Read the Docs build information Build id: 425685 Project: cyverse-kallisto-tutorial Version: latest Commit: c6930c467ae36a289f944de43a1df4c138bd446c Date: 2020-09-18T15:43:19.037941Z State: finished Success: True [rtd-command-info] start-time: 2020-09-18T15:47:53.013359Z, end-time: 2020-09-18T15:47:53.714521Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/kallisto_tutorial.git . Cloning into '.'... [rtd-command-info] start-time: 2020-09-18T15:47:54.657376Z, end-time: 2020-09-18T15:47:54.728839Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at c6930c4 add triage issue template [rtd-command-info] start-time: 2020-09-18T15:47:54.949660Z, end-time: 2020-09-18T15:47:55.004886Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-18T15:47:57.415478Z, end-time: 2020-09-18T15:48:00.618890Z, duration: 3, exit-code: 0 python2.7 -mvirtualenv New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-18T15:48:00.745618Z, end-time: 2020-09-18T15:48:01.413170Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/envs/latest/lib/python2.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-18T15:48:01.802922Z, end-time: 2020-09-18T15:48:09.875396Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py2-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp27-cp27mu-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting typing; python_version < "3.5" Downloading typing-3.7.4.3-py2-none-any.whl (26 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.10-py2.py3-none-any.whl (127 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py2-none-any.whl size=23754 sha256=fcdc61bb0dd0e6d5a2f247343b71d266d8b5b2bba3dea1d3de438b8844701200 Stored in directory: /tmp/pip-ephem-wheel-cache-q_4NqZ/wheels/ad/62/e0/a06cc957652749e64c7904e899eca3ecb2ec47c60d52653660 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py2-none-any.whl size=502566 sha256=2aaafb38aaf414b6ee9bd981df5f6eda0a8d78c903fc6556a4b1b97f9ef1d4fd Stored in directory: /tmp/pip-ephem-wheel-cache-q_4NqZ/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, typing, MarkupSafe, Jinja2, six, pyparsing, packaging, snowballstemmer, pytz, babel, urllib3, certifi, idna, chardet, requests, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 44.1.1 Uninstalling setuptools-44.1.1: Successfully uninstalled setuptools-44.1.1 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.3 urllib3-1.25.10 [rtd-command-info] start-time: 2020-09-18T15:48:11.113891Z, end-time: 2020-09-18T15:48:11.183752Z, 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 = 'RNA-Seq with Kallisto Tutorial' copyright = '2020, CyVerse' author = 'CyVerse' version = '2.0' version = '2.0' 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 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", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("html", "//learning.cyverse.org/_/downloads/kallisto_tutorial/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'cyverse-kallisto-tutorial', 'name': u'kallisto_tutorial', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/kallisto_tutorial/en/latest/', 'analytics_code': 'UA-72224033-6', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', 'github_repo': 'kallisto_tutorial', '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': 'c6930c46', } 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-09-18T15:48:11.293614Z, end-time: 2020-09-18T15:48:12.821484Z, duration: 1, 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... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 9 source files that are out of date updating environment: 9 added, 0 changed, 0 removed reading sources... 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[100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/index.rst:173: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step1.rst:119: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step1.rst:105: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step2.rst:99: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step2.rst:85: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step3.rst:122: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step3.rst:108: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step4.rst:296: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step4.rst:337: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step4.rst:323: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[rtd-command-info] start-time: 2020-09-18T15:48:13.011151Z, end-time: 2020-09-18T15:48:14.335163Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 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: 9 added, 0 changed, 0 removed reading sources... [ 11%] .github/ISSUE_TEMPLATE/triage-for-2-0-release /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) reading sources... [ 22%] Contributors_maintainers reading sources... [ 33%] License reading sources... [ 44%] index reading sources... 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[100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/index.rst:173: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step1.rst:119: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step1.rst:105: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step2.rst:99: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step2.rst:85: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step3.rst:122: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step3.rst:108: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step4.rst:296: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step4.rst:337: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/step4.rst:323: WARNING: Undefined substitution referenced: "Github Repo Link". cyverse_rst_defined_substitutions.txt:106: WARNING: image file not readable: ./img/cyverse_learning.png cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-kallisto-tutorial/checkouts/latest/slides/README.md: WARNING: document isn't included in any toctree done preparing documents... done assembling single document... step1 step2 step3 step4 writing... done writing additional files... copying images... 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