5.5 pandocfilters-1.5.0 parso-0.8.3 path-and-address-2.0.1 pexpect-4.8.0 pickleshare-0.7.5 pkginfo-1.8.3 pkgutil-resolve-name-1.3.10 platformdirs-2.5.2 pluggy-1.0.0 prompt-toolkit-3.0.31 psutil-5.9.2 ptyprocess-0.7.0 py-1.11.0 pycodestyle-2.9.1 pycparser-2.21 pydyf-0.2.0 pyflakes-2.5.0 pygments-2.11.2 pymdown-extensions-9.3 pyrsistent-0.18.1 python-dateutil-2.8.2 pytkdocs-0.16.1 pyyaml-env-tag-0.1 pyzmq-23.2.1 readme-renderer-37.1 requests-toolbelt-0.9.1 rfc3986-2.0.0 rich-12.5.1 smmap-5.0.0 soupsieve-2.3.2.post1 tinycss2-1.1.1 toml-0.10.2 tomli-2.0.1 tornado-6.2 tox-3.26.0 traitlets-5.3.0 twine-4.0.1 typing-extensions-4.3.0 virtualenv-20.16.2 watchdog-2.1.9 wcwidth-0.2.5 weasyprint-56.1 webencodings-0.5.1 zipp-3.8.1 zopfli-0.2.1

[rtd-command-info] start-time: 2022-09-10T14:38:23.808964Z, end-time: 2022-09-10T14:38:23.872607Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-

from __future__ import division, print_function, unicode_literals

from datetime import datetime

from recommonmark.parser import CommonMarkParser

extensions = []
templates_path = ['templates', '_templates', '.templates']
source_suffix = ['.rst', '.md']
source_parsers = {
            '.md': CommonMarkParser,
        }
master_doc = 'index'
project = u'foss'
copyright = str(datetime.now().year)
version = 'latest'
release = 'latest'
exclude_patterns = ['_build']
pygments_style = 'sphinx'
htmlhelp_basename = 'cyverse-foss'
html_theme = 'sphinx_rtd_theme'
file_insertion_enabled = False
latex_documents = [
  ('index', 'cyverse-foss.tex', u'foss Documentation',
   u'', 'manual'),
]




###########################################################################
#          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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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://assets.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://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("foss-2021-spring", "/en/foss-2021-spring/"),
    ("foss-2020-spring", "/en/foss-2020-spring/"),
    ("foss-2020-fall", "/en/foss-2020-fall/"),
    ("foss-2019-spring", "/en/foss-2019-spring/"),
    ],
    'downloads': [ 
    ("html", "//cyverse-foss.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-foss',
    'name': u'foss',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://cyverse-foss.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'UA-72224033-6',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'proxied_api_host': '/_',
    'github_repo': 'foss',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-72224033-6',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '035156a2',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/cyverse-foss/builds/1091164/'

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'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-09-10T14:38:24.088757Z, end-time: 2022-09-10T14:38:26.565329Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 15 source files that are out of date
updating environment: 15 added, 0 changed, 0 removed
reading sources... [  6%] 00_basics
reading sources... [ 13%] 01_intro_open_sci
reading sources... [ 20%] 02_project_management
reading sources... [ 26%] 03_managing_data
reading sources... [ 33%] 04_documentation_communication
reading sources... [ 40%] 05_version_control
reading sources... [ 46%] 06_repetition
reading sources... [ 53%] 07_reproducibility
reading sources... [ 60%] code_of_conduct
reading sources... [ 66%] documentation/githubpages
reading sources... [ 73%] final_project/overview
reading sources... [ 80%] glossary
reading sources... [ 86%] index
reading sources... [ 93%] installation
reading sources... [100%] schedule

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/01_intro_open_sci.md:: WARNING: image file not readable: ../assets/logos/deviceIcon.svg
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/03_managing_data.md:0: WARNING: Document may not end with a transition.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/04_documentation_communication.md:0: WARNING: Document may not end with a transition.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/00_basics.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/01_intro_open_sci.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/02_project_management.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/03_managing_data.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/04_documentation_communication.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/05_version_control.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/06_repetition.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/07_reproducibility.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/code_of_conduct.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/documentation/githubpages.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/final_project/overview.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/glossary.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/installation.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/schedule.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  6%] 00_basics
writing output... [ 13%] 01_intro_open_sci
writing output... [ 20%] 02_project_management
writing output... [ 26%] 03_managing_data
writing output... [ 33%] 04_documentation_communication
writing output... [ 40%] 05_version_control
writing output... [ 46%] 06_repetition
writing output... [ 53%] 07_reproducibility
writing output... [ 60%] code_of_conduct
writing output... [ 66%] documentation/githubpages
writing output... [ 73%] final_project/overview
writing output... [ 80%] glossary
writing output... [ 86%] index
writing output... [ 93%] installation
writing output... [100%] schedule

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/final_project/overview.md:35: WARNING: None:any reference target not found: 
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/final_project/overview.md:39: WARNING: None:any reference target not found: 
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/final_project/overview.md:52: WARNING: None:any reference target not found: 
generating indices... genindex
writing additional pages... search
copying images... [  3%] assets/git_1.png
copying images... [  6%] assets/git_2.png
copying images... [  9%] assets/git_3.png
copying images... [ 12%] assets/git_5.png
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copying images... [ 45%] assets/git_16.png
copying images... [ 48%] assets/git_17.png
copying images... [ 51%] assets/git_18.png
copying images... [ 54%] assets/git_19.png
copying images... [ 58%] assets/git_20.png
copying images... [ 61%] assets/git_21.png
copying images... [ 64%] assets/open_science_components.png
copying images... [ 67%] assets/five_schools.png
copying images... [ 70%] assets/layercake.png
copying images... [ 74%] assets/data_store/datastore_plchldr.png
copying images... [ 77%] assets/logos/deIcon.png
copying images... [ 80%] assets/atmosphere/atmosphere-icon.png
copying images... [ 83%] assets/DataCommons_DrkBlue.png
copying images... [ 87%] assets/Learningcenter_DkBlue.png
copying images... [ 90%] assets/intercomlogo.png
copying images... [ 93%] assets/organizing_searching_tradeoff.png
copying images... [ 96%] assets/journal.pcbi.1006750.g002.png
copying images... [100%] assets/reproducibility-spectrum.png

copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 20 warnings.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2022-09-10T14:38:26.829411Z, end-time: 2022-09-10T14:38:28.375657Z, duration: 1, exit-code: 0
python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 15 added, 0 changed, 0 removed
reading sources... [  6%] 00_basics
reading sources... [ 13%] 01_intro_open_sci
reading sources... [ 20%] 02_project_management
reading sources... [ 26%] 03_managing_data
reading sources... [ 33%] 04_documentation_communication
reading sources... [ 40%] 05_version_control
reading sources... [ 46%] 06_repetition
reading sources... [ 53%] 07_reproducibility
reading sources... [ 60%] code_of_conduct
reading sources... [ 66%] documentation/githubpages
reading sources... [ 73%] final_project/overview
reading sources... [ 80%] glossary
reading sources... [ 86%] index
reading sources... [ 93%] installation
reading sources... [100%] schedule

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/01_intro_open_sci.md:: WARNING: image file not readable: ../assets/logos/deviceIcon.svg
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/03_managing_data.md:0: WARNING: Document may not end with a transition.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/04_documentation_communication.md:0: WARNING: Document may not end with a transition.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/00_basics.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/latest/docs/01_intro_open_sci.md: WARNING: document isn't included in any toctree
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build succeeded, 17 warnings.

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