Read the Docs build information
Build id: 189910
Project: cyverse-container-camp-workshop-2019
Version: latest
Commit: c05605c87d01a19a3d2dabe00373f0cabb345c57
Date: 2019-03-07T14:04:24.112563Z
State: finished
Success: True
[rtd-command-info] start-time: 2019-03-07T14:04:24.655025Z, end-time: 2019-03-07T14:04:24.661593Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/container_camp_workshop_2019.git
[rtd-command-info] start-time: 2019-03-07T14:04:24.721265Z, end-time: 2019-03-07T14:04:25.776721Z, duration: 1, exit-code: 0
git fetch --tags --prune --prune-tags --depth 50
From https://github.com/CyVerse-learning-materials/container_camp_workshop_2019
a09ace6..c05605c master -> origin/master
[rtd-command-info] start-time: 2019-03-07T14:04:25.940368Z, end-time: 2019-03-07T14:04:26.339458Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was a09ace6 Update agenda.rst
HEAD is now at c05605c Fixed schedule
[rtd-command-info] start-time: 2019-03-07T14:04:26.409925Z, end-time: 2019-03-07T14:04:26.434230Z, duration: 0, exit-code: 0
git clean -d -f -f
Removing misc/__init__.pyc
Removing misc/cyverse_sphinx_conf.pyc
[rtd-command-info] start-time: 2019-03-07T14:04:27.513157Z, end-time: 2019-03-07T14:04:29.556165Z, duration: 2, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python2.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.
[rtd-command-info] start-time: 2019-03-07T14:04:29.617818Z, end-time: 2019-03-07T14:04:31.424802Z, duration: 1, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip pip
Collecting pip
Using cached https://files.pythonhosted.org/packages/d8/f3/413bab4ff08e1fc4828dfc59996d721917df8e8583ea85385d51125dceff/pip-19.0.3-py2.py3-none-any.whl
Installing collected packages: pip
Found existing installation: pip 18.1
Uninstalling pip-18.1:
Successfully uninstalled pip-18.1
Successfully installed pip-19.0.3
[rtd-command-info] start-time: 2019-03-07T14:04:31.482997Z, end-time: 2019-03-07T14:04:38.966976Z, duration: 7, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting Pygments==2.2.0
Using cached https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl
Collecting setuptools<40
Using cached https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl
Collecting docutils==0.13.1
Using cached https://files.pythonhosted.org/packages/5f/6d/e864b3c61b81eec57386ac62082fccfe694c7c3046d8723258a37da6d5fc/docutils-0.13.1-py2-none-any.whl
Collecting mock==1.0.1
Collecting pillow==2.6.1
Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting commonmark==0.5.4
Collecting recommonmark==0.4.0
Using cached https://files.pythonhosted.org/packages/df/a5/8ee4b84af7f997dfdba71254a88008cfc19c49df98983c9a4919e798f8ce/recommonmark-0.4.0-py2.py3-none-any.whl
Collecting sphinx<1.8
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Collecting sphinx-rtd-theme<0.5
Using cached https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl
Collecting readthedocs-sphinx-ext<0.6
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Collecting snowballstemmer>=1.1 (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx<1.8)
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Collecting packaging (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/91/32/58bc30e646e55eab8b21abf89e353f59c0cc02c417e42929f4a9546e1b1d/packaging-19.0-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl
Collecting Jinja2>=2.3 (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting typing; python_version < "3.5" (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/cc/3e/29f92b7aeda5b078c86d14f550bf85cff809042e3429ace7af6193c3bc9f/typing-3.6.6-py2-none-any.whl
Collecting imagesize (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl
Collecting urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<1.8)
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Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests>=2.0.0->sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8)
Using cached https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, snowballstemmer, sphinxcontrib-websupport, pyparsing, six, packaging, pytz, babel, urllib3, certifi, chardet, idna, requests, MarkupSafe, Jinja2, typing, imagesize, sphinx, sphinx-rtd-theme, readthedocs-sphinx-ext
Found existing installation: setuptools 40.6.3
Uninstalling setuptools-40.6.3:
Successfully uninstalled setuptools-40.6.3
Successfully installed Jinja2-2.10 MarkupSafe-1.1.1 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 certifi-2018.11.29 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.0 pillow-2.6.1 pyparsing-2.3.1 pytz-2018.9 readthedocs-sphinx-ext-0.5.17 recommonmark-0.4.0 requests-2.21.0 setuptools-39.2.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.0 typing-3.6.6 urllib3-1.24.1
[rtd-command-info] start-time: 2019-03-07T14:04:39.028238Z, end-time: 2019-03-07T14:04:40.326265Z, duration: 1, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip -r requirements.txt
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (1.7.9)
Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 2)) (0.4.0)
Collecting sphinxcontrib-images (from -r requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/19/09/da51642f401be838476d5f02fb6b382600f731cdbcbf0579d431f2be3378/sphinxcontrib_images-0.8.0-py2-none-any.whl
Collecting sphinx_bootstrap_theme (from -r requirements.txt (line 4))
Collecting guzzle_sphinx_theme==0.7.11 (from -r requirements.txt (line 5))
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.1)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.2.0)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.6.0)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.21.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (39.2.0)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.13.1)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (19.0)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.10)
Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (3.6.6)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.0)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.12.0)
Requirement already satisfied: commonmark<=0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from recommonmark->-r requirements.txt (line 2)) (0.5.4)
Requirement already satisfied: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2018.9)
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Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2018.11.29)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.8)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.3.1)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1)
Installing collected packages: sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme
Successfully installed guzzle-sphinx-theme-0.7.11 sphinx-bootstrap-theme-0.6.5 sphinxcontrib-images-0.8.0
[rtd-command-info] start-time: 2019-03-07T14:04:40.834343Z, end-time: 2019-03-07T14:04:40.892289Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# General information about the project.
import sys
import os
sys.path.insert(0, os.path.dirname(__file__))
from misc.cyverse_sphinx_conf import * # noqa
project = 'CyVerse Container Camp 2019'
copyright = '2019, CyVerse'
author = 'CyVerse'
epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright
###########################################################################
# 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 mulitple 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': [
("pdf", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/pdf/latest/"),
("htmlzip", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/htmlzip/latest/"),
("epub", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/epub/latest/"),
],
'subprojects': [
],
'slug': 'cyverse-container-camp-workshop-2019',
'name': u'container_camp_workshop_2019',
'rtd_language': u'en',
'programming_language': u'words',
'canonical_url': 'https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/',
'analytics_code': 'None',
'single_version': False,
'conf_py_path': '/',
'api_host': 'https://readthedocs.com',
'github_user': 'CyVerse-learning-materials',
'github_repo': 'container_camp_workshop_2019',
'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': 'c05605c8',
}
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"]
[rtd-command-info] start-time: 2019-03-07T14:04:40.962251Z, end-time: 2019-03-07T14:04:49.503962Z, duration: 8, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short.
**Biocontainers**
================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
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maximum 1 argument(s) allowed, 3 supplied.
.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.
.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/boot.rst:70: WARNING: Content block expected for the "important" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub".
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:449: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 3 supplied.
.. code-block:: bash
-v /home/username/your_data_folder:/data:ro
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:578: WARNING: Error in "code-block" directive:
1 argument(s) required, 0 supplied.
.. code-block::
$ docker inspect jupytertest
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:417: WARNING: Unknown target name: "see here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile".
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:470: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image".
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**Workshop Code of Conduct and Other Information**
============================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:484: WARNING: Title underline too short.
Exercise 3: Creating the Singularity file (30 minutes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
looking for now-outdated files... none found
pickling environment... done
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done
preparing documents... done
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copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/_static' does not exist
done
copying readthedocs static files... done
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dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 57 warnings.
The HTML pages are in _build/html.
[rtd-command-info] start-time: 2019-03-07T14:04:49.652327Z, end-time: 2019-03-07T14:04:51.812608Z, duration: 2, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.7.9
loading translations [en]... done
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done
preparing documents... done
assembling single document... getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity topics/breakout_session docker/dockerintro docker/dockeradvanced docker/dockerhandson singularity/singularityintro singularity/singularityadvanced breakout/biocontainers breakout/nvidia-docker breakout/workflows breakout/datascience cyverse/boot cyverse/de_docker cyverse/vice_docker useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems
writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/index.rst:104: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
done
writing additional files...
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done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 33 warnings.
The HTML page is in _build/localmedia.
[rtd-command-info] start-time: 2019-03-07T14:04:51.968420Z, end-time: 2019-03-07T14:04:54.163829Z, duration: 2, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 0 added, 3 changed, 0 removed
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pickling environment... done
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Chapter 10.
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[]\T1/ptm/m/n/10 You should be greeted by your own con-tainer-ised Jupyter ser-
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Chapter 24.
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Chapter 9.
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Chapter 10.
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[]\T1/ptm/m/n/10 You should be greeted by your own con-tainer-ised Jupyter ser-
vice! Now open \T1/pcr/m/n/10 galaxy/
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Chapter 11.
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Chapter 14.
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Chapter 15.
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Chapter 16.
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l.3905 ...your version of Linux/Windows/OSX/OS9
— well this is where D...
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l.3905 ...ersion of Linux/Windows/OSX/OS9 —
well this is where Docker ...
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Chapter 17.
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Chapter 19.
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Chapter 20.
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Chapter 23.
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Chapter 24.
(./CyVerseDocumentation.ind) [141] (./CyVerseDocumentation.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}
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build succeeded, 33 warnings.
The ePub file is in _build/epub.
[rtd-command-info] start-time: 2019-03-07T14:08:04.523754Z, end-time: 2019-03-07T14:08:04.579073Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/./_build/epub/CyVerseContainerCamp2019.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/artifacts/latest/sphinx_epub/cyverse-container-camp-workshop-2019.epub